Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 439 of 444
Found at i:127291143 original size:31 final size:31
Alignment explanation
Indices: 127291100--127291279 Score: 279
Period size: 31 Copynumber: 5.8 Consensus size: 31
127291090 CTTGTCACTT
* *
127291100 GTAGCCGAAGCTACCACTATTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
127291131 GTAGCCGGAGCTACCATTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
127291162 GTAGCAGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
127291193 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
127291224 GTAGTCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
127291255 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
127291280 TGTCATTTGT
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 139 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:127291357 original size:50 final size:51
Alignment explanation
Indices: 127291255--127291383 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
127291245 CACTGATCAG
* * * *
127291255 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
127291306 GTAGCCGAAGCTATTACTTATCACTT-TCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
127291356 GTAGCCGAAGCTATCACTGATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
127291384 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 46 0.66
51 24 0.34
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
Found at i:127295796 original size:30 final size:31
Alignment explanation
Indices: 127295751--127295825 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
127295741 CACAAGCCAA
*
127295751 ACTTAAGAAAAAAAAACTT-AATAATTCAATG
1 ACTTAA-ATAAAAAAACTTGAATAATTCAATG
**
127295782 ACTTAAATAAAAAAACTTGAATGGTTCAATG
1 ACTTAAATAAAAAAACTTGAATAATTCAATG
*
127295813 ACTTAAATGAAAA
1 ACTTAAATAAAAA
127295826 TTATCAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (31 bp):
ACTTAAATAAAAAAACTTGAATAATTCAATG
Found at i:127296546 original size:24 final size:24
Alignment explanation
Indices: 127296519--127296567 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
127296509 CTAATGAGGG
127296519 AGCAATTGCCAAGTTTATGGCCTA
1 AGCAATTGCCAAGTTTATGGCCTA
127296543 AGCAATTGCCAAGTTTATGGCCTA
1 AGCAATTGCCAAGTTTATGGCCTA
127296567 A
1 A
127296568 CTTGGATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (24 bp):
AGCAATTGCCAAGTTTATGGCCTA
Found at i:127297313 original size:19 final size:19
Alignment explanation
Indices: 127297291--127297359 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
127297281 AACTACAAAT
127297291 TAAAAAAATAAAAATTTTA
1 TAAAAAAATAAAAATTTTA
**
127297310 TAAAATTATAAAAA--TTA
1 TAAAAAAATAAAAATTTTA
*
127297327 TAAAAAAATATATAATTGTT-
1 TAAAAAAATA-AAAATT-TTA
*
127297347 TAAAAAATTAAAA
1 TAAAAAAATAAAA
127297360 TTATGTTGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 11 0.28
18 3 0.08
19 14 0.36
20 9 0.23
21 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (19 bp):
TAAAAAAATAAAAATTTTA
Found at i:127297323 original size:9 final size:9
Alignment explanation
Indices: 127297287--127297332 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
127297277 AAAAAACTAC
127297287 AAATTA-AA
1 AAATTATAA
127297295 AAA--ATAA
1 AAATTATAA
*
127297302 AAATTTTATA
1 AAATTATA-A
127297312 AAATTATAA
1 AAATTATAA
127297321 AAATTATAA
1 AAATTATAA
127297330 AAA
1 AAA
127297333 AATATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
6 1 0.03
7 5 0.16
8 3 0.09
9 15 0.47
10 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAATTATAA
Found at i:127297387 original size:11 final size:10
Alignment explanation
Indices: 127297369--127297424 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 10
127297359 ATTATGTTGG
127297369 AATTTAAAAA
1 AATTTAAAAA
127297379 AATTGTAAAAA
1 AATT-TAAAAA
127297390 ATATTT--AAA
1 A-ATTTAAAAA
127297399 AA-TT-AAAA
1 AATTTAAAAA
127297407 AATTT--AAA
1 AATTTAAAAA
127297415 AATTTAAAAA
1 AATTTAAAAA
127297425 TGATTAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 2 0.05
8 14 0.35
9 6 0.15
10 7 0.17
11 8 0.20
12 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:127297407 original size:8 final size:8
Alignment explanation
Indices: 127297387--127297425 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
127297377 AAAATTGTAA
127297387 AAAATATTT
1 AAAA-ATTT
*
127297396 AAAAATTA
1 AAAAATTT
127297404 AAAAATTT
1 AAAAATTT
127297412 AAAAATTT
1 AAAAATTT
127297420 AAAAAT
1 AAAAAT
127297426 GATTAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 24 0.86
9 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:127297896 original size:22 final size:21
Alignment explanation
Indices: 127297866--127297911 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
127297856 TGGAATAATT
127297866 TAAAATATTATT-TAATTTAAA
1 TAAAATATT-TTATAATTTAAA
*
127297887 TAAAATTATTTTATTATTTAAA
1 TAAAA-TATTTTATAATTTAAA
127297909 TAA
1 TAA
127297912 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAATATTTTATAATTTAAA
Found at i:127298166 original size:17 final size:17
Alignment explanation
Indices: 127298135--127298180 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
127298125 GTATTGTTGT
127298135 AATTTTTTAATTTTTTAA
1 AATTTTTT-ATTTTTTAA
*
127298153 TACTTTTTTATTTTTTAA
1 -AATTTTTTATTTTTTAA
127298171 AATTTTTTAT
1 AATTTTTTAT
127298181 GATGACATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 9 0.36
19 7 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
AATTTTTTATTTTTTAA
Found at i:127301594 original size:12 final size:11
Alignment explanation
Indices: 127301573--127301602 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
127301563 ATAGTATGCA
127301573 GTTTTTTGTTT
1 GTTTTTTGTTT
127301584 GTTTGTTTGTTT
1 GTTT-TTTGTTT
127301596 GTTTTTT
1 GTTTTTT
127301603 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (11 bp):
GTTTTTTGTTT
Found at i:127301633 original size:5 final size:5
Alignment explanation
Indices: 127301623--127301647 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
127301613 TGAAAGTAAA
127301623 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
127301648 TATGTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:127309345 original size:13 final size:13
Alignment explanation
Indices: 127309327--127309361 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
127309317 AGACAAAGGC
127309327 AAGTATAAATTAT
1 AAGTATAAATTAT
127309340 AAGTATAAA--AT
1 AAGTATAAATTAT
127309351 AAGTATAAATT
1 AAGTATAAATT
127309362 TATACGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (13 bp):
AAGTATAAATTAT
Found at i:127312454 original size:31 final size:30
Alignment explanation
Indices: 127312415--127312500 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
127312405 TTTGAGAAGT
127312415 CCTTATTTGAGCACTTTTGAAATAG-TTTA
1 CCTTATTTGAGCACTTTTGAAATAGATTTA
*
127312444 GCACTTATTTGAGTA-TTTTCGAAA-AGATTTTA
1 -C-CTTATTTGAGCACTTTT-GAAATAGA-TTTA
*
127312476 CCTCATTTGAGCACTTTTGTAAATA
1 CCTTATTTGAGCACTTTTG-AAATA
127312501 TTAGACACCA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
30 18 0.39
31 23 0.50
32 5 0.11
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (30 bp):
CCTTATTTGAGCACTTTTGAAATAGATTTA
Found at i:127313010 original size:23 final size:22
Alignment explanation
Indices: 127312966--127313009 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
127312956 AAAAGGAAAG
127312966 AAACAAAAGGATAGTTTTTTTT
1 AAACAAAAGGATAGTTTTTTTT
127312988 AAACAAAAGGATAGTTTTTTTT
1 AAACAAAAGGATAGTTTTTTTT
127313010 TTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (22 bp):
AAACAAAAGGATAGTTTTTTTT
Found at i:127317456 original size:2 final size:2
Alignment explanation
Indices: 127317449--127317490 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
127317439 TCCTCAAGCC
*
127317449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127317491 TTAAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:127317498 original size:6 final size:6
Alignment explanation
Indices: 127317450--127317507 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
127317440 CCTCAAGCCA
* * * * * *
127317450 TATATA TATATA TATATA TATATA TATATA TATATT TATATT TAAATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
127317498 TATATT TATA
1 TATATT TATA
127317508 ATGAATTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TATATT
Found at i:127319794 original size:57 final size:57
Alignment explanation
Indices: 127319679--127319802 Score: 142
Period size: 57 Copynumber: 2.2 Consensus size: 57
127319669 AGGAGGAGGT
* * * * *
127319679 GGTGGTGGTGGAAGTGGTGCTCCGGTTGCCACTACTTTTGACTGCAATAGGACTGGA
1 GGTGGTGGTGGAAGGGGTGCTCCGATAGCCACTACATTTGACTGCAATAGGACCGGA
* * * *
127319736 GGTGGTGGTGGAAGGGGTGCTCCTATAGCCACTACATTTGGCTTCGAT-GAGACCGGA
1 GGTGGTGGTGGAAGGGGTGCTCCGATAGCCACTACATTTGACTGCAATAG-GACCGGA
*
127319793 GGTGGAGGTG
1 GGTGGTGGTG
127319803 AGGGCGGACG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 1 0.02
57 55 0.98
ACGTcount: A:0.18, C:0.17, G:0.40, T:0.26
Consensus pattern (57 bp):
GGTGGTGGTGGAAGGGGTGCTCCGATAGCCACTACATTTGACTGCAATAGGACCGGA
Found at i:127320252 original size:24 final size:24
Alignment explanation
Indices: 127320225--127320277 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
127320215 TAGTGGTGAC
* *
127320225 GGTGATGGCAATTGTGACGCTGAT
1 GGTGATGGCAATGGTGACGCTGAA
*
127320249 GGTGATGGCAATGGTGATGCTGAA
1 GGTGATGGCAATGGTGACGCTGAA
127320273 GGTGA
1 GGTGA
127320278 CGGTGATGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.42, T:0.26
Consensus pattern (24 bp):
GGTGATGGCAATGGTGACGCTGAA
Found at i:127320317 original size:27 final size:27
Alignment explanation
Indices: 127320279--127320374 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 27
127320269 TGAAGGTGAC
* *
127320279 GGTGATGGCAATAGGGATGTTGATAGT
1 GGTGATGACAATAGCGATGTTGATAGT
* * * *
127320306 GGTGATGACAATTGTGATGCTGATGGT
1 GGTGATGACAATAGCGATGTTGATAGT
*
127320333 GACGGTGATGGCAATAGCGATGTTGATAGT
1 ---GGTGATGACAATAGCGATGTTGATAGT
127320363 GGTGATGACAAT
1 GGTGATGACAAT
127320375 TGTGATGCTG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
27 33 0.60
30 22 0.40
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (27 bp):
GGTGATGACAATAGCGATGTTGATAGT
Found at i:127320328 original size:57 final size:57
Alignment explanation
Indices: 127320218--127320400 Score: 255
Period size: 57 Copynumber: 3.3 Consensus size: 57
127320208 TTTCTGATAG
* * * * * *
127320218 TGGTGACGGTGATGGCAATTGTGACGCTG--A-TGGTGATGGCAATGGTGATGCTGA
1 TGGTGACGGTGATGGCAATAGCGATGTTGATAGTGGTGATGACAATTGTGATGCTGA
* *
127320272 AGGTGACGGTGATGGCAATAGGGATGTTGATAGTGGTGATGACAATTGTGATGCTGA
1 TGGTGACGGTGATGGCAATAGCGATGTTGATAGTGGTGATGACAATTGTGATGCTGA
127320329 TGGTGACGGTGATGGCAATAGCGATGTTGATAGTGGTGATGACAATTGTGATGCTGA
1 TGGTGACGGTGATGGCAATAGCGATGTTGATAGTGGTGATGACAATTGTGATGCTGA
* *
127320386 TGGTGATGGTAATGG
1 TGGTGACGGTGATGG
127320401 TGATGCTGAC
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 24 0.21
56 1 0.01
57 90 0.78
ACGTcount: A:0.23, C:0.08, G:0.39, T:0.29
Consensus pattern (57 bp):
TGGTGACGGTGATGGCAATAGCGATGTTGATAGTGGTGATGACAATTGTGATGCTGA
Found at i:127320381 original size:27 final size:27
Alignment explanation
Indices: 127320248--127320450 Score: 119
Period size: 30 Copynumber: 7.3 Consensus size: 27
127320238 GTGACGCTGA
* *
127320248 TGGTGATGGCAATGGTGATGCTGA-AGG
1 TGGTGATGACAATAGTGATGCTGATA-G
* * *
127320275 TGACGGTGATGGCAATAGGGATGTTGATAG
1 T---GGTGATGACAATAGTGATGCTGATAG
* *
127320305 TGGTGATGACAATTGTGATGCTGATGG
1 TGGTGATGACAATAGTGATGCTGATAG
* * *
127320332 TGACGGTGATGGCAATAGCGATGTTGATAG
1 T---GGTGATGACAATAGTGATGCTGATAG
*
127320362 TGGTGATGACAATTGTGATGCTG--A-
1 TGGTGATGACAATAGTGATGCTGATAG
** * *
127320386 TGGTGATGGTAATGGTGATGCTGACAG
1 TGGTGATGACAATAGTGATGCTGATAG
* *
127320413 TGACGGTGACGGA-AATAGGGATGCTGATAG
1 T---GGTGA-TGACAATAGTGATGCTGATAG
127320443 TGGTGATG
1 TGGTGATG
127320451 GTGATGGCAA
Statistics
Matches: 136, Mismatches: 26, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
24 20 0.15
25 1 0.01
26 2 0.01
27 47 0.35
30 64 0.47
31 2 0.01
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.28
Consensus pattern (27 bp):
TGGTGATGACAATAGTGATGCTGATAG
Found at i:127320391 original size:12 final size:12
Alignment explanation
Indices: 127320376--127320409 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
127320366 GATGACAATT
127320376 GTGATGCTGATG
1 GTGATGCTGATG
* *
127320388 GTGATGGTAATG
1 GTGATGCTGATG
127320400 GTGATGCTGA
1 GTGATGCTGA
127320410 CAGTGACGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.41, T:0.32
Consensus pattern (12 bp):
GTGATGCTGATG
Found at i:127321847 original size:19 final size:19
Alignment explanation
Indices: 127321811--127321849 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
127321801 TAAAATTTGA
* * *
127321811 TACTTTTTTTTTTCAATTT
1 TACTTTTCTTTGTAAATTT
127321830 TACTTTTCTTTGTAAATTT
1 TACTTTTCTTTGTAAATTT
127321849 T
1 T
127321850 TCACATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (19 bp):
TACTTTTCTTTGTAAATTT
Found at i:127326182 original size:42 final size:42
Alignment explanation
Indices: 127326124--127326214 Score: 173
Period size: 42 Copynumber: 2.1 Consensus size: 42
127326114 TATTTTATGA
127326124 AAACTAAAGAGCTGATTCAGTTCTCAGTAATCATGTGAATTTG
1 AAACT-AAGAGCTGATTCAGTTCTCAGTAATCATGTGAATTTG
127326167 AAACTAAGAGCTGATTCAGTTCTCAGTAATCATGTGAATTTG
1 AAACTAAGAGCTGATTCAGTTCTCAGTAATCATGTGAATTTG
127326209 AAACTA
1 AAACTA
127326215 CTAATTTTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 43 0.90
43 5 0.10
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (42 bp):
AAACTAAGAGCTGATTCAGTTCTCAGTAATCATGTGAATTTG
Found at i:127328340 original size:2 final size:2
Alignment explanation
Indices: 127328333--127328360 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
127328323 ATGTCTTTTG
127328333 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
127328361 TTGGTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127334930 original size:17 final size:15
Alignment explanation
Indices: 127334895--127334924 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
127334885 ATCGACTCGT
127334895 TTAATTTTATTAAAA
1 TTAATTTTATTAAAA
127334910 TTAATTTTATTAAAA
1 TTAATTTTATTAAAA
127334925 AATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTTTATTAAAA
Found at i:127337161 original size:196 final size:196
Alignment explanation
Indices: 127336822--127337381 Score: 676
Period size: 196 Copynumber: 2.8 Consensus size: 196
127336812 TGCTGTTGAT
* * *
127336822 TTGTTAGTTGACATAGTGAATTTTGCCCAATGTTACTCGGACT-TGGGTGTGAGTGTCAAATACC
1 TTGTTAGTTGACATAGTGAATTTTGCCCTATGTTATTCGGACTCT-GGTGTGAGTGTCAAATACG
* * * *
127336886 GGTATGTATTTAACACGAGTAACGTTTGACTTTTCAAAGGTTTTCCATGTAATATACATATGTCA
65 GGTATGTATTTAAGA-GAGTATCGTTAGACTTTTCAAAGGTTTTCCATGTAATATCCATATGTCA
* * * * * *
127336951 AACATTGGTGCTTCAAGAAAAATGAAGAGCCTGAGCAA-GA-TAGCATTGTGTGATCGCTTGGTG
129 AACA-CGGTGCTTCAAGAAAAATGAAGAGCCTGAGCAACAACTAGCATTGTGTGATCCCTAGCTC
127337014 TCAA
193 TCAA
* * * *
127337018 TTGTCAGTTGACATAGTTAATTTTGCCCTATGTTATTCGGACTCTGGTGTAAGTGTCAAATATGG
1 TTGTTAGTTGACATAGTGAATTTTGCCCTATGTTATTCGGACTCTGGTGTGAGTGTCAAATACGG
* * * **
127337083 GTATGTATTTAATGAGAGTATTGTTAGACTTTTCAAAGGTTTTCTATGTAATATCCATGTGTCCG
66 GTATGTATTTAA-GAGAGTATCGTTAGACTTTTCAAAGGTTTTCCATGTAATATCCATATGTCAA
* * *
127337148 ACACGAGTGCTTCAAGAAAAATGAAGAGTCTGAGCAACAACCTATCATTTTGTGATCCCTAGCTC
130 ACACG-GTGCTTCAAGAAAAATGAAGAGCCTGAGCAACAA-CTAGCATTGTGTGATCCCTAGCTC
127337213 TCAA
193 TCAA
*
127337217 TTGTTAGTTGACATAGTGAATTTTGCCCTATGTTATTCGGACTCGGGTGTGAGTGTCAAATACGG
1 TTGTTAGTTGACATAGTGAATTTTGCCCTATGTTATTCGGACTCTGGTGTGAGTGTCAAATACGG
* * * * *
127337282 GTGTGCATTTGACACGGGTATCGTTAGATTTTTCATTTTTCAAAGGTTTTCCATGTAATATCCAT
66 GTATGTATTTAAGA-GAGTATCGTTAGA-----C--TTTTCAAAGGTTTTCCATGTAATATCCAT
*
127337347 CTGTCAAACACTGGTGCTTCAAGAAAAATGAAGAG
123 ATGTCAAACAC-GGTGCTTCAAGAAAAATGAAGAG
127337382 TCCGAACAAC
Statistics
Matches: 309, Mismatches: 40, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
195 1 0.00
196 143 0.46
197 3 0.01
198 1 0.00
199 101 0.33
204 1 0.00
206 58 0.19
207 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (196 bp):
TTGTTAGTTGACATAGTGAATTTTGCCCTATGTTATTCGGACTCTGGTGTGAGTGTCAAATACGG
GTATGTATTTAAGAGAGTATCGTTAGACTTTTCAAAGGTTTTCCATGTAATATCCATATGTCAAA
CACGGTGCTTCAAGAAAAATGAAGAGCCTGAGCAACAACTAGCATTGTGTGATCCCTAGCTCTCA
A
Found at i:127338808 original size:4 final size:4
Alignment explanation
Indices: 127338801--127338855 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
127338791 ACACACACAC
* * *
127338801 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT GCAT TCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
127338849 ACAT ACA
1 ACAT ACA
127338856 CACACATGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:127339299 original size:25 final size:25
Alignment explanation
Indices: 127339265--127339313 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
127339255 CACACTTTTG
127339265 GATTTCCTCATAAAAAATCTACACC
1 GATTTCCTCATAAAAAATCTACACC
*
127339290 GATTTCCTCATCAAAAATCTACAC
1 GATTTCCTCATAAAAAATCTACAC
127339314 AGGTTTGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.29
Consensus pattern (25 bp):
GATTTCCTCATAAAAAATCTACACC
Found at i:127339722 original size:2 final size:2
Alignment explanation
Indices: 127339715--127339747 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
127339705 ATGTTCAAAG
127339715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127339748 ATTTCTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127341627 original size:25 final size:22
Alignment explanation
Indices: 127341571--127341618 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
127341561 TCAAGTTTAT
127341571 ATATGATATTGATTATTACAAA
1 ATATGATATTGATTATTACAAA
127341593 ATATGATATTGATTATTACAAA
1 ATATGATATTGATTATTACAAA
127341615 ATAT
1 ATAT
127341619 TATCTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (22 bp):
ATATGATATTGATTATTACAAA
Found at i:127344344 original size:23 final size:23
Alignment explanation
Indices: 127344318--127344363 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
127344308 TTTACGTTAG
127344318 ATCAAAAAGCAAATTGATCATTT
1 ATCAAAAAGCAAATTGATCATTT
* *
127344341 ATCAAAAAGTAAATTGGTCATTT
1 ATCAAAAAGCAAATTGATCATTT
127344364 CTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (23 bp):
ATCAAAAAGCAAATTGATCATTT
Found at i:127346334 original size:26 final size:27
Alignment explanation
Indices: 127346279--127346340 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
127346269 ATAAATAATT
*
127346279 TAATAT-ATATTTTTTATATTTACATTA
1 TAATATAATATTTTTTATATATACA-TA
127346306 TAATATAATATTTTTTATGATATA-A-A
1 TAATATAATATTTTTTAT-ATATACATA
127346332 TAATATAAT
1 TAATATAAT
127346341 GGACTTGGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.31
27 6 0.19
28 12 0.38
29 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATATAATATTTTTTATATATACATA
Found at i:127356662 original size:31 final size:32
Alignment explanation
Indices: 127356596--127356662 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
127356586 CAAAATGTTA
127356596 TTTTTGGGATAATTCCACAAAAAGTTCTCAAC
1 TTTTTGGGATAATTCCACAAAAAGTTCTCAAC
* * *
127356628 TTTTTTGGTTAATTCTACAAAAAGTTC-CAAC
1 TTTTTGGGATAATTCCACAAAAAGTTCTCAAC
127356659 TTTT
1 TTTT
127356663 AAATTGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (32 bp):
TTTTTGGGATAATTCCACAAAAAGTTCTCAAC
Found at i:127362026 original size:29 final size:29
Alignment explanation
Indices: 127361966--127362022 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
127361956 GAGTAAATTA
*
127361966 ATTATTCTATTAAAAATTTCATGCATTTT
1 ATTATTCTATTAAAAATTTCATCCATTTT
*
127361995 ATTATT-TATTAAAAATTTTATCCATTTT
1 ATTATTCTATTAAAAATTTCATCCATTTT
127362023 TATTTAGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (29 bp):
ATTATTCTATTAAAAATTTCATCCATTTT
Found at i:127362115 original size:28 final size:28
Alignment explanation
Indices: 127362075--127362129 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
127362065 AAATGGATAA
127362075 ATTTTTTAATAGAAAGATTAATTTGTTC
1 ATTTTTTAATAGAAAGATTAATTTGTTC
127362103 ATTTTTTAATAGAAAGATTAATTTGTT
1 ATTTTTTAATAGAAAGATTAATTTGTT
127362130 TATTAATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (28 bp):
ATTTTTTAATAGAAAGATTAATTTGTTC
Found at i:127372314 original size:3 final size:3
Alignment explanation
Indices: 127372306--127372358 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
127372296 AGTTTATCCC
127372306 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127372354 TAA TA
1 TAA TA
127372359 CTTTTCGCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:127376730 original size:20 final size:20
Alignment explanation
Indices: 127376693--127376730 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
127376683 TGATGGGGAG
*
127376693 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
127376713 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
127376731 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:127378696 original size:46 final size:46
Alignment explanation
Indices: 127378643--127378814 Score: 229
Period size: 46 Copynumber: 3.7 Consensus size: 46
127378633 AGTGTGCTCT
* *
127378643 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
127378689 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
127378735 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGTAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
127378781 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGA
127378815 CGCTATGGCA
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 111 0.99
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:127379176 original size:23 final size:23
Alignment explanation
Indices: 127379146--127379199 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
127379136 TCTTTGATAT
127379146 GTTGAGACAAGGAAATTATGTAA
1 GTTGAGACAAGGAAATTATGTAA
127379169 GTTGAGACAAGGAAATTATGTAA
1 GTTGAGACAAGGAAATTATGTAA
127379192 GTTGAGAC
1 GTTGAGAC
127379200 TATTATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.26
Consensus pattern (23 bp):
GTTGAGACAAGGAAATTATGTAA
Found at i:127379745 original size:13 final size:13
Alignment explanation
Indices: 127379727--127379752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127379717 CAAAAATCGA
127379727 TAACCAATCAAAT
1 TAACCAATCAAAT
127379740 TAACCAATCAAAT
1 TAACCAATCAAAT
127379753 CGAGGTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
TAACCAATCAAAT
Found at i:127386935 original size:21 final size:20
Alignment explanation
Indices: 127386898--127386943 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
127386888 AACTCCCTAA
*
127386898 AATT-ATAAAAATTAAATTT
1 AATTCATAAAAATAAAATTT
127386917 AATTCATAAAAATAAAAATTT
1 AATTCATAAAAAT-AAAATTT
127386938 AATTCA
1 AATTCA
127386944 ATTGTTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.17
20 8 0.33
21 12 0.50
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTCATAAAAATAAAATTT
Found at i:127388183 original size:13 final size:13
Alignment explanation
Indices: 127388165--127388190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127388155 TGTTTCTTTC
127388165 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
127388178 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
127388191 ATGGTTCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:127393734 original size:18 final size:18
Alignment explanation
Indices: 127393686--127393735 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
127393676 TTTAAGGTAA
127393686 AATCGAATTAATTTAGTT
1 AATCGAATTAATTTAGTT
* *
127393704 AAT-TAATCGAATTTAGTT
1 AATCGAAT-TAATTTAGTT
127393722 AATCGAATTAATTT
1 AATCGAATTAATTT
127393736 GGTTGAGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (18 bp):
AATCGAATTAATTTAGTT
Found at i:127394776 original size:5 final size:5
Alignment explanation
Indices: 127394755--127394807 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
127394745 TGTTAAAATA
* *
127394755 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
127394803 TATAT
1 TATAT
127394808 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:127394786 original size:10 final size:9
Alignment explanation
Indices: 127394752--127394808 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
127394742 ATGTGTTAAA
127394752 ATATATATT
1 ATATATATT
*
127394761 AAAT-TATT
1 ATATATATT
127394769 AT-TATATT
1 ATATATATT
127394777 ATAGTATATT
1 ATA-TATATT
127394787 ATAT-TA-T
1 ATATATATT
127394794 ATATTATATT
1 ATA-TATATT
127394804 ATATA
1 ATATA
127394809 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:127394798 original size:12 final size:12
Alignment explanation
Indices: 127394753--127394808 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
127394743 TGTGTTAAAA
*
127394753 TATATATTAAAT
1 TATATATTATAT
127394765 TAT-TATTATATT
1 TATATATTATA-T
127394777 ATAGTATATTATAT
1 -TA-TATATTATAT
127394791 TATATATTATAT
1 TATATATTATAT
127394803 TATATA
1 TATATA
127394809 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:127396147 original size:18 final size:19
Alignment explanation
Indices: 127396126--127396164 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
127396116 ATATATAGAT
127396126 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
127396144 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
127396163 AT
1 AT
127396165 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:127396513 original size:39 final size:39
Alignment explanation
Indices: 127396403--127396537 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
127396393 GACCTCGAGT
* * * *
127396403 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
127396444 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
127396482 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
127396521 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
127396538 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:127396681 original size:18 final size:19
Alignment explanation
Indices: 127396660--127396700 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
127396650 AATGAAATGA
127396660 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
127396678 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
127396697 GAAA
1 GAAA
127396701 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:127398318 original size:2 final size:2
Alignment explanation
Indices: 127398311--127398339 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
127398301 TAAGCTTCTC
127398311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127398340 CTTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127398446 original size:19 final size:21
Alignment explanation
Indices: 127398408--127398446 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
127398398 CGGTCAAGCC
*
127398408 TTAATAAGATTTTAAGCTTAT
1 TTAATAAGATTTTAAACTTAT
127398429 TTAATAA-A-TTTAAACTTA
1 TTAATAAGATTTTAAACTTA
127398447 AAAATTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
TTAATAAGATTTTAAACTTAT
Found at i:127407166 original size:54 final size:54
Alignment explanation
Indices: 127407108--127407274 Score: 153
Period size: 54 Copynumber: 3.1 Consensus size: 54
127407098 TTTCAGATTT
*
127407108 CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGCGATCAACTTC
1 CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGAGATCAACTTC
* * * * * * * *
127407162 CTAG-AGCGGAATTAACGT-CAACTCCTGATAAGG-TCATTATTGGAAACCAAACTT-
1 CTAGAAG-GGAATCAAC-TCCCACTTCTGGT-GGGCTCATTACTGGAGATC-AACTTC
* ** *
127407216 CTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTTGTTACTGGGGATCAACTTC
1 CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGAGATCAACTTC
127407270 CTAGA
1 CTAGA
127407275 GCGGAATTAA
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
53 10 0.12
54 64 0.76
55 10 0.12
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (54 bp):
CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGAGATCAACTTC
Found at i:127407246 original size:108 final size:108
Alignment explanation
Indices: 127407106--127407339 Score: 380
Period size: 108 Copynumber: 2.2 Consensus size: 108
127407096 GATTTCAGAT
*
127407106 TTCTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG
1 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG
* *
127407171 AATTAACGT-CAACTCCTGATAAGGTCATTATTGGAAACCAAAC
66 AATTAACGTCCAA-TCCAGATAAGGTCATTACTGGAAACCAAAC
** *
127407214 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTTGTTACTGGGGATCAACTTCCTAGAGCGG
1 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG
*
127407279 AATTAATGTCCAATCCAGATAAGGTCATTACTGGAAACCAAAC
66 AATTAACGTCCAATCCAGATAAGGTCATTACTGGAAACCAAAC
*
127407322 TTCTAGAAAGGAATCAAC
1 TTCTAGAAGGGAATCAAC
127407340 CATAACCCCT
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 114 0.97
109 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (108 bp):
TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG
AATTAACGTCCAATCCAGATAAGGTCATTACTGGAAACCAAAC
Found at i:127407328 original size:54 final size:54
Alignment explanation
Indices: 127407156--127407328 Score: 126
Period size: 54 Copynumber: 3.2 Consensus size: 54
127407146 ACTGGCGATC
* *
127407156 AACTTCCTAGAGCGGAATTAACGT-CAACTCCTGATAAGGTCATTATTGGAAACCA
1 AACTTCCTAGAGCGGAATTAATGTCCAA-TCC-GATAAGGTCATTACTGGAAACCA
* * * * * ** ** *
127407211 AACTT-CTAGAAG-GGAATCAACT-CCCACTTCCGGT-GGGCTTGTTACTGGGGATC-
1 AACTTCCTAG-AGCGGAATTAA-TGTCCA-ATCCGATAAGG-TCATTACTGGAAACCA
127407264 AACTTCCTAGAGCGGAATTAATGTCCAATCCAGATAAGGTCATTACTGGAAACCA
1 AACTTCCTAGAGCGGAATTAATGTCCAATCC-GATAAGGTCATTACTGGAAACCA
127407319 AACTT-CTAGA
1 AACTTCCTAGA
127407329 AAGGAATCAA
Statistics
Matches: 85, Mismatches: 22, Indels: 23
0.65 0.17 0.18
Matches are distributed among these distances:
53 13 0.15
54 53 0.62
55 19 0.22
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (54 bp):
AACTTCCTAGAGCGGAATTAATGTCCAATCCGATAAGGTCATTACTGGAAACCA
Found at i:127410878 original size:25 final size:23
Alignment explanation
Indices: 127410807--127410879 Score: 62
Period size: 25 Copynumber: 3.1 Consensus size: 23
127410797 TGGATCAAAA
*
127410807 TTAAATTATATAATTTTATAAGA-G
1 TTAAA-TATATAATTTTATAA-ATT
*
127410831 TTAAA-ATATAATTTTCAT-CATT
1 TTAAATATATAATTTT-ATAAATT
127410853 TTAATAATATATAATTTTATAAATT
1 TT-A-AATATATAATTTTATAAATT
127410878 TT
1 TT
127410880 TAAAAAGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
21 1 0.03
22 12 0.30
23 3 0.08
24 9 0.22
25 15 0.38
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
TTAAATATATAATTTTATAAATT
Found at i:127413107 original size:155 final size:155
Alignment explanation
Indices: 127412842--127413130 Score: 409
Period size: 155 Copynumber: 1.9 Consensus size: 155
127412832 GTACGGTCAT
** * *
127412842 TATTAGTATTCTGACAATTCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATTATTGTTGG
1 TATTAGTATTCCAACAATTCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATGATTGTTAG
** * *
127412907 ATGTATAAGCTTGTCATAATGTTTGATAAGAACAACCTGAAGTTCGAATCCCGCAAAGGGTTTGC
66 ATGTATAAGCTTGTCATAACATTTGATAAGAACAACCTAAAGTTCGAATCCCCCAAAGGGTTTGC
127412972 CGTTGCAGCGTTTCCGTACAGTGTC
131 CGTTGCAGCGTTTCCGTACAGTGTC
** * ** *
127412997 TATTAGTATTCCAACAATTCTTGATGTTGCTGTGAATGATGTTTCATGATTTCAATGATTGTTAG
1 TATTAGTATTCCAACAATTCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATGATTGTTAG
* * *
127413062 ATGTATAAGCTTGTCCTTACATTTGATAAGAACGATCC-AAAGTTCGAATCCCCCAAAGGGTTTG
66 ATGTATAAGCTTGTCATAACATTTGATAAGAAC-AACCTAAAGTTCGAATCCCCCAAAGGGTTTG
127413126 CCGTT
130 CCGTT
127413131 TGCACTAGCT
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
155 113 0.97
156 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (155 bp):
TATTAGTATTCCAACAATTCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATGATTGTTAG
ATGTATAAGCTTGTCATAACATTTGATAAGAACAACCTAAAGTTCGAATCCCCCAAAGGGTTTGC
CGTTGCAGCGTTTCCGTACAGTGTC
Found at i:127413369 original size:185 final size:185
Alignment explanation
Indices: 127412988--127413391 Score: 490
Period size: 185 Copynumber: 2.2 Consensus size: 185
127412978 AGCGTTTCCG
* * * ** *
127412988 TACAGTGTCTATTAGTATTCCAACAATTCTTGATGTTGCTGTGAATGATGTTTCATGATTTCAAT
1 TACAGTCTTTATTAGTATTCCGACAATTCTTGATGTCACTGTGAATGATGTTTCA-GACTTCAAT
* * *
127413053 GATTGTTAGATGTATAAGCTTGTCCTTACATTTGATAAGAACGATCCAAAGTTCGAATCCCCCAA
65 GATAGTTAGATGTATAAACTTGTCCTAACATTTGATAAGAACGATCCAAAGTTCGAATCCCCCAA
* * * * * * *
127413118 AGGGTTTGCCGTTTGCACTAGCTACGTAATGTAGGTTGGCTCGTGCAACGTTTACG
130 AGGGTTTGCCATTTGAACTAGCTACATAATATAGGTTGGCTCATGCAACATTTACA
* *
127413174 TACGGTCTTTATTAGTATTTCGACAATTCTTGATGTCACTGTGAATGATGTTTTGCA-ACTTCAA
1 TACAGTCTTTATTAGTATTCCGACAATTCTTGATGTCACTGTGAATGATG-TTT-CAGACTTCAA
* ** *
127413238 TGGTAGTTAGA-GTATAAACTTGTCCTAATGTTTGATAAGAATGATCCAAAGTTCGAA-CCCCGC
64 TGATAGTTAGATGTATAAACTTGTCCTAACATTTGATAAGAACGATCCAAAGTTCGAATCCCC-C
* ** *
127413301 AAAGGGTTTGCCATTTGAACTAGTTACATAATATAGGTTGGCTCATGTGATATTTACA
128 AAAGGGTTTGCCATTTGAACTAGCTACATAATATAGGTTGGCTCATGCAACATTTACA
* **
127413359 TTCAGTCTTTATCGGTATTCCGACAATTCTTGA
1 TACAGTCTTTATTAGTATTCCGACAATTCTTGA
127413392 CATTGCCGTG
Statistics
Matches: 184, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
184 4 0.02
185 117 0.64
186 58 0.32
187 3 0.02
188 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (185 bp):
TACAGTCTTTATTAGTATTCCGACAATTCTTGATGTCACTGTGAATGATGTTTCAGACTTCAATG
ATAGTTAGATGTATAAACTTGTCCTAACATTTGATAAGAACGATCCAAAGTTCGAATCCCCCAAA
GGGTTTGCCATTTGAACTAGCTACATAATATAGGTTGGCTCATGCAACATTTACA
Found at i:127424506 original size:25 final size:26
Alignment explanation
Indices: 127424450--127424506 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
127424440 GATTATATTC
127424450 ATATATAATTTATATGTATATAATTA
1 ATATATAATTTATATGTATATAATTA
* * *
127424476 AGATAT-ATTTGTATGTGTATAAATT-
1 ATATATAATTTATATGTATAT-AATTA
127424501 ATATAT
1 ATATAT
127424507 TAAATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (26 bp):
ATATATAATTTATATGTATATAATTA
Found at i:127430827 original size:31 final size:32
Alignment explanation
Indices: 127430787--127430864 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
127430777 ACTTTTCTTA
* *
127430787 TTTTTATACAAGAA-GGAAAATACAATTTAAC
1 TTTTAATACAAGAATGGAAAATACAATCTAAC
** **
127430818 TTTTAATACAAGAATTTTAAAATGTAATCTAAC
1 TTTTAATACAAGAA-TGGAAAATACAATCTAAC
127430851 TTTTAATACAAGAA
1 TTTTAATACAAGAA
127430865 CTTTAAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 13 0.33
33 26 0.67
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (32 bp):
TTTTAATACAAGAATGGAAAATACAATCTAAC
Found at i:127445770 original size:3 final size:3
Alignment explanation
Indices: 127445762--127445803 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
127445752 GTAGTGATTT
127445762 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
127445804 AAAGGGTGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:127445931 original size:18 final size:18
Alignment explanation
Indices: 127445892--127445933 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
127445882 TTCATGCTCT
*
127445892 GGTTCTGGTTCGGCTTCC
1 GGTTCTGGTTCGGCTTCA
* *
127445910 GGTTCTGGTTCTGTTTCA
1 GGTTCTGGTTCGGCTTCA
127445928 GGTTCT
1 GGTTCT
127445934 TGTATTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.21, G:0.31, T:0.45
Consensus pattern (18 bp):
GGTTCTGGTTCGGCTTCA
Found at i:127454824 original size:16 final size:16
Alignment explanation
Indices: 127454803--127454834 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
127454793 TTTAAAATCA
*
127454803 GAAATGATCTGAACTT
1 GAAATGATCGGAACTT
127454819 GAAATGATCGGAACTT
1 GAAATGATCGGAACTT
127454835 AAACTTGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (16 bp):
GAAATGATCGGAACTT
Found at i:127455686 original size:21 final size:20
Alignment explanation
Indices: 127455662--127455703 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
127455652 ATAAATAATA
*
127455662 TATATTATATAATATATTTTT
1 TATATTA-ACAATATATTTTT
*
127455683 TATATTAACAATTTATTTTT
1 TATATTAACAATATATTTTT
127455703 T
1 T
127455704 GAACTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTAACAATATATTTTT
Found at i:127460580 original size:19 final size:18
Alignment explanation
Indices: 127460529--127460569 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
127460519 GAAGATCCAA
*
127460529 TTAAAATGT-TTTAAATT
1 TTAAAATTTATTTAAATT
127460546 TTGAAAATTTATTTAAATT
1 TT-AAAATTTATTTAAATT
127460565 TTAAA
1 TTAAA
127460570 TTATAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
19 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TTAAAATTTATTTAAATT
Found at i:127460768 original size:23 final size:23
Alignment explanation
Indices: 127460738--127460785 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
127460728 AGGGCTAAAA
127460738 AGATACTTGCTTTATTTATTACG
1 AGATACTTGCTTTATTTATTACG
*
127460761 AGATACTTGCTTTATTTATTTCG
1 AGATACTTGCTTTATTTATTACG
127460784 AG
1 AG
127460786 TGTCAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (23 bp):
AGATACTTGCTTTATTTATTACG
Found at i:127466424 original size:3 final size:3
Alignment explanation
Indices: 127466416--127466449 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
127466406 TATGAGGCTT
127466416 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
127466450 ATAAATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:127467969 original size:24 final size:24
Alignment explanation
Indices: 127467942--127467987 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
127467932 TTATGTACAT
* *
127467942 GAAATTTTAATTGTGTTTCAATAC
1 GAAACTTTAATTGTATTTCAATAC
*
127467966 GAAACTTTAATTTTATTTCAAT
1 GAAACTTTAATTGTATTTCAAT
127467988 CATACACGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
GAAACTTTAATTGTATTTCAATAC
Found at i:127468915 original size:25 final size:26
Alignment explanation
Indices: 127468841--127468916 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 26
127468831 TATTCGAGCC
* *
127468841 AAATTGAATTTATATTTTAAATA-GTGA
1 AAATTGACTTT-T-TTTTAAATACTTGA
**
127468868 AAATTGACTTTTTTTTATTTACTTGA
1 AAATTGACTTTTTTTTAAATACTTGA
127468894 AAATT-A-TTTTTTTTAAAATACTT
1 AAATTGACTTTTTTTT-AAATACTT
127468917 ACTAAAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
24 8 0.20
25 14 0.34
26 9 0.22
27 10 0.24
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (26 bp):
AAATTGACTTTTTTTTAAATACTTGA
Found at i:127476962 original size:19 final size:18
Alignment explanation
Indices: 127476938--127476973 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
127476928 TTTTTTGAGG
*
127476938 GGGGAAGTGAAATGTTTGA
1 GGGGAAGT-AAAAGTTTGA
127476957 GGGGAAGTAAAAGTTTG
1 GGGGAAGTAAAAGTTTG
127476974 GGAGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (18 bp):
GGGGAAGTAAAAGTTTGA
Found at i:127485155 original size:16 final size:16
Alignment explanation
Indices: 127485136--127485167 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
127485126 CTCAAATTGA
127485136 TTGAATCTAAAATAAT
1 TTGAATCTAAAATAAT
127485152 TTGAATCTAAAATAAT
1 TTGAATCTAAAATAAT
127485168 CCCACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
TTGAATCTAAAATAAT
Found at i:127487424 original size:15 final size:16
Alignment explanation
Indices: 127487406--127487435 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
127487396 AAGCAATCCA
127487406 AATT-CAACTCAAAAT
1 AATTCCAACTCAAAAT
127487421 AATTCCAACTCAAAA
1 AATTCCAACTCAAAA
127487436 ATTAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
AATTCCAACTCAAAAT
Found at i:127492887 original size:131 final size:133
Alignment explanation
Indices: 127492588--127492923 Score: 369
Period size: 131 Copynumber: 2.5 Consensus size: 133
127492578 TATTGTTGTT
* * * ** * * *
127492588 AATAAGTAGAAAATTAAATTATGTAACGACATTTTAAGATT-TTTTCTAATATTTTAACATTT--
1 AATAAGCATAAAACTAAATTACATAACAACATTTTAAGGTTGTTGT-TAATATTTTAACATTTAA
* * * *
127492650 -AACAACTTGTTTTGTTGTTACAAATTTGATTAAGGATTTGCAACAACGTACGGATCGTGTCACT
65 CAACAACTTATTTTGTTGTTACAAATTTGATCAAGAATTTGCAACAACG-AC-AATCGTGTCACT
**
127492714 GCAATG
128 GCAACC
* * *
127492720 AGTAAGCATAAAATTAAATTACATAACAACAGTTTAAGGTTGTTGTTAATATTTTAACATTTAAC
1 AATAAGCATAAAACTAAATTACATAACAACATTTTAAGGTTGTTGTTAATATTTTAACATTTAAC
* *
127492785 AACAACTTATTTTGTTGTTACAAATTTTATCAAGAATTTGCAACAAC-A-AATCGTGTCATTGCA
66 AACAACTTATTTTGTTGTTACAAATTTGATCAAGAATTTGCAACAACGACAATCGTGTCACTGCA
127492848 ACC
131 ACC
* * * * ** *
127492851 AATAAGCATGAAACTAAATTACATACCAACATTTTAAAGTTGTTGCTAATATTTTAATGTTCAAC
1 AATAAGCATAAAACTAAATTACATAACAACATTTTAAGGTTGTTGTTAATATTTTAACATTTAAC
127492916 AACAACTT
66 AACAACTT
127492924 GTTTGATCGT
Statistics
Matches: 173, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
131 77 0.45
132 49 0.28
133 4 0.02
135 43 0.25
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (133 bp):
AATAAGCATAAAACTAAATTACATAACAACATTTTAAGGTTGTTGTTAATATTTTAACATTTAAC
AACAACTTATTTTGTTGTTACAAATTTGATCAAGAATTTGCAACAACGACAATCGTGTCACTGCA
ACC
Found at i:127501054 original size:17 final size:18
Alignment explanation
Indices: 127501023--127501056 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
127501013 GTGAGAAAAA
127501023 TAAAAAAATATAAATTAT
1 TAAAAAAATATAAATTAT
*
127501041 TAAAATAATA-AAATTA
1 TAAAAAAATATAAATTA
127501057 CATTTTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAAATATAAATTAT
Found at i:127501405 original size:15 final size:14
Alignment explanation
Indices: 127501365--127501408 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
127501355 TTTAATGGAT
*
127501365 TTTTTTATTTGGTAA
1 TTTTTTATTT-TTAA
*
127501380 TTTTTTCTTTTTATA
1 TTTTTTATTTTTA-A
127501395 TTTTTTATTTTTAA
1 TTTTTTATTTTTAA
127501409 AATTTGAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (14 bp):
TTTTTTATTTTTAA
Found at i:127503489 original size:10 final size:10
Alignment explanation
Indices: 127503448--127503493 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
127503438 ATCACAAAAT
*
127503448 AAAAATATCA
1 AAAAAAATCA
*
127503458 AAAAAAATCT
1 AAAAAAATCA
*
127503468 AAACAAAT--
1 AAAAAAATCA
127503476 AAAAAAATCA
1 AAAAAAATCA
127503486 AAAAAAAT
1 AAAAAAAT
127503494 TAATAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 7 0.23
10 23 0.77
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:127503493 original size:18 final size:18
Alignment explanation
Indices: 127503458--127503493 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
127503448 AAAAATATCA
* *
127503458 AAAAAAATCTAAACAAAT
1 AAAAAAATCAAAAAAAAT
127503476 AAAAAAATCAAAAAAAAT
1 AAAAAAATCAAAAAAAAT
127503494 TAATAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAATCAAAAAAAAT
Found at i:127503540 original size:12 final size:12
Alignment explanation
Indices: 127503496--127503540 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
127503486 AAAAAAATTA
127503496 ATAAACATAAAT
1 ATAAACATAAAT
127503508 A-AATA-AT-AAT
1 ATAA-ACATAAAT
*
127503518 ATAAATATAAAT
1 ATAAACATAAAT
127503530 ATAAACATAAA
1 ATAAACATAAA
127503541 CATTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 5 0.18
11 8 0.29
12 15 0.54
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAACATAAAT
Found at i:127504002 original size:15 final size:15
Alignment explanation
Indices: 127503968--127504005 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
127503958 ATCCATTCAG
127503968 ATAAAAAAAATATAT
1 ATAAAAAAAATATAT
*
127503983 GTAAAAAAAAT-TGAT
1 ATAAAAAAAATAT-AT
127503998 ATAAAAAA
1 ATAAAAAA
127504006 CAAACGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAAAAAAAATATAT
Found at i:127507489 original size:17 final size:16
Alignment explanation
Indices: 127507447--127507494 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
127507437 TACATATCTC
*
127507447 AAATTTATATAATTTT
1 AAATTTAAATAATTTT
** *
127507463 GGATTCAAATTAATTTT
1 AAATTTAAA-TAATTTT
127507480 AAATTTAAATAATTT
1 AAATTTAAATAATTT
127507495 GTGTTCAAAG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (16 bp):
AAATTTAAATAATTTT
Found at i:127517811 original size:2 final size:2
Alignment explanation
Indices: 127517806--127517831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
127517796 GTGTTTGAGT
127517806 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
127517832 TTACCAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:127521682 original size:7 final size:7
Alignment explanation
Indices: 127521670--127521706 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
127521660 ACACAAGTAA
127521670 AATTAAT
1 AATTAAT
127521677 AATTAAT
1 AATTAAT
127521684 AATTAAT
1 AATTAAT
127521691 AA-TAAT
1 AATTAAT
127521697 AA-TAAT
1 AATTAAT
127521703 AATT
1 AATT
127521707 TTTATCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATTAAT
Found at i:127521942 original size:9 final size:9
Alignment explanation
Indices: 127521928--127521954 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
127521918 AATTAAATAG
127521928 TTTGAGTTA
1 TTTGAGTTA
127521937 TTTGAGTTA
1 TTTGAGTTA
127521946 TTTGAGTTA
1 TTTGAGTTA
127521955 ATCAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (9 bp):
TTTGAGTTA
Found at i:127523101 original size:13 final size:13
Alignment explanation
Indices: 127523043--127523101 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
127523033 ATTAAAAACA
* *
127523043 AAATTTGATATAT
1 AAATTTTATATTT
*
127523056 AAA-TATATATTTT
1 AAATTTTATA-TTT
127523069 AAATATTTATATTT
1 AAAT-TTTATATTT
127523083 -AATTTTATATTT
1 AAATTTTATATTT
127523095 AAATTTT
1 AAATTTT
127523102 GTTCCTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 13 0.34
13 17 0.45
14 3 0.08
15 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
AAATTTTATATTT
Found at i:127523966 original size:15 final size:16
Alignment explanation
Indices: 127523945--127524002 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 16
127523935 GAATTTTTAT
127523945 TTATTTTATATAAAAA
1 TTATTTTATATAAAAA
127523961 -TATTTTCATAATAATATAA
1 TTATTTT-AT-ATAA-A-AA
127523980 TTTATTTTATA-AAAAA
1 -TTATTTTATATAAAAA
127523996 TTATTTT
1 TTATTTT
127524003 TTAATCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
15 13 0.36
16 4 0.11
17 5 0.14
18 3 0.08
19 3 0.08
20 2 0.06
21 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTTTATATAAAAA
Found at i:127525871 original size:2 final size:2
Alignment explanation
Indices: 127525866--127525891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
127525856 AATCATTCAA
127525866 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
127525892 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127529078 original size:21 final size:21
Alignment explanation
Indices: 127529053--127529092 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
127529043 AAAACATGAG
*
127529053 ATAATAAAAATATATAATTGA
1 ATAATAAAAATATAAAATTGA
* *
127529074 ATAATCACAATATAAAATT
1 ATAATAAAAATATAAAATT
127529093 AAATTAATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
ATAATAAAAATATAAAATTGA
Found at i:127536794 original size:26 final size:26
Alignment explanation
Indices: 127536765--127536817 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
127536755 ATAATGGACA
127536765 TTATTTTTAGATTTAAACTTAAATTT
1 TTATTTTTAGATTTAAACTTAAATTT
*
127536791 TTATTTTTAGATTTAAATTTAAATTT
1 TTATTTTTAGATTTAAACTTAAATTT
127536817 T
1 T
127536818 AATTGATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (26 bp):
TTATTTTTAGATTTAAACTTAAATTT
Found at i:127537285 original size:38 final size:39
Alignment explanation
Indices: 127537231--127537310 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
127537221 TATATAAAAA
* *
127537231 AAGTTAATATTGTTTAATTTAAGTTTAAGTTTT-GTCCT
1 AAGTTAATATTATTTAATTTAAGTTTAAGTTTTAATCCT
*
127537269 AAGTTAATATTATTTAATTTAAGTTTTAGTTTTAATCCT
1 AAGTTAATATTATTTAATTTAAGTTTAAGTTTTAATCCT
127537308 AAG
1 AAG
127537311 ACAAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 31 0.82
39 7 0.18
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (39 bp):
AAGTTAATATTATTTAATTTAAGTTTAAGTTTTAATCCT
Found at i:127541552 original size:9 final size:9
Alignment explanation
Indices: 127541490--127541607 Score: 68
Period size: 9 Copynumber: 13.1 Consensus size: 9
127541480 CATGTAGTAA
*
127541490 AAAAATGAT
1 AAAAATTAT
127541499 AAAAA--AT
1 AAAAATTAT
127541506 AAAAATTAAT
1 AAAAATT-AT
*
127541516 AAAAGTTAT
1 AAAAATTAT
127541525 AAAAATT-T
1 AAAAATTAT
127541533 AAAAA-T-T
1 AAAAATTAT
127541540 -AAAATTAT
1 AAAAATTAT
*
127541548 AAAAATCATAA
1 AAAAAT--TAT
127541559 AAAAATATAT
1 AAAAAT-TAT
*
127541569 AAAAAATTGT
1 -AAAAATTAT
**
127541579 AAATTTTTAT
1 AAA-AATTAT
**
127541589 AAAAACCAT
1 AAAAATTAT
127541598 AAAAATTAT
1 AAAAATTAT
127541607 A
1 A
127541608 GTATATAGAT
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
6 4 0.05
7 10 0.12
8 7 0.08
9 31 0.36
10 19 0.22
11 14 0.16
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:127541560 original size:23 final size:24
Alignment explanation
Indices: 127541497--127541561 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 24
127541487 TAAAAAAATG
127541497 ATAAAAA-ATAAAAATTAATAAAAGTT
1 ATAAAAATATAAAAA-T--TAAAAGTT
*
127541523 ATAAAAATTTAAAAATTAAAA-TT
1 ATAAAAATATAAAAATTAAAAGTT
127541546 ATAAAAATCATAAAAA
1 ATAAAAAT-ATAAAAA
127541562 AATATATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 10 0.29
24 11 0.31
26 8 0.23
27 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
ATAAAAATATAAAAATTAAAAGTT
Found at i:127541562 original size:33 final size:33
Alignment explanation
Indices: 127541500--127541561 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
127541490 AAAAATGATA
* *
127541500 AAAAATAAAAATTAATAAAAGTTATAAAAATTT
1 AAAAATAAAAATTAATAAAAATCATAAAAATTT
*
127541533 AAAAATTAAAATT-ATAAAAATCATAAAAA
1 AAAAATAAAAATTAATAAAAATCATAAAAA
127541562 AATATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (33 bp):
AAAAATAAAAATTAATAAAAATCATAAAAATTT
Found at i:127541666 original size:37 final size:38
Alignment explanation
Indices: 127541625--127541709 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 38
127541615 GATAATATAG
* * *
127541625 AAAAATTTATAA-AATTTTATAAAGTCGTAAGAAAATTA
1 AAAAATTTATAAGAAATATA-AAAGTCGTAAAAAAATTA
* *
127541663 AAAAATGTA-AAGAAATATAAAATTCGTAAAAAAATTA
1 AAAAATTTATAAGAAATATAAAAGTCGTAAAAAAATTA
*
127541700 TAAAATTTAT
1 AAAAATTTAT
127541710 CATACAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
37 25 0.66
38 13 0.34
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (38 bp):
AAAAATTTATAAGAAATATAAAAGTCGTAAAAAAATTA
Found at i:127541703 original size:20 final size:20
Alignment explanation
Indices: 127541635--127541706 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 20
127541625 AAAAATTTAT
* * *
127541635 AAAATTTTATAAAGTCGTAAG
1 AAAATTATA-AAATTCGTAAA
*
127541656 AAAATTA-AAAAAT-GTAAA
1 AAAATTATAAAATTCGTAAA
*
127541674 GAAA-TATAAAATTCGTAAA
1 AAAATTATAAAATTCGTAAA
127541693 AAAATTATAAAATT
1 AAAATTATAAAATT
127541707 TATCATACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.05
18 12 0.29
19 12 0.29
20 10 0.24
21 6 0.14
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAATTATAAAATTCGTAAA
Found at i:127541924 original size:29 final size:29
Alignment explanation
Indices: 127541870--127541934 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
127541860 TACATTTTAT
127541870 AATTTTTTTATGATTTTATAAAATTTTTC
1 AATTTTTTTATGATTTTATAAAATTTTTC
* **
127541899 AATTTCTTTTAT-ATTTTCTAGGATTTTTC
1 AATTT-TTTTATGATTTTATAAAATTTTTC
*
127541928 TATTTTT
1 AATTTTT
127541935 AATTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 2 0.06
29 23 0.74
30 6 0.19
ACGTcount: A:0.25, C:0.06, G:0.05, T:0.65
Consensus pattern (29 bp):
AATTTTTTTATGATTTTATAAAATTTTTC
Found at i:127544619 original size:11 final size:11
Alignment explanation
Indices: 127544603--127544628 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
127544593 AGGGGTTTAT
127544603 ATATATATATA
1 ATATATATATA
127544614 ATATATATATA
1 ATATATATATA
127544625 ATAT
1 ATAT
127544629 TTCAATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATATA
Found at i:127550027 original size:18 final size:18
Alignment explanation
Indices: 127549986--127550028 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
127549976 ATAATTATCT
*
127549986 TAAACAAGAAAAAGACAA
1 TAAAAAAGAAAAAGACAA
127550004 -AGAAAAAGAAAAAGACAA
1 TA-AAAAAGAAAAAGACAA
127550022 TAAAAAA
1 TAAAAAA
127550029 TTAGCAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.77, C:0.07, G:0.12, T:0.05
Consensus pattern (18 bp):
TAAAAAAGAAAAAGACAA
Found at i:127557092 original size:13 final size:13
Alignment explanation
Indices: 127557074--127557098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127557064 TCAATTTTAA
127557074 AAAATAGAAAATT
1 AAAATAGAAAATT
127557087 AAAATAGAAAAT
1 AAAATAGAAAAT
127557099 ACTTTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AAAATAGAAAATT
Found at i:127557260 original size:25 final size:27
Alignment explanation
Indices: 127557208--127557267 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
127557198 TTTATATTTT
* *
127557208 TGAAAATTGAAAAATATGTTTTGTATA
1 TGAAAATAGAAAAATATGTTTTGAATA
127557235 TGAAAATAG-AAAAT-TGTTTTGAATA
1 TGAAAATAGAAAAATATGTTTTGAATA
*
127557260 TAAAAATA
1 TGAAAATA
127557268 ATGAAAACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 17 0.57
26 5 0.17
27 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (27 bp):
TGAAAATAGAAAAATATGTTTTGAATA
Found at i:127561728 original size:25 final size:25
Alignment explanation
Indices: 127561700--127561778 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
127561690 ATTTCTGCCA
127561700 CATATCCTTTAGTTGATTTCTATCC
1 CATATCCTTTAGTTGATTTCTATCC
* * *
127561725 CATAAT-C-TTATTTTCCATTTCT-GCC
1 CAT-ATCCTTTA-GTT-GATTTCTATCC
127561750 ACATATCCTTTAGTTGATTTCTATCC
1 -CATATCCTTTAGTTGATTTCTATCC
127561776 CAT
1 CAT
127561779 GCATATAGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
24 3 0.07
25 19 0.46
26 16 0.39
27 3 0.07
ACGTcount: A:0.22, C:0.25, G:0.06, T:0.47
Consensus pattern (25 bp):
CATATCCTTTAGTTGATTTCTATCC
Found at i:127561753 original size:51 final size:51
Alignment explanation
Indices: 127561677--127561778 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
127561667 GGAGTACCAA
127561677 AATCTTATTTTCCATTTCTGCCACATATCCTTTAGTTGATTTCTATCCCAT
1 AATCTTATTTTCCATTTCTGCCACATATCCTTTAGTTGATTTCTATCCCAT
127561728 AATCTTATTTTCCATTTCTGCCACATATCCTTTAGTTGATTTCTATCCCAT
1 AATCTTATTTTCCATTTCTGCCACATATCCTTTAGTTGATTTCTATCCCAT
127561779 GCATATAGGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.22, C:0.25, G:0.06, T:0.47
Consensus pattern (51 bp):
AATCTTATTTTCCATTTCTGCCACATATCCTTTAGTTGATTTCTATCCCAT
Found at i:127561754 original size:26 final size:26
Alignment explanation
Indices: 127561677--127561754 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
127561667 GGAGTACCAA
127561677 AATCTTATTTTCCATTTCTGCCACAT
1 AATCTTATTTTCCATTTCTGCCACAT
* * *
127561703 -ATCCTT-TAGTT-GATTTCTATCC-CAT
1 AAT-CTTAT-TTTCCATTTCT-GCCACAT
127561728 AATCTTATTTTCCATTTCTGCCACAT
1 AATCTTATTTTCCATTTCTGCCACAT
127561754 A
1 A
127561755 TCCTTTAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.23, C:0.26, G:0.05, T:0.46
Consensus pattern (26 bp):
AATCTTATTTTCCATTTCTGCCACAT
Found at i:127566958 original size:28 final size:29
Alignment explanation
Indices: 127566900--127566958 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
127566890 TAGACCAAAA
* **
127566900 AATTTATACCCAATGTGAGAATAATTGTC
1 AATTTAGACCCAATGTGAGAATAATAATC
127566929 AATTTAGACCCAA-GTGAGAATAATAATC
1 AATTTAGACCCAATGTGAGAATAATAATC
127566957 AA
1 AA
127566959 ATTCAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (29 bp):
AATTTAGACCCAATGTGAGAATAATAATC
Found at i:127566961 original size:29 final size:30
Alignment explanation
Indices: 127566899--127566961 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
127566889 TTAGACCAAA
* **
127566899 AAATTTATACCCAATGTGAGAATAATTGTC
1 AAATTTAGACCCAATGTGAGAATAATAATC
127566929 -AATTTAGACCCAA-GTGAGAATAATAATC
1 AAATTTAGACCCAATGTGAGAATAATAATC
127566957 AAATT
1 AAATT
127566962 CAAAACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (30 bp):
AAATTTAGACCCAATGTGAGAATAATAATC
Found at i:127567002 original size:24 final size:23
Alignment explanation
Indices: 127566957--127567008 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
127566947 AATAATAATC
**
127566957 AAATTCAAAACTTAATTTAAAAA
1 AAATTCAAAACTTAATAGAAAAA
*
127566980 AAATTCAAACTCTTAATAGAAAAA
1 AAATTCAAA-ACTTAATAGAAAAA
*
127567004 TAATT
1 AAATT
127567009 GTAAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATTCAAAACTTAATAGAAAAA
Found at i:127571591 original size:29 final size:27
Alignment explanation
Indices: 127571527--127571591 Score: 67
Period size: 31 Copynumber: 2.3 Consensus size: 27
127571517 ATTTCATGTG
* *
127571527 TATAATTGTACCAAATCAAAGTTCATG
1 TATAATTGTACCAAATCAAAATTCATA
*
127571554 TATTAAATTGAATACTAAATCAAAATTCATA
1 TA-T-AATTG--TACCAAATCAAAATTCATA
127571585 TATAATT
1 TATAATT
127571592 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 9 0.29
30 1 0.03
31 18 0.58
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (27 bp):
TATAATTGTACCAAATCAAAATTCATA
Found at i:127572360 original size:21 final size:21
Alignment explanation
Indices: 127572312--127572367 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
127572302 TTATTAAGAT
*
127572312 TTAT-TTTAAATATATAACAT
1 TTATATTTAAATATATAACAG
* *
127572332 TATATATTTAAATTTGTAACAG
1 T-TATATTTAAATATATAACAG
*
127572354 TTATATTTTAATAT
1 TTATATTTAAATAT
127572368 TTAAAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 14 0.48
22 14 0.48
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
TTATATTTAAATATATAACAG
Found at i:127572369 original size:23 final size:21
Alignment explanation
Indices: 127572313--127572370 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
127572303 TATTAAGATT
*
127572313 TATTTTAAATATATAACATTA
1 TATTTTAAATTTATAACATTA
*
127572334 TATATTTAAATTTGTAACAGTTA
1 TAT-TTTAAATTTATAACA-TTA
127572357 TATTTTAATATTTA
1 TATTTTAA-ATTTA
127572371 AAATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (21 bp):
TATTTTAAATTTATAACATTA
Found at i:127572382 original size:19 final size:20
Alignment explanation
Indices: 127572355--127572392 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
127572345 TTGTAACAGT
*
127572355 TATATTTTA-ATATTTAAAA
1 TATAATTTATATATTTAAAA
127572374 TATAATTTATATATTTAAA
1 TATAATTTATATATTTAAA
127572393 TTAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTTATATATTTAAAA
Found at i:127577129 original size:15 final size:15
Alignment explanation
Indices: 127577109--127577159 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
127577099 TCAAAATTAA
127577109 TATTTTTGAAACATC
1 TATTTTTGAAACATC
** *
127577124 TATTTTCAAAATAT-
1 TATTTTTGAAACATC
*
127577138 TCATTCTTGAAACATC
1 T-ATTTTTGAAACATC
127577154 TATTTT
1 TATTTT
127577160 CAAAATATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (15 bp):
TATTTTTGAAACATC
Found at i:127577135 original size:30 final size:31
Alignment explanation
Indices: 127577099--127577165 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
127577089 TTCAAAAACC
*
127577099 TCAAAATTAAT-ATTTTTGAAACATCTATTT
1 TCAAAATTAATCATTCTTGAAACATCTATTT
*
127577129 TCAAAA-TATTCATTCTTGAAACATCTATTT
1 TCAAAATTAATCATTCTTGAAACATCTATTT
127577159 TCAAAAT
1 TCAAAAT
127577166 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (31 bp):
TCAAAATTAATCATTCTTGAAACATCTATTT
Found at i:127577174 original size:15 final size:15
Alignment explanation
Indices: 127577124--127577174 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
127577114 TTGAAACATC
127577124 TATTTTCAAAATATT
1 TATTTTCAAAATATT
* * * *
127577139 CATTCTT-GAAACATC
1 TATT-TTCAAAATATT
127577154 TATTTTCAAAATATT
1 TATTTTCAAAATATT
127577169 TATTTT
1 TATTTT
127577175 TTTCCTTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTTTCAAAATATT
Found at i:127578251 original size:31 final size:31
Alignment explanation
Indices: 127578216--127578280 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
127578206 AAAAATAGTA
127578216 ATTGAACTATTCGAAAA-ATTTCATTCAAGTC
1 ATTGAACTATTC-AAAACATTTCATTCAAGTC
* * *
127578247 ATTGAACTATTCAAAACTTTTTATTTAAGTC
1 ATTGAACTATTCAAAACATTTCATTCAAGTC
127578278 ATT
1 ATT
127578281 AGATTGTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.42
Consensus pattern (31 bp):
ATTGAACTATTCAAAACATTTCATTCAAGTC
Found at i:127578334 original size:21 final size:21
Alignment explanation
Indices: 127578308--127578349 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
127578298 TTTTTTAAAG
127578308 TCCAGCTAGTGAGTTCCAACT
1 TCCAGCTAGTGAGTTCCAACT
127578329 TCCAGCTAGTGAGTTCCAACT
1 TCCAGCTAGTGAGTTCCAACT
127578350 GATGATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (21 bp):
TCCAGCTAGTGAGTTCCAACT
Found at i:127580961 original size:12 final size:12
Alignment explanation
Indices: 127580944--127580971 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
127580934 ACAAGTATTG
127580944 AATTTAATAATT
1 AATTTAATAATT
127580956 AATTTAATAATT
1 AATTTAATAATT
127580968 AATT
1 AATT
127580972 CATTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTTAATAATT
Found at i:127588536 original size:16 final size:16
Alignment explanation
Indices: 127588515--127588547 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
127588505 ACTATACTTA
127588515 AAAATCTCTAAAATTG
1 AAAATCTCTAAAATTG
127588531 AAAATCTCTAAAATTG
1 AAAATCTCTAAAATTG
127588547 A
1 A
127588548 GTTGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (16 bp):
AAAATCTCTAAAATTG
Found at i:127588721 original size:17 final size:16
Alignment explanation
Indices: 127588692--127588726 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
127588682 ACACTATATA
127588692 TTTTTTTTCTTCTATT
1 TTTTTTTTCTTCTATT
*
127588708 TTTTTTATTTTTCTATT
1 TTTTTT-TTCTTCTATT
127588725 TT
1 TT
127588727 AACCAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTCTTCTATT
Found at i:127589413 original size:21 final size:22
Alignment explanation
Indices: 127589389--127589432 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
127589379 GATTTTCTTG
* *
127589389 ATTTTA-ATAAATTATTTTAAA
1 ATTTTATAAAAATAATTTTAAA
127589410 ATTTTATAAAAATAATTTTAAA
1 ATTTTATAAAAATAATTTTAAA
127589432 A
1 A
127589433 AAAATTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTATAAAAATAATTTTAAA
Found at i:127591072 original size:13 final size:13
Alignment explanation
Indices: 127591054--127591095 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
127591044 AAATTTAAAT
127591054 TATTTAGTGATAA
1 TATTTAGTGATAA
127591067 TATTTAG-GAT--
1 TATTTAGTGATAA
127591077 TATTTAGTGATAA
1 TATTTAGTGATAA
127591090 TATTTA
1 TATTTA
127591096 AAAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Done.