Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 1 of 150
Found at i:3489 original size:31 final size:30
Alignment explanation
Indices: 3397--3493 Score: 113
Period size: 31 Copynumber: 3.2 Consensus size: 30
3387 AAACCCCTAG
* *
3397 ATCCCAAGCAGGGATATCCTAGAATAGGAT
1 ATCCCAAGCCGGGATATCCTGGAATAGGAT
* * * *
3427 AACCCAAACCGGGATGTCCCTGAAATAGGAT
1 ATCCCAAGCCGGGATAT-CCTGGAATAGGAT
*
3458 ATCCCAAGCCGGGATATACCTGGAATGGGAT
1 ATCCCAAGCCGGGATAT-CCTGGAATAGGAT
3489 ATCCC
1 ATCCC
3494 TGGCTGGAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
30 13 0.24
31 41 0.76
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (30 bp):
ATCCCAAGCCGGGATATCCTGGAATAGGAT
Found at i:3757 original size:31 final size:31
Alignment explanation
Indices: 3675--3758 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
3665 AGAATAAGAA
* *
3675 TGAATTAAATTCAGTGCTTACTAAAACGTTG
1 TGAAATAAATTCAGTGCTTATTAAAACGTTG
* *
3706 TAAAATAAATTTAGTGCTTATTAAAACGTTG
1 TGAAATAAATTCAGTGCTTATTAAAACGTTG
3737 TGAAATAAATTCAGTGCTTATT
1 TGAAATAAATTCAGTGCTTATT
3759 TACAAGGACT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (31 bp):
TGAAATAAATTCAGTGCTTATTAAAACGTTG
Found at i:10332 original size:31 final size:31
Alignment explanation
Indices: 10297--10355 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
10287 AAAAACCATA
*
10297 AAAATGTGAAGTAAGATGATATAGTTAGTAT
1 AAAATGTGAAATAAGATGATATAGTTAGTAT
* *
10328 AAAATGTGAAATAAGTTGATATGGTTAG
1 AAAATGTGAAATAAGATGATATAGTTAG
10356 GAAATTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (31 bp):
AAAATGTGAAATAAGATGATATAGTTAGTAT
Found at i:18338 original size:29 final size:29
Alignment explanation
Indices: 18300--18385 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
18290 AACATTTGTT
* *
18300 AATATGCATTAATTAAAACAAATATATAA
1 AATATACATTAATTATAACAAATATATAA
* *
18329 AATATACATTAATTATACCAAATGTATAA
1 AATATACATTAATTATAACAAATATATAA
*
18358 AATATACATTAGTTATAACAAATATATA
1 AATATACATTAATTATAACAAATATATA
18386 TTATTATTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (29 bp):
AATATACATTAATTATAACAAATATATAA
Found at i:18604 original size:31 final size:31
Alignment explanation
Indices: 18540--18676 Score: 213
Period size: 31 Copynumber: 4.5 Consensus size: 31
18530 AGATAAGCTC
18540 GAACCGGGATATCCTAAACTGGAATA-CATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
* * *
18570 GAACCGGGACATCCTAAACTGGAAAATCATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
* *
18601 GAACAGGGATATCCTAAACTGGAACACCATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
*
18632 GAACCGGGATACCCTAAACTGGAATACCATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
18663 GAACCGGGATATCC
1 GAACCGGGATATCC
18677 GCATAACGGG
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 24 0.25
31 72 0.75
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
GAACCGGGATATCCTAAACTGGAATACCATT
Found at i:19929 original size:66 final size:66
Alignment explanation
Indices: 19857--20057 Score: 343
Period size: 66 Copynumber: 3.1 Consensus size: 66
19847 AAAAAAAAAG
* *
19857 AAAAAGAATATACAATTTATTGTTTACTACTATTATTTCCATTATTTAGTTATTAATATCTACAA
1 AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
19922 A
66 A
*
19923 AAAAAGAATATTCATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
1 AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
19988 A
66 A
* *
19989 AAAAAG--TATACATTTTATTGTTTACTAATATTATTTCCATTTTTTAGCTATTAATATCTACAA
1 AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
20052 A
66 A
20053 AAAAA
1 AAAAA
20058 AAGAAAAAAG
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
64 60 0.47
66 69 0.53
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (66 bp):
AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
A
Found at i:38372 original size:24 final size:24
Alignment explanation
Indices: 38345--38396 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38335 CCTAGCTACC
**
38345 CACACCCACACACTTGCACTCACT
1 CACACCCACACACACGCACTCACT
**
38369 CACATGCACACACACGCACTCACT
1 CACACCCACACACACGCACTCACT
38393 CACA
1 CACA
38397 TATACACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.13
Consensus pattern (24 bp):
CACACCCACACACACGCACTCACT
Found at i:38397 original size:24 final size:24
Alignment explanation
Indices: 38351--38468 Score: 87
Period size: 24 Copynumber: 4.8 Consensus size: 24
38341 TACCCACACC
** *
38351 CACACACTTGCACTCACTCACATG
1 CACACACACGCACACACTCACATG
*
38375 CACACACACGCACTCACTCACAT-
1 CACACACACGCACACACTCACATG
* * * **
38398 -ATACACATGCATACACACACACACA
1 CACACACACGC--ACACACTCACATG
*
38423 CACACACACACACACACTCACATG
1 CACACACACGCACACACTCACATG
*
38447 CACACATGCATGCACACACTCA
1 CACACA--CACGCACACACTCA
38469 TTTTTAAAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
22 8 0.11
24 46 0.63
26 19 0.26
ACGTcount: A:0.38, C:0.42, G:0.06, T:0.14
Consensus pattern (24 bp):
CACACACACGCACACACTCACATG
Found at i:38464 original size:2 final size:2
Alignment explanation
Indices: 38410--38444 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38400 ACACATGCAT
*
38410 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC TC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
38445 TGCACACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:39484 original size:54 final size:54
Alignment explanation
Indices: 39414--39516 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
39404 AATATACCTA
* * *
39414 TTTCATCGCAAGCAGAGGCTATGAATGTTGATAATCAGGTAATATGAACAATCT
1 TTTCATCGCAAGCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
* * * *
39468 TTTCATCTCAATCAGAGTATATGGATGTTGAGAATCAGGTAACATGAAC
1 TTTCATCGCAAGCAGAGGATATGAATGTTGAGAATCAGGTAACATGAAC
39517 TTTCTTCCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (54 bp):
TTTCATCGCAAGCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
Found at i:42410 original size:27 final size:27
Alignment explanation
Indices: 42370--42427 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
42360 GACTTTGGAA
42370 TTTATAATATAAAAATATATAAATTTATT
1 TTTATAATATAAAAATATAT-AATTT-TT
* *
42399 TTTATAA-A-AAAATTGTATAATTTTT
1 TTTATAATATAAAAATATATAATTTTT
42424 TTTA
1 TTTA
42428 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 5 0.19
27 8 0.30
28 1 0.04
29 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTATAATATAAAAATATATAATTTTT
Found at i:42640 original size:23 final size:24
Alignment explanation
Indices: 42609--42653 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42599 TCTACTTTAA
*
42609 AATTGTTAA-AAAAATATTAAAGC
1 AATTATTAAGAAAAATATTAAAGC
*
42632 AATTATTAAGAAAAGTATTAAA
1 AATTATTAAGAAAAATATTAAA
42654 AATACCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (24 bp):
AATTATTAAGAAAAATATTAAAGC
Found at i:42894 original size:3 final size:3
Alignment explanation
Indices: 42886--42938 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
42876 CTGAGTAGAG
42886 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42934 ATA AT
1 ATA AT
42939 GTGCGGTGTT
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):
ATA
Found at i:45513 original size:18 final size:18
Alignment explanation
Indices: 45490--45525 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
45480 AAAAAGAAAT
45490 TCAAAATAATTTT-TAAAA
1 TCAAAAT-ATTTTATAAAA
45508 TCAAAATATTTTATAAAA
1 TCAAAATATTTTATAAAA
45526 ATTTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
TCAAAATATTTTATAAAA
Found at i:49473 original size:4 final size:4
Alignment explanation
Indices: 49464--49495 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
49454 TTGCTAGCTC
49464 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
49496 ATATTCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:52749 original size:26 final size:27
Alignment explanation
Indices: 52720--52778 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
52710 ATTCATTAGT
*
52720 AAAATAATTATTTAA-TATGTAATT-TA
1 AAAATAATTAATTAATTAT-TAATTGTA
*
52746 AAAAAAATTAATTAATTATTAATTGTA
1 AAAATAATTAATTAATTATTAATTGTA
*
52773 TAAATA
1 AAAATA
52779 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AAAATAATTAATTAATTATTAATTGTA
Found at i:54076 original size:20 final size:19
Alignment explanation
Indices: 54038--54076 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54028 ATATTAATTT
* *
54038 TTTTAAAAAAATTATATAA
1 TTTTAAAAAAAATAAATAA
54057 TTTTAAAAAAAATACAATAA
1 TTTTAAAAAAAATA-AATAA
54077 ACTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTTAAAAAAAATAAATAA
Found at i:56195 original size:47 final size:47
Alignment explanation
Indices: 56100--56229 Score: 127
Period size: 47 Copynumber: 2.8 Consensus size: 47
56090 AGTCAGTAAT
* * * *
56100 TCATCTACTTGACTAGTGGTTTATCCACAACGTATTCTAATCAGTAG
1 TCATCTGCTTGACCAATAGTTTATCCACAACGTATTCTAATCAGTAG
* * *
56147 TCATCTGTTTGACCAATAGTTTATCCACAACGTATTCTACT-TGATAG
1 TCATCTGCTTGACCAATAGTTTATCCACAACGTATTCTAATCAG-TAG
* * * * * *
56194 TCATTTGCTTGACTAGTGGTTTACCCACAACATATT
1 TCATCTGCTTGACCAATAGTTTATCCACAACGTATT
56230 AGTGACTTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
46 1 0.01
47 67 0.99
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (47 bp):
TCATCTGCTTGACCAATAGTTTATCCACAACGTATTCTAATCAGTAG
Found at i:56315 original size:91 final size:91
Alignment explanation
Indices: 56199--56367 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 91
56189 GATAGTCATT
* * * * *
56199 TGCTTGACTAGTGGTTTACCCACAACATATTAG-TGACTTTTATCTGCACAAATGGATGATTCAT
1 TGCTCGACCAGTGGTTTACCCACAACATATTAGCAG-CTTTTATATGCACAAA-GGATGATTCAC
56263 CCACCAATAT-TTTAGTCGGTAGACATA
64 CCACCAATATATTTAGTCGGTAGACATA
* * *
56290 TGCTCGACCAGTGGTTTATCCACAACATATTAGCAGCTTTTATATGCACAGAGGATGGTTCACCC
1 TGCTCGACCAGTGGTTTACCCACAACATATTAGCAGCTTTTATATGCACAAAGGATGATTCACCC
*
56355 ATCAATATATTTA
66 ACCAATATATTTA
56368 TCATTAGCAG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 18 0.27
91 48 0.72
92 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (91 bp):
TGCTCGACCAGTGGTTTACCCACAACATATTAGCAGCTTTTATATGCACAAAGGATGATTCACCC
ACCAATATATTTAGTCGGTAGACATA
Found at i:64378 original size:88 final size:88
Alignment explanation
Indices: 64228--64405 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
64218 TGTTGGACCG
64228 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
1 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
64293 TTTTAAAACTGGTGTTTAATTAT
66 TTTTAAAACTGGTGTTTAATTAT
*
64316 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATGTTTAATC
1 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
64381 TTTTAAAACTGGTGTTTAATTAT
66 TTTTAAAACTGGTGTTTAATTAT
64404 TG
1 TG
64406 TTATCTTTTT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (88 bp):
TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
TTTTAAAACTGGTGTTTAATTAT
Found at i:68403 original size:5 final size:6
Alignment explanation
Indices: 68386--68412 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
68376 TGGTGGGGAA
68386 GAGGGG GAGGGG GAGGGG GAGGGG GAG
1 GAGGGG GAGGGG GAGGGG GAGGGG GAG
68413 AGCGAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
GAGGGG
Found at i:68662 original size:17 final size:17
Alignment explanation
Indices: 68640--68673 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
68630 TTAATGGTAA
68640 ATTATACCAACAGTCAC
1 ATTATACCAACAGTCAC
68657 ATTATACCAACAGTCAC
1 ATTATACCAACAGTCAC
68674 TCAACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
ATTATACCAACAGTCAC
Found at i:70460 original size:22 final size:22
Alignment explanation
Indices: 70419--70462 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
70409 CATCAAAATA
*
70419 ATAAAATAAGATTCACAAGTTT
1 ATAAAATAAGATTCAAAAGTTT
70441 ATAAAATAAGATT-ATAAAGTTT
1 ATAAAATAAGATTCA-AAAGTTT
70463 CCTCAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
ATAAAATAAGATTCAAAAGTTT
Found at i:70889 original size:2 final size:2
Alignment explanation
Indices: 70884--70924 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
70874 TTAACTGGTT
* *
70884 TA TA TA TA TA TA TA TA TT TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70925 TCCTTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:77808 original size:4 final size:4
Alignment explanation
Indices: 77799--77823 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
77789 GGAAAAGGTA
77799 TAGC TAGC TAGC TAGC TAGC TAGC T
1 TAGC TAGC TAGC TAGC TAGC TAGC T
77824 CTAAAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (4 bp):
TAGC
Found at i:87791 original size:153 final size:153
Alignment explanation
Indices: 87513--87823 Score: 622
Period size: 153 Copynumber: 2.0 Consensus size: 153
87503 AAACTAGACT
87513 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
1 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
87578 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTAGTGCAAAATGTTGATAACCAAGTTTAT
66 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTAGTGCAAAATGTTGATAACCAAGTTTAT
87643 TACACTCTCCTTTCTTTTCTCTA
131 TACACTCTCCTTTCTTTTCTCTA
87666 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
1 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
87731 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTAGTGCAAAATGTTGATAACCAAGTTTAT
66 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTAGTGCAAAATGTTGATAACCAAGTTTAT
87796 TACACTCTCCTTTCTTTTCTCTA
131 TACACTCTCCTTTCTTTTCTCTA
87819 CAATA
1 CAATA
87824 TTTCTCATCA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 158 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (153 bp):
CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTAGTGCAAAATGTTGATAACCAAGTTTAT
TACACTCTCCTTTCTTTTCTCTA
Found at i:93855 original size:5 final size:5
Alignment explanation
Indices: 93845--93869 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
93835 GTCCATATTC
93845 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
93870 GTGGGTGATA
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:101199 original size:69 final size:69
Alignment explanation
Indices: 101081--101328 Score: 257
Period size: 69 Copynumber: 3.6 Consensus size: 69
101071 AGGGGTACCT
** ** *
101081 GGAACAGAATCAGCAAAAATAGACGAGGT-TTGCCCCTTGAACAACTTATCCT-CATAGACAGGA
1 GGAACAGAATCAGCAAAAATAGACGAACTCTT-CCCCTTGAACATGTTAT-CTGCATAGGCAGGA
*
101144 GAGCTT
64 GAGCTA
* * * * * * * * *
101150 GGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACATGTTATCTGTATAGGCAGGAGT
1 GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
101215 GCTA
66 GCTA
* * *
101219 GGAACAGAATCAGCAAAAATAGATGAGCTCTTTCCCTTGAACATGTTATCTGCATAGGCAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
**
101284 ATTA
66 GCTA
* * *
101288 GGAACAGAATCTGCAAAAATAGATGAGCTCTTCCCCTTGAA
1 GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAA
101329 GACTTTGTTT
Statistics
Matches: 147, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
68 2 0.01
69 143 0.97
70 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (69 bp):
GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
GCTA
Found at i:101320 original size:138 final size:137
Alignment explanation
Indices: 101081--101402 Score: 337
Period size: 138 Copynumber: 2.3 Consensus size: 137
101071 AGGGGTACCT
* * **
101081 GGAACAGAATCAGCAAAAATAGACGAGGTTTGCCCCTTGAACAACTTATCCTCATAGACAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAGCTTT-TCCCTTGAACATGTTATCCTCATAGACAGGAGA
* * * * * * * *
101146 GCTTGGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACA-TGTTATCTGTATAGGCA
65 GATTGGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACT-TTATCTGTATAAGCA
101210 GGAG-TGCTA
129 GG-GCTGCTA
* *
101219 GGAACAGAATCAGCAAAAATAGATGAGCTCTTTCCCTTGAACATGTTAT-CTGCATAGGCAGGAG
1 GGAACAGAATCAGCAAAAATAGACGAGCT-TTTCCCTTGAACATGTTATCCT-CATAGACAGGAG
* * * * * *
101283 A-ATTAGGAACAGAATCTGCAAAAATAGATGAGCTCTTCCCCTTGAAGACTTTGTTTTTATAAGC
64 AGATT-GGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACTTTATCTGTATAAGC
*
101347 AGGGCTGCTT
128 AGGGCTGCTA
* * *
101357 GGAATAGAATCCGCAAAAATAGACGAGCTTTTCCCGTGGAACATGT
1 GGAACAGAATCAGCAAAAATAGACGAGCTTTTCCC-TTGAACATGT
101403 CCCCTATGTA
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
137 11 0.07
138 139 0.91
139 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (137 bp):
GGAACAGAATCAGCAAAAATAGACGAGCTTTTCCCTTGAACATGTTATCCTCATAGACAGGAGAG
ATTGGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACTTTATCTGTATAAGCAGG
GCTGCTA
Found at i:107366 original size:4 final size:4
Alignment explanation
Indices: 107357--107383 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
107347 CCCACTATTA
107357 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
107384 ATTTATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:110267 original size:6 final size:6
Alignment explanation
Indices: 110258--110306 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
110248 GAAGGCGAGT
* * *
110258 GTGAGG GTGAGG GTGAGG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG
1 GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG
110306 G
1 G
110307 AGGAGATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.27, C:0.00, G:0.57, T:0.16
Consensus pattern (6 bp):
GTGAAG
Found at i:110316 original size:18 final size:18
Alignment explanation
Indices: 110277--110317 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
110267 AGGGTGAGGG
* *
110277 TGAAGGTGAAGGTGAAGG
1 TGAAGGTGAAGGAGAAGA
*
110295 TGAAGGTGAAGGAGGAGA
1 TGAAGGTGAAGGAGAAGA
110313 TGAAG
1 TGAAG
110318 AGGAAGAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.15
Consensus pattern (18 bp):
TGAAGGTGAAGGAGAAGA
Found at i:122964 original size:4 final size:4
Alignment explanation
Indices: 122955--123020 Score: 88
Period size: 4 Copynumber: 17.8 Consensus size: 4
122945 CCCCATTCGT
*
122955 TTTC TTTC -TTC -TTC -TTC -TTC -TTC TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
122998 TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT
123021 TTTATTTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 15 0.25
4 44 0.75
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:135615 original size:12 final size:11
Alignment explanation
Indices: 135598--135640 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 11
135588 ATTTTGATGC
135598 TTAATTTTTTAT
1 TTAATTTTTT-T
135610 TTAATTTTTTGT
1 TTAATTTTTT-T
135622 TTAATTTTTCTT
1 TTAATTTTT-TT
135634 TTAATTT
1 TTAATTT
135641 GATATCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 28 0.97
13 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (11 bp):
TTAATTTTTTT
Found at i:144542 original size:5 final size:5
Alignment explanation
Indices: 144534--144559 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
144524 TGAAATATTA
144534 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
144560 TTAGGGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:148438 original size:3 final size:3
Alignment explanation
Indices: 148430--148456 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
148420 GCCTTTAAGG
148430 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
148457 TTCTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:148849 original size:3 final size:3
Alignment explanation
Indices: 148841--148877 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
148831 ATGCTTTTAC
148841 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
148878 CTATACAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:153172 original size:17 final size:16
Alignment explanation
Indices: 153150--153202 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
153140 TCAAACAATT
153150 TTATTTAAATCACTAAA
1 TTATTTAAA-CACTAAA
153167 TTATTTAAA-A--AAA
1 TTATTTAAACACTAAA
153180 TTTATTTAAGACACTAAA
1 -TTATTTAA-ACACTAAA
153198 TTATT
1 TTATT
153203 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.10
14 8 0.26
15 2 0.06
16 1 0.03
17 14 0.45
18 3 0.10
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (16 bp):
TTATTTAAACACTAAA
Found at i:156395 original size:5 final size:5
Alignment explanation
Indices: 156385--156413 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
156375 TTCATACATA
156385 TGTTT TGTTT TGTTT TGTTT TGTTT TGTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTT
156414 ATGGTGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
TGTTT
Found at i:175027 original size:26 final size:28
Alignment explanation
Indices: 174988--175039 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
174978 CAATATAGGC
*
174988 TTTTACAATATTATCATAA-TTTTTTCA
1 TTTTACAATATTATAATAACTTTTTTCA
*
175015 TTTTATAA-ATTATAATAACTTTTTT
1 TTTTACAATATTATAATAACTTTTTT
175040 TTTACTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTACAATATTATAATAACTTTTTTCA
Found at i:179458 original size:33 final size:33
Alignment explanation
Indices: 179416--179480 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
179406 CATGCTAAAA
* *
179416 TTTGTGTATAAGTTTATATTTTAGTCGAGTTAT
1 TTTGGGTATAAATTTATATTTTAGTCGAGTTAT
*
179449 TTTGGGTATAAATTTATATTTTTGTCGAGTTA
1 TTTGGGTATAAATTTATATTTTAGTCGAGTTA
179481 CAAAATAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (33 bp):
TTTGGGTATAAATTTATATTTTAGTCGAGTTAT
Found at i:192810 original size:25 final size:25
Alignment explanation
Indices: 192781--192843 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
192771 CTAATTTCTC
* *
192781 CTTTCTTTCTT-TCCCTTTTTCTTTT
1 CTTTCTTT-TTCTCCCTGTTTCGTTT
192806 CTTTCTTTTTCTCCCTGTTTCGTTT
1 CTTTCTTTTTCTCCCTGTTTCGTTT
*
192831 CTATTCTATTTCT
1 CT-TTCTTTTTCT
192844 TTTATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 22 0.67
26 9 0.27
ACGTcount: A:0.03, C:0.27, G:0.03, T:0.67
Consensus pattern (25 bp):
CTTTCTTTTTCTCCCTGTTTCGTTT
Found at i:194896 original size:29 final size:30
Alignment explanation
Indices: 194853--194915 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
194843 TTCAAGACTC
* *
194853 AAATTTCATAATTCAAAAAA-A-AAGTACT
1 AAATTTAATAATTCAAAAAATATAAGAACT
194881 AAATTTAATCAATTCAAAAAATATAAGAACT
1 AAATTTAAT-AATTCAAAAAATATAAGAACT
194912 AAAT
1 AAAT
194916 CCGCAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 1 0.03
31 10 0.33
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATTTAATAATTCAAAAAATATAAGAACT
Found at i:195396 original size:20 final size:20
Alignment explanation
Indices: 195355--195397 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
195345 TAAATATATA
**
195355 TTTTATTTTAAAATACTTTT
1 TTTTATTTTAAAATACAATT
195375 TTTTATTTTTAAAATA-AATT
1 TTTTA-TTTTAAAATACAATT
195395 TTT
1 TTT
195398 GGTGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATTTTAAAATACAATT
Found at i:195396 original size:21 final size:20
Alignment explanation
Indices: 195355--195397 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
195345 TAAATATATA
**
195355 TTTTATTTTAAAATACTTTT
1 TTTTATTTTAAAATAAATTT
195375 TTTTATTTTTAAAATAAATTT
1 TTTTA-TTTTAAAATAAATTT
195396 TT
1 TT
195398 GGTGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATTTTAAAATAAATTT
Found at i:197548 original size:21 final size:22
Alignment explanation
Indices: 197513--197567 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
197503 TTTCCCCCCA
* *
197513 TTGCATGTGTCTATACAA-TTGT
1 TTGCA-GTGGCTATACAATTTAT
*
197535 TTGCAGTGGCTATATAATTTAT
1 TTGCAGTGGCTATACAATTTAT
197557 TTGCAGTGGCT
1 TTGCAGTGGCT
197568 CCATCTGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (22 bp):
TTGCAGTGGCTATACAATTTAT
Found at i:197801 original size:52 final size:52
Alignment explanation
Indices: 197738--197884 Score: 216
Period size: 52 Copynumber: 2.9 Consensus size: 52
197728 TGCATAGTCC
*
197738 TGGTGCTGTTAATTTGGTACTGTTAATTTTGAATGCTTTGAAATGTTTGAAA
1 TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
*
197790 TGGTGTTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
1 TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
* *
197842 TGGTGCTGTT-A----CTACT-TCAACTTTGAATGCTTTGAAATGTTTG
1 TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTG
197885 CTCACTGATA
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
46 26 0.29
47 4 0.04
51 1 0.01
52 59 0.66
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (52 bp):
TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
Found at i:199102 original size:23 final size:23
Alignment explanation
Indices: 199033--199105 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
199023 GTATATTAAA
199033 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
*** * * *
199056 ATATAA-TATTTTTA-ATTGA-A
1 ATATAATTAAAATCATTTTGATT
199076 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
199099 ATATAAT
1 ATATAAT
199106 ATTAATATAA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 8 0.23
23 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATAATTAAAATCATTTTGATT
Found at i:202484 original size:92 final size:91
Alignment explanation
Indices: 202327--202535 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
202317 TTGATTTTAG
** *
202327 TAAATTCATATAAGAACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
202392 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
202419 TAAATTCATATAAGAAAATTTATTATCAAGCATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
202483 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
202511 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
202536 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 28 0.27
92 70 0.69
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:202646 original size:15 final size:15
Alignment explanation
Indices: 202565--202652 Score: 55
Period size: 15 Copynumber: 6.1 Consensus size: 15
202555 ATTTTAAATC
*
202565 ATATATTATAATTAAA
1 ATATATT-TAATTATA
202581 ATATATTTAA-TAT-
1 ATATATTTAATTATA
*
202594 -TA-ATTT-ATTAAGA
1 ATATATTTAATT-ATA
* *
202607 ATTTTATTAAATTAT-
1 A-TATATTTAATTATA
202622 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
202636 ATATATTTAATAATA
1 ATATATTTAATTATA
202651 AT
1 AT
202653 TATGGTTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
10 1 0.02
11 5 0.09
12 3 0.05
13 8 0.15
14 8 0.15
15 16 0.29
16 11 0.20
17 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:202671 original size:55 final size:55
Alignment explanation
Indices: 202558--202683 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 55
202548 TTAAATTATT
* * * *
202558 TTAAATCATATATTATAATTAAAATATATTTAATATTAATTTATTAAGAATTTTA
1 TTAAATTATATATTATAATTAAAATATATTTAATAATAATTTATTAAGAATATGA
* * *
202613 TTAAATTATATATTTTAATTATAATATATTTAATAATAA-TTATGGTTA-AATATGA
1 TTAAATTATATATTATAATTAAAATATATTTAATAATAATTTAT--TAAGAATATGA
*
202668 TTAAATTATTTATTAT
1 TTAAATTATATATTAT
202684 TGATATTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
54 4 0.07
55 54 0.90
56 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (55 bp):
TTAAATTATATATTATAATTAAAATATATTTAATAATAATTTATTAAGAATATGA
Found at i:202691 original size:156 final size:154
Alignment explanation
Indices: 202602--202910 Score: 474
Period size: 156 Copynumber: 2.0 Consensus size: 154
202592 ATTAATTTAT
*
202602 TAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGGTTAAATATG
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGGTTAAATATG
* * *
202667 ATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATAATAAT
66 ATTAAAATATTTATTACTGATATTAATAATATTATTAAAATTTAAATAACAATAACAATAATAAT
* *
202732 TTACCAAAACAAATTTCTGCTAATTA
131 TT--CAAAACAAATTTATACTAATTA
*
202758 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATG
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGGTTAAATATG
* * * *
202823 ATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAACAACAATAATCAT
66 ATTAAAATATTTATTACTGATATTAATAATATTATTAAAATTTAAATAACAATAACAATAATAAT
*
202888 TTACCAAAACAAATTTATGCTAA
131 TT--CAAAACAAATTTATACTAA
202911 GGGTATTCTA
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 145 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (154 bp):
TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGGTTAAATATG
ATTAAAATATTTATTACTGATATTAATAATATTATTAAAATTTAAATAACAATAACAATAATAAT
TTCAAAACAAATTTATACTAATTA
Found at i:202791 original size:18 final size:17
Alignment explanation
Indices: 202763--202797 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
202753 AATTATAAGA
*
202763 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
202780 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
202798 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:212806 original size:57 final size:58
Alignment explanation
Indices: 212729--212851 Score: 187
Period size: 57 Copynumber: 2.1 Consensus size: 58
212719 AAAACTCGAA
* *
212729 TTTTTTTACTGTACTAGGTGCCGGCCGTTGACAGGCCAGCACCTAAAATTTTTTTTTCC
1 TTTTTTTACTGTACTAGGTGCCGGCCATTGACAGGCCAGCACC-AAAAATTTTTTTTCC
*
212788 TTTTTTT-C-GTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTCC
1 TTTTTTTACTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTCC
212844 TTCTTTTT
1 TT-TTTTT
212852 TGTATATCAG
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 16 0.27
57 36 0.60
58 1 0.02
59 7 0.12
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (58 bp):
TTTTTTTACTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTCC
Found at i:214825 original size:2 final size:2
Alignment explanation
Indices: 214820--214848 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
214810 TAGTAATCTA
214820 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
214849 CAGTAATTAA
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:217817 original size:26 final size:26
Alignment explanation
Indices: 217788--217845 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
217778 TTAGATTTAT
* *
217788 ATTATTTTATAAGCTATAGAGTAAGA
1 ATTATTTGATAAACTATAGAGTAAGA
217814 ATTATTTGATAAACTATAGAGTAAGA
1 ATTATTTGATAAACTATAGAGTAAGA
217840 ATTATT
1 ATTATT
217846 ATGCAACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (26 bp):
ATTATTTGATAAACTATAGAGTAAGA
Found at i:218236 original size:12 final size:12
Alignment explanation
Indices: 218219--218243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
218209 CAGGATAGTG
218219 AAAATTATGAAC
1 AAAATTATGAAC
218231 AAAATTATGAAC
1 AAAATTATGAAC
218243 A
1 A
218244 GTTTCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATTATGAAC
Found at i:220141 original size:8 final size:8
Alignment explanation
Indices: 220124--220193 Score: 62
Period size: 7 Copynumber: 9.2 Consensus size: 8
220114 CTTGACACCA
220124 TAAA-CCC
1 TAAACCCC
*
220131 TAAATCCC
1 TAAACCCC
220139 T-AACCCC
1 TAAACCCC
220146 T-AACCCC
1 TAAACCCC
220153 TAAATCCCCC
1 TAAA--CCCC
220163 T-AACCCC
1 TAAACCCC
*
220170 TAAATCCC
1 TAAACCCC
220178 T-AACCCC
1 TAAACCCC
220185 T-AACCCC
1 TAAACCCC
220192 TA
1 TA
220194 CCCCCTACTC
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
7 35 0.65
8 12 0.22
9 2 0.04
10 5 0.09
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.19
Consensus pattern (8 bp):
TAAACCCC
Found at i:220154 original size:22 final size:22
Alignment explanation
Indices: 220128--220193 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
220118 ACACCATAAA
220128 CCCTAAATCCCTAACCCCTAAC
1 CCCTAAATCCCTAACCCCTAAC
220150 CCCTAAAT--C---CCCCTAAC
1 CCCTAAATCCCTAACCCCTAAC
220167 CCCTAAATCCCTAACCCCTAAC
1 CCCTAAATCCCTAACCCCTAAC
220189 CCCTA
1 CCCTA
220194 CCCCCTACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 16 0.41
19 1 0.03
20 1 0.03
22 21 0.54
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.18
Consensus pattern (22 bp):
CCCTAAATCCCTAACCCCTAAC
Found at i:220164 original size:17 final size:16
Alignment explanation
Indices: 220142--220200 Score: 79
Period size: 17 Copynumber: 3.8 Consensus size: 16
220132 AAATCCCTAA
220142 CCCCTAACCCCTAAAT
1 CCCCTAACCCCTAAAT
220158 CCCCCTAACCCCTAAAT
1 -CCCCTAACCCCTAAAT
220175 -CCCTAACCCCT-AA-
1 CCCCTAACCCCTAAAT
*
220188 CCCCTACCCCCTA
1 CCCCTAACCCCTA
220201 CTCCTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
14 12 0.31
15 11 0.28
17 16 0.41
ACGTcount: A:0.27, C:0.56, G:0.00, T:0.17
Consensus pattern (16 bp):
CCCCTAACCCCTAAAT
Found at i:220201 original size:7 final size:7
Alignment explanation
Indices: 220136--220200 Score: 76
Period size: 7 Copynumber: 8.7 Consensus size: 7
220126 AACCCTAAAT
220136 CCCTAAC
1 CCCTAAC
220143 CCCTAAC
1 CCCTAAC
220150 CCCTAAATCC
1 CCCT-AA--C
220160 CCCTAAC
1 CCCTAAC
*
220167 CCCTAAAT
1 CCCT-AAC
220175 CCCTAAC
1 CCCTAAC
220182 CCCTAAC
1 CCCTAAC
*
220189 CCCTACC
1 CCCTAAC
220196 CCCTA
1 CCCTA
220201 CTCCTTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
7 36 0.71
8 8 0.16
9 2 0.04
10 5 0.10
ACGTcount: A:0.28, C:0.55, G:0.00, T:0.17
Consensus pattern (7 bp):
CCCTAAC
Found at i:220796 original size:22 final size:22
Alignment explanation
Indices: 220753--220797 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
220743 GAATTTGAAT
*
220753 TTAAATTAAAATTAATACTATA
1 TTAAATTAAAATCAATACTATA
*
220775 TTAAATTAATATCATATA-TATA
1 TTAAATTAAAATCA-ATACTATA
220797 T
1 T
220798 ACCTTAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATTAAAATCAATACTATA
Found at i:221183 original size:42 final size:41
Alignment explanation
Indices: 221114--221243 Score: 158
Period size: 41 Copynumber: 3.1 Consensus size: 41
221104 AATATTTTTT
* *
221114 GCGGCGC-TTCAACAAAATCGCCGCTAAAACCCCTAACATTA
1 GCGGCGCTTTCAACAAAAACGCCGCTAAAA-CCTTAACATTA
* *
221155 GCGGCGCTTCTCAA-AAAAACGCCGCTAAAAATCTTAACTTTA
1 GCGGCGCTT-TCAACAAAAACGCCGCT-AAAACCTTAACATTA
*
221197 GCGGCGCTTT-AACGAAAACGCCGCTAAATACCTTAACATTA
1 GCGGCGCTTTCAACAAAAACGCCGCTAAA-ACCTTAACATTA
221238 GCGGCG
1 GCGGCG
221244 GTTGATTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
40 5 0.06
41 35 0.45
42 29 0.38
43 8 0.10
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTCAACAAAAACGCCGCTAAAACCTTAACATTA
Found at i:221255 original size:83 final size:82
Alignment explanation
Indices: 221114--221266 Score: 195
Period size: 83 Copynumber: 1.9 Consensus size: 82
221104 AATATTTTTT
* *
221114 GCGGCGCTTCAACAAAATCGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAAAAAAACGCCG
1 GCGGCGCTTCAACAAAATCGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCAAAAAAA-GCCA
221179 CTAAAAATCTTAACTTTA
65 CTAAAAATCTTAACTTTA
* * * *
221197 GCGGCGCTTTAACGAAAA-CGCCGCTAAATA-CCTTAACATTAGCGGCGGTTGAT-TAAAAAAGC
1 GCGGCGCTTCAAC-AAAATCGCCGCTAAA-ACCCCTAACATTAGCGGCGCTT-ATCAAAAAAAGC
221259 CACTAAAA
63 CACTAAAA
221267 CCCCCGACCA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
82 9 0.15
83 46 0.75
84 6 0.10
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (82 bp):
GCGGCGCTTCAACAAAATCGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCAAAAAAAGCCAC
TAAAAATCTTAACTTTA
Found at i:221445 original size:39 final size:40
Alignment explanation
Indices: 221399--221475 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
221389 GTTTTTTGCA
*
221399 GAAACGCTGCT-AA-TGCATATTTTTAGCGGCGTTTTCTTT
1 GAAACGCTGCTAAAGTGCAT-TTTTTAGCGGCATTTTCTTT
*
221438 GAAACGCTGCTAAAGTTCATTTTTTAGCGGCATTTTCT
1 GAAACGCTGCTAAAGTGCATTTTTTAGCGGCATTTTCT
221476 CACAAGCGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 11 0.32
40 19 0.56
41 4 0.12
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (40 bp):
GAAACGCTGCTAAAGTGCATTTTTTAGCGGCATTTTCTTT
Found at i:225173 original size:13 final size:11
Alignment explanation
Indices: 225137--225167 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
225127 CCGCCCGTAT
225137 TAATTTTTATA
1 TAATTTTTATA
*
225148 TTATTTTTATA
1 TAATTTTTATA
225159 TAATTTTTA
1 TAATTTTTA
225168 AATATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:225320 original size:30 final size:30
Alignment explanation
Indices: 225286--225348 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
225276 ACTTAACAAC
*
225286 CAAATATCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
225316 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
225346 CAA
1 CAA
225349 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:228027 original size:6 final size:6
Alignment explanation
Indices: 228016--228041 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
228006 GCTTGGTTGA
228016 GATGTT GATGTT GATGTT GATGTT GA
1 GATGTT GATGTT GATGTT GATGTT GA
228042 CCTTGACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (6 bp):
GATGTT
Found at i:228651 original size:13 final size:13
Alignment explanation
Indices: 228633--228697 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
228623 AATTCTTCAT
228633 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
228646 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
228659 TGCTGTGGAAAA-
1 TGCTTTTGAAAAG
* *
228671 TGCTTTTGAGAAT
1 TGCTTTTGAAAAG
*
228684 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
228697 T
1 T
228698 TTGGTTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 9 0.21
13 31 0.74
14 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:230420 original size:83 final size:84
Alignment explanation
Indices: 230290--230444 Score: 208
Period size: 83 Copynumber: 1.8 Consensus size: 84
230280 TTAGAGGAGC
* * *
230290 TAAAGTGAAATTTTACTATATATATTAATTTATAATTTCTTTATTTATAAGAGGA-TTCAATTGA
1 TAAAGGGAAATTTCAC-ATATATATTAATTTATAATTTCTCTATTTATAAGAGGACTT-AATTGA
230354 AAATTTTTCATTTTGAGGGGT
64 AAATTTTTCATTTTGAGGGGT
* * *
230375 TAAAGGGAAATTTCAC-TATATATT-ACTTATTAGTTTCTCTATTTATAAGATGACTTAATTGAA
1 TAAAGGGAAATTTCACATATATATTAATTTA-TAATTTCTCTATTTATAAGAGGACTTAATTGAA
230438 AATTTTT
65 AATTTTT
230445 TTTAGGGAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
82 4 0.06
83 42 0.68
84 2 0.03
85 14 0.23
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (84 bp):
TAAAGGGAAATTTCACATATATATTAATTTATAATTTCTCTATTTATAAGAGGACTTAATTGAAA
ATTTTTCATTTTGAGGGGT
Found at i:238107 original size:27 final size:28
Alignment explanation
Indices: 238069--238122 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
238059 TAGGATCGGG
*
238069 GTTTGAGGTTTAAAGTTCAA-GTTCAGA
1 GTTTAAGGTTTAAAGTTCAAGGTTCAGA
*
238096 GTTTAAGGTTTAAGGTTCAAGGTTCAG
1 GTTTAAGGTTTAAAGTTCAAGGTTCAG
238123 GATAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (28 bp):
GTTTAAGGTTTAAAGTTCAAGGTTCAGA
Found at i:239919 original size:8 final size:8
Alignment explanation
Indices: 239902--239932 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
239892 TTTTCATTGC
*
239902 ATTTTGTT
1 ATTTTATT
239910 ATTTTATT
1 ATTTTATT
239918 ATTTTATT
1 ATTTTATT
239926 ATTTTAT
1 ATTTTAT
239933 AGACATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
ATTTTATT
Found at i:250552 original size:2 final size:2
Alignment explanation
Indices: 250545--250570 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
250535 GCAAAACATC
250545 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
250571 CCTCCAATCT
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:255472 original size:11 final size:12
Alignment explanation
Indices: 255441--255471 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
255431 ACAATTTATC
255441 TTATTTTTGTAA
1 TTATTTTTGTAA
255453 TTATTTTTGTAA
1 TTATTTTTGTAA
255465 TTATTTT
1 TTATTTT
255472 GATTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATTTTTGTAA
Found at i:264456 original size:28 final size:29
Alignment explanation
Indices: 264424--264487 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
264414 GAAATTTTTT
264424 TAAATTTTTCATAATTTTTTA-AAATA-TA
1 TAAATTTTTCA-AATTTTTTATAAATATTA
* *
264452 TAAA-TTTTGAAATTTTTTATAAATATTT
1 TAAATTTTTCAAATTTTTTATAAATATTA
264480 TAAATTTT
1 TAAATTTT
264488 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 9 0.29
27 10 0.32
28 9 0.29
29 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TAAATTTTTCAAATTTTTTATAAATATTA
Found at i:267438 original size:24 final size:25
Alignment explanation
Indices: 267411--267469 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
267401 TATTGTTTTT
267411 TATTTTAAAAAATAATG-AG-TAATA
1 TATTTTAAAAAAT-ATGTAGTTAATA
*
267435 TATTTTATAAAATATGTAGTTTAATA
1 TATTTTAAAAAATATGTAG-TTAATA
267461 TATTTTAAA
1 TATTTTAAA
267470 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 14 0.47
26 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
TATTTTAAAAAATATGTAGTTAATA
Found at i:267896 original size:3 final size:3
Alignment explanation
Indices: 267888--267947 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
267878 TATTGCTGCA
267888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
267936 AAT AAT AAT AAT
1 AAT AAT AAT AAT
267948 TTATTCATCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:269618 original size:172 final size:164
Alignment explanation
Indices: 269299--269621 Score: 373
Period size: 172 Copynumber: 1.9 Consensus size: 164
269289 GACCACTTTC
* *
269299 TTTTGGAAGTCAAAACACATCATCACTGAAACCAAGCATTTGTTACAACTGCAACACCTATGGTC
1 TTTTGGAAGTCAAAACACAACATCACTGAAACCAAGCATTTGTTACAAATGCAACACCTATGGTC
*
269364 CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGACAATAATAATCAAT
66 CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGAAAATAATAATCAAT
** *
269429 GAGTGTATCTTAAAGTGCATTGTTAGAACTTTTA
131 GAACGTATCTCAAAGTGCATTGTTAGAACTTTTA
**
269463 TTTTGGAAGTCACAACACAACAACATCACTGAAACCTGGCATTTGTTACAAATGCAA-ATCC-AC
1 TTTTGGAAGTCA-AA-AC-ACAACATCACTGAAACCAAGCATTTGTTACAAATGCAACA-CCTA-
* * * ** * *
269526 TGGTCCCTTATCATTTTTTTTTTGGCCAAATCCTTAGTGAATTCTTAGAGCTTTGACGA-GAAAA
61 TGGTCCC---T--TTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGA-AATGAAAA
**
269590 TAATAATCGGTGAACGTATCTCAAAGTGCATT
120 TAATAATCAATGAACGTATCTCAAAGTGCATT
269622 ATTTCTTGAC
Statistics
Matches: 131, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
164 12 0.09
165 2 0.02
166 4 0.03
167 43 0.33
170 1 0.01
172 68 0.52
173 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (164 bp):
TTTTGGAAGTCAAAACACAACATCACTGAAACCAAGCATTTGTTACAAATGCAACACCTATGGTC
CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGAAAATAATAATCAAT
GAACGTATCTCAAAGTGCATTGTTAGAACTTTTA
Found at i:272467 original size:15 final size:16
Alignment explanation
Indices: 272440--272470 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
272430 TCGATCTAGT
272440 CAATCTAAATTTGATC
1 CAATCTAAATTTGATC
272456 CAATCT-AATTTGATC
1 CAATCTAAATTTGATC
272471 ATAAAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
CAATCTAAATTTGATC
Found at i:280248 original size:4 final size:4
Alignment explanation
Indices: 280239--280266 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
280229 CCATCAAATA
280239 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
280267 ATTCCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:285708 original size:30 final size:29
Alignment explanation
Indices: 285642--285752 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 29
285632 GATTAAATCA
* * * *
285642 AAATTAAAGGTTCAAGTATACATTTGAACC
1 AAATTAAA-GTTCATGTATACAATTGCACT
* * *
285672 ACAATTAGAGTTTCATGTGTATAATTGCACT
1 A-AATTAAAG-TTCATGTATACAATTGCACT
285703 AAATTAAAGTTCATGTATACAATTGCACATT
1 AAATTAAAGTTCATGTATACAATTGCAC--T
**
285734 AAATCGAAGTTCATGTATA
1 AAATTAAAGTTCATGTATA
285753 ATTTTGAGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 17 0.26
30 9 0.14
31 39 0.60
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATACAATTGCACT
Found at i:297138 original size:20 final size:20
Alignment explanation
Indices: 297110--297159 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
297100 TGCCTACGGA
*
297110 ACACTCCAAAAGCATAAGTC
1 ACACCCCAAAAGCATAAGTC
297130 ACACCCCAAAAGCATAAGTC
1 ACACCCCAAAAGCATAAGTC
297150 ACACCCCAAA
1 ACACCCCAAA
297160 CAAGGTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.36, G:0.08, T:0.10
Consensus pattern (20 bp):
ACACCCCAAAAGCATAAGTC
Found at i:297584 original size:2 final size:2
Alignment explanation
Indices: 297577--297602 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
297567 ATAATAATAA
297577 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
297603 TCAATTTAAA
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:300349 original size:4 final size:4
Alignment explanation
Indices: 300340--300367 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
300330 AAGAATATTA
300340 AAAC AAAC AAAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC
300368 TAGAGCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:302259 original size:4 final size:4
Alignment explanation
Indices: 302250--302276 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
302240 ACACACGTGC
302250 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
302277 ACGACGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:313718 original size:21 final size:21
Alignment explanation
Indices: 313685--313866 Score: 96
Period size: 21 Copynumber: 8.7 Consensus size: 21
313675 ACTGTACCCA
* *
313685 GGAGAAGTGGGGCTATATGCT
1 GGAGAAGTAGGGCTATATGAT
* *
313706 GGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* * *
313727 GGAGATGTAGGGCTATAGGAG
1 GGAGAAGTAGGGCTATATGAT
* * * * * *
313748 GGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTAGGGCTATATGAT
* * * *
313769 GGAGATGTCGGACTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* * * *
313790 GGCGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* *
313811 GGAGAAGTGGGGCTGTATGCA-
1 GGAGAAGTAGGGCTATATG-AT
* * **
313832 GGTGAAGTTGGGCTATATGCC
1 GGAGAAGTAGGGCTATATGAT
*
313853 GGTGAAGTAGGGCT
1 GGAGAAGTAGGGCT
313867 GTAGCTTGGT
Statistics
Matches: 127, Mismatches: 32, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
21 126 0.99
22 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.25
Consensus pattern (21 bp):
GGAGAAGTAGGGCTATATGAT
Found at i:313731 original size:42 final size:42
Alignment explanation
Indices: 313685--313850 Score: 147
Period size: 42 Copynumber: 4.0 Consensus size: 42
313675 ACTGTACCCA
* *
313685 GGAGAAGTGGGGCTATATGCTGGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
* * * * * *
313727 GGAGATGTAGGGCTATA-GGAGGGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTGGGGCTATATGCAGGG-GAAGTTGGGCTGTATGAT
* * * * * *
313769 GGAGATGTCGGACTGTATG-ATGGCGATGTTGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGCA-GGGGAAGTTGGGCTGTATGAT
* * *
313811 GGAGAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATG
1 GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATG
313851 CCGGTGAAGT
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
41 4 0.04
42 91 0.92
43 4 0.04
ACGTcount: A:0.23, C:0.07, G:0.45, T:0.25
Consensus pattern (42 bp):
GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
Found at i:313860 original size:42 final size:42
Alignment explanation
Indices: 313685--313890 Score: 114
Period size: 42 Copynumber: 4.9 Consensus size: 42
313675 ACTGTACCCA
* * * * * *
313685 GGAGAAGTGGGGCTATATGCT-GGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTAGGGCTGTA-GCTAGGTGAAGTTGGGCTATATGAC
* * * * * * *
313727 GGAGATGTAGGGCTATAG-GAGGGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTAGGGCTGTAGCTA-GGTGAAGTTGGGCTATATGAC
* * * * * * * *
313769 GGAGATGTCGGACTGTATGAT-GGCGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTGTA-GCTAGGTGAAGTTGGGCTATATGAC
* *
313811 GGAGAAGTGGGGCTGTATGC-AGGTGAAGTTGGGCTATATGCC
1 GGAGAAGTAGGGCTGTA-GCTAGGTGAAGTTGGGCTATATGAC
* * *
313853 GGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATA
1 GGAGAAGTAGGGCTGTAGCTAGGTGAAGTTGGGCTATA
313891 GCTGGGAGAT
Statistics
Matches: 129, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
41 3 0.02
42 125 0.97
43 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.43, T:0.26
Consensus pattern (42 bp):
GGAGAAGTAGGGCTGTAGCTAGGTGAAGTTGGGCTATATGAC
Found at i:313920 original size:63 final size:63
Alignment explanation
Indices: 313853--313983 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 63
313843 GCTATATGCC
* * * * *
313853 GGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGATGT-GGGACTATAACTT
1 GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGG-CTATAACTT
* * * * *
313916 GGTGAAGTAGGACTGTAACTTGGAGACGTAGGGCTGTAGCTTGGAGAGGTAGGGCTATAGCTT
1 GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGGCTATAACTT
313979 GGTGA
1 GGTGA
313984 GGTTGGAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 54 0.95
64 3 0.05
ACGTcount: A:0.24, C:0.10, G:0.40, T:0.27
Consensus pattern (63 bp):
GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGGCTATAACTT
Found at i:313980 original size:42 final size:42
Alignment explanation
Indices: 313859--313980 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
313849 TGCCGGTGAA
* * *
313859 GTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGAT
1 GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
* * * *
313901 GT-GGGACTATAACTTGGTGAAGTAGGACTGTAACTTGGAGAC
1 GTAGGG-CTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
* * *
313943 GTAGGGCTGTAGCTTGGAGAGGTAGGGCTATAGCTTGG
1 GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGG
313981 TGAGGTTGGA
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 3 0.05
42 58 0.91
43 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (42 bp):
GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
Found at i:313986 original size:21 final size:21
Alignment explanation
Indices: 313832--313983 Score: 119
Period size: 21 Copynumber: 7.2 Consensus size: 21
313822 GCTGTATGCA
* *
313832 GGTGAAGTTGGGCTATATGC-C
1 GGTGAAGTAGGGCTATA-GCTT
*
313853 GGTGAAGTAGGGCTGTAGCTT
1 GGTGAAGTAGGGCTATAGCTT
* * *
313874 GGTGAAGTTGGACTATAGCTG
1 GGTGAAGTAGGGCTATAGCTT
* * *
313895 GGAGATGT-GGGACTATAACTT
1 GGTGAAGTAGGG-CTATAGCTT
* * *
313916 GGTGAAGTAGGACTGTAACTT
1 GGTGAAGTAGGGCTATAGCTT
* * *
313937 GGAGACGTAGGGCTGTAGCTT
1 GGTGAAGTAGGGCTATAGCTT
* *
313958 GGAGAGGTAGGGCTATAGCTT
1 GGTGAAGTAGGGCTATAGCTT
313979 GGTGA
1 GGTGA
313984 GGTTGGAGAA
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
20 4 0.04
21 99 0.94
22 2 0.02
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (21 bp):
GGTGAAGTAGGGCTATAGCTT
Found at i:314076 original size:42 final size:43
Alignment explanation
Indices: 314030--314169 Score: 169
Period size: 42 Copynumber: 3.3 Consensus size: 43
314020 TGGACTTGTT
* * ** * * *
314030 GGGCTGTAACCTGGTGAACTAGGACTGTAAG-TAGGTGATGTG
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
314072 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGTA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
*
314114 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGAA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
* *
314156 GGACTGTAGCCAGG
1 GGGCTGTAACCAGG
314170 AGATGATGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 2 0.02
42 85 0.98
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.19
Consensus pattern (43 bp):
GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
Found at i:314099 original size:21 final size:21
Alignment explanation
Indices: 314075--314172 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
314065 TGATGTGGGG
* *
314075 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
314096 CTGTAGCCAGGAGATGTAGGG
1 CTGTAGCCAGGAGAGGTAGGA
* *
314117 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
314138 CTGTAGCCAGGAGATGAAGGA
1 CTGTAGCCAGGAGAGGTAGGA
314159 CTGTAGCCAGGAGA
1 CTGTAGCCAGGAGA
314173 TGATGGGCTG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.39, T:0.15
Consensus pattern (21 bp):
CTGTAGCCAGGAGAGGTAGGA
Found at i:314173 original size:21 final size:21
Alignment explanation
Indices: 314092--314196 Score: 120
Period size: 21 Copynumber: 5.0 Consensus size: 21
314082 CAGGCGAGGT
*
314092 AGGACTGTAGCCAGGAGATGT
1 AGGACTGTAGCCAGGAGATGA
* * * * *
314113 AGGGCTGTAACCAGGCGAGGT
1 AGGACTGTAGCCAGGAGATGA
314134 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
314155 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
* * * *
314176 TGGGCTGTAACCAGGGGATGA
1 AGGACTGTAGCCAGGAGATGA
314197 CGTGGGAGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.16
Consensus pattern (21 bp):
AGGACTGTAGCCAGGAGATGA
Found at i:314184 original size:42 final size:42
Alignment explanation
Indices: 314075--314196 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
314065 TGATGTGGGG
* * * *
314075 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGTAGGG
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* *
314117 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGAAGGA
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* * * *
314159 CTGTAGCCAGGAGATGAT-GGGCTGTAACCAGGGGATGA
1 CTGTAACCAGGAGA-GATAGGACTGTAGCCAGGAGATGA
314197 CGTGGGAGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.39, T:0.16
Consensus pattern (42 bp):
CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
Found at i:323189 original size:29 final size:29
Alignment explanation
Indices: 323146--323229 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
323136 TTTAGAAATC
*
323146 TAAATAATTTAAGGACTAAATTTTAAAAAA
1 TAAA-AATATAAGGACTAAATTTTAAAAAA
** * *
323176 TAAAAATATAAGGAAAAAATTTCAAATAA
1 TAAAAATATAAGGACTAAATTTTAAAAAA
** *
323205 -AAAAATATAAAAACTAAATTCTAAA
1 TAAAAATATAAGGACTAAATTTTAAA
323230 TTTTTGAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
28 19 0.44
29 20 0.47
30 4 0.09
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (29 bp):
TAAAAATATAAGGACTAAATTTTAAAAAA
Found at i:323223 original size:28 final size:30
Alignment explanation
Indices: 323160--323224 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
323150 TAATTTAAGG
*
323160 ACTAAATTTTAAAAAATAAAAATATAAGGAA
1 ACTAAATTTCAAAAAATAAAAATATAA-GAA
*
323191 A--AAATTTCAAATAA-AAAAATATAA-AA
1 ACTAAATTTCAAAAAATAAAAATATAAGAA
323217 ACTAAATT
1 ACTAAATT
323225 CTAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 3 0.10
28 15 0.50
29 11 0.37
31 1 0.03
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (30 bp):
ACTAAATTTCAAAAAATAAAAATATAAGAA
Found at i:333820 original size:31 final size:31
Alignment explanation
Indices: 333783--333851 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
333773 TGGACCCCAA
333783 AAAGTTTA-AGTACCAACTTAAGAAAAAGTGT
1 AAAGTTTAGA-TACCAACTTAAGAAAAAGTGT
* *
333814 AAAGTTTAGATACCAAGTTAGGAAAAAGTGT
1 AAAGTTTAGATACCAACTTAAGAAAAAGTGT
*
333845 CAAGTTT
1 AAAGTTT
333852 GGGTATCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (31 bp):
AAAGTTTAGATACCAACTTAAGAAAAAGTGT
Found at i:334703 original size:18 final size:18
Alignment explanation
Indices: 334664--334706 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
334654 GAATAGATTT
*
334664 TTAATTAAATAATTTTAT
1 TTAATTAAATAATTTTAA
334682 TTAATTAAA-AATTTTAAA
1 TTAATTAAATAATTTT-AA
334700 TTAATTA
1 TTAATTA
334707 TACCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTAAATAATTTTAA
Found at i:338512 original size:2 final size:2
Alignment explanation
Indices: 338505--338538 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
338495 AGGCAACAAC
338505 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
338539 TATATAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:338918 original size:4 final size:4
Alignment explanation
Indices: 338909--338938 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
338899 TTTGAATTCA
338909 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
338939 AAAAGCAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:339559 original size:5 final size:5
Alignment explanation
Indices: 339551--339591 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
339541 GACATCAATT
* *
339551 AAAAC AAAAAC CAGAC AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
339592 TCATTTCTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.76, C:0.22, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:345800 original size:14 final size:13
Alignment explanation
Indices: 345754--345816 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
345744 ACAATAATTA
345754 TAAAA-ATAAAATT
1 TAAAATATAAAA-T
345767 TAAAAGTATACCAAAT
1 TAAAA-TATA--AAAT
345783 TAAAATATAAAGAT
1 TAAAATATAAA-AT
* *
345797 TAAATTATAAATT
1 TAAAATATAAAAT
345810 TAAAATA
1 TAAAATA
345817 GTATAGGGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 14 0.33
14 12 0.29
15 7 0.17
16 6 0.14
17 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (13 bp):
TAAAATATAAAAT
Found at i:347512 original size:28 final size:26
Alignment explanation
Indices: 347462--347514 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
347452 TTTAAAATAC
*
347462 TTTTAAAATATTTTTATTTTTATTAT
1 TTTTAAAATATTTTTATGTTTATTAT
347488 TTTTAAAATAATTTTTAATGTTTATTA
1 TTTTAAAAT-ATTTTT-ATGTTTATTA
347515 AAAAATGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 6 0.25
28 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTAAAATATTTTTATGTTTATTAT
Found at i:347515 original size:22 final size:21
Alignment explanation
Indices: 347477--347517 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
347467 AAATATTTTT
*
347477 ATTTTTATTATTTTTAAAATA
1 ATTTTTAATATTTTTAAAATA
*
347498 ATTTTTAATGTTTATTAAAA
1 ATTTTTAATATTT-TTAAAA
347518 AATGGGTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTTAATATTTTTAAAATA
Found at i:350846 original size:26 final size:26
Alignment explanation
Indices: 350814--350867 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
350804 TAACCAAAAT
** *
350814 ATTATAACTTTTTTTTATTTATCAAA
1 ATTATAAAGTTTTTTTATTTACCAAA
350840 ATTATAAAGTTTTTTTATTTACCAAA
1 ATTATAAAGTTTTTTTATTTACCAAA
350866 AT
1 AT
350868 ATACAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTATAAAGTTTTTTTATTTACCAAA
Found at i:350897 original size:16 final size:15
Alignment explanation
Indices: 350878--350907 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
350868 ATACAAAAAA
350878 AAAAACAAAAACCTGC
1 AAAAA-AAAAACCTGC
350894 AAAAAAAAAACCTG
1 AAAAAAAAAACCTG
350908 TGATTTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAACCTGC
Found at i:351111 original size:18 final size:18
Alignment explanation
Indices: 351090--351127 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
351080 AGTAATAACT
*
351090 CTATTTTAATTTAATAAA
1 CTATTCTAATTTAATAAA
*
351108 CTATTCTCATTTAATAAA
1 CTATTCTAATTTAATAAA
351126 CT
1 CT
351128 CNNNNNNNNN
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (18 bp):
CTATTCTAATTTAATAAA
Found at i:351848 original size:17 final size:17
Alignment explanation
Indices: 351826--351859 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
351816 GGTGCCGCCA
*
351826 CAGGTTTTTTTTTTTTG
1 CAGGTTTTTGTTTTTTG
351843 CAGGTTTTTGTTTTTTG
1 CAGGTTTTTGTTTTTTG
351860 TTTTTGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.68
Consensus pattern (17 bp):
CAGGTTTTTGTTTTTTG
Found at i:351920 original size:26 final size:28
Alignment explanation
Indices: 351868--351929 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 28
351858 TGTTTTTGGT
*
351868 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTTGATAAATAAAAAAATTTTATA
351896 ATATTTTGATAAAT-AAAAAA-TTTATA
1 ATATTTTGATAAATAAAAAAATTTTATA
351922 ATATTTTG
1 ATATTTTG
351930 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 14 0.42
27 6 0.18
28 13 0.39
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAATTTTATA
Found at i:353878 original size:19 final size:20
Alignment explanation
Indices: 353846--353884 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
353836 AATAAACACC
353846 AAAAATATAATTTAAAAATA
1 AAAAATATAATTTAAAAATA
*
353866 AAAAAT-TATTTTAAAAATA
1 AAAAATATAATTTAAAAATA
353885 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATATAATTTAAAAATA
Found at i:355996 original size:18 final size:17
Alignment explanation
Indices: 355968--356002 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
355958 ATTATTAAGA
*
355968 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
355985 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
356003 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:356116 original size:18 final size:17
Alignment explanation
Indices: 356088--356122 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
356078 ATTATTAAGA
*
356088 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
356105 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
356123 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:361757 original size:18 final size:20
Alignment explanation
Indices: 361734--361795 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 20
361724 TAAAAAAAAA
361734 TATAAAT-TTTT-AAATTTT
1 TATAAATATTTTGAAATTTT
361752 TATAAATATTTTGAAA--TT
1 TATAAATATTTTGAAATTTT
*
361770 TAAAAATCATTTTG-AATTTT
1 TATAAAT-ATTTTGAAATTTT
361790 T-TAAAT
1 TATAAAT
361796 TTATTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 17 0.46
19 14 0.38
20 6 0.16
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATAAATATTTTGAAATTTT
Found at i:361795 original size:19 final size:18
Alignment explanation
Indices: 361736--361795 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
361726 AAAAAAAATA
*
361736 TAAAT-TTTTAAATTTTT
1 TAAATATTTTGAATTTTT
* *
361753 ATAAATATTTTGAAATTTA
1 -TAAATATTTTGAATTTTT
*
361772 AAAATCATTTTGAATTTTT
1 TAAAT-ATTTTGAATTTTT
361791 TAAAT
1 TAAAT
361796 TTATTTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (18 bp):
TAAATATTTTGAATTTTT
Found at i:363685 original size:10 final size:10
Alignment explanation
Indices: 363658--363707 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
363648 ATTTTAAAAA
*
363658 TATAAGTTTT
1 TATAATTTTT
363668 TATGAATTTTT
1 TAT-AATTTTT
363679 TATAATTTTT
1 TATAATTTTT
*
363689 T-GAATATTTT
1 TATAAT-TTTT
363699 TAT-ATTTTT
1 TATAATTTTT
363708 AAATTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 7 0.21
10 18 0.53
11 9 0.26
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (10 bp):
TATAATTTTT
Found at i:363692 original size:19 final size:21
Alignment explanation
Indices: 363658--363708 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
363648 ATTTTAAAAA
363658 TATAAGTTTTTATGAAT-TTTT
1 TATAA-TTTTTATGAATATTTT
363679 TATAATTTTT-TGAATATTTT
1 TATAATTTTTATGAATATTTT
363699 TAT-ATTTTTA
1 TATAATTTTTA
363709 AATTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.39
20 12 0.43
21 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
TATAATTTTTATGAATATTTT
Found at i:363715 original size:19 final size:20
Alignment explanation
Indices: 363675--363718 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
363665 TTTTATGAAT
*
363675 TTTTTATAATTTTTTGAATA
1 TTTTTATAATTTTTTAAATA
363695 TTTTTAT-A-TTTTTAAATTA
1 TTTTTATAATTTTTTAAA-TA
363714 TTTTT
1 TTTTT
363719 TGACACGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATAATTTTTTAAATA
Found at i:368235 original size:249 final size:246
Alignment explanation
Indices: 367826--368478 Score: 898
Period size: 250 Copynumber: 2.7 Consensus size: 246
367816 CCTTTTAATT
*
367826 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTTC
1 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
367891 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACG-------TAT-CAATTTTTATAATTTT
66 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTATTTATACAATTTTTA-AATTTT
* *
367948 TTT--TAAATA-TATGTTTAATTTCAATCAAGTAAGCACTTTACATAATTTTTTTAGAACATTTA
130 TTTAATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACAGAATTTTTTTAGAACATTTA
* *
368010 GCTTAACATTCTCTTCTACTTAATCTCGCGACGCTTTTGTAACAG-TTCTTC
195 GCTTAACATTCTCTTCTACTTAATCTCGCGACACTTTTGTAACAGCTTCATC
* * * ** * *
368061 AATTTTGCCTGCTCAACTAATAAAACTTTAGCATTGATTTTTTGTTGGTTCACTTTACTTACACC
1 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
*
368126 ACCCATTGAAGCGCTCAATGTGAAATTGAGCAATTACGAATTATTATATACTAATTTTTACAATT
66 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTATT-TATAC-AATTTTTA-AATT
* *
368191 TTTTTCAATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACCGATTTTTTTTAGAACAT
128 TTTTT-AATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACAGAATTTTTTTAGAACAT
* * * *
368256 TTGGCTTAACATTCTCTTCTACTTAATCTTGTGACACTTTTGTCACAGCTTCATC
192 TTAGCTTAACATTCTCTTCTACTTAATCTCGCGACACTTTTGTAACAGCTTCATC
* * *
368311 AATTTTGCCTGCCCAATTTATAAAAATTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCT
1 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
* * * * *
368376 ACCCCTTGAAGCACTCGATGTGAAATCGAACAATTACGAATTATTTTGATACCAATTTTTATATT
66 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTA-TTT-ATA-CAATTTTTAAATT
368441 TTTTTGAATATATATTATGTTTAATTTCAATCAAGTAA
128 TTTTT-AATATATATTATGTTTAATTTCAATCAAGTAA
368479 ACTTTATGAC
Statistics
Matches: 363, Mismatches: 37, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
235 94 0.26
243 3 0.01
244 1 0.00
245 17 0.05
248 5 0.01
249 90 0.25
250 139 0.38
251 13 0.04
252 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (246 bp):
AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTATTTATACAATTTTTAAATTTTT
TTAATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACAGAATTTTTTTAGAACATTTAG
CTTAACATTCTCTTCTACTTAATCTCGCGACACTTTTGTAACAGCTTCATC
Found at i:378181 original size:17 final size:16
Alignment explanation
Indices: 378159--378190 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
378149 TCAATGTCAT
378159 AAAAAAAGCAAAAAAAG
1 AAAAAAAG-AAAAAAAG
378176 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
378191 CTATACCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAG
Done.