Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold298
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: 553964
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 6992 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4482 original size:6 final size:6
Alignment explanation
Indices: 4466--4503 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
4456 TGGAAGAAAC
4466 TTCTG- TTCTGT TTCTGT TTCTGT TTCTGT TTCATGT TT
1 TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT TTC-TGT TT
4504 TAAGTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.03, C:0.16, G:0.16, T:0.66
Consensus pattern (6 bp):
TTCTGT
Found at i:18338 original size:24 final size:24
Alignment explanation
Indices: 18309--18359 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
18299 GAAAAATATT
*
18309 AAATATATATA-TATTTTATTTTTA
1 AAATATA-ATAGTATTTTATTTTAA
*
18333 AAATATAATAGTTTTTTATTTTAA
1 AAATATAATAGTATTTTATTTTAA
18357 AAA
1 AAA
18360 ACGGGCCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AAATATAATAGTATTTTATTTTAA
Found at i:21642 original size:19 final size:20
Alignment explanation
Indices: 21606--21658 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
21596 AAAAATTACA
*
21606 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
21625 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
21645 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
21659 TTATATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:21648 original size:18 final size:18
Alignment explanation
Indices: 21626--21663 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
21616 AATAATTTTC
21626 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
21645 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
21663 A
1 A
21664 TTGATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:21649 original size:20 final size:20
Alignment explanation
Indices: 21605--21692 Score: 63
Period size: 20 Copynumber: 4.2 Consensus size: 20
21595 CAAAAATTAC
*
21605 AAAAAAATCAAAATAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
*
21625 CAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
21645 -AAAAATTCCAAAATTTATATTGAT
1 AAAAAATT-CAAAA--TAT-TT-AT
* *
21669 AAAAAAATTCAAAAAATATAT
1 -AAAAAATTCAAAATATTTAT
21690 AAA
1 AAA
21693 TAAGTTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
19 11 0.20
20 21 0.38
21 2 0.04
22 4 0.07
23 4 0.07
24 2 0.04
25 5 0.09
26 7 0.12
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:21978 original size:19 final size:19
Alignment explanation
Indices: 21940--21978 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21930 TTCGCTCGAC
* *
21940 TCAATTTAAAAAAATTAAA
1 TCAAATTAAAAAAATAAAA
*
21959 TCAAATTAAAATAATAAAA
1 TCAAATTAAAAAAATAAAA
21978 T
1 T
21979 AAAACTCATT
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:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
TCAAATTAAAAAAATAAAA
Found at i:22731 original size:9 final size:9
Alignment explanation
Indices: 22717--22792 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
22707 GTAGTGATTC
22717 AATTCGGTT
1 AATTCGGTT
*
22726 AATTCGGGT
1 AATTCGGTT
22735 AATTCGGTT
1 AATTCGGTT
*
22744 AATTCGGGT
1 AATTCGGTT
22753 AA-TCAGGTT
1 AATTC-GGTT
* *
22762 AATTCAGAT
1 AATTCGGTT
*
22771 AATTCGGGT
1 AATTCGGTT
22780 AATTCGGTT
1 AATTCGGTT
22789 AATT
1 AATT
22793 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 2 0.04
9 52 0.93
10 2 0.04
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:25705 original size:10 final size:11
Alignment explanation
Indices: 25667--25719 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
25657 TATCAATGAG
*
25667 ATAAAAAAATT
1 ATAAAATAATT
25678 ACTAAAAT-ATT
1 A-TAAAATAATT
25689 AGT-AAATAATT
1 A-TAAAATAATT
25700 A-AAAATAA-T
1 ATAAAATAATT
25709 ATAAAATAATT
1 ATAAAATAATT
25720 TCTAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
9 2 0.06
10 17 0.49
11 11 0.31
12 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAAATAATT
Found at i:32041 original size:177 final size:176
Alignment explanation
Indices: 31788--32173 Score: 630
Period size: 177 Copynumber: 2.2 Consensus size: 176
31778 TGTATGTAGA
31788 GTTGGTGAAACATACAACGGAAA-GCCAGAGAATGCTCCAGCAGATAGGGAAGGCAAACCACAGC
1 GTTGGTGAAACATACAAC-GAAAGGCCAGAGAA-GCTCCAGCAGATAGGGAAGGCAAACCACAGC
* *
31852 ACCATAAGAACCGATCCATCACTCTCGGGTCAGTTAAAGAATTCAATTTCGACAATATTAATGGA
64 ACCATAAGAACCGATCCATCACTCTCGGGTCACTTAAAGAATTCAATTTCGACAATATTAATGCA
* *
31917 GAGATAGAAGAAAATGCTACTAAGTCAGTGGAAACTTATGAAGGTCGT
129 GAGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
*
31965 GTTGGTGAAACATGCAACGAAAGGCCAGAGCAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
1 GTTGGTGAAACATACAACGAAAGGCCAGAG-AAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
* * *
32030 CCATAAGAACCGATCCATCACTCTTGGGTCACTTAAAGAATTCAATTTCGACAATGTTAATGCCG
65 CCATAAGAACCGATCCATCACTCTCGGGTCACTTAAAGAATTCAATTTCGACAATATTAATGCAG
* *
32095 AGATAGAAGAAAATGCTACCAAGTCGGTGGAAACTCATGAATGTCGT
130 AGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
* *
32142 GTTGGTGAAACATACAATGAAAGACCAGAGAA
1 GTTGGTGAAACATACAACGAAAGGCCAGAGAA
32174 AGCTGAAGTA
Statistics
Matches: 194, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
176 6 0.03
177 186 0.96
178 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (176 bp):
GTTGGTGAAACATACAACGAAAGGCCAGAGAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCAC
CATAAGAACCGATCCATCACTCTCGGGTCACTTAAAGAATTCAATTTCGACAATATTAATGCAGA
GATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
Found at i:33769 original size:24 final size:23
Alignment explanation
Indices: 33729--33773 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
33719 TATAAATAAA
* *
33729 TTAAAAATAATATAAATATATTT
1 TTAAAAATAAAAAAAATATATTT
33752 TTAAAAATTAAAAAAAATATAT
1 TTAAAAA-TAAAAAAAATATAT
33774 AAATGTGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAAATAAAAAAAATATATTT
Found at i:34560 original size:18 final size:17
Alignment explanation
Indices: 34537--34574 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
34527 TTTAAGAAAC
34537 ATTTTTGAGACAAAAAGT
1 ATTTTTGAGACAAAAA-T
*
34555 ATTTTTGAGATAAAAAT
1 ATTTTTGAGACAAAAAT
34572 ATT
1 ATT
34575 GTCAAACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (17 bp):
ATTTTTGAGACAAAAAT
Found at i:35840 original size:30 final size:32
Alignment explanation
Indices: 35804--35873 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
35794 ATTCATCAAA
*
35804 ACAAAAAAC-AG-ATCTTGTAATAAAATGGTG
1 ACAAAAAACTAGAATCTTGTAATAAAATGATG
*
35834 ACAAAAAACTCGAATCTTGTAATAAAATGATG
1 ACAAAAAACTAGAATCTTGTAATAAAATGATG
35866 ACAAAAAA
1 ACAAAAAA
35874 GTGAAGAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 9 0.25
31 1 0.03
32 26 0.72
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.21
Consensus pattern (32 bp):
ACAAAAAACTAGAATCTTGTAATAAAATGATG
Found at i:41996 original size:16 final size:16
Alignment explanation
Indices: 41966--42000 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41956 ATTTTTATCA
41966 TTTTTAAATTAAAAAT
1 TTTTTAAATTAAAAAT
41982 TTTTATAAATT-AAAAT
1 TTTT-TAAATTAAAAAT
41998 TTT
1 TTT
42001 ACTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTTAAATTAAAAAT
Found at i:45581 original size:18 final size:17
Alignment explanation
Indices: 45540--45585 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
45530 CTAAATAGTC
*
45540 TTAAAAAAT-ATTATAT
1 TTAAAAAATAATTAAAT
45556 TTATAAAAATAATTCAAAT
1 TTA-AAAAATAATT-AAAT
45575 TT-AAAAATAAT
1 TTAAAAAATAAT
45586 CACAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 15 0.58
18 3 0.12
19 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAATAATTAAAT
Found at i:45776 original size:6 final size:7
Alignment explanation
Indices: 45759--45785 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
45749 ACTGATATAC
45759 AAAAAAG
1 AAAAAAG
45766 AAAAAAG
1 AAAAAAG
45773 AAAAAAG
1 AAAAAAG
45780 AAAAAA
1 AAAAAA
45786 AATTTGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:46504 original size:222 final size:221
Alignment explanation
Indices: 46096--46608 Score: 592
Period size: 222 Copynumber: 2.3 Consensus size: 221
46086 TCAGTATACA
* * * *
46096 AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTAGTGTCGGCCATTGGCAAACCAGCACAAAA
1 AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAA
* * *
46161 AAAAATTTCTCCTTTTTTGGTATACTGATACATGCTATTGACACGAAAAAAGTGAAAAAAAAATT
66 AAAAATTTCTACTTTTTTCGTATACTGATACATGCAATTGACACGAAAAAAGTGAAAAAAAAATT
*******
46226 TCCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCACAAATTTTGTTTTTTTTTTTTACT
131 TCCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CA-AAA--AAAAACATTTTTTTTACT
46291 TTTTTAGTATACTGATAC-C-A-GGACACG
192 TTTTTAGTATACTGATACTCAATGGACACG
* * *
46318 AAAAAAGTAAAAAAAAAATTTCCCCCAAAAAAGGTGGTGCCGGCCATTGGCAAGTCACCACAAAT
1 AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAA
***** * * * *
46383 TTTTTTTTTTACTTTTTTCGTATATTGATACTTGCAATTGACACGAAAAGAGTGTAAAAAAAAA-
66 AAAAATTTCTACTTTTTTCGTATACTGATACATGCAATTGACACGAAAAAAGTG-AAAAAAAAAT
46447 TTCTC-AAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTT
130 TTC-CGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTT
* * *
46511 TTTCGTATATTGATACTTGCAATTGACACG
194 TTTAGTATACTGATAC-T-CAATGGACACG
* * * *
46541 AAAAGAGTGTAAAAAAAAA-TT--CTCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAA
1 AAAAAAGT-AAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAA
46603 AAAAAA
65 AAAAAA
46609 CATTTTTTTT
Statistics
Matches: 243, Mismatches: 40, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
218 27 0.11
220 3 0.01
221 41 0.17
222 138 0.57
223 25 0.10
224 9 0.04
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.27
Consensus pattern (221 bp):
AAAAAAGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCATTGGCAAGCCACCACAAAA
AAAAATTTCTACTTTTTTCGTATACTGATACATGCAATTGACACGAAAAAAGTGAAAAAAAAATT
TCCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTT
TAGTATACTGATACTCAATGGACACG
Found at i:46534 original size:113 final size:113
Alignment explanation
Indices: 46121--46627 Score: 537
Period size: 113 Copynumber: 4.6 Consensus size: 113
46111 AAATTTCCCA
* * ** * * * *
46121 CAAAAAAGGTAGTGTCGGCCATTGGCAAACCAGCAC-AAAAAAAA-A---TTTCTCCTTTTTTGG
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCG
* *
46181 TATACTGATACATGCTATTGACACGAAAAAAGTG-AAAAAAAAATT-T
66 TATACTGATACTTGCAATTGACACGAAAAAAGTGTAAAAAAAAATTCT
*******
46227 CCGAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCACAAATTTTGTTTTTTTTTTTTACTT
1 -C-AAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CA-AAA--AAAAACATTTTTTTTACTT
* * * *
46292 TTTTAGTATACTGATAC---C-A-GGACACGAAAAAAGT-AAAAAAAAAATTTCCCC
60 TTTTCGTATACTGATACTTGCAATTGACACGAAAAAAGTGTAAAAAAAAA-TT--CT
* * ***
46343 CAAAAAAGGTGGTGCCGGCCATTGGCAAGTCACCAC-----AAATTTTTTTTTTTACTTTTTTCG
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCG
* *
46403 TATATTGATACTTGCAATTGACACGAAAAGAGTGTAAAAAAAAATTCT
66 TATACTGATACTTGCAATTGACACGAAAAAAGTGTAAAAAAAAATTCT
46451 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCG
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCG
* *
46516 TATATTGATACTTGCAATTGACACGAAAAGAGTGTAAAAAAAAATTCT
66 TATACTGATACTTGCAATTGACACGAAAAAAGTGTAAAAAAAAATTCT
46564 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTC
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTC
46628 ATGTCTTGGT
Statistics
Matches: 342, Mismatches: 32, Indels: 46
0.81 0.08 0.11
Matches are distributed among these distances:
105 30 0.09
107 1 0.00
108 65 0.19
109 2 0.01
110 15 0.04
111 12 0.04
112 23 0.07
113 137 0.40
114 33 0.10
115 1 0.00
117 23 0.07
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (113 bp):
CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCG
TATACTGATACTTGCAATTGACACGAAAAAAGTGTAAAAAAAAATTCT
Found at i:46668 original size:113 final size:113
Alignment explanation
Indices: 46343--46675 Score: 383
Period size: 113 Copynumber: 3.0 Consensus size: 113
46333 AAATTTCCCC
* * *** *
46343 CAAAAAAGGTGGTGCCGGCCATTGGCAAGTCACCAC-----AAATTTTTTTTTTTACTTTTTTCG
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCA
** * * **
46403 TATATTGATACTTGCAATTGACACGAAAAGAGTGTAAAAAAAAATTCT
66 TATATTGATACCGGCAATTAACACGAAAAGACTCAAAAAAAAAATTCT
*
46451 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCG
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCA
** * * **
46516 TATATTGATACTTGCAATTGACACGAAAAGAGTGTAAAAAAAAATTCT
66 TATATTGATACCGGCAATTAACACGAAAAGACTCAAAAAAAAAATTCT
46564 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCA
1 CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCA
* * * * *
46629 TGTCTTGGTGCCGGCCATTAACA-GACCAAA-ACTCAAAAAAAAAATTC
66 TATATTGATACCGGCAATTAACACGA--AAAGACTCAAAAAAAAAATTC
46676 CGTGTACAGG
Statistics
Matches: 201, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
108 34 0.17
112 2 0.01
113 162 0.81
114 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (113 bp):
CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAACATTTTTTTTACTTTTTTCA
TATATTGATACCGGCAATTAACACGAAAAGACTCAAAAAAAAAATTCT
Found at i:50462 original size:48 final size:50
Alignment explanation
Indices: 50374--50476 Score: 147
Period size: 48 Copynumber: 2.1 Consensus size: 50
50364 GTTTCTTCAT
50374 CATCAAACTTAAAAAGCAACCACCAGCTTTTATGTTGTAACGTGGCAATCG
1 CATCAAACTTAAAAAGCAACCACCAGC-TTTATGTTGTAACGTGGCAATCG
* * * *
50425 CATCAACCTT-AAATGCGACCACCAGC-TTATGTTGTAACGTGGCAATTG
1 CATCAAACTTAAAAAGCAACCACCAGCTTTATGTTGTAACGTGGCAATCG
50473 CATC
1 CATC
50477 TTCTTTAGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 25 0.52
50 14 0.29
51 9 0.19
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
CATCAAACTTAAAAAGCAACCACCAGCTTTATGTTGTAACGTGGCAATCG
Found at i:56544 original size:29 final size:29
Alignment explanation
Indices: 56502--56561 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
56492 CAGATCTGGG
56502 TATTAAGCATCTTTCAAGAAAAAAGGTTC
1 TATTAAGCATCTTTCAAGAAAAAAGGTTC
56531 TATTAAGCATCTTTCAAGAAAAAAGGTTC
1 TATTAAGCATCTTTCAAGAAAAAAGGTTC
56560 TA
1 TA
56562 ACTTCGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
TATTAAGCATCTTTCAAGAAAAAAGGTTC
Found at i:65340 original size:19 final size:17
Alignment explanation
Indices: 65294--65341 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
65284 TTCAATTAAA
65294 ATTTATTA-AAAATATT
1 ATTTATTACAAAATATT
65310 ATTTTATATACAAAATAAATT
1 A-TTTAT-TACAAAAT--ATT
65331 ATTTATTACAA
1 ATTTATTACAA
65342 GGTTGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 2 0.07
19 10 0.37
20 5 0.19
21 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATTACAAAATATT
Found at i:65754 original size:33 final size:34
Alignment explanation
Indices: 65694--65768 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
65684 AATATAGTTG
* * * * *
65694 ATATTTAATTAACTTGTGACGTTAATTTAAT-TA
1 ATATTTAATTAACTTCTCACATCAATTTAATCAA
*
65727 ATATTTAATTAATTTCTCACATCAATTTAATCAA
1 ATATTTAATTAACTTCTCACATCAATTTAATCAA
65761 ATATTTAA
1 ATATTTAA
65769 GGTTGACTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATTTAATTAACTTCTCACATCAATTTAATCAA
Found at i:86789 original size:33 final size:33
Alignment explanation
Indices: 86752--86818 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
86742 GATCAATATG
86752 AAAAAGCATGAACTTTTTATAAACCCAACACAT
1 AAAAAGCATGAACTTTTTATAAACCCAACACAT
86785 AAAAAGCATGAACTTTTTATAAACCCAACACAT
1 AAAAAGCATGAACTTTTTATAAACCCAACACAT
86818 A
1 A
86819 TCCTACCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (33 bp):
AAAAAGCATGAACTTTTTATAAACCCAACACAT
Found at i:90525 original size:34 final size:34
Alignment explanation
Indices: 90482--90547 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
90472 TCCCTCGTAA
*
90482 GCACCCCACAACTTTGTTTCAACGCAAGCGAAAG
1 GCACCCCACAACTCTGTTTCAACGCAAGCGAAAG
90516 GCACCCCACAACTCTGTTTCAACGCAAGCGAA
1 GCACCCCACAACTCTGTTTCAACGCAAGCGAA
90548 GGGTTTCCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.17, T:0.17
Consensus pattern (34 bp):
GCACCCCACAACTCTGTTTCAACGCAAGCGAAAG
Found at i:98026 original size:14 final size:15
Alignment explanation
Indices: 98002--98034 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
97992 ACATCTTTTA
98002 ATAATTGCTTCATCC
1 ATAATTGCTTCATCC
98017 ATAA-TGCTTCATCC
1 ATAATTGCTTCATCC
98031 ATAA
1 ATAA
98035 ATTTGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
ATAATTGCTTCATCC
Found at i:103116 original size:22 final size:22
Alignment explanation
Indices: 103086--103131 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
103076 GATATTATTG
* *
103086 AATTGAATTTGAATAATTTTCA
1 AATTAAATTTGAATAATTTGCA
*
103108 AATTAAATTTGAGTAATTTGCA
1 AATTAAATTTGAATAATTTGCA
103130 AA
1 AA
103132 CACAAATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (22 bp):
AATTAAATTTGAATAATTTGCA
Found at i:103403 original size:17 final size:18
Alignment explanation
Indices: 103356--103395 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
103346 AATGTTTCTT
* *
103356 AAAAGTGCTTTTGGGACA
1 AAAAGTACTTTTAGGACA
103374 AAAAGTACTTTTAGGACA
1 AAAAGTACTTTTAGGACA
103392 AAAA
1 AAAA
103396 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (18 bp):
AAAAGTACTTTTAGGACA
Found at i:106924 original size:20 final size:18
Alignment explanation
Indices: 106886--106938 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
106876 GTACTTTGTG
*
106886 TTAATATTTTTAAAT-TTT
1 TTAAT-TTTTTATATATTT
106904 TATAATTCTTTTATATATTT
1 T-TAATT-TTTTATATATTT
*
106924 TTTATTTTTTATATA
1 TTAATTTTTTATATA
106939 AATTATTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 11 0.37
19 15 0.50
20 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAATTTTTTATATATTT
Found at i:107715 original size:37 final size:37
Alignment explanation
Indices: 107674--107748 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
107664 AGAATAATTC
*
107674 TATAATAGCTAAATTGACCAAAAGTGTATACGTGAGG
1 TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
**
107711 TATAATAGCCAAATTGACTGAAAGTGTATACGTGAGG
1 TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
107748 T
1 T
107749 CCACTAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (37 bp):
TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
Found at i:112271 original size:26 final size:27
Alignment explanation
Indices: 112242--112294 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
112232 AACGTAAAAG
*
112242 CTTTTAC-GTATTTTTTCACA-ATTTCA
1 CTTTTACAATATTTTTT-ACATATTTCA
112268 CTTTTACAATATTTTTTACATATTTCA
1 CTTTTACAATATTTTTTACATATTTCA
112295 TCATCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (27 bp):
CTTTTACAATATTTTTTACATATTTCA
Found at i:112994 original size:17 final size:17
Alignment explanation
Indices: 112968--113002 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
112958 CCTCCTCGCA
* *
112968 CGTGTTGCGCCTGCGCG
1 CGTGTAGCGCCTCCGCG
112985 CGTGTAGCGCCTCCGCG
1 CGTGTAGCGCCTCCGCG
113002 C
1 C
113003 CAAATCCACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.40, G:0.37, T:0.20
Consensus pattern (17 bp):
CGTGTAGCGCCTCCGCG
Found at i:123709 original size:34 final size:35
Alignment explanation
Indices: 123660--123727 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
123650 AACGTTCAAG
* * **
123660 GTTTAGGGTTTGAGTTTGATGTTT-GGGGTCTAGT
1 GTTTAAGGTTCGAGTTCAATGTTTAGGGGTCTAGT
*
123694 GTTTAAGGTTCGAGTTCAATGTTTAGGGTTCTAG
1 GTTTAAGGTTCGAGTTCAATGTTTAGGGGTCTAG
123728 AGTTCGAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.16, C:0.06, G:0.34, T:0.44
Consensus pattern (35 bp):
GTTTAAGGTTCGAGTTCAATGTTTAGGGGTCTAGT
Found at i:131889 original size:20 final size:19
Alignment explanation
Indices: 131864--131902 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
131854 CCAATTTTTT
131864 TGAAAATTTTAATTATACCC
1 TGAAAATTTTAATTA-ACCC
131884 TGAAAATTTTAATTAACCC
1 TGAAAATTTTAATTAACCC
131903 CCTCCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (19 bp):
TGAAAATTTTAATTAACCC
Found at i:133810 original size:239 final size:230
Alignment explanation
Indices: 133232--133839 Score: 732
Period size: 239 Copynumber: 2.6 Consensus size: 230
133222 CCAAAGTAAC
* * *
133232 AAATAAAAAATGAACCCCATTATTATAAATCAAGTTATTAAATATTTCAAACAAATCTTGATATT
1 AAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAATT
* * * * * *
133297 CGAAACTTCCTATTATCTAATAAAAAACCTAAAATTTCTAATAATAAGCCAAAATCGCCTATAT-
66 TGAAACTTCCCATTATCCAAT-AAAAACCTAAGATTTCTAATAATAAACCAAAACCG-C-ATATC
* **** *
133361 GATTAATTACAAATACTTTTTGACAAGTATTTACTGTTGGGAGTCATGTGAACCAAAAACCTATT
128 GATTAATTACAAATACTTTTTGACAAGCATTTACCACCGGGAGTCATGTGAACCAAAAACCTATC
* * * * * *
133426 AATAAATAAGAATTCATTTCAGTAAAAAACTTATTAAC
193 AATAAATAAGAATACATTCCAATAAAAAACTAATAAAA
* * **
133464 AAATAAAAACTGAACCTCAATATTATAAATCAAATTATTAAATATTTTGAACAAATCTTGAAATT
1 AAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAATT
* * *
133529 TGAAACTTCCCAGTATCCAATAAAAACTTAAGATTTCTAATAATAAACCGAAACCGCATATCGAA
66 TGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATATCG-A
* * * * *
133594 TTAGTTACAAATACTTTTTGACAAGCGTTTGCCACCGTGAGTCTTGTGAACCAAAAACCTATCAA
130 TTAATTACAAATACTTTTTGACAAGCATTTACCACCGGGAGTCATGTGAACCAAAAACCTATCAA
133659 TAAATAAGAATACATTCCAATAAAAACCTACTAACAAATAAAA
195 TAAATAAGAATACATTCCAATAAAAA---ACT----AATAAAA
* *
133702 AAATAAAAAAATAAACCTCATTATTATGAATCAAATTATTAAATATTTCAAACAAATCTTGAAAT
1 AAAT-AAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAAT
* * * * *
133767 TTAAAATTTCCCATTATCCAATAAAAACCTAAGATTCCTAATAATAACCCAAAACCGCCTATCTG
65 TTGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATATC-G
133832 ATTAATTA
129 ATTAATTA
133840 TATTTTTTTT
Statistics
Matches: 317, Mismatches: 48, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
229 4 0.01
230 2 0.01
231 108 0.34
232 75 0.24
234 3 0.01
238 8 0.03
239 116 0.37
240 1 0.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (230 bp):
AAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAATT
TGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATATCGAT
TAATTACAAATACTTTTTGACAAGCATTTACCACCGGGAGTCATGTGAACCAAAAACCTATCAAT
AAATAAGAATACATTCCAATAAAAAACTAATAAAA
Found at i:134494 original size:34 final size:35
Alignment explanation
Indices: 134428--134494 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
134418 CAAACACTAG
*
134428 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
134463 AAAATATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
134495 TATTTTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:139325 original size:51 final size:51
Alignment explanation
Indices: 139248--139357 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 51
139238 ATGCTACAGG
* * *
139248 CTAAATTTGTTAAATTAAAATCAAATTAATA-GAATGTGTAAATGTTATGGA
1 CTAAATTTATTAAATTAAAATCAAATTAACACG-ATGTGTAAATCTTATGGA
* * * *
139299 CTAAATTTATTAAATTAAAGTTAAATTGACACGATGTGTAAATCTTGTGGA
1 CTAAATTTATTAAATTAAAATCAAATTAACACGATGTGTAAATCTTATGGA
*
139350 CTGAATTT
1 CTAAATTT
139358 GTTATCATAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
51 49 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (51 bp):
CTAAATTTATTAAATTAAAATCAAATTAACACGATGTGTAAATCTTATGGA
Found at i:143083 original size:21 final size:23
Alignment explanation
Indices: 143047--143089 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
143037 TTTTGTTTTT
143047 TTTTTATATATTTGAATGATTTC
1 TTTTTATATATTTGAATGATTTC
*
143070 TTTTTAT-T-TTTGAATTATTT
1 TTTTTATATATTTGAATGATTT
143090 TTGTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTTATATATTTGAATGATTTC
Found at i:146506 original size:11 final size:11
Alignment explanation
Indices: 146473--146520 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
146463 TAACAACAAT
* *
146473 AAAATAGTAAC
1 AAAATAATAGC
*
146484 AATATAATAGC
1 AAAATAATAGC
*
146495 AAAATGATAGC
1 AAAATAATAGC
*
146506 AAAATAATAAC
1 AAAATAATAGC
146517 AAAA
1 AAAA
146521 CACAGCAGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:146572 original size:20 final size:20
Alignment explanation
Indices: 146526--146573 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
146516 CAAAACACAG
146526 CAGCAAAACAATAGAAACAA
1 CAGCAAAACAATAGAAACAA
* * *
146546 CAACAAAACAGTGGAAACAA
1 CAGCAAAACAATAGAAACAA
*
146566 TAGCAAAA
1 CAGCAAAA
146574 TATAGCAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (20 bp):
CAGCAAAACAATAGAAACAA
Found at i:147867 original size:11 final size:11
Alignment explanation
Indices: 147834--147881 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
147824 TAACAACAAT
* *
147834 AAAATAGTAAC
1 AAAATAATAGC
*
147845 AATATAATAGC
1 AAAATAATAGC
*
147856 AAAATGATAGC
1 AAAATAATAGC
*
147867 AAAATAATAAC
1 AAAATAATAGC
147878 AAAA
1 AAAA
147882 CACAGCAGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:147933 original size:20 final size:20
Alignment explanation
Indices: 147887--147934 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
147877 CAAAACACAG
147887 CAGCAAAACAATAGAAACAA
1 CAGCAAAACAATAGAAACAA
* * *
147907 CAACAAAACAGTGGAAACAA
1 CAGCAAAACAATAGAAACAA
*
147927 TAGCAAAA
1 CAGCAAAA
147935 TATAGCAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (20 bp):
CAGCAAAACAATAGAAACAA
Found at i:151461 original size:6 final size:6
Alignment explanation
Indices: 151445--151480 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
151435 GTTAGACACA
151445 ATTTATT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTT-TT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
151481 GTGATGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:153956 original size:60 final size:60
Alignment explanation
Indices: 153883--154016 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
153873 TTAATATAAC
* * * *
153883 ATTTTGTATCTAAACTTGACA-TTTTTTCTTAATTT-GATTACTAAACTTTTTTTGGGC-CTA
1 ATTTGGTACCTAAACTTGACATTTTTTTC-TAATTTAGA-AACTAAACTTTTTTTAGGCTC-A
* * *
153943 ATTTGGTACCTAAACTTGACATTTTTTTCTATTTTAGAAACTAAGCTTTTTTTAGGTTCA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTAGAAACTAAACTTTTTTTAGGCTCA
154003 ATTTGGTACCTAAA
1 ATTTGGTACCTAAA
154017 TTTATTAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 54 0.84
61 10 0.16
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTAGAAACTAAACTTTTTTTAGGCTCA
Found at i:154442 original size:31 final size:30
Alignment explanation
Indices: 154407--154533 Score: 94
Period size: 31 Copynumber: 4.2 Consensus size: 30
154397 GATTAGGTAT
*
154407 CAAATTAAGAAAAATAGTCAAGTTCATGTAC
1 CAAATTAAGAAAAATA-TCAAGTTCAAGTAC
* * *** ** *
154438 CAAATT-GGACACCCAAAAAGTTTAAGTAC
1 CAAATTAAGAAAAATATCAAGTTCAAGTAC
* * * *
154467 CAACTTAACAAAAAGTATCAAGTTTAGGTAC
1 CAAATTAAGAAAAA-TATCAAGTTCAAGTAC
*
154498 CAAATTAAGAAAAAATGTCAAGTTCAAGTAC
1 CAAATTAAG-AAAAATATCAAGTTCAAGTAC
154529 CAAAT
1 CAAAT
154534 ATTATATTAA
Statistics
Matches: 69, Mismatches: 24, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
29 15 0.22
30 6 0.09
31 43 0.62
32 5 0.07
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.24
Consensus pattern (30 bp):
CAAATTAAGAAAAATATCAAGTTCAAGTAC
Found at i:159829 original size:42 final size:42
Alignment explanation
Indices: 159770--159937 Score: 336
Period size: 42 Copynumber: 4.0 Consensus size: 42
159760 AACAGACGAG
159770 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
1 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
159812 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
1 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
159854 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
1 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
159896 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
1 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
159938 CCTTATATTA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (42 bp):
GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
Found at i:161581 original size:175 final size:174
Alignment explanation
Indices: 161279--161669 Score: 606
Period size: 175 Copynumber: 2.2 Consensus size: 174
161269 ACCTTGATTA
* *
161279 TTACCTGCATGCTGAA-GATGGTGGATCTCATAGTTGAACAGGTGGCAAAAGTGTTTCTCTTCCT
1 TTACCTGCATGCT-AAGGATGGTGGATCTCATAGTCGAACAGGAGGCAAAAGTGTTTCTCTTCCT
* * * * *
161343 ACTCTTGTCGGTCATGCCATAGGTGGCGGGATGACAACATTTATAGCATCCGACCTGATTCAGTA
65 ACCCTTGACGGTCATGCCATAGGTGGCGGGATGACAACATTGATAGCATCCAACCTAATTCAGTA
*
161408 ACCTTAAGTGTAGTTTATCCTTTGAAATACCATGCTTGTCGGGTTC
130 ACCTTAAGTGTAGTTTATCCTTTGAAA-ACCATGCTTGTCGGCTTC
* *
161454 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTTCTA
1 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCAAAAGTGTTTCTCTTCCTA
* *
161519 CCCTTGACGGTTATGTCATAGGTGGCGGGATCG-CAACATTGATAGCATCCAACCTAATTCAGTA
66 CCCTTGACGGTCATGCCATAGGTGGCGGGAT-GACAACATTGATAGCATCCAACCTAATTCAGTA
* * *
161583 ACCTTAAGTGTAGTTTATCCTTTGAAAACTATTCTTGTCGGCTTT
130 ACCTTAAGTGTAGTTTATCCTTTGAAAACCATGCTTGTCGGCTTC
161628 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGG
1 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGG
161670 GGGGGGGGGG
Statistics
Matches: 199, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
174 58 0.29
175 140 0.70
176 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (174 bp):
TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCAAAAGTGTTTCTCTTCCTA
CCCTTGACGGTCATGCCATAGGTGGCGGGATGACAACATTGATAGCATCCAACCTAATTCAGTAA
CCTTAAGTGTAGTTTATCCTTTGAAAACCATGCTTGTCGGCTTC
Found at i:167610 original size:45 final size:45
Alignment explanation
Indices: 167546--167637 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
167536 AATATAAACA
* * *
167546 AGAGCTAACTCTTTAAAAGGAATGGTATGCCTTGTAAGCAATCAC
1 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
167591 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
1 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
167636 AG
1 AG
167638 TTCTCGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (45 bp):
AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
Found at i:179961 original size:13 final size:13
Alignment explanation
Indices: 179943--179967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179933 CGATGGTCCA
179943 AGGTCCAAGGTTG
1 AGGTCCAAGGTTG
179956 AGGTCCAAGGTT
1 AGGTCCAAGGTT
179968 TAAGATTTAA
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:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (13 bp):
AGGTCCAAGGTTG
Found at i:180283 original size:28 final size:28
Alignment explanation
Indices: 180221--180301 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 28
180211 ATCGAGAGTC
* ** * *
180221 TAGGGTGTAAGGTTTGGGGTCCATAGTT
1 TAGGGTTTAAGGTTTAAGGTCCAGAATT
*
180249 T-GAGGTTTAAGGTTTATGGTCCAGAATT
1 TAG-GGTTTAAGGTTTAAGGTCCAGAATT
*
180277 TAGGGTTTGAA-GTTTAAGATCCAGA
1 TAGGGTTT-AAGGTTTAAGGTCCAGA
180302 TTAAAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.02
28 39 0.91
29 3 0.07
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (28 bp):
TAGGGTTTAAGGTTTAAGGTCCAGAATT
Found at i:188123 original size:18 final size:17
Alignment explanation
Indices: 188100--188143 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
188090 TAATATATAT
188100 TATATTCTAAAATATAAA
1 TATATT-TAAAATATAAA
188118 TATA-TTAAAATATAAA
1 TATATTTAAAATATAAA
188134 -ATATTATAAA
1 TATATT-TAAA
188144 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 5 0.21
18 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATTTAAAATATAAA
Found at i:188126 original size:16 final size:15
Alignment explanation
Indices: 188107--188145 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
188097 TATTATATTC
188107 TAAAATATAAATATAT
1 TAAAATATAAA-ATAT
188123 TAAAATATAAAATAT
1 TAAAATATAAAATAT
188138 TATAAATA
1 TA-AAATA
188146 ATTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATAAAATAT
Found at i:188167 original size:25 final size:26
Alignment explanation
Indices: 188113--188167 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
188103 ATTCTAAAAT
**
188113 ATAAATATATTAAAATATAAAATATT
1 ATAAATATATTAAAATATAAAATAGA
*
188139 ATAAATA-ATTTAAAA-ATAATATAGA
1 ATAAATATA-TTAAAATATAAAATAGA
188164 ATAA
1 ATAA
188168 GTTATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
ATAAATATATTAAAATATAAAATAGA
Found at i:189923 original size:21 final size:22
Alignment explanation
Indices: 189893--189937 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
189883 GAACAAATTG
189893 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
189915 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
189936 TT
1 TT
189938 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:194238 original size:13 final size:13
Alignment explanation
Indices: 194203--194239 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
194193 GATATATTTG
*
194203 TAATTTGAAAGCT
1 TAATTTGAAAACT
194216 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
194230 TAATTTGAAA
1 TAATTTGAAA
194240 TTTTGGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:194249 original size:21 final size:20
Alignment explanation
Indices: 194220--194276 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
194210 AAAGCTTAAG
*
194220 TTTGAAAACTTAATTTGAAAT
1 TTTGAAAACTTAAATT-AAAT
*
194241 TTTGGAAACTTAAAAATTAAAT
1 TTTGAAAACTT--AAATTAAAT
*
194263 TTTGTAAACTTAAA
1 TTTGAAAACTTAAA
194277 AGTTTTGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.10
21 10 0.32
22 14 0.45
23 4 0.13
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTGAAAACTTAAATTAAAT
Found at i:215819 original size:26 final size:27
Alignment explanation
Indices: 215790--215848 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
215780 AAGCCTATTT
* *
215790 AGGCGTAAC-AACCTTATACTAATTGA
1 AGGCATAACAAACCTCATACTAATTGA
215816 AGGCATAACGAAACCTCATACTAATTGA
1 AGGCATAAC-AAACCTCATACTAATTGA
215844 AGGCA
1 AGGCA
215849 ATAAGTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.28
28 21 0.72
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (27 bp):
AGGCATAACAAACCTCATACTAATTGA
Found at i:217209 original size:18 final size:19
Alignment explanation
Indices: 217176--217232 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
217166 ATTAAATTTG
*
217176 ATTAAGATAATATATTTTT-
1 ATTAAAATAAT-TATTTTTA
*
217195 ATTAAAATAGTTATTTTTA
1 ATTAAAATAATTATTTTTA
217214 ATTAAAATAATTCATTTTT
1 ATTAAAATAATT-ATTTTT
217233 TAGCATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.21
19 20 0.61
20 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATTAAAATAATTATTTTTA
Found at i:236922 original size:2 final size:2
Alignment explanation
Indices: 236915--236956 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
236905 ATCTTTGATT
*
236915 AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
236957 TAAAGTTCAA
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:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:238275 original size:17 final size:18
Alignment explanation
Indices: 238238--238275 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
238228 AATAAAAATT
*
238238 TATTTTCTAATGAAATAA
1 TATTTTATAATGAAATAA
*
238256 TATTTTATAAT-AATTAA
1 TATTTTATAATGAAATAA
238273 TAT
1 TAT
238276 CATATAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTTATAATGAAATAA
Found at i:238663 original size:17 final size:18
Alignment explanation
Indices: 238641--238675 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
238631 AACCCGCCGT
238641 AATTT-GTAATTTTTATA
1 AATTTGGTAATTTTTATA
*
238658 AATTTGGTGATTTTTATA
1 AATTTGGTAATTTTTATA
238676 CTAAATTTTC
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:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
AATTTGGTAATTTTTATA
Found at i:248359 original size:30 final size:29
Alignment explanation
Indices: 248325--248383 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
248315 AAATTGAGTC
* *
248325 AAATCAAAATATTATGTATAAAATTACACA
1 AAATCAAAAT-TTATATACAAAATTACACA
*
248355 AAATCAAAATTTATATACAAAGTTACACA
1 AAATCAAAATTTATATACAAAATTACACA
248384 TCAGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (29 bp):
AAATCAAAATTTATATACAAAATTACACA
Found at i:256449 original size:14 final size:14
Alignment explanation
Indices: 256430--256469 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
256420 TTGATTGTCA
256430 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
256444 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
256458 GGAAAATGTTTT
1 GTAAAATGTTTT
256470 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:256478 original size:20 final size:20
Alignment explanation
Indices: 256453--256492 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
256443 CGTAAAATGA
*
256453 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
256473 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
256493 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:256482 original size:34 final size:35
Alignment explanation
Indices: 256438--256504 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
256428 CAGTAAAATG
*
256438 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
256472 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
256505 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:256508 original size:14 final size:15
Alignment explanation
Indices: 256432--256508 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
256422 GATTGTCAGT
* *
256432 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
256446 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
256460 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
256480 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
256495 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
256509 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:262475 original size:20 final size:21
Alignment explanation
Indices: 262433--262500 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
262423 ATTAATTATT
262433 TTTTAAAAA-A-AT-TTAAAA
1 TTTTAAAAATATATATTAAAA
*
262451 TTTTTAAAAATATATA-TATAA
1 -TTTTAAAAATATATATTAAAA
* * *
262472 TTTTTAAAATTTTTATTAAAA
1 TTTTAAAAATATATATTAAAA
262493 TTTTAAAA
1 TTTTAAAA
262501 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.23
20 13 0.33
21 17 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAAATATATATTAAAA
Found at i:262494 original size:21 final size:21
Alignment explanation
Indices: 262445--262509 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
262435 TTAAAAAAAT
*
262445 TTAAAATTTTTAAAA-ATATA
1 TTAAAATTTTTAAAATTTATA
* *
262465 TATATAATTTTTAAAATTTTTA
1 T-TAAAATTTTTAAAATTTATA
262487 TTAAAA-TTTTAAAATTTA-A
1 TTAAAATTTTTAAAATTTATA
262506 TTAA
1 TTAA
262510 TTCCTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
19 5 0.13
20 12 0.32
21 17 0.45
22 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAATTTTTAAAATTTATA
Found at i:273065 original size:41 final size:39
Alignment explanation
Indices: 273008--273127 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 39
272998 TGATCGAATG
*
273008 TAATTCAGACTTATTGTCTAGCAGGCTAGATGCCGGTGATA
1 TAATTCAGAC-TATTGTCTAGCAGGCTA-ATGCCGGTGAAA
*
273049 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACT-ATTGTCTAGCAGGC-TAATGCCGGTGAAA
* * * *
273090 TTATTCGGACTATAAGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTAT-TGTCTAGCAGGCT-AATGCCGGTG
273128 TATTAAATCA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.06
41 62 0.91
42 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (39 bp):
TAATTCAGACTATTGTCTAGCAGGCTAATGCCGGTGAAA
Found at i:273448 original size:2 final size:2
Alignment explanation
Indices: 273441--273469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
273431 TACTCGGTGC
273441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
273470 GTATTTTGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:275595 original size:86 final size:85
Alignment explanation
Indices: 275495--275651 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 85
275485 TTCCGATATG
* * *
275495 TGATTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAAT-TTTAGATTTACGTGTAAGGCCA
1 TGATTTCGTGTAAGACC-CTGTCTGAGACAG-TGGCATCAATATTT-GATTT-CATGTAAGACCA
275557 TGTCTGGGACATTAGCATCGTATA
62 TGTCTGGGACATTAGCATCGTATA
* *
275581 TGATTTCGTGTAAGACCCTGTCTGAGACAGTGTCATCGATATTTGATTTCATGTAAGACCATGTC
1 TGATTTCGTGTAAGACCCTGTCTGAGACAGTGGCATCAATATTTGATTTCATGTAAGACCATGTC
275646 TGGGAC
66 TGGGAC
275652 GTTGGCATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
85 21 0.33
86 38 0.60
87 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (85 bp):
TGATTTCGTGTAAGACCCTGTCTGAGACAGTGGCATCAATATTTGATTTCATGTAAGACCATGTC
TGGGACATTAGCATCGTATA
Found at i:275636 original size:43 final size:42
Alignment explanation
Indices: 275488--275651 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 42
275478 CATAGGATTC
* *
275488 CGATATGTGATTTCGTGTAAGACCACGTCTGGGAC-GTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAG-T-GCAT
* * *
275531 CAAT-TTTAGATTTACGTGTAAGGCCATGTCTGGGACATTAGCAT
1 CGATATTT-GATTT-CGTGTAAGACCATGTCTGGGACAGT-GCAT
* * *
275575 CG-TATATGATTTCGTGTAAGACCCTGTCTGAGACAGTGTCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTG-CAT
*
275617 CGATATTTGATTTCATGTAAGACCATGTCTGGGAC
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGAC
275652 GTTGGCATTG
Statistics
Matches: 99, Mismatches: 16, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 28 0.28
43 42 0.42
44 28 0.28
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGCAT
Found at i:275674 original size:86 final size:86
Alignment explanation
Indices: 275497--275674 Score: 184
Period size: 86 Copynumber: 2.1 Consensus size: 86
275487 CCGATATGTG
* * *
275497 ATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATTTTAGATTTACGTGTAAGGCCATGTCT
1 ATTTCGTGTAAGACCACGTCTGAGACGTTGGCATCAATTTTAGATTTACATGTAAGACCATGTCT
* * *
275562 GGGACATTAGCATCGTATATG
66 GGGACATTAGCATCGAAAATC
* *
275583 ATTTCGTGTAAGACC-CTGTCTGAGACAG-TGTCATCGATATTT-GATTT-CATGTAAGACCATG
1 ATTTCGTGTAAGACCAC-GTCTGAGAC-GTTGGCATCAAT-TTTAGATTTACATGTAAGACCATG
* * *
275644 TCTGGGACGTTGGCATTGAACAATC
63 TCTGGGACATTAGCATCGAA-AATC
*
275669 TTTTCG
1 ATTTCG
275675 AGCTATCTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
85 29 0.38
86 43 0.57
87 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (86 bp):
ATTTCGTGTAAGACCACGTCTGAGACGTTGGCATCAATTTTAGATTTACATGTAAGACCATGTCT
GGGACATTAGCATCGAAAATC
Found at i:278162 original size:9 final size:9
Alignment explanation
Indices: 278144--278321 Score: 74
Period size: 10 Copynumber: 18.3 Consensus size: 9
278134 GCCCATTTTT
278144 ATTTTAAAA
1 ATTTTAAAA
278153 ATTTTTAAAA
1 A-TTTTAAAA
**
278163 ATTAAAAAAA
1 ATT-TTAAAA
278173 GTATTTTAAAA
1 --ATTTTAAAA
*
278184 ATATTTTAAA
1 AT-TTTAAAA
**
278194 ATTAAAAAAA
1 ATT-TTAAAA
*
278204 ATTTAAAAAA
1 ATTT-TAAAA
278214 GTATTTTAAAA
1 --ATTTTAAAA
*
278225 ATATTTTAAA
1 AT-TTTAAAA
*
278235 A-TTAAAAA
1 ATTTTAAAA
278243 TATTTTAAAA
1 -ATTTTAAAA
*
278253 ATATTTTAAA
1 AT-TTTAAAA
*
278263 A-TTAAAAA
1 ATTTTAAAA
278271 TATTTTAAAA
1 -ATTTTAAAA
*
278281 ATATTTTAAA
1 AT-TTTAAAA
*
278291 A-TTAAAAA
1 ATTTTAAAA
278299 TATTTTAAAA
1 -ATTTTAAAA
*
278309 ATATTTTAAA
1 AT-TTTAAAA
278319 ATT
1 ATT
278322 AATCCGGCCC
Statistics
Matches: 127, Mismatches: 23, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
8 15 0.12
9 18 0.14
10 79 0.62
11 8 0.06
12 7 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:278188 original size:11 final size:11
Alignment explanation
Indices: 278143--278319 Score: 137
Period size: 11 Copynumber: 17.9 Consensus size: 11
278133 GGCCCATTTT
278143 TATTTTAAAAA
1 TATTTTAAAAA
278154 T-TTTT-AAAA
1 TATTTTAAAAA
**
278163 -ATTAAAAAAA
1 TATTTTAAAAA
278173 GTATTTTAAAAA
1 -TATTTTAAAAA
278185 TATTTT--AAA
1 TATTTTAAAAA
*
278194 -A-TTAAAAAA
1 TATTTTAAAAA
* *
278203 AATTTAAAAAA
1 TATTTTAAAAA
278214 GTATTTTAAAAA
1 -TATTTTAAAAA
278226 TATTTT--AAA
1 TATTTTAAAAA
278235 -A--TTAAAAA
1 TATTTTAAAAA
278243 TATTTTAAAAA
1 TATTTTAAAAA
278254 TATTTT--AAA
1 TATTTTAAAAA
278263 -A--TTAAAAA
1 TATTTTAAAAA
278271 TATTTTAAAAA
1 TATTTTAAAAA
278282 TATTTT--AAA
1 TATTTTAAAAA
278291 -A--TTAAAAA
1 TATTTTAAAAA
278299 TATTTTAAAAA
1 TATTTTAAAAA
278310 TATTTTAAAA
1 TATTTTAAAA
278320 TTAATCCGGC
Statistics
Matches: 135, Mismatches: 7, Indels: 48
0.71 0.04 0.25
Matches are distributed among these distances:
6 6 0.04
7 2 0.01
8 13 0.10
9 24 0.18
10 9 0.07
11 64 0.47
12 17 0.13
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:278209 original size:28 final size:28
Alignment explanation
Indices: 278178--278323 Score: 222
Period size: 28 Copynumber: 5.1 Consensus size: 28
278168 AAAAAGTATT
* ***
278178 TTAAAAATATTTTAAAATTA-AAAAAAA
1 TTAAAAATATTTTAAAAATATTTTAAAA
278205 TTTAAAAAAGTATTTTAAAAATATTTTAAAA
1 -TT-AAAAA-TATTTTAAAAATATTTTAAAA
278236 TTAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAAATATTTTAAAA
278264 TTAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAAATATTTTAAAA
278292 TTAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAAATATTTTAAAA
278320 TTAA
1 TTAA
278324 TCCGGCCCAT
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
28 83 0.75
29 10 0.09
30 14 0.13
31 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
TTAAAAATATTTTAAAAATATTTTAAAA
Found at i:278323 original size:17 final size:17
Alignment explanation
Indices: 278178--278308 Score: 97
Period size: 17 Copynumber: 8.0 Consensus size: 17
278168 AAAAAGTATT
278178 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
278195 TTAAAAAAAATTTAAAAAAGTA
1 TT-AAAAATATTT--TAAA--A
278217 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
278236 TTAAAAATA--TT----
1 TTAAAAATATTTTAAAA
278247 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
278264 TTAAAAATA--TT----
1 TTAAAAATATTTTAAAA
278275 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
278292 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
278309 ATATTTTAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 38
0.68 0.03 0.29
Matches are distributed among these distances:
11 18 0.20
13 4 0.04
15 4 0.04
17 37 0.41
18 9 0.10
19 1 0.01
20 3 0.03
21 3 0.03
22 1 0.01
23 9 0.10
24 2 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:282925 original size:6 final size:6
Alignment explanation
Indices: 282914--282957 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
282904 ATATAAAACA
282914 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AA
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AA
282958 CGTGAGCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AATGAT
Found at i:289513 original size:258 final size:258
Alignment explanation
Indices: 289056--289566 Score: 943
Period size: 258 Copynumber: 2.0 Consensus size: 258
289046 CTAAACATTC
289056 CTATGTGGAACATTTTCCAACCTGCACGATACCATTACCCACTCCACTACTTGCATCAACCTAAA
1 CTATGTGGAACATTTTCCAACCTGCACGATACCATTACCCACTCCACTACTTGCATCAACCTAAA
* *
289121 TAATATCAGATGCATAAAGAAAATTATGTTTAAGATCATCATTAATCCTAAATCAAATTTTTTCT
66 TAATATCAGATGCACAAAGAAAATTATGTTTAAGATCATCATTAATCCTAAATCAAATTTTCTCT
* * *
289186 TTTATAACCAGAAGTCCACAAAACAGCAATTGAACCAATAAGCAAAATCATGTCCATCTGTTGTC
131 TTTATAACCAGAAGTCCACAAAACAGCAAGTGAACCAATAAGCAAAATCATGTCCAGCAGTTGTC
289251 TGTAAAGTGCACCTCTCTGTATTTCAGTTAACATATTATTCTTAAAAAAGGACCAAATTATTT
196 TGTAAAGTGCACCTCTCTGTATTTCAGTTAACATATTATTCTTAAAAAAGGACCAAATTATTT
289314 CTATGTGGAACATTTTCCAACCTGCACGATACCATTACCCACTCCACTACTTGCATCAACCTAAA
1 CTATGTGGAACATTTTCCAACCTGCACGATACCATTACCCACTCCACTACTTGCATCAACCTAAA
*
289379 TAATATCGGATGCACAAAGAAAATTATGTTTAAGATCATCATTAATCCTAAATCAAAGTTTTCT-
66 TAATATCAGATGCACAAAGAAAATTATGTTTAAGATCATCATTAATCCTAAATCAAA-TTTTCTC
289443 TTTTATAACCAGAAGTCCACAAAACAGCAAGTGAACCAATAAGCAAAATCATGTCCAGCAGTTGT
130 TTTTATAACCAGAAGTCCACAAAACAGCAAGTGAACCAATAAGCAAAATCATGTCCAGCAGTTGT
*
289508 CTGTAAAGTGCACCTCTCTGTATTTCAGTTAACATATTATTCTTAAAAAGGGACCAAAT
195 CTGTAAAGTGCACCTCTCTGTATTTCAGTTAACATATTATTCTTAAAAAAGGACCAAAT
289567 AAGGATTGAA
Statistics
Matches: 245, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
258 240 0.98
259 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (258 bp):
CTATGTGGAACATTTTCCAACCTGCACGATACCATTACCCACTCCACTACTTGCATCAACCTAAA
TAATATCAGATGCACAAAGAAAATTATGTTTAAGATCATCATTAATCCTAAATCAAATTTTCTCT
TTTATAACCAGAAGTCCACAAAACAGCAAGTGAACCAATAAGCAAAATCATGTCCAGCAGTTGTC
TGTAAAGTGCACCTCTCTGTATTTCAGTTAACATATTATTCTTAAAAAAGGACCAAATTATTT
Found at i:290548 original size:30 final size:30
Alignment explanation
Indices: 290514--290573 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
290504 CTGCTTGGAG
*
290514 GAAAAATTGTCATTAGATATACATAAGCTT
1 GAAAAATTGTCAATAGATATACATAAGCTT
290544 GAAAAATTGTCAATAGATATACATAAGCTT
1 GAAAAATTGTCAATAGATATACATAAGCTT
290574 CATCCTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (30 bp):
GAAAAATTGTCAATAGATATACATAAGCTT
Found at i:292362 original size:3 final size:3
Alignment explanation
Indices: 292354--292403 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
292344 CACCTACAGA
*
292354 AAT AAT AAT AAT AAT AAT AAC 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
292402 AA
1 AA
292404 AACAGCACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:303818 original size:6 final size:6
Alignment explanation
Indices: 303807--303840 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
303797 AAAGAGGGAT
303807 TAAATC TAAATC TAAATC TAAATC TAAAT- TAAAT
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAAT
303841 AATAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:303846 original size:18 final size:18
Alignment explanation
Indices: 303807--303846 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
303797 AAAGAGGGAT
*
303807 TAAATCTAAATCTAAATC
1 TAAATCTAAATCTAAATA
303825 TAAATCTAAAT-TAAATAA
1 TAAATCTAAATCTAAAT-A
303843 TAAA
1 TAAA
303847 AATTAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATCTAAATCTAAATA
Found at i:303860 original size:25 final size:25
Alignment explanation
Indices: 303836--303888 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
303826 AAATCTAAAT
*
303836 TAAATAATA-AAAATTAAATAAAAA
1 TAAATAAAACAAAATTAAATAAAAA
* **
303860 TAAGTAAAACAAAATTAAATCTAAA
1 TAAATAAAACAAAATTAAATAAAAA
303885 TAAA
1 TAAA
303889 ACAAATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (25 bp):
TAAATAAAACAAAATTAAATAAAAA
Found at i:303878 original size:21 final size:21
Alignment explanation
Indices: 303854--303893 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
303844 AAAAATTAAA
*
303854 TAAAAATAAGTAAAACAAAAT
1 TAAAAATAAATAAAACAAAAT
**
303875 TAAATCTAAATAAAACAAA
1 TAAAAATAAATAAAACAAA
303894 TAAATGAAAA
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:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAAAATAAATAAAACAAAAT
Found at i:304155 original size:14 final size:14
Alignment explanation
Indices: 304115--304160 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
304105 TCAAAATCTA
304115 AAATAAATAAT-AT
1 AAATAAATAATAAT
304128 AAATTAAATAATAAT
1 AAA-TAAATAATAAT
304143 GAAATAAA-AATAAGT
1 -AAATAAATAATAA-T
304158 AAA
1 AAA
304161 ACAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 7 0.24
16 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
AAATAAATAATAAT
Found at i:304171 original size:21 final size:21
Alignment explanation
Indices: 304147--304186 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
304137 AATAATGAAA
*
304147 TAAAAATAAGTAAAACAAAAT
1 TAAAAATAAATAAAACAAAAT
**
304168 TAAATCTAAATAAAACAAA
1 TAAAAATAAATAAAACAAA
304187 TAAATGAAAA
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:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAAAATAAATAAAACAAAAT
Found at i:304256 original size:293 final size:292
Alignment explanation
Indices: 303679--304262 Score: 717
Period size: 294 Copynumber: 2.0 Consensus size: 292
303669 TTGTTATGCT
* * * * *
303679 TAAACCAAAATTAAATTAAATTTGCAGTATAGTGAGTATGGTCGATCCCACAAACACTGAACTGG
1 TAAACCAAAATTAAATTAAATTTACAGAATAGTAACTATGGTCGATCCCACAAACACTGAACTGA
* * * * * ** *
303744 TTAATTTTACGATTTCTTATGACCAAGATTAGACAAATTTTCAAAAATAAATAAAAGAGGGATTA
66 TTAATTTTACAATTTCTTATGACCAAAAGTAGACAAATCTGCAAAAATAAATAAAAGAAAGAATA
* ** * *
303809 AATCTAAATCTAAATCTAAATCTAAATTAAATAATAAAAATTAAATAAAAATAAGTAAAACAAAA
131 AATCAAAATCTAAATAAAAATATAAATTAAATAAT--AAATGAAATAAAAATAAGTAAAACAAAA
**
303874 TTAAATCTAAATAAAACAAATAAATGAAAACTCTAACCTCAAGTGTGATTTTGACTCCGACTACA
194 TTAAATCTAAATAAAACAAATAAATGAAAACTCTAACCTCAAGCATGATTTTGACTCCGACTACA
* ** *
303939 AACTGATCTTAGACAATGGATTTTCTCTTTCGCC
259 AACTGACCCGAGACAATAGATTTTCTCTTTCGCC
* ** * *
303973 TAAATCAAAATTAAATTAAATTTACAGAATAGTAACTA-GGATCGATCCCACTGAGATTGAACTG
1 TAAACCAAAATTAAATTAAATTTACAGAATAGTAACTATGG-TCGATCCCACAAACACTGAACTG
* * * * *
304037 ATTAATTTTACAATTTCTTATGACCAAAAGTAGACAAATCTGCTAAATTAAATTAAATAAATAAT
65 ATTAATTTTACAATTTCTTATGACCAAAAGTAGACAAATCTGCAAAAATAAATAAAAGAAAGAAT
*
304102 AGATCAAAATCTAAAATAAATAATATAAATTAAATAAT-AATGAAATAAAAATAAGTAAAACAAA
130 AAATCAAAATCT-AAATAAA-AATATAAATTAAATAATAAATGAAATAAAAATAAGTAAAACAAA
* *
304166 ATTAAATCTAAATAAAACAAATAAATGAAAACTCTAACTTTAAGCATGATTTTGACTCC-AGCTA
193 ATTAAATCTAAATAAAACAAATAAATGAAAACTCTAACCTCAAGCATGATTTTGACTCCGA-CTA
** *
304230 TGAATTGAGCCCGA-ACAATAGATTTTCTCTTTC
257 CAAACTGA-CCCGAGACAATAGATTTTCTCTTTC
304263 AATTGATAAA
Statistics
Matches: 245, Mismatches: 40, Indels: 11
0.83 0.14 0.04
Matches are distributed among these distances:
292 1 0.00
293 108 0.44
294 115 0.47
295 5 0.02
296 16 0.07
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (292 bp):
TAAACCAAAATTAAATTAAATTTACAGAATAGTAACTATGGTCGATCCCACAAACACTGAACTGA
TTAATTTTACAATTTCTTATGACCAAAAGTAGACAAATCTGCAAAAATAAATAAAAGAAAGAATA
AATCAAAATCTAAATAAAAATATAAATTAAATAATAAATGAAATAAAAATAAGTAAAACAAAATT
AAATCTAAATAAAACAAATAAATGAAAACTCTAACCTCAAGCATGATTTTGACTCCGACTACAAA
CTGACCCGAGACAATAGATTTTCTCTTTCGCC
Found at i:307000 original size:16 final size:16
Alignment explanation
Indices: 306975--307009 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
306965 TTTCTATTGA
*
306975 TCTGTTCTTCCAATTT
1 TCTGTCCTTCCAATTT
*
306991 TCTGTCCTTCCTATTT
1 TCTGTCCTTCCAATTT
307007 TCT
1 TCT
307010 TTTCACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (16 bp):
TCTGTCCTTCCAATTT
Found at i:309790 original size:6 final size:6
Alignment explanation
Indices: 309779--309803 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
309769 TATTGATAAA
309779 CACACG CACACG CACACG CACACG C
1 CACACG CACACG CACACG CACACG C
309804 TTCTTACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACACG
Found at i:318980 original size:22 final size:22
Alignment explanation
Indices: 318940--318990 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
318930 TTAGCATCTG
*
318940 GTGCTCTCTGCTTGACACTTCA
1 GTGCTCTCTGCTTGACACTACA
*
318962 GTGCTCTCTG-TTTAGCACTACA
1 GTGCTCTCTGCTTGA-CACTACA
*
318984 ATGCTCT
1 GTGCTCT
318991 TTGGTGTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGCTCTCTGCTTGACACTACA
Found at i:325640 original size:20 final size:20
Alignment explanation
Indices: 325606--325647 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
325596 AACTATTTAA
** *
325606 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
325626 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
325646 AT
1 AT
325648 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:330393 original size:20 final size:20
Alignment explanation
Indices: 330359--330400 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
330349 AACTATTTAA
** *
330359 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
330379 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
330399 AT
1 AT
330401 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:333108 original size:14 final size:15
Alignment explanation
Indices: 333080--333110 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
333070 CGAATATCAA
333080 ATTTCTATGTATTTC
1 ATTTCTATGTATTTC
333095 ATTTCTAT-TATTTC
1 ATTTCTATGTATTTC
333109 AT
1 AT
333111 CTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTCTATGTATTTC
Found at i:334447 original size:31 final size:31
Alignment explanation
Indices: 334409--334467 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
334399 CATTTGAGTT
*
334409 AATTAAGTTATTCGGATAAACTCGAATAAAA
1 AATTAAGTTATTCAGATAAACTCGAATAAAA
* * *
334440 AATTAAGTTTTTCAGCTTAACTCGAATA
1 AATTAAGTTATTCAGATAAACTCGAATA
334468 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
AATTAAGTTATTCAGATAAACTCGAATAAAA
Found at i:335569 original size:2 final size:2
Alignment explanation
Indices: 335564--335588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
335554 TCTTAAAAAA
335564 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
335589 AAAGATGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:360471 original size:33 final size:33
Alignment explanation
Indices: 360424--360493 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
360414 CCATAAAGAG
* **
360424 TCATACAAAGTCATTTTGGTTACTTTAGAAAAA
1 TCATACAAAATCATTAGGGTTACTTTAGAAAAA
*
360457 TCATACAAAATCATTAGGGTTACTTTAGATAAA
1 TCATACAAAATCATTAGGGTTACTTTAGAAAAA
360490 -CATA
1 TCATA
360494 AACATTTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (33 bp):
TCATACAAAATCATTAGGGTTACTTTAGAAAAA
Found at i:369882 original size:7 final size:7
Alignment explanation
Indices: 369870--369898 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
369860 TACCCTACTA
369870 CTTAATG
1 CTTAATG
369877 CTTAATG
1 CTTAATG
369884 CTTAATG
1 CTTAATG
369891 CTTAATG
1 CTTAATG
369898 C
1 C
369899 CATTCCCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (7 bp):
CTTAATG
Found at i:380847 original size:13 final size:13
Alignment explanation
Indices: 380829--380892 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
380819 AGTTCTTCAT
380829 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
380842 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
380855 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
380868 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
380881 TGCTTTTGAAAA
1 TGCTTTTGAAAA
380893 ATTTGGTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:393650 original size:32 final size:32
Alignment explanation
Indices: 393599--393678 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
393589 ATCATACATT
* * * *
393599 TTAAATAAACATAATTATTCAAGTAATATATC
1 TTAAATAAATATAACTATTCAAATAACATATC
* *
393631 TTAAATAGATATAACTATTCAAATAACATTTC
1 TTAAATAAATATAACTATTCAAATAACATATC
*
393663 ATAAATAAATATAACT
1 TTAAATAAATATAACT
393679 CCAAGTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (32 bp):
TTAAATAAATATAACTATTCAAATAACATATC
Found at i:395959 original size:43 final size:42
Alignment explanation
Indices: 395905--396029 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
395895 TGTATCATCA
395905 GATAAAGCGAAGTAAATACACTAGCACACATAA-TGCATCATTG
1 GATAAAGCGAAGTAAATACACTA--ACACATAAGTGCATCATTG
* * * *
395948 GATAAATCGAAGTAAATATACTAACACATAAGTGTATCATTC
1 GATAAAGCGAAGTAAATACACTAACACATAAGTGCATCATTG
* * * * * * *
395990 GATGAACCAAAGCAAATATATTAGCACATAAGTGCATCAT
1 GATAAAGCGAAGTAAATACACTAACACATAAGTGCATCAT
396030 CAGATAAACT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 8 0.11
42 41 0.59
43 21 0.30
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (42 bp):
GATAAAGCGAAGTAAATACACTAACACATAAGTGCATCATTG
Found at i:397375 original size:6 final size:6
Alignment explanation
Indices: 397364--397392 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
397354 AAAATTAAAT
397364 TTACAG TTACAG TTACAG TTACAG TTACA
1 TTACAG TTACAG TTACAG TTACAG TTACA
397393 TATTATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
TTACAG
Found at i:407387 original size:14 final size:13
Alignment explanation
Indices: 407370--407413 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
407360 TTTAGTTTTT
407370 TTTTTTATTTTAGA
1 TTTTTTATTTTA-A
*
407384 TTTTTAATTTTAA
1 TTTTTTATTTTAA
407397 TTTTTTATTTT-A
1 TTTTTTATTTTAA
407409 TTTTT
1 TTTTT
407414 AAGACGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 11 0.39
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTTAA
Found at i:413370 original size:21 final size:19
Alignment explanation
Indices: 413342--413381 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
413332 GGCAAGCACT
413342 AATATTAAAATAAAAATAAA
1 AATATTAAAAT-AAAATAAA
*
413362 AATACTTAAAATTAAATAAA
1 AATA-TTAAAATAAAATAAA
413382 TAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATTAAAATAAAATAAA
Found at i:414420 original size:2 final size:2
Alignment explanation
Indices: 414413--414444 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
414403 TTCCATGTTC
414413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
414445 TCATGTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416513 original size:14 final size:14
Alignment explanation
Indices: 416490--416529 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
416480 ACAGAAAAGT
*
416490 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
416504 AAATCATTTTACGG
1 AAAACATTTTACAG
416518 AAAACATTTTAC
1 AAAACATTTTAC
416530 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:419249 original size:2 final size:2
Alignment explanation
Indices: 419242--419277 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
419232 ATTGAAACCA
419242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
419278 GGGAAAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:433840 original size:15 final size:16
Alignment explanation
Indices: 433818--433848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
433808 AATTTTTATT
*
433818 AAATTTTTTTAAAATA
1 AAATTTTTATAAAATA
433834 AAATTTTTATAAAAT
1 AAATTTTTATAAAAT
433849 TTGATTGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTTATAAAATA
Found at i:434719 original size:12 final size:11
Alignment explanation
Indices: 434691--434720 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
434681 TTATTTTTTT
434691 TATTTTTAAAA
1 TATTTTTAAAA
434702 TATTTTTAAAA
1 TATTTTTAAAA
434713 TACTTTTT
1 TA-TTTTT
434721 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:436995 original size:33 final size:32
Alignment explanation
Indices: 436939--437099 Score: 97
Period size: 33 Copynumber: 4.8 Consensus size: 32
436929 ACATTTGTAG
* * * *
436939 TGTCATAACCTAGTTATGATCTTATCATCAAAA
1 TGTCATAGCCCAGCTATGGTCTTA-CATCAAAA
*
436972 TGTCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGTCATAGCCCAGCTATGGTCTTACAT-CAAA-A
* * * * * * * *
437006 CTGCCATGGTCCAACCATGGTCTTACGTTCATAG
1 -TGTCATAGCCCAGCTATGGTCTTAC-ATCAAAA
* ** * *
437040 TGTCATAACCCAATTATGGTCTTATTATCAGAA
1 TGTCATAGCCCAGCTATGGTCTTA-CATCAAAA
*
437073 TATCATAGCCCAGCTATGGTCTTACAT
1 TGTCATAGCCCAGCTATGGTCTTACAT
437100 ATATTCATAG
Statistics
Matches: 94, Mismatches: 29, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
32 5 0.05
33 65 0.69
34 1 0.01
35 22 0.23
36 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTCATAGCCCAGCTATGGTCTTACATCAAAA
Found at i:437029 original size:101 final size:101
Alignment explanation
Indices: 436919--437102 Score: 287
Period size: 101 Copynumber: 1.8 Consensus size: 101
436909 CATGGCCCTG
** * * *
436919 CCATGGTCTTACATTTGTAGTGTCATAACCTAGTTATGATCTTATCATCAAAATGTCATAGCCCA
1 CCATGGTCTTACATTCATAGTGTCATAACCCAATTATGATCTTATCATCAAAATATCATAGCCCA
436984 GCTATGGTCTTACATATAAACACTGCCATGGTCCAA
66 GCTATGGTCTTACATATAAACACTGCCATGGTCCAA
* * * *
437020 CCATGGTCTTACGTTCATAGTGTCATAACCCAATTATGGTCTTATTATCAGAATATCATAGCCCA
1 CCATGGTCTTACATTCATAGTGTCATAACCCAATTATGATCTTATCATCAAAATATCATAGCCCA
437085 GCTATGGTCTTACATATA
66 GCTATGGTCTTACATATA
437103 TTCATAGTGC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (101 bp):
CCATGGTCTTACATTCATAGTGTCATAACCCAATTATGATCTTATCATCAAAATATCATAGCCCA
GCTATGGTCTTACATATAAACACTGCCATGGTCCAA
Found at i:445861 original size:17 final size:17
Alignment explanation
Indices: 445832--445880 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
445822 TAAATTTTAC
445832 TAAAAATTTTTAAAATAT
1 TAAAAA-TTTTAAAATAT
* * *
445850 TAGAAATTTTAACATTT
1 TAAAAATTTTAAAATAT
445867 TAAAAATTTCTAAA
1 TAAAAATTT-TAAA
445881 TCACCATCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAAATTTTAAAATAT
Found at i:449190 original size:101 final size:102
Alignment explanation
Indices: 448969--449201 Score: 290
Period size: 103 Copynumber: 2.3 Consensus size: 102
448959 TTTACATTTG
* * * *
448969 TAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCTCAGCTAAGGTCTTACATAT
1 TAGTGACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTAAGGTATTACATAT
* *
449034 GAACGTAAGACCATGGTCCAACCATGGTCTTACGTTCA
66 AAACG-AAGACCATGGTCCAACCATGGTCCTACGTTCA
* * * * *
449072 TAGTGATATAACTCAGTTATAGTCTTATCATCAGAATGTCATAGCCCAACTATGGTATTACATAT
1 TAGTGACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTAAGGTATTACATAT
* * *
449137 AAAC-ACTG-TCGTGGTCCAACCATGGTCCTACGTTCA
66 AAACGA-AGACCATGGTCCAACCATGGTCCTACGTTCA
**
449173 TAGTTCCATAACCCAGTTATGGTCTTATC
1 TAGTGACATAACCCAGTTATGGTCTTATC
449202 CGTCAATTCA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
101 50 0.45
102 1 0.01
103 59 0.54
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (102 bp):
TAGTGACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTAAGGTATTACATAT
AAACGAAGACCATGGTCCAACCATGGTCCTACGTTCA
Found at i:452698 original size:17 final size:17
Alignment explanation
Indices: 452676--452709 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
452666 TCCAAGTACC
*
452676 AAAATTAAATGAAAAAA
1 AAAATTAAAAGAAAAAA
452693 AAAATTAAAAGAAAAAA
1 AAAATTAAAAGAAAAAA
452710 GCAATGATAG
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:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAATTAAAAGAAAAAA
Found at i:469195 original size:24 final size:26
Alignment explanation
Indices: 469153--469203 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
469143 AAGCGTTAAA
* *
469153 ATTAAGTTATATATTTTTATCATTTT
1 ATTAAGTTATATATATTTATAATTTT
469179 ATTAA-TT-TATATATTTATAATTTT
1 ATTAAGTTATATATATTTATAATTTT
469203 A
1 A
469204 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 2 0.09
26 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTAAGTTATATATATTTATAATTTT
Found at i:469849 original size:6 final size:6
Alignment explanation
Indices: 469838--469862 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
469828 AACAAAATAA
469838 ACTCTC ACTCTC ACTCTC ACTCTC A
1 ACTCTC ACTCTC ACTCTC ACTCTC A
469863 TACAAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (6 bp):
ACTCTC
Found at i:482080 original size:15 final size:15
Alignment explanation
Indices: 482057--482086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
482047 TATGAAATGA
482057 TTTAATCTTCTTCTT
1 TTTAATCTTCTTCTT
*
482072 TTTAGTCTTCTTCTT
1 TTTAATCTTCTTCTT
482087 CCCTCTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTAATCTTCTTCTT
Found at i:494625 original size:8 final size:8
Alignment explanation
Indices: 494612--494645 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
494602 TTTCTATAAC
494612 ACATTATT
1 ACATTATT
494620 ACATTATT
1 ACATTATT
494628 ACATTATT
1 ACATTATT
494636 ACATTATT
1 ACATTATT
494644 AC
1 AC
494646 CCTTTCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (8 bp):
ACATTATT
Found at i:494955 original size:2 final size:2
Alignment explanation
Indices: 494948--494975 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
494938 TGAAAGCTTT
494948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
494976 GATCCAATTA
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):
TA
Found at i:495893 original size:40 final size:42
Alignment explanation
Indices: 495845--495922 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
495835 ATTTAAAAAT
*
495845 TATTTTAAAAATAAATAAA-AAA-CTAAAAATAT-TTTTAAAG
1 TATTTTAAAAATAAA-AAATAAATATAAAAATATATTTTAAAG
*
495885 TATTTTAAAATTAAAAAATAAATATAAAAATATATTTT
1 TATTTTAAAAATAAAAAATAAATATAAAAATATATTTT
495923 TATTAAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 3 0.09
40 17 0.52
41 9 0.27
42 4 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (42 bp):
TATTTTAAAAATAAAAAATAAATATAAAAATATATTTTAAAG
Found at i:501898 original size:22 final size:21
Alignment explanation
Indices: 501871--501951 Score: 96
Period size: 22 Copynumber: 4.0 Consensus size: 21
501861 TAGATTAGAA
*
501871 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTAT-AATT
501893 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
501914 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
* *
501932 TGTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
501952 ATTATAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.06
19 14 0.26
20 13 0.24
21 8 0.15
22 16 0.30
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Done.