Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 87 of 313
Found at i:28963658 original size:21 final size:20
Alignment explanation
Indices: 28963626--28963699 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
28963616 CTAAGACCCT
*
28963626 AACCCTATACCATAAATGATA
1 AACCCTAAACCATAAAT-ATA
* ***
28963647 AACCATAAACCATAAACCCCA
1 AACCCTAAACCATAAA-TATA
28963668 AACCCTAAACCATAAATACTA
1 AACCCTAAACCATAAATA-TA
28963689 AACCCTAAACC
1 AACCCTAAACC
28963700 TTAATTAACC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.50, C:0.32, G:0.01, T:0.16
Consensus pattern (20 bp):
AACCCTAAACCATAAATATA
Found at i:28963696 original size:7 final size:7
Alignment explanation
Indices: 28963645--28963699 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
28963635 CCATAAATGA
*
28963645 TAAACCA
1 TAAACCC
*
28963652 TAAACCA
1 TAAACCC
28963659 TAAACCC
1 TAAACCC
*
28963666 CAAACCC
1 TAAACCC
*
28963673 TAAACCA
1 TAAACCC
**
28963680 TAAATAC
1 TAAACCC
28963687 TAAACCC
1 TAAACCC
28963694 TAAACC
1 TAAACC
28963700 TTAATTAACC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:28964110 original size:14 final size:13
Alignment explanation
Indices: 28964062--28964125 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 13
28964052 AAACCTCAAG
28964062 CCCTAAATCATAAA
1 CCCTAAATCAT-AA
* *
28964076 ACATAAATCATCAA
1 CCCTAAATCAT-AA
28964090 CCCTAAATCATAA
1 CCCTAAATCATAA
*
28964103 CCCTTAAACCCATAA
1 CCC-TAAA-TCATAA
28964118 CCCCTAAA
1 -CCCTAAA
28964126 CCTATAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
13 5 0.12
14 24 0.59
15 9 0.22
16 3 0.07
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (13 bp):
CCCTAAATCATAA
Found at i:28964118 original size:15 final size:15
Alignment explanation
Indices: 28964098--28964132 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28964088 AACCCTAAAT
*
28964098 CATAACCCTTAAACC
1 CATAACCCCTAAACC
28964113 CATAACCCCTAAACC
1 CATAACCCCTAAACC
*
28964128 TATAA
1 CATAA
28964133 AAATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAACCCCTAAACC
Found at i:28964119 original size:28 final size:29
Alignment explanation
Indices: 28964050--28964134 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 29
28964040 CTTCTAAATT
*
28964050 ATAAACC-TCAAGCCCTAAATCATAAAAC
1 ATAAACCATCAACCCCTAAATCATAAAAC
* **
28964078 ATAAATCATCAA-CCCTAAATCATAACCC
1 ATAAACCATCAACCCCTAAATCATAAAAC
* *
28964106 TTAAACCCAT-AACCCCTAAACCTATAAAA
1 ATAAA-CCATCAACCCCTAAATC-ATAAAA
28964135 ATATTAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 26 0.58
29 15 0.33
30 4 0.09
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (29 bp):
ATAAACCATCAACCCCTAAATCATAAAAC
Found at i:28970158 original size:52 final size:48
Alignment explanation
Indices: 28970096--28970288 Score: 180
Period size: 47 Copynumber: 4.0 Consensus size: 48
28970086 GAAATGTGAT
*
28970096 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCTTC-GAG---TGTGATATGTGC
* *
28970148 TTCCGTATAAGACCATATCCGGGATATGG-TATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCT-TCGAGTGTGATATGTGC
* * * *
28970195 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCTTCGAGTGTGATATGTGC
* * * * *
28970241 ATCCGTGTAAGACCATTGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCTTCGAG--TGTGATATGTG
28970289 ACTATGTGCA
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
46 26 0.22
47 52 0.43
48 11 0.09
50 1 0.01
51 2 0.02
52 28 0.23
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCTTCGAGTGTGATATGTGC
Found at i:28970269 original size:93 final size:97
Alignment explanation
Indices: 28970100--28970307 Score: 221
Period size: 93 Copynumber: 2.1 Consensus size: 97
28970090 TGTGATTTCC
* * *
28970100 GTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTTCCGTATAAGACCATA
1 GTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATATGTGCATCCGTATAAGACCATA
*
28970165 TCCGGGATATGGTATCGG-TGTGATATGTG-CTACT
63 TCCGGGATATGGCATCGGATGTGATATGTGACTA-T
* *
28970199 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-ATCCGTGTAAGACCAT-TGC
1 GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAT-C
* * *
28970260 TGGGCTATGGCCTCGGTATGTGATATGTGACTAT
65 CGGGATATGGCATCGG-ATGTGATATGTGACTAT
**
28970294 GTGCAAGACCATAG
1 GTATAAGACCATAG
28970308 TTTTACTATG
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
92 1 0.01
93 27 0.29
94 11 0.12
95 23 0.25
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (97 bp):
GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATATCC
GGGATATGGCATCGGATGTGATATGTGACTAT
Found at i:28973107 original size:10 final size:10
Alignment explanation
Indices: 28973092--28973143 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
28973082 TAAATTTAGG
28973092 ATTTATTTTT
1 ATTTATTTTT
*
28973102 ATTTATCTTT
1 ATTTATTTTT
* *
28973112 AATTATCTTT
1 ATTTATTTTT
*
28973122 ATTTATTTGT
1 ATTTATTTTT
28973132 ATTTATCTTTT
1 ATTTAT-TTTT
28973143 A
1 A
28973144 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:28976839 original size:5 final size:5
Alignment explanation
Indices: 28976831--28976936 Score: 81
Period size: 5 Copynumber: 20.6 Consensus size: 5
28976821 CAACCCAACC
* * * * *
28976831 TTTAT TTTAT TTTAC TTTAC TTAATT TTTAT TATT-T ATTAT TTTAT TTCAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT T-TTAT TTTAT TTTAT TTTAT
* * *
28976882 TTTAT TAGTATT TTTAT TTTAT TTTAC TTTAT TTTAT TATT-T ATTAT
1 TTTAT T-TTA-T TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT
28976929 TTTAT TTT
1 TTTAT TTT
28976937 TGGATATTAA
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
4 4 0.05
5 63 0.79
6 11 0.14
7 2 0.03
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:28976902 original size:27 final size:30
Alignment explanation
Indices: 28976862--28976935 Score: 100
Period size: 27 Copynumber: 2.6 Consensus size: 30
28976852 TAATTTTTAT
28976862 TATTTATTATTTTATTTCA-TTT-TATTAG
1 TATTTATTATTTTATTTCACTTTATATTAG
* * *
28976890 TATTT-TTATTTTATTTTACTTTATTTTAT
1 TATTTATTATTTTATTTCACTTTATATTAG
28976919 TATTTATTATTTTATTT
1 TATTTATTATTTTATTT
28976936 TTGGATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.30
28 8 0.20
29 9 0.22
30 11 0.28
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (30 bp):
TATTTATTATTTTATTTCACTTTATATTAG
Found at i:28976961 original size:57 final size:57
Alignment explanation
Indices: 28976836--28976964 Score: 136
Period size: 57 Copynumber: 2.2 Consensus size: 57
28976826 CAACCTTTAT
* * * * **
28976836 TTTATTTTACTTTACTTAATTTTTATTATTTATTATTTTATTTCATTTTATTAGTATT
1 TTTATCTTATTTTACTTAATTTTTATTATTTATTATTTTATTT-ATTATATTAATAAA
* *
28976894 TTTATTTTATTTTACTTTA-TTTTATTATTTATTATTTTATTT-TTGGATATTAATAAA
1 TTTATCTTATTTTACTTAATTTTTATTATTTATTATTTTATTTATT--ATATTAATAAA
*
28976951 TTTCTCTTATTTTA
1 TTTATCTTATTTTA
28976965 TCTAGGTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
55 2 0.03
57 42 0.69
58 17 0.28
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (57 bp):
TTTATCTTATTTTACTTAATTTTTATTATTTATTATTTTATTTATTATATTAATAAA
Found at i:28978907 original size:10 final size:10
Alignment explanation
Indices: 28978889--28978922 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
28978879 AATTTAGAAT
*
28978889 TTATTTTTAA
1 TTATCTTTAA
28978899 TTATCTTTAA
1 TTATCTTTAA
*
28978909 TTATCTTTAT
1 TTATCTTTAA
28978919 TTAT
1 TTAT
28978923 TTGCATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:28982164 original size:36 final size:36
Alignment explanation
Indices: 28982123--28982196 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
28982113 TGATTTTTAG
28982123 AATTTCAACTAAAAATGGTTGCGACAACCCCAAATT
1 AATTTCAACTAAAAATGGTTGCGACAACCCCAAATT
*
28982159 AATTTCAACTAAAAATGGTTGTGACAACCCCAAATT
1 AATTTCAACTAAAAATGGTTGCGACAACCCCAAATT
28982195 AA
1 AA
28982197 CAAATGATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (36 bp):
AATTTCAACTAAAAATGGTTGCGACAACCCCAAATT
Found at i:28983445 original size:9 final size:9
Alignment explanation
Indices: 28983427--28983494 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
28983417 TCAACAAAAT
28983427 AATT-TAAA
1 AATTATAAA
28983435 AATTATAAA
1 AATTATAAA
*
28983444 AA-TAGAAA
1 AATTATAAA
*
28983452 ATAATATAAA
1 A-ATTATAAA
*
28983462 AATTCAAAAAA
1 AATT--ATAAA
28983473 AATTATAAA
1 AATTATAAA
* *
28983482 AAGTATAAG
1 AATTATAAA
28983491 AATT
1 AATT
28983495 CAAAAAAGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 10 0.21
9 23 0.49
10 6 0.13
11 8 0.17
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (9 bp):
AATTATAAA
Found at i:28984174 original size:31 final size:31
Alignment explanation
Indices: 28984139--28984219 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
28984129 TATTTGAGAA
*
28984139 GCTCTTATTTGAACACTTTTAAAAAGATTTG
1 GCTCTTATTTGAACACTTTCAAAAAGATTTG
* *
28984170 GCTCTTATTAGAACACTTTCAAAAAGTTTTG
1 GCTCTTATTTGAACACTTTCAAAAAGATTTG
* *
28984201 GCTCGTATTTGAGCACTTT
1 GCTCTTATTTGAACACTTT
28984220 GAAAGTTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (31 bp):
GCTCTTATTTGAACACTTTCAAAAAGATTTG
Found at i:28985353 original size:12 final size:12
Alignment explanation
Indices: 28985336--28985381 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
28985326 AACTTTTTAT
28985336 ATTTATTTATTC
1 ATTTATTTATTC
28985348 ATTTATTTATT-
1 ATTTATTTATTC
*
28985359 ATTTCTTTA-TC
1 ATTTATTTATTC
*
28985370 CTTTATTATATT
1 ATTTATT-TATT
28985382 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 1 0.04
11 13 0.46
12 13 0.46
13 1 0.04
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTATTTATTC
Found at i:28985367 original size:23 final size:22
Alignment explanation
Indices: 28985331--28985381 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
28985321 TCATTAACTT
28985331 TTTA-TATTTATTTATTCATTTA
1 TTTATTATTTATTTA-TCATTTA
* *
28985353 TTTATTATTTCTTTATCCTTTA
1 TTTATTATTTATTTATCATTTA
28985375 TTATATT
1 TT-TATT
28985382 TAAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTATTTATTTATCATTTA
Found at i:28985586 original size:13 final size:14
Alignment explanation
Indices: 28985553--28985597 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
28985543 TGTATTTATT
28985553 TTTATTT-TATCAA
1 TTTATTTATATCAA
*
28985566 TCTA-TTATATC-A
1 TTTATTTATATCAA
28985578 TTTATTTATA-CAA
1 TTTATTTATATCAA
28985591 TTTATTT
1 TTTATTT
28985598 TATTTTATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTTATATCAA
Found at i:28989891 original size:17 final size:17
Alignment explanation
Indices: 28989871--28989904 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28989861 AAATAGATTT
28989871 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
28989888 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
28989905 ACTTAAACCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:28993562 original size:4 final size:4
Alignment explanation
Indices: 28993548--28993581 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
28993538 GTCACATAGC
*
28993548 CAGA TAGA CAGA CAGA CAGA CAGA CAGA CAGA CA
1 CAGA CAGA CAGA CAGA CAGA CAGA CAGA CAGA CA
28993582 CAAAATTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.24, T:0.03
Consensus pattern (4 bp):
CAGA
Found at i:28997342 original size:20 final size:20
Alignment explanation
Indices: 28997296--28997343 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
28997286 TAATTTAAAC
28997296 TAAAAATGTTACTAAATTTA
1 TAAAAATGTTACTAAATTTA
* *
28997316 CATAAAATTTTA-TAAATTCTA
1 TA-AAAATGTTACTAAATT-TA
28997337 TAAAAAT
1 TAAAAAT
28997344 AAATCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAAATGTTACTAAATTTA
Found at i:28998026 original size:30 final size:30
Alignment explanation
Indices: 28997992--28998052 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28997982 CATGGATAGG
28997992 ATTGATAGATTAAGAGCTTACTTAACTACA
1 ATTGATAGATTAAGAGCTTACTTAACTACA
*
28998022 ATTGATAGATTAAGAGCTTACTTAAGTACA
1 ATTGATAGATTAAGAGCTTACTTAACTACA
28998052 A
1 A
28998053 AAATAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (30 bp):
ATTGATAGATTAAGAGCTTACTTAACTACA
Found at i:29000326 original size:22 final size:22
Alignment explanation
Indices: 29000293--29000344 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
29000283 GATTTAGGAG
* * *
29000293 TAATATAA-AATGGTAAAATTT
1 TAATTTAATAATGATAAAATTA
29000314 TAATTTAATAATGATAAAATTA
1 TAATTTAATAATGATAAAATTA
*
29000336 TATTTTAAT
1 TAATTTAAT
29000345 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (22 bp):
TAATTTAATAATGATAAAATTA
Found at i:29000351 original size:30 final size:30
Alignment explanation
Indices: 29000336--29000393 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
29000326 GATAAAATTA
29000336 TATTTTAATTTTTTAAAAATAATAAAAAAT
1 TATTTTAATTTTTTAAAAATAATAAAAAAT
*
29000366 TATTTTAATTTTTTAAAAATTATAAAAA
1 TATTTTAATTTTTTAAAAATAATAAAAA
29000394 TAATAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTTTAATTTTTTAAAAATAATAAAAAAT
Found at i:29000392 original size:29 final size:30
Alignment explanation
Indices: 29000317--29000395 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
29000307 AAAATTTTAA
* * *
29000317 TTTAATAATGATAAAATTATATTTTAATTT
1 TTTAAAAATAATAAAAATATATTTTAATTT
29000347 TTTAAAAATAATAAAAA-ATTATTTTAATTT
1 TTTAAAAATAATAAAAATA-TATTTTAATTT
*
29000377 TTTAAAAATTATAAAAATA
1 TTTAAAAATAATAAAAATA
29000396 ATAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTAAAAATAATAAAAATATATTTTAATTT
Found at i:29000405 original size:30 final size:30
Alignment explanation
Indices: 29000341--29000405 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
29000331 AATTATATTT
* **
29000341 TAATTTTTTAAAAATAATAAAAAATTATTT
1 TAATTTTTTAAAAATAATAAAAAAATATAA
*
29000371 TAATTTTTTAAAAATTATAAAAATAATA-AA
1 TAATTTTTTAAAAATAATAAAAA-AATATAA
29000401 TAATT
1 TAATT
29000406 AAAATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATTTTTTAAAAATAATAAAAAAATATAA
Found at i:29001899 original size:56 final size:56
Alignment explanation
Indices: 29001820--29001927 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
29001810 CGCCCTTGCC
* *
29001820 TCGAGTCCCTCGCCACCTTGCTAAGTGCCAACACCACCTAAGCACTTCGCCCAGAG
1 TCGAGTCCCTCACCACCTCGCTAAGTGCCAACACCACCTAAGCACTTCGCCCAGAG
* * * **
29001876 TCGAGTCCTTCACCACCTCGCTAAGTTCTAACACCACCTGGGCACTTCGCCC
1 TCGAGTCCCTCACCACCTCGCTAAGTGCCAACACCACCTAAGCACTTCGCCC
29001928 TGAACCCCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.20
Consensus pattern (56 bp):
TCGAGTCCCTCACCACCTCGCTAAGTGCCAACACCACCTAAGCACTTCGCCCAGAG
Found at i:29003554 original size:1 final size:1
Alignment explanation
Indices: 29003520--29003544 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29003510 TCACTTCCTT
29003520 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
29003545 CCCAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29004771 original size:21 final size:21
Alignment explanation
Indices: 29004747--29004789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29004737 AAATTATATT
* *
29004747 AATAATGTTTTATTAAATGAA
1 AATAATCTTTTAGTAAATGAA
*
29004768 AATAATCTTTTAGTCAATGAA
1 AATAATCTTTTAGTAAATGAA
29004789 A
1 A
29004790 TTACATATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATCTTTTAGTAAATGAA
Found at i:29005456 original size:12 final size:11
Alignment explanation
Indices: 29005437--29005479 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
29005427 ATTAATTATT
*
29005437 TTTAAAAAAAA
1 TTTAAAAAATA
29005448 TTATAAAAAATA
1 TT-TAAAAAATA
*
29005460 TTTTATAAAATA
1 -TTTAAAAAATA
29005472 TTTAAAAA
1 TTTAAAAA
29005480 TATAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.33
12 16 0.59
13 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:29009445 original size:5 final size:5
Alignment explanation
Indices: 29009435--29009472 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
29009425 GTAATTGTTT
29009435 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
29009473 AACAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:29009547 original size:13 final size:11
Alignment explanation
Indices: 29009521--29009596 Score: 55
Period size: 12 Copynumber: 6.4 Consensus size: 11
29009511 TAAATGAAAC
29009521 AAAAAGAATAGA
1 AAAAAGAA-AGA
29009533 AAAAGAGAAAG-
1 AAAA-AGAAAGA
*
29009544 GAAAAGAAACGA
1 AAAAAGAAA-GA
*
29009556 AACAAAGAAGGGA
1 AA-AAAGAA-AGA
29009569 AAGAAAGAAAGA
1 AA-AAAGAAAGA
*
29009581 AAAAGGGAAAGA
1 AAAA-AGAAAGA
29009593 AAAA
1 AAAA
29009597 GAAGGATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
10 5 0.10
11 6 0.12
12 21 0.40
13 20 0.38
ACGTcount: A:0.71, C:0.03, G:0.25, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:29010304 original size:17 final size:17
Alignment explanation
Indices: 29010275--29010318 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
29010265 TGTGTGATTA
29010275 ATTGAATTGATATGAAT
1 ATTGAATTGATATGAAT
*
29010292 ATTG-ATTGTATATGAAA
1 ATTGAATTG-ATATGAAT
*
29010309 AGTGAATTGA
1 ATTGAATTGA
29010319 AGAACCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (17 bp):
ATTGAATTGATATGAAT
Found at i:29015906 original size:49 final size:48
Alignment explanation
Indices: 29015831--29015924 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
29015821 GTCGGTAATT
* * *
29015831 CCAAACCAAATTGTAAACATTATAATAAGTATCATTTTGGGGAATNATC
1 CCAAACCAAAGTGGAAACATTATAATAAGTATCATTTTGAGGAAT-ATC
*
29015880 CCAAACCAAAGTGGAAACATTGTAATAAGTATCATTTTGAGGAAT
1 CCAAACCAAAGTGGAAACATTATAATAAGTATCATTTTGAGGAAT
29015925 GCCGATTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (48 bp):
CCAAACCAAAGTGGAAACATTATAATAAGTATCATTTTGAGGAATATC
Found at i:29019835 original size:18 final size:17
Alignment explanation
Indices: 29019802--29019837 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29019792 ACTAAATTGG
29019802 AAATGAGAAAAATTAAT
1 AAATGAGAAAAATTAAT
*
29019819 AAATGATAAATAATTAAT
1 AAATGAGAAA-AATTAAT
29019837 A
1 A
29019838 GGAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (17 bp):
AAATGAGAAAAATTAAT
Found at i:29027188 original size:21 final size:21
Alignment explanation
Indices: 29027156--29027196 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29027146 AGGCTCGAGG
29027156 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
29027177 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
29027197 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:29031664 original size:24 final size:23
Alignment explanation
Indices: 29031637--29031689 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
29031627 TGCACATTAT
* * *
29031637 ATATATCCTAATTAAATTTATTTA
1 ATATATACTAAATAAATTTA-TCA
*
29031661 ATATATATTAAATAAATTTATCA
1 ATATATACTAAATAAATTTATCA
29031684 ATATAT
1 ATATAT
29031690 GTATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATACTAAATAAATTTATCA
Found at i:29032258 original size:17 final size:17
Alignment explanation
Indices: 29032221--29032264 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29032211 GTAAAAAAGA
*
29032221 AATATAAAAAAAATAAT
1 AATATAAAAAAAATAAC
* *
29032238 AATATAAAAAATATAGC
1 AATATAAAAAAAATAAC
29032255 AATAGTAAAA
1 AATA-TAAAA
29032265 TTATGATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (17 bp):
AATATAAAAAAAATAAC
Found at i:29032328 original size:25 final size:24
Alignment explanation
Indices: 29032300--29032391 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 24
29032290 ATAGAGATAT
*
29032300 AATACTTAAAATATAATAATAAAAA
1 AATAC-TAAAATATAATAAGAAAAA
29032325 AATA-T-AAATA-AATAAGAAATAA
1 AATACTAAAATATAATAAGAAA-AA
29032347 AA-ACTAGATAA-ATAATAAGAAAATA
1 AATACTA-A-AATATAATAAGAAAA-A
*
29032372 AATAGATGAAAATATAATAA
1 AATA-CT-AAAATATAATAA
29032392 TAGTAATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
21 9 0.17
22 10 0.19
23 1 0.02
24 3 0.06
25 18 0.33
26 3 0.06
27 9 0.17
28 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (24 bp):
AATACTAAAATATAATAAGAAAAA
Found at i:29032344 original size:11 final size:11
Alignment explanation
Indices: 29032308--29032364 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
29032298 ATAATACTTA
29032308 AAATATAATAAT
1 AAATA-AATAAT
*
29032320 AAAAAAAT-AT
1 AAATAAATAAT
*
29032330 AAATAAATAAG
1 AAATAAATAAT
29032341 AAATAAA-AACT
1 AAATAAATAA-T
*
29032352 AGATAAATAAT
1 AAATAAATAAT
29032363 AA
1 AA
29032365 GAAAATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
10 11 0.31
11 19 0.53
12 6 0.17
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:29032349 original size:26 final size:26
Alignment explanation
Indices: 29032320--29032373 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
29032310 ATATAATAAT
*
29032320 AAAAAAATATAAATAAATAAG-AAATA
1 AAAAAAAGATAAAT-AATAAGAAAATA
**
29032346 AAAACTAGATAAATAATAAGAAAATA
1 AAAAAAAGATAAATAATAAGAAAATA
29032372 AA
1 AA
29032374 TAGATGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (26 bp):
AAAAAAAGATAAATAATAAGAAAATA
Found at i:29032393 original size:3 final size:3
Alignment explanation
Indices: 29032385--29032544 Score: 57
Period size: 3 Copynumber: 55.0 Consensus size: 3
29032375 AGATGAAAAT
* * * * *
29032385 ATA ATA ATA GTA ATA AT- ACA ATA GTA GTA ATA ATA AAA AGTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * * * * * *
29032430 ATA AT- ATA TTAA ATA GTA A-A AAA ATA ATA GTA ACA GTA AT- TTA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
29032473 A-A A-A ATG ATA ATA GTA ATA ATC ATA ATG ATA ATA AT- ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * *
29032516 ATA GTA A-A ATA ATG ATA GTA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29032545 TATATTAAAT
Statistics
Matches: 112, Mismatches: 35, Indels: 20
0.67 0.21 0.12
Matches are distributed among these distances:
2 14 0.12
3 92 0.82
4 6 0.05
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:29032431 original size:16 final size:17
Alignment explanation
Indices: 29032395--29032435 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
29032385 ATAATAATAG
* *
29032395 TAATAATACAATAGTAG
1 TAATAATACAAAAGTAA
29032412 TAATAATA-AAAAGTAA
1 TAATAATACAAAAGTAA
29032428 TAATAATA
1 TAATAATA
29032436 TATTAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (17 bp):
TAATAATACAAAAGTAA
Found at i:29032527 original size:15 final size:15
Alignment explanation
Indices: 29032354--29032527 Score: 69
Period size: 15 Copynumber: 11.3 Consensus size: 15
29032344 TAAAAACTAG
29032354 ATAAATAATAAG-AAA
1 ATAAATAAT-AGTAAA
29032369 ATAAATAGAT-G-AAA
1 ATAAATA-ATAGTAAA
29032383 ATATAATAATAGTAATA
1 ATA-AATAATAGTAA-A
*
29032400 ATACAATAGTAGTAATA
1 ATA-AATAATAGTAA-A
*
29032417 ATAAA-AAGTAATAATA
1 ATAAATAA-TAGTAA-A
*
29032433 ATATATTAAATAGTAAA
1 ATA-AAT-AATAGTAAA
29032450 A-AAATAATAGTAACA
1 ATAAATAATAGTAA-A
* * *
29032465 GT-AAT-TTA-AAAA
1 ATAAATAATAGTAAA
*
29032477 AT-GATAATAGTAATA
1 ATAAATAATAGTAA-A
* * *
29032492 ATCATAATGATAATAAT
1 AT-A-AATAATAGTAAA
29032509 ATAAATAATAGTAAA
1 ATAAATAATAGTAAA
29032524 ATAA
1 ATAA
29032528 TGATAGTAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
12 4 0.03
13 4 0.03
14 21 0.17
15 35 0.29
16 18 0.15
17 24 0.20
18 13 0.11
19 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (15 bp):
ATAAATAATAGTAAA
Found at i:29033225 original size:6 final size:6
Alignment explanation
Indices: 29033214--29033243 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29033204 AAAGAAGGAA
29033214 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
29033244 GAAATCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:29035934 original size:20 final size:21
Alignment explanation
Indices: 29035909--29035961 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 21
29035899 AAAAAAATGA
29035909 ATTTTGGAATTTTTATAAA-T
1 ATTTTGGAATTTTTATAAATT
29035929 ATTTT-GAA-TTTTATAAATT
1 ATTTTGGAATTTTTATAAATT
*
29035948 ATTTTGCAATTTTT
1 ATTTTGGAATTTTT
29035962 GTTGATAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.31
19 9 0.31
20 7 0.24
21 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (21 bp):
ATTTTGGAATTTTTATAAATT
Found at i:29035939 original size:19 final size:20
Alignment explanation
Indices: 29035909--29035961 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 20
29035899 AAAAAAATGA
29035909 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
29035929 ATTTTGAA-TTTTATAAATT
1 ATTTTGAATTTTTATAAATT
29035948 ATTTTGCAATTTTT
1 ATTTTG-AATTTTT
29035962 GTTGATAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.30
19 10 0.33
20 7 0.23
21 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:29035942 original size:18 final size:19
Alignment explanation
Indices: 29035909--29035960 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
29035899 AAAAAAATGA
29035909 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTATAAATT
29035929 ATTTTGAATTTTATAAATT
1 ATTTTGAATTTTATAAATT
29035948 ATTTTGCAATTTT
1 ATTTTG-AATTTT
29035961 TGTTGATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.30
19 10 0.33
20 11 0.37
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTATAAATT
Found at i:29037586 original size:40 final size:40
Alignment explanation
Indices: 29037505--29037586 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 40
29037495 CGTACCTGGG
*
29037505 AAAAAAATAAAAAAAAACAGAATTAAAAGTTTTGATATGA
1 AAAAAAACAAAAAAAAACAGAATTAAAAGTTTTGATATGA
29037545 AAAAAAACAAAATAAAAACAGAATTAAAAGTTTTGAT-TGA
1 AAAAAAACAAAA-AAAAACAGAATTAAAAGTTTTGATATGA
29037585 AA
1 AA
29037587 TTTCGAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 16 0.40
41 24 0.60
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.22
Consensus pattern (40 bp):
AAAAAAACAAAAAAAAACAGAATTAAAAGTTTTGATATGA
Found at i:29038353 original size:20 final size:20
Alignment explanation
Indices: 29038330--29038384 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
29038320 TAAATTCTAA
29038330 AAGATAAATAAAAATAATTT
1 AAGATAAATAAAAATAATTT
* * *
29038350 AAGATAATTTAAGATAATTT
1 AAGATAAATAAAAATAATTT
*
29038370 AAGATAAATGAAAAT
1 AAGATAAATAAAAAT
29038385 GAATCCTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (20 bp):
AAGATAAATAAAAATAATTT
Found at i:29038356 original size:10 final size:10
Alignment explanation
Indices: 29038343--29038376 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
29038333 ATAAATAAAA
29038343 ATAATTTAAG
1 ATAATTTAAG
29038353 ATAATTTAAG
1 ATAATTTAAG
29038363 ATAATTTAAG
1 ATAATTTAAG
29038373 ATAA
1 ATAA
29038377 ATGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (10 bp):
ATAATTTAAG
Found at i:29039786 original size:29 final size:31
Alignment explanation
Indices: 29039738--29039801 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
29039728 TTTATAATTA
*
29039738 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
29039769 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
29039798 TTTA
1 TTTA
29039802 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:29039790 original size:8 final size:8
Alignment explanation
Indices: 29039779--29039803 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29039769 TTTAATAAGA
29039779 TATTTTAT
1 TATTTTAT
29039787 TATTTTAT
1 TATTTTAT
29039795 TATTTTAT
1 TATTTTAT
29039803 T
1 T
29039804 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:29039826 original size:2 final size:2
Alignment explanation
Indices: 29039821--29039850 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29039811 TATATATATA
29039821 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29039851 GAAAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29043642 original size:46 final size:46
Alignment explanation
Indices: 29043584--29043750 Score: 146
Period size: 46 Copynumber: 3.6 Consensus size: 46
29043574 TGGTATGTGT
*
29043584 GCTACTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGGGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGGGA
* * *
29043630 GCCAGTGTAAGACATGTCTGAGACCTGCATC-G--ATATTGA-GACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATATT-ATG--G-GA
* * * **
29043676 GCTAGTGTAAGACATGCCTAGGACATGCATCGGGCTCGA-GTTATACGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GGC-C-ATATTATGGGA
*
29043724 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
29043751 GCGTCAGCTT
Statistics
Matches: 95, Mismatches: 15, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 2 0.02
46 55 0.58
48 27 0.28
50 1 0.01
51 2 0.02
52 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGGGA
Found at i:29043864 original size:49 final size:49
Alignment explanation
Indices: 29043770--29043900 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 49
29043760 TATTGTGTGT
* * *
29043770 CAGTGTAAGACCTGTCTGGGACATGGCATTGACACCAATAGATGAAAGC
1 CAGTGTAAAAACTGTCTGGGACATGGCATCGACACCAATAGATGAAAGC
* * * * *
29043819 CATTGTAAAAACTGTCTGGGACACGGCATCGAC-CTCGATATATGAAAGT
1 CAGTGTAAAAACTGTCTGGGACATGGCATCGACAC-CAATAGATGAAAGC
* * * *
29043868 CGGTGTAAGACCTGTTTGGGACATGGCATCGAC
1 CAGTGTAAAAACTGTCTGGGACATGGCATCGAC
29043901 TTTGATGTGC
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 1 0.01
49 66 0.99
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (49 bp):
CAGTGTAAAAACTGTCTGGGACATGGCATCGACACCAATAGATGAAAGC
Found at i:29047143 original size:30 final size:30
Alignment explanation
Indices: 29047109--29047165 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
29047099 GCCTAGGGGT
* *
29047109 AAAATCGTAATTTTTAC-AAAGTTTAAGGGC
1 AAAATAGTAA-TTTTACTAAAGTATAAGGGC
*
29047139 AAAATAGTCATTTTACTAAAGTATAAG
1 AAAATAGTAATTTTACTAAAGTATAAG
29047166 TTTTAAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.26
30 17 0.74
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (30 bp):
AAAATAGTAATTTTACTAAAGTATAAGGGC
Found at i:29050354 original size:21 final size:20
Alignment explanation
Indices: 29050330--29050369 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29050320 ATATTCAAGT
*
29050330 TCCACACGGGCGTGTTGCCCA
1 TCCACACAGGCGTG-TGCCCA
*
29050351 TCCACATAGGCGTGTGCCC
1 TCCACACAGGCGTGTGCCC
29050370 TGTGTCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (20 bp):
TCCACACAGGCGTGTGCCCA
Found at i:29052584 original size:5 final size:5
Alignment explanation
Indices: 29052574--29052630 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
29052564 TCAACATCTA
* * *
29052574 AAAAT AAAAT AATAA- ATAAT AAAAT AAAGT ACAAT AAAAT AAAAT -AAA-
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
29052622 AAAAT AAAA
1 AAAAT AAAA
29052631 ATTGGGTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 8 0.19
5 32 0.76
6 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29060864 original size:16 final size:16
Alignment explanation
Indices: 29060843--29060873 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29060833 GTAACGCCCC
*
29060843 AAAAATCTCGAAATCT
1 AAAAATCCCGAAATCT
29060859 AAAAATCCCGAAATC
1 AAAAATCCCGAAATC
29060874 CCAAATTTTC
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:0.23, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAATCCCGAAATCT
Found at i:29062274 original size:29 final size:29
Alignment explanation
Indices: 29062220--29062275 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
29062210 AATGTGACTG
* *
29062220 GGCCTAATGGGTCATATAAGTGTGATTTA
1 GGCCTAATGGGCCATATAAGTATGATTTA
29062249 GGCCTAATGGGCCATATGAA-TATGATT
1 GGCCTAATGGGCCATAT-AAGTATGATT
29062276 GGGCTTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAGTATGATTTA
Found at i:29069593 original size:8 final size:8
Alignment explanation
Indices: 29069580--29069624 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
29069570 AGGAAAAAGT
29069580 CGAAATGC
1 CGAAATGC
29069588 CGAAATGC
1 CGAAATGC
* *
29069596 CGAAAAGT
1 CGAAATGC
29069604 CGAAATGC
1 CGAAATGC
* *
29069612 TGAAAAGC
1 CGAAATGC
29069620 CGAAA
1 CGAAA
29069625 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (8 bp):
CGAAATGC
Found at i:29069605 original size:24 final size:24
Alignment explanation
Indices: 29069574--29069624 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
29069564 ATGTATAGGA
*
29069574 AAAAGTCGAAATGCCGAAATGCCG
1 AAAAGTCGAAATGCCGAAAAGCCG
*
29069598 AAAAGTCGAAATGCTGAAAAGCCG
1 AAAAGTCGAAATGCCGAAAAGCCG
29069622 AAA
1 AAA
29069625 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (24 bp):
AAAAGTCGAAATGCCGAAAAGCCG
Found at i:29069607 original size:16 final size:16
Alignment explanation
Indices: 29069580--29069624 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
29069570 AGGAAAAAGT
*
29069580 CGAAATGCCGAAATGC
1 CGAAAAGCCGAAATGC
*
29069596 CGAAAAGTCGAAATGC
1 CGAAAAGCCGAAATGC
*
29069612 TGAAAAGCCGAAA
1 CGAAAAGCCGAAA
29069625 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (16 bp):
CGAAAAGCCGAAATGC
Found at i:29069883 original size:29 final size:29
Alignment explanation
Indices: 29069850--29069934 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
29069840 AATATGACTG
*
29069850 GGCCTAACGGGCCATATAAATGTGATTTA
1 GGCCTAATGGGCCATATAAATGTGATTTA
* * * *
29069879 GGCCTAATGGGCCATATACAGGTAATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTA
* *
29069908 GGCCTAATGGGCCATATGAATATGATT
1 GGCCTAATGGGCCATATAAATGTGATT
29069935 GGGCTTAGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAATGTGATTTA
Found at i:29078828 original size:13 final size:13
Alignment explanation
Indices: 29078810--29078834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29078800 TGTGGGTTCA
29078810 CACGGCCATGTCG
1 CACGGCCATGTCG
29078823 CACGGCCATGTC
1 CACGGCCATGTC
29078835 TTGCTTCTTT
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:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (13 bp):
CACGGCCATGTCG
Found at i:29085746 original size:127 final size:127
Alignment explanation
Indices: 29085590--29086041 Score: 559
Period size: 127 Copynumber: 3.5 Consensus size: 127
29085580 AGTCCAACGA
* * * * * *
29085590 AAAACCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGC
1 AAAATCGAAACCCAGCACGATAGGACACGATTCCTCGAATTTCCAAACACTAAACATTGCCTTGT
* * * * * * *
29085655 TTTAGCATTTAGAAAACACGAGTAAAATTCTAAAGGAAAATTCAATCATTTTGAACAAACCG
66 TTTAGTATTTGGAAAACACGAGTGAAATTATAAAGGAATATTCGATTATTTTGAACAAACCG
* * * * *
29085717 AAAATCGTAACCCAGCACGATTGGACACGATTCCCCGCATTTCCAAACACTAAATATTGCCTTGT
1 AAAATCGAAACCCAGCACGATAGGACACGATTCCTCGAATTTCCAAACACTAAACATTGCCTTGT
* *
29085782 TTTAGTATTTGGAAAACACAAGTGAAATTTTAAAGGAATATTCGATTATTTTGAACAAACCG
66 TTTAGTATTTGGAAAACACGAGTGAAATTATAAAGGAATATTCGATTATTTTGAACAAACCG
* * * * * * *
29085844 GAAATCGAAACCCAGCACGATTGGACACTATTCC-CCACATTTCCAAACACTGAATATTTCCTTG
1 AAAATCGAAACCCAGCACGATAGGACACGATTCCTCGA-ATTTCCAAACACTAAACATTGCCTTG
*
29085908 TTTTAGTATTTGGAAAACACGAGTGAAATTATAAAAGGAATATTCGATTATTTTGAACGAA-CG
65 TTTTAGTATTTGGAAAACACGAGTGAAATTAT-AAAGGAATATTCGATTATTTTGAACAAACCG
* * *
29085971 AGAAATCGAAACCTAGTACGATAGGGCACGATTCCTCGAATTTCCAAACA-TCAAACATTGCCTT
1 A-AAATCGAAACCCAGCACGATAGGACACGATTCCTCGAATTTCCAAACACT-AAACATTGCCTT
29086035 CGTTTTA
64 -GTTTTA
29086042 AAGAATTTTC
Statistics
Matches: 280, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
126 1 0.00
127 196 0.70
128 75 0.27
129 8 0.03
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (127 bp):
AAAATCGAAACCCAGCACGATAGGACACGATTCCTCGAATTTCCAAACACTAAACATTGCCTTGT
TTTAGTATTTGGAAAACACGAGTGAAATTATAAAGGAATATTCGATTATTTTGAACAAACCG
Found at i:29088358 original size:22 final size:24
Alignment explanation
Indices: 29088330--29088374 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
29088320 TTGCTTGTAG
29088330 GTACGGGG-TGTGCG-TGGCGTAT
1 GTACGGGGCTGTGCGTTGGCGTAT
29088352 GTACGGGGCTGTGCGTTGGCGTA
1 GTACGGGGCTGTGCGTTGGCGTA
29088375 CGGAAGGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.09, C:0.16, G:0.49, T:0.27
Consensus pattern (24 bp):
GTACGGGGCTGTGCGTTGGCGTAT
Found at i:29090800 original size:10 final size:10
Alignment explanation
Indices: 29090779--29090830 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
29090769 AATTAAATTC
29090779 TAAAAGATAAA
1 TAAAA-ATAAA
29090790 TAAAAATAAA
1 TAAAAATAAA
*
29090800 TAAAAATAAT
1 TAAAAATAAA
*
29090810 TAAATATAAA
1 TAAAAATAAA
*
29090820 TGAAAATAAA
1 TAAAAATAAA
29090830 T
1 T
29090831 CCTAAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
10 31 0.86
11 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:29101600 original size:16 final size:16
Alignment explanation
Indices: 29101576--29101609 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29101566 AATGCCGAAG
29101576 TTTCAGCTTTTCGACT
1 TTTCAGCTTTTCGACT
*
29101592 TTTCGGCTTTTCGACT
1 TTTCAGCTTTTCGACT
29101608 TT
1 TT
29101610 CGCCGATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.53
Consensus pattern (16 bp):
TTTCAGCTTTTCGACT
Found at i:29109081 original size:16 final size:16
Alignment explanation
Indices: 29109060--29109101 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
29109050 AGACAACCCA
29109060 ATTTTTATTTT-TCTTT
1 ATTTTTATTTTAT-TTT
29109076 ATTTTTATTTTATTTT
1 ATTTTTATTTTATTTT
29109092 ATTATTTATT
1 ATT-TTTATT
29109102 ACTTTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTATTTTATTTT
Found at i:29109098 original size:8 final size:8
Alignment explanation
Indices: 29109089--29109117 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
29109079 TTTATTTTAT
29109089 TTTATTA-
1 TTTATTAC
29109096 TTTATTAC
1 TTTATTAC
29109104 TTTATTAC
1 TTTATTAC
29109112 TTTATT
1 TTTATT
29109118 TGTTTGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTATTAC
Found at i:29109116 original size:20 final size:18
Alignment explanation
Indices: 29109060--29109118 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
29109050 AGACAACCCA
29109060 ATTTTTA-TTT-TTCTTT
1 ATTTTTACTTTATTCTTT
* *
29109076 ATTTTTATTTTATTTTATT
1 ATTTTTACTTTATTCT-TT
29109095 ATTTATTACTTTATTACTTT
1 ATTT-TTACTTTATT-CTTT
29109115 ATTT
1 ATTT
29109119 GTTTGGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 7 0.20
17 3 0.09
18 3 0.09
19 6 0.17
20 15 0.43
21 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTACTTTATTCTTT
Found at i:29111473 original size:42 final size:42
Alignment explanation
Indices: 29111426--29111534 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
29111416 TAAGATTCCT
* * *
29111426 TATAAGACCATATCCGAGATATGGCCTCGATATG-TGATTTCG
1 TATAAGACCATATCAGGGATATGGCCTCGATATGAT-ATTTCA
* * * *
29111468 TATAAGACCATGTCAGGGACATGACGTCGATATGATATTTCA
1 TATAAGACCATATCAGGGATATGGCCTCGATATGATATTTCA
* *
29111510 TGTAAGACCATATCGGGGATATGGC
1 TATAAGACCATATCAGGGATATGGC
29111535 ATTGAAACGA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 53 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
TATAAGACCATATCAGGGATATGGCCTCGATATGATATTTCA
Found at i:29114273 original size:49 final size:49
Alignment explanation
Indices: 29114105--29114314 Score: 157
Period size: 49 Copynumber: 4.4 Consensus size: 49
29114095 GTGGTGTGTG
* * * * *
29114105 AGCCAGTGTAAGACATGTCTAGGACAT-GCATCGGCCTCGAGATAT-ACA
1 AGCCAGTGTAAGACCTGTCTAGAACATGGCATCGACCTCGATAGATGA-A
* * * * * * *
29114153 AGCTAGTGTAAGACCTGTCTGGGACATGGCGTC-AGCTTG-TTG-TG--
1 AGCCAGTGTAAGACCTGTCTAGAACATGGCATCGACCTCGATAGATGAA
* * * * * *
29114197 TGTCAGTGTAAGACCTGCCTGGGACATGGCATCGACAC-CGATAGATGAG
1 AGCCAGTGTAAGACCTGTCTAGAACATGGCATCGAC-CTCGATAGATGAA
* * *
29114246 AGCCAGTGTAAGAGCTGTCTAGAACATGGCATTGACCTCGATATATGAA
1 AGCCAGTGTAAGACCTGTCTAGAACATGGCATCGACCTCGATAGATGAA
29114295 AGCCAGTGTAAGACCTGTCT
1 AGCCAGTGTAAGACCTGTCT
29114315 GGGACACGAC
Statistics
Matches: 125, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
44 28 0.22
45 2 0.02
46 4 0.03
47 2 0.02
48 28 0.22
49 61 0.49
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (49 bp):
AGCCAGTGTAAGACCTGTCTAGAACATGGCATCGACCTCGATAGATGAA
Found at i:29137009 original size:116 final size:117
Alignment explanation
Indices: 29136845--29137071 Score: 266
Period size: 117 Copynumber: 1.9 Consensus size: 117
29136835 GAGTTTTTAA
*
29136845 AACCCACACGGCCCGGACACACGAGCGTGCCCTTGGCCATATGAAA-TTTCAGACTTAGTTTTAA
1 AACCCACACGGCCCGGACACACGAGCGTGCCCTTGACCATATGAAATTTTCAGACTTAGTTTTAA
** *
29136909 A-CATTTTAAAGAAATTGACATTGAGTTACACGGCCTGG-CGACACGGCCGTGT
66 ATCATTTTAAA-AAATCAACAGTGAGTTACACGGCCTGGAC-ACACGGCCGTGT
* * * * * *
29136961 AACCCACATGGCCTGGACACAC-AGGCGTGTCCC-TGACCGTGTGGAATTTTTAGACTTAGTTTT
1 AACCCACACGGCCCGGACACACGA-GCGTG-CCCTTGACCATATGAAATTTTCAGACTTAGTTTT
** *
29137024 AAATTTTTTTTAAAAATCAACAGTGAGTTACACGGCCTGGACACACGG
64 AAATCATTTTAAAAAATCAACAGTGAGTTACACGGCCTGGACACACGG
29137072 GCTTGTCCTT
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
115 1 0.01
116 34 0.37
117 51 0.55
118 7 0.08
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (117 bp):
AACCCACACGGCCCGGACACACGAGCGTGCCCTTGACCATATGAAATTTTCAGACTTAGTTTTAA
ATCATTTTAAAAAATCAACAGTGAGTTACACGGCCTGGACACACGGCCGTGT
Found at i:29138085 original size:18 final size:18
Alignment explanation
Indices: 29138064--29138122 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
29138054 ACTATTATTA
29138064 TTATTTATTTTTTCTTAT
1 TTATTTATTTTTTCTTAT
*
29138082 TTATTTATTTATTC-TA-
1 TTATTTATTTTTTCTTAT
* *
29138098 TTATTTTATTTCTTTATTGT
1 TTA-TTTATTT-TTTCTTAT
29138118 TTATT
1 TTATT
29138123 AGTATTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.09
17 9 0.27
18 15 0.45
19 3 0.09
20 3 0.09
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (18 bp):
TTATTTATTTTTTCTTAT
Found at i:29138093 original size:29 final size:28
Alignment explanation
Indices: 29138056--29138134 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
29138046 ATATTATTAC
29138056 TATTA-TTATTAT-TTATTTTTTCTTATT
1 TATTATTTATTATATTATTTTTT-TTATT
* * *
29138083 TATTTATTTATTCTATTATTTTATTTCTT
1 TA-TTATTTATTATATTATTTTTTTTATT
*
29138112 TATTGTTTATTAGTATTATTTTT
1 TATTATTTATTA-TATTATTTTT
29138135 CAGGTTCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.05
28 11 0.26
29 21 0.50
30 8 0.19
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.72
Consensus pattern (28 bp):
TATTATTTATTATATTATTTTTTTTATT
Found at i:29140630 original size:6 final size:6
Alignment explanation
Indices: 29140621--29140667 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
29140611 TCTAAGTCTA
* *
29140621 TTTATT TTTA-T TTTATT TTTGTT TTTATT TTTATT TTT-CT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
29140667 T
1 T
29140668 ACTTTTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:29140637 original size:11 final size:11
Alignment explanation
Indices: 29140621--29140667 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
29140611 TCTAAGTCTA
29140621 TTTATTTTTAT
1 TTTATTTTTAT
*
29140632 TTTATTTTTGTT
1 TTTATTTTT-AT
29140644 TTTATTTTTAT
1 TTTATTTTTAT
29140655 TTT-TCTTTTAT
1 TTTAT-TTTTAT
29140666 TT
1 TT
29140668 ACTTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 1 0.03
11 21 0.66
12 10 0.31
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:29140647 original size:17 final size:16
Alignment explanation
Indices: 29140625--29140667 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
29140615 AGTCTATTTA
29140625 TTTTTATTTTATTTTT
1 TTTTTATTTTATTTTT
29140641 GTTTTTATTTTTATTTTT
1 -TTTTTA-TTTTATTTTT
*
29140659 CTTTTATTT
1 TTTTTATTT
29140668 ACTTTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 11 0.46
18 10 0.42
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTATTTTATTTTT
Found at i:29143917 original size:6 final size:5
Alignment explanation
Indices: 29143893--29143957 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 5
29143883 ATTGAGTCCA
*
29143893 TTTAT TTTAT TTTATT TTTAGT TTTAGT TTTAT TTCTATT TTTAGG TTTATT
1 TTTAT TTTAT TTTA-T TTTA-T TTTA-T TTTAT TT-TA-T TTTA-T TTTA-T
29143945 TTTAT TTT-T TTTA
1 TTTAT TTTAT TTTA
29143958 GACTTCTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.08
5 16 0.31
6 28 0.55
7 3 0.06
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:29143925 original size:18 final size:17
Alignment explanation
Indices: 29143893--29143952 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 17
29143883 ATTGAGTCCA
29143893 TTTATTTTA-TTTTATT
1 TTTATTTTAGTTTTATT
29143909 TTTAGTTTTAGTTTTATT
1 TTTA-TTTTAGTTTTATT
* *
29143927 TCTATTTTTAGGTTTATT
1 TTTA-TTTTAGTTTTATT
29143945 TTTATTTT
1 TTTATTTT
29143953 TTTTAGACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 4 0.11
17 9 0.24
18 25 0.66
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.75
Consensus pattern (17 bp):
TTTATTTTAGTTTTATT
Found at i:29143937 original size:24 final size:22
Alignment explanation
Indices: 29143893--29143956 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 22
29143883 ATTGAGTCCA
*
29143893 TTTATTTTATTTTATTTTTAGT
1 TTTATTTTATTTTATTTTTAGG
29143915 TTTAGTTTTATTTCTATTTTTAGG
1 TTTA-TTTTATTT-TATTTTTAGG
29143939 TTTATTTTTATTTT-TTTT
1 TTTA-TTTTATTTTATTTT
29143957 AGACTTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.21
23 9 0.24
24 21 0.55
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTATTTTATTTTATTTTTAGG
Found at i:29148128 original size:147 final size:151
Alignment explanation
Indices: 29147942--29148214 Score: 364
Period size: 147 Copynumber: 1.8 Consensus size: 151
29147932 AAGACTTTAG
* * *
29147942 CACAAACAATTTTTTTTACAATCAAAAATATAATCTTAAACATTAAAT-TTAAGTATTAAAAATA
1 CACAAACAATTTTTTATACAATCAAAAATATAATATTAAACATTAAATCTAAAG-ATTAAAAATA
29148006 AA-A-AA-ATAAACATAAAATATAAAAATTATTATTACAAACTAA-AAAAAAAC-TTAAAACTAT
65 AATAGAATATAAACATAAAATATAAAAATTATTATTAC-AAC-AATAAAAAAACATTAAAACTAT
29148066 CATAAACTATCTCTAAAACTCCGA
128 CATAAACTATCTCTAAAACTCCGA
* *
29148090 CACAAACAAATTTTTTATA-AA-CAAAAATATAATATTAAATATTTAATCTAAAGATTAAAAATA
1 CACAAAC-AATTTTTTATACAATCAAAAATATAATATTAAACATTAAATCTAAAGATTAAAAATA
* * * *
29148153 AATTAGAATATAAATATATAATATACAAATTATTATTACAACAATAAAAACACATTAAAACT
65 AA-TAGAATATAAACATAAAATATAAAAATTATTATTACAACAATAAAAAAACATTAAAACT
29148215 TTCACAATTT
Statistics
Matches: 108, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
147 35 0.32
148 13 0.12
149 13 0.12
150 12 0.11
151 35 0.32
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.31
Consensus pattern (151 bp):
CACAAACAATTTTTTATACAATCAAAAATATAATATTAAACATTAAATCTAAAGATTAAAAATAA
ATAGAATATAAACATAAAATATAAAAATTATTATTACAACAATAAAAAAACATTAAAACTATCAT
AAACTATCTCTAAAACTCCGA
Found at i:29148256 original size:151 final size:148
Alignment explanation
Indices: 29147943--29148256 Score: 350
Period size: 151 Copynumber: 2.1 Consensus size: 148
29147933 AGACTTTAGC
* *
29147943 ACAAACAATTTTTTTTACAATCAAAAATATAATCTTAAACATTAAATTTAAGTATTAAAAATAAA
1 ACAAACAATTTTTTTTACAATCAAAAATATAATATTAAACATTAAATTAAAGTATTAAAAATAAA
*
29148008 AAAATAAACATAAAATATAAAAATTATTATTACAAACTAAAAAAAAACTTAAAACTATCATAAAC
66 AAAATAAACATAAAATATAAAAATTATTATTACAAACTAAAAAAAAACTTAAAACTATCACAAAC
* * *
29148073 TATCTCTAAAACTCCGAC
131 TATCCCTAAAACTCCAAA
* * *
29148091 ACAAACAAATTTTTTATA-AA-CAAAAATATAATATTAAATATTTAATCTAAAG-ATTAAAAATA
1 ACAAAC-AATTTTTTTTACAATCAAAAATATAATATTAAACATTAAAT-TAAAGTATTAAAAATA
* * * * *
29148153 AATTAGAATATAAATATATAATATACAAATTATTATTAC-AAC-AATAAAAACACATTAAAACTT
64 AA--A-AA-ATAAACATAAAATATAAAAATTATTATTACAAACTAA-AAAAAAAC-TTAAAACTA
** * * *
29148216 TCACAATTTCTCCCTAAAATTCTAAA
123 TCACAAACTATCCCTAAAACTCCAAA
29148242 ACAAACAATTTTTTT
1 ACAAACAATTTTTTT
29148257 CCTTCCAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
147 35 0.25
148 12 0.09
149 13 0.09
150 20 0.14
151 58 0.42
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.32
Consensus pattern (148 bp):
ACAAACAATTTTTTTTACAATCAAAAATATAATATTAAACATTAAATTAAAGTATTAAAAATAAA
AAAATAAACATAAAATATAAAAATTATTATTACAAACTAAAAAAAAACTTAAAACTATCACAAAC
TATCCCTAAAACTCCAAA
Found at i:29152133 original size:355 final size:355
Alignment explanation
Indices: 29151131--29152194 Score: 2004
Period size: 354 Copynumber: 3.0 Consensus size: 355
29151121 TTTTAATAAA
29151131 TATCTCCCCCATGCACCAACCCACTAACAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
1 TATCTCCCCCATGCACCAACCCACTAACAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
29151196 CCTTTATTTTCATTTTTAAAGGGACAAAAATACATATAGCCTTATGATTCGGAACAAAATCTTTG
66 CCTTTATTTTCATTTTTAAAGGGACAAAAATACATATAGCCTTATGATTCGGAACAAAATCTTTG
*
29151261 AAGGGTTACAAAGTCGAGATGTGGATATCCACTAAGAACCAAACCAATAGCGGGCATGGTTGACC
131 AAGGGTTACAAAGTCGAGATGTGGATATCCACTAAGAACCAAACCAATAGCGGGCGTGGTTGACC
*
29151326 AACAGCCATTTTACGAAGCACTCAGCTTTCAACCCGTTTTGGATAAGAACTTGGTGGATGTTAAG
196 AACAGCCATTTTACGAAGCACTCAGCTTTCAACCCGTTTTGGATAAGAACTTGGTGGATGTCAAG
*
29151391 ATCATACCAGTAAATGAACTAAACTCATAATTCTTTCATACTTCATTAATGCGAGAGTACATGTA
261 ATCATACCAGTAAATGAACGAAACTCATAATTCTTTCATACTTCATTAATGCGAGAGTACATGTA
29151456 TTTAATAGATGGAAGAGAGAGGTTAGCACT
326 TTTAATAGATGGAAGAGAGAGGTTAGCACT
*
29151486 TATCTCCCCCATGCACCAACCCACTAATAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
1 TATCTCCCCCATGCACCAACCCACTAACAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
29151551 CCTTTATTTTCATTTTTAAAGGGACAAAAATACATATAG-CTTATGATTCGGAACAAAATCTTTG
66 CCTTTATTTTCATTTTTAAAGGGACAAAAATACATATAGCCTTATGATTCGGAACAAAATCTTTG
*
29151615 AAGGGTTACAAAGTCGAGATGTGGATATCCACTAAGAACCAAACGAATAGCGGGCGTGGTTGACC
131 AAGGGTTACAAAGTCGAGATGTGGATATCCACTAAGAACCAAACCAATAGCGGGCGTGGTTGACC
* *
29151680 AACAGCCATTTTACGAAGCACTCAACTTTCAACCCATTTTGGATAAGAACTTGGTGGATGTCAAG
196 AACAGCCATTTTACGAAGCACTCAGCTTTCAACCCGTTTTGGATAAGAACTTGGTGGATGTCAAG
29151745 ATCATACCAGTAAATGAACGAAACTCATAATTCTTTCATACTTCATTAATGCGAGAGTACATGTA
261 ATCATACCAGTAAATGAACGAAACTCATAATTCTTTCATACTTCATTAATGCGAGAGTACATGTA
*
29151810 TTTAATAGATGGAAGAGAGAGGTTAGCATT
326 TTTAATAGATGGAAGAGAGAGGTTAGCACT
29151840 TATCTCCCCCATGCACCAACCCACTAACAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
1 TATCTCCCCCATGCACCAACCCACTAACAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
*
29151905 CTTTTATTTTCATTTTTAAAGGGACAAAAATACATATAGCCTTATGATTCGGAACAAAATCTTTG
66 CCTTTATTTTCATTTTTAAAGGGACAAAAATACATATAGCCTTATGATTCGGAACAAAATCTTTG
* * *
29151970 AAGGGTTACAAAGTCTAGATGTGGATATCCACCAAGAACCAAACCAATAGCAGGCGTGGTTGACC
131 AAGGGTTACAAAGTCGAGATGTGGATATCCACTAAGAACCAAACCAATAGCGGGCGTGGTTGACC
29152035 AACAGCCATTTTACGAAGCACTCAGCTTTCAACCCGTTTTGGATAAGAACTTGGTGGATGTCAAG
196 AACAGCCATTTTACGAAGCACTCAGCTTTCAACCCGTTTTGGATAAGAACTTGGTGGATGTCAAG
*
29152100 ATCATACCAGTAAATGAACGAAACTCATAATTCTTTCATACTTCATTAATGCGATAGTACATGTA
261 ATCATACCAGTAAATGAACGAAACTCATAATTCTTTCATACTTCATTAATGCGAGAGTACATGTA
29152165 TTTAATAGATGGAAGAGAGAGGTTAGCACT
326 TTTAATAGATGGAAGAGAGAGGTTAGCACT
29152195 AACTAACTTG
Statistics
Matches: 690, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
354 345 0.50
355 345 0.50
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (355 bp):
TATCTCCCCCATGCACCAACCCACTAACAGTCCCAATCCAAATGCCTTAATGCATCTGCATAATT
CCTTTATTTTCATTTTTAAAGGGACAAAAATACATATAGCCTTATGATTCGGAACAAAATCTTTG
AAGGGTTACAAAGTCGAGATGTGGATATCCACTAAGAACCAAACCAATAGCGGGCGTGGTTGACC
AACAGCCATTTTACGAAGCACTCAGCTTTCAACCCGTTTTGGATAAGAACTTGGTGGATGTCAAG
ATCATACCAGTAAATGAACGAAACTCATAATTCTTTCATACTTCATTAATGCGAGAGTACATGTA
TTTAATAGATGGAAGAGAGAGGTTAGCACT
Found at i:29159607 original size:13 final size:13
Alignment explanation
Indices: 29159589--29159615 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29159579 AAAATAATGT
29159589 TTACTACTTATTA
1 TTACTACTTATTA
29159602 TTACTACTTATTA
1 TTACTACTTATTA
29159615 T
1 T
29159616 GTAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TTACTACTTATTA
Found at i:29159975 original size:14 final size:14
Alignment explanation
Indices: 29159956--29159984 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29159946 CTCTTGAGAT
29159956 TAATCTTTATCGAG
1 TAATCTTTATCGAG
29159970 TAATCTTTATCGAG
1 TAATCTTTATCGAG
29159984 T
1 T
29159985 CAAAGGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (14 bp):
TAATCTTTATCGAG
Found at i:29164852 original size:9 final size:9
Alignment explanation
Indices: 29164835--29164909 Score: 66
Period size: 9 Copynumber: 8.6 Consensus size: 9
29164825 CATCTGGCAA
29164835 AAAAATTAT
1 AAAAATTAT
*
29164844 AAAAGTTAT
1 AAAAATTAT
*
29164853 AAAAATCAAT
1 AAAAAT-TAT
*
29164863 AAAAGTTAT
1 AAAAATTAT
29164872 AAAAATTAT
1 AAAAATTAT
*
29164881 -TAAATTA-
1 AAAAATTAT
*
29164888 AAAAAAT-T
1 AAAAATTAT
*
29164896 AAAAATTAG
1 AAAAATTAT
29164905 AAAAA
1 AAAAA
29164910 AATTTATAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
8 16 0.31
9 28 0.55
10 7 0.14
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29164884 original size:19 final size:18
Alignment explanation
Indices: 29164835--29164909 Score: 84
Period size: 19 Copynumber: 4.3 Consensus size: 18
29164825 CATCTGGCAA
29164835 AAAAATTATAAAAGTTAT
1 AAAAATTATAAAAGTTAT
*
29164853 AAAAATCAATAAAAGTTAT
1 AAAAAT-TATAAAAGTTAT
* *
29164872 AAAAATTATTAAA-TTAA
1 AAAAATTATAAAAGTTAT
*
29164889 AAAAATTA-AAAA-TTAG
1 AAAAATTATAAAAGTTAT
29164905 AAAAA
1 AAAAA
29164910 AATTTATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.22
17 11 0.22
18 11 0.22
19 17 0.34
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAGTTAT
Found at i:29165219 original size:29 final size:27
Alignment explanation
Indices: 29165165--29165241 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
29165155 AACTTTATAA
29165165 AATTTTATAATTTTTTTTCTATATTTCCAT
1 AATTTTATAA--TTTTTT-TATATTTCCAT
**
29165195 ATATTTTATAATTTTTTTATGATTTTTAT
1 A-ATTTTATAATTTTTTTAT-ATTTCCAT
*
29165224 AATTTT-TAATATTTTTAT
1 AATTTTATAATTTTTTTAT
29165242 TAAAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 11 0.26
28 8 0.19
29 13 0.31
30 1 0.02
31 9 0.21
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (27 bp):
AATTTTATAATTTTTTTATATTTCCAT
Found at i:29165239 original size:19 final size:19
Alignment explanation
Indices: 29165193--29165269 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 19
29165183 CTATATTTCC
*
29165193 ATATATTTTATAATTTTT-
1 ATATTTTTTATAATTTTTA
*
29165211 TTATGATTTTTATAATTTTTA
1 ATAT--TTTTTATAATTTTTA
**
29165232 ATA-TTTTTATTAAAATTTA
1 ATATTTTTTA-TAATTTTTA
* *
29165251 ATAATTTGTATAATTTTTA
1 ATATTTTTTATAATTTTTA
29165270 TTTTTATCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
18 9 0.20
19 17 0.37
20 18 0.39
21 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATATTTTTTATAATTTTTA
Found at i:29174913 original size:108 final size:109
Alignment explanation
Indices: 29174576--29174962 Score: 724
Period size: 109 Copynumber: 3.6 Consensus size: 109
29174566 GTTATTAATT
* *
29174576 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTTATGAATGTAAATTTTTTTGTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATGTTTTTATGAATGTAAATTTTTTTGTT
29174641 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
66 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
* *
29174685 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTTATGAATGTAAATTTTTTTGTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATGTTTTTATGAATGTAAATTTTTTTGTT
29174750 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
66 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
29174794 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGA-GTTTTTATGAATGTAAATTTTTTTGTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATGTTTTTATGAATGTAAATTTTTTTGTT
29174858 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
66 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
29174902 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGA-GTTTTTATGAATGTAAATTTTTTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATGTTTTTATGAATGTAAATTTTTTT
29174963 TAAAGTCATT
Statistics
Matches: 276, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
108 131 0.47
109 145 0.53
ACGTcount: A:0.24, C:0.01, G:0.15, T:0.60
Consensus pattern (109 bp):
ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATGTTTTTATGAATGTAAATTTTTTTGTT
TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAG
Found at i:29174963 original size:217 final size:207
Alignment explanation
Indices: 29174576--29175374 Score: 944
Period size: 217 Copynumber: 3.8 Consensus size: 207
29174566 GTTATTAATT
*
29174576 ATTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTTATGAATGTAAATTTTTTTGTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGA-TTTTTTATGAATGTAAATTTTTTTGTT
*
29174641 TTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTA
65 TTTTTAATTATTTTAAAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTA
29174706 GTTTAGTGTTTTGTGATTTTTTTATGAATGTAAATTTTTTTGTTTTTTTAATTATTTTATAGCTA
130 GTTTAGTGTTTTGTGA-TTTTTTATGAATGT-AA-----TT-TTTTTTTAATTATTTTATAG-TA
29174771 TTTTGTTAGTAATTTATGATTAG
186 TTTTGTTAGTAATTTAT-ATTAG
*
29174794 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGAGTTTTTATGAATGTAAATTTTTTTGTTT
1 ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATTTTTTATGAATGTAAATTTTTTTGTTT
*
29174859 TTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAG
66 TTTTAATTATTTTAAAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAG
* * * *
29174924 TTTAGTATTTTGTGAGTTTTTATGAATGTAA--ATTTTTT--TTA----A-AGTCATTTTGTCAG
131 TTTAGTGTTTTGTGATTTTTTATGAATGTAATTTTTTTTTAATTATTTTATAGT-ATTTTGTTAG
*
29174980 TAATTTATGGTTAG
195 TAATTTAT-ATTAG
* * *
29174994 ATTATAAATTGTTTGGGTTTTGTTTAATGT-TTATTGTGATTTTTTATGAATGTAAATTTTTTTA
1 ATTATAAATTGTTTGTGTTTAGTTT-A-GTATT-TTGTGATTTTTTATGAATGTAAATTTTTTTG
* * *
29175058 TTTTTTTAAATTATTTGAAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTCTGT
63 TTTTTTT-AATTATTTTAAAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGT
* * *
29175123 TT-TTTTAGTGTTTATTGTGATTTTTTATGAATGTAA-TTTTTTTTAATTATTTCAAAGT-TGTT
127 TTAGTTTAGTG-TT-TTGTGATTTTTTATGAATGTAATTTTTTTTTAATTATTTTATAGTAT-TT
*
29175185 TTTTAGTAATTTATTATTAG
189 TGTTAGTAATTTA-TATTAG
* * * * * *
29175205 GTTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGACTTGTTATAAATGT-TATTTTTTGTG
1 ATTATAAATTGTTTGTGTTTAGTTTAGT-ATT-TTGTGATTTTTTATGAATGTAAATTTTTT-TG
* * * * *
29175269 TTTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATTATTAGATTATAAATTATTAATTTG
63 TTTTTTTAATTATTTTAAAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTT--TGTG
* * *
29175334 TTTAGTTTAATGTGTATCGTGATTTGTTAT-AATGTAATTTT
126 TTTAGTTT-A-GTGTTTTGTGATTTTTTATGAATGTAATTTT
29175375 ATTTGTTTTT
Statistics
Matches: 516, Mismatches: 39, Indels: 57
0.84 0.06 0.09
Matches are distributed among these distances:
199 1 0.00
200 47 0.09
201 4 0.01
202 44 0.09
203 57 0.11
204 21 0.04
205 9 0.02
207 9 0.02
209 2 0.00
210 58 0.11
211 67 0.13
212 17 0.03
213 18 0.03
214 2 0.00
215 5 0.01
216 13 0.03
217 106 0.21
218 36 0.07
ACGTcount: A:0.25, C:0.01, G:0.15, T:0.59
Consensus pattern (207 bp):
ATTATAAATTGTTTGTGTTTAGTTTAGTATTTTGTGATTTTTTATGAATGTAAATTTTTTTGTTT
TTTTAATTATTTTAAAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAG
TTTAGTGTTTTGTGATTTTTTATGAATGTAATTTTTTTTTAATTATTTTATAGTATTTTGTTAGT
AATTTATATTAG
Found at i:29174987 original size:92 final size:94
Alignment explanation
Indices: 29174878--29175056 Score: 283
Period size: 92 Copynumber: 1.9 Consensus size: 94
29174868 TTTTATAGCT
* *
29174878 ATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTT-A-GTATT-TTGTGAG
1 ATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGGGTTTAGTTTAATGT-TTATTGTGAG
29174940 TTTTTATGAATGTAAATTTTTTTTAAAGTC
65 TTTTTATGAATGTAAATTTTTTTTAAAGTC
* * *
29174970 ATTTTGTCAGTAATTTATGGTTAGATTATAAATTGTTTGGGTTTTGTTTAATGTTTATTGTGATT
1 ATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGGGTTTAGTTTAATGTTTATTGTGAGT
29175035 TTTTATGAATGTAAATTTTTTT
66 TTTTATGAATGTAAATTTTTTT
29175057 ATTTTTTTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
92 45 0.57
93 3 0.04
94 31 0.39
ACGTcount: A:0.26, C:0.01, G:0.17, T:0.56
Consensus pattern (94 bp):
ATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGGGTTTAGTTTAATGTTTATTGTGAGT
TTTTATGAATGTAAATTTTTTTTAAAGTC
Found at i:29175085 original size:111 final size:109
Alignment explanation
Indices: 29174964--29175393 Score: 484
Period size: 110 Copynumber: 4.0 Consensus size: 109
29174954 AATTTTTTTT
* * * * *
29174964 AAAGTCATTTTGTCAGTAATTTATGGTTAGATTATAAATTGTTTGGGTTTTGTTTAATGTTTATT
1 AAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAATGTTTATT
* *
29175029 GTGATTTTTTATGAATGTAAATTTTTTTATTTTTTTAAATTATTTG
66 GTGATTTGTTATGAATGT-AATTTTTTT-TTTTTTTAAATTATTTC
* * *
29175075 AAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTCTGTTT-TTTTAGTGTTTATT
1 AAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAATGTTTATT
*
29175139 GTGATTTTTTATGAATGTAA------TTTTTTTT-AATTATTTC
66 GTGATTTGTTATGAATGTAATTTTTTTTTTTTTTAAATTATTTC
* * * *
29175176 AAAGTTGTTTT-TTAGTAATTTATTATTAGGTTATAAATTGTTTGTGTTTAGTTTAGTGTTTATT
1 AAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAATGTTTATT
* * * * *
29175240 GTGACTTGTTATAAATGTTATTTTTTGTGTTTTTTAAATTATTTT
66 GTGATTTGTTATGAATGTAATTTTTT-TTTTTTTTAAATTATTTC
* * * *
29175285 AAAGTTATTTTGTTAGTAATTTATTATTAGATTATAAATTATTAATTTGTTTAGTTTAATGTGTA
1 AAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTT--TGTGTTTAGTTTAATGTTTA
* * * * *
29175350 TCGTGATTTGTTAT-AATGTAATTTTATTTGTTTTTGATTTATTT
64 TTGTGATTTGTTATGAATGTAATTTTTTTTTTTTTTAAATTATTT
29175394 GACAATTTTT
Statistics
Matches: 274, Mismatches: 33, Indels: 25
0.83 0.10 0.08
Matches are distributed among these distances:
100 35 0.13
101 47 0.17
102 7 0.03
103 1 0.00
108 7 0.03
109 20 0.07
110 72 0.26
111 56 0.20
112 29 0.11
ACGTcount: A:0.26, C:0.01, G:0.14, T:0.58
Consensus pattern (109 bp):
AAAGTTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAATGTTTATT
GTGATTTGTTATGAATGTAATTTTTTTTTTTTTTAAATTATTTC
Found at i:29175096 original size:311 final size:301
Alignment explanation
Indices: 29174661--29175232 Score: 835
Period size: 311 Copynumber: 1.9 Consensus size: 301
29174651 TTTTATAGCT
* * *
29174661 ATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTGATTTT
1 ATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGGGTTTAGTTTAATGTTTTGTGATTTT
* * *
29174726 TTTATGAATGTAAATTTTTTTGTTTTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGAT
66 TTTATGAATGTAAATTTTTTTATTTTTTTAATTATTTGAAAGCTATTTTGTTAGTAATTTATGAT
*
29174791 TAGATTATAAATTGTTTGTGTTTAGTTTAGT-ATT-TTGTGAGTTTTTATGAATGTAAATTTTTT
131 TAGATTATAAATTGTTTCTGTTT-GTTTAGTGATTATTGTGAGTTTTTATGAATGT-AA------
* *
29174854 TGTTTTTTTAATTATTTTATAGCTATTTTGTTAGTAATTTATGATTAGATTATAAATTGTTTGTG
188 T-TTTTTTTAATTATTTCAAAGCTATTTT-TTAGTAATTTATGATTAGATTATAAATTGTTTGTG
29174919 TTTAGTTTAGTATTTTGTGAGTTTTTATGAATGTAAATTTTTTTTAAAGTC
251 TTTAGTTTAGTATTTTGTGAGTTTTTATGAATGTAAATTTTTTTTAAAGTC
* *
29174970 ATTTTGTCAGTAATTTATGGTTAGATTATAAATTGTTTGGGTTTTGTTTAATGTTTATTGTGA-T
1 ATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGGGTTTAGTTTAATG-TT-TTGTGATT
*
29175034 TTTTTATGAATGTAAATTTTTTTATTTTTTTAAATTATTTGAAAGTTATTTTGTTAGTAATTTAT
64 TTTTTATGAATGTAAATTTTTTTATTTTTTT-AATTATTTGAAAGCTATTTTGTTAGTAATTTAT
* * *
29175099 GATTAGATTATAAATTGTTTCTGTTTTTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTT
128 GATTAGATTATAAATTGTTTCTGTTTGTTTAGTGATTATTGTGAGTTTTTATGAATGTAATTTTT
* * * *
29175164 TTTAATTATTTCAAAGTTGTTTTTTAGTAATTTATTATTAGGTTATAAATTGTTTGTGTTTAGTT
193 TTTAATTATTTCAAAGCTATTTTTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTT
29175229 TAGT
258 TAGT
29175233 GTTTATTGTG
Statistics
Matches: 239, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
303 44 0.18
304 23 0.10
305 1 0.00
309 48 0.20
310 39 0.16
311 65 0.27
312 19 0.08
ACGTcount: A:0.25, C:0.01, G:0.15, T:0.59
Consensus pattern (301 bp):
ATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGGGTTTAGTTTAATGTTTTGTGATTTT
TTTATGAATGTAAATTTTTTTATTTTTTTAATTATTTGAAAGCTATTTTGTTAGTAATTTATGAT
TAGATTATAAATTGTTTCTGTTTGTTTAGTGATTATTGTGAGTTTTTATGAATGTAATTTTTTTT
AATTATTTCAAAGCTATTTTTTAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAG
TATTTTGTGAGTTTTTATGAATGTAAATTTTTTTTAAAGTC
Found at i:29175274 original size:110 final size:111
Alignment explanation
Indices: 29175159--29175384 Score: 298
Period size: 112 Copynumber: 2.0 Consensus size: 111
29175149 ATGAATGTAA
* * * *
29175159 TTTTTTTTAATTATTTCAAAGTTGTTTT-TTAGTAATTTATTATTAGGTTATAAATTGTT-TGTG
1 TTTTTTTAAATTATTTCAAAGTTATTTTGTTAGTAATTTATTATTAGATTATAAATTATTATGTG
* * * *
29175222 TTTAGTTTAGTGTTTATTGTGACTTGTTATAAATGTTA-TTT-TTTG
66 TTTAGTTTAATGTGTATCGTGACTTGTTAT-AATGTAATTTTATTTG
* *
29175267 TGTTTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATTATTAGATTATAAATTATTAATT
1 T-TTTTTTAAATTATTTCAAAGTTATTTTGTTAGTAATTTATTATTAGATTATAAATTATT-ATG
*
29175332 TGTTTAGTTTAATGTGTATCGTGATTTGTTATAATGTAATTTTATTTG
64 TGTTTAGTTTAATGTGTATCGTGACTTGTTATAATGTAATTTTATTTG
29175380 TTTTT
1 TTTTT
29175385 GATTTATTTG
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
108 1 0.01
109 24 0.24
110 29 0.29
111 6 0.06
112 36 0.36
113 5 0.05
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.60
Consensus pattern (111 bp):
TTTTTTTAAATTATTTCAAAGTTATTTTGTTAGTAATTTATTATTAGATTATAAATTATTATGTG
TTTAGTTTAATGTGTATCGTGACTTGTTATAATGTAATTTTATTTG
Found at i:29176315 original size:24 final size:23
Alignment explanation
Indices: 29176288--29176341 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
29176278 TATGTATTTG
29176288 TTATTAAATAGATATT-TATTATAA
1 TTATTAAATAG-TATTATATTA-AA
*
29176312 TTATT--ATAGTTTTATATTAAA
1 TTATTAAATAGTATTATATTAAA
29176333 TTATTAAAT
1 TTATTAAAT
29176342 TATGATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 2 0.08
24 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TTATTAAATAGTATTATATTAAA
Found at i:29176317 original size:3 final size:3
Alignment explanation
Indices: 29176303--29176373 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
29176293 AAATAGATAT
* * *
29176303 TTA TTA TAA TTA TTA -TA GTT- TTA -TA TTA -AA TTA TTA -AA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
29176344 TGA TTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29176374 AAATAAATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
2 8 0.15
3 43 0.83
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:29177196 original size:21 final size:21
Alignment explanation
Indices: 29177170--29177230 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
29177160 GGCTTTGCAA
29177170 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGT-T
* *
29177192 T-AGGCACCACATGTGTCGTT
1 TCAGGCACTATATGTGTCGTT
*
29177212 TCAGGCACTTTATGTGTCG
1 TCAGGCACTATATGTGTCG
29177231 CATATTGCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (21 bp):
TCAGGCACTATATGTGTCGTT
Found at i:29177744 original size:44 final size:44
Alignment explanation
Indices: 29177676--29177764 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
29177666 TCAGCATATG
* *
29177676 ATTGTTTCCATACGCAGGTCAGTAGCAGTCAAAGGTCCCGGTTC
1 ATTGTTTCCATACGCAAGTCAGTAGAAGTCAAAGGTCCCGGTTC
* *
29177720 ATTGTTTCCATGCGCAAGTTAGTAGAAGTCAAAGGTCCCGGTTC
1 ATTGTTTCCATACGCAAGTCAGTAGAAGTCAAAGGTCCCGGTTC
29177764 A
1 A
29177765 ACATCCAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (44 bp):
ATTGTTTCCATACGCAAGTCAGTAGAAGTCAAAGGTCCCGGTTC
Found at i:29177998 original size:15 final size:15
Alignment explanation
Indices: 29177978--29178007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29177968 AATGAAGTTA
29177978 TTAGTCAATTTGAAT
1 TTAGTCAATTTGAAT
29177993 TTAGTCAATTTGAAT
1 TTAGTCAATTTGAAT
29178008 GATATCATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TTAGTCAATTTGAAT
Found at i:29178447 original size:13 final size:13
Alignment explanation
Indices: 29178429--29178454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29178419 GGACCCTTTA
29178429 GAAATTAATTATC
1 GAAATTAATTATC
29178442 GAAATTAATTATC
1 GAAATTAATTATC
29178455 TCAGTTTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GAAATTAATTATC
Found at i:29184171 original size:108 final size:110
Alignment explanation
Indices: 29184039--29184238 Score: 280
Period size: 108 Copynumber: 1.8 Consensus size: 110
29184029 TTTATAATAG
* * * * *
29184039 TTACTAACAAAATAATTTTTAAATAAATTAAAAAATATTAAAACA-TTACATTTATAACCTAA-C
1 TTACTAACAAAATAACTTTAAAATAAATTAAAAAATAATAAAA-ATTTACATTCATAACCTAATA
* *
29184102 AAATTACAATAAACCCTAAA-CAAACAATTAACCTAATCACGAAAC
65 AAATCACAATAAACACTAAACCAAACAATTAACCTAATCACGAAAC
**
29184147 TTACTAACAAAATAACTTTAAAATAAATTAAAAGTTAATAAAAATTTACATTCATAACCTAATAA
1 TTACTAACAAAATAACTTTAAAATAAATTAAAAAATAATAAAAATTTACATTCATAACCTAATAA
*
29184212 AATCACAATAAACATTAAACCAAACAA
66 AATCACAATAAACACTAAACCAAACAA
29184239 ATAATTTATA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 1 0.01
108 54 0.68
109 17 0.22
110 7 0.09
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (110 bp):
TTACTAACAAAATAACTTTAAAATAAATTAAAAAATAATAAAAATTTACATTCATAACCTAATAA
AATCACAATAAACACTAAACCAAACAATTAACCTAATCACGAAAC
Found at i:29188898 original size:14 final size:14
Alignment explanation
Indices: 29188879--29188905 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29188869 GTTGCGTTCG
29188879 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
29188893 TAGTTAAATTAGA
1 TAGTTAAATTAGA
29188906 CTAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:29195130 original size:94 final size:94
Alignment explanation
Indices: 29194969--29195221 Score: 425
Period size: 94 Copynumber: 2.7 Consensus size: 94
29194959 CACGGCCTGA
* * * ** *
29194969 CCACACGGGCGTGTGTGATCTCACGTGGGCGTGGGAGAAGCGAAGGAAAACACACATTGGCACAA
1 CCACATGGGCGTGTGAGATTTCATATGAGCGTGGGAGAAGCGAAGGAAAACACACATTGGCACAA
*
29195034 AATACGCCCGTGTGAGAGACACAAGCAAG
66 AATACGACCGTGTGAGAGACACAAGCAAG
29195063 CCACATGGGCGTGTGAGATTTCATATGAGCGTGGGAGAAGCGAAGGAAAACACACATTGGCACAA
1 CCACATGGGCGTGTGAGATTTCATATGAGCGTGGGAGAAGCGAAGGAAAACACACATTGGCACAA
29195128 AATACGACCGTGTGAGAGACACAAGCAAG
66 AATACGACCGTGTGAGAGACACAAGCAAG
*
29195157 CCACATGGGCGTGTGAGATTTCATATGAGCGTGGGAGAAGCGAAGGAAAACACACACCTGGCACA
1 CCACATGGGCGTGTGAGATTTCATATGAGCGTGGGAGAAGCGAAGGAAAACACACA-TTGGCACA
29195222 TGGTTGTGTG
Statistics
Matches: 150, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 143 0.95
95 7 0.05
ACGTcount: A:0.34, C:0.21, G:0.31, T:0.14
Consensus pattern (94 bp):
CCACATGGGCGTGTGAGATTTCATATGAGCGTGGGAGAAGCGAAGGAAAACACACATTGGCACAA
AATACGACCGTGTGAGAGACACAAGCAAG
Found at i:29195393 original size:15 final size:15
Alignment explanation
Indices: 29195369--29195447 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
29195359 AGCCACCCAT
29195369 TTTATT-TTATTTTA
1 TTTATTATTATTTTA
29195383 TTTATTATTATTTT-
1 TTTATTATTATTTTA
29195397 TTATATTATTTATTTTTA
1 TT-TATTA-TTA-TTTTA
* *
29195415 TTTTACTAATA-TTTA
1 -TTTATTATTATTTTA
29195430 TTTATTTATTATTCTTA
1 TTTA-TTATTATT-TTA
29195447 T
1 T
29195448 ATTTAGATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
14 12 0.23
15 20 0.38
16 4 0.08
17 10 0.19
18 4 0.08
19 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATTATTTTA
Found at i:29195405 original size:22 final size:22
Alignment explanation
Indices: 29195373--29195450 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 22
29195363 ACCCATTTTA
*
29195373 TTTTATTTTATTTATTATTATT
1 TTTTATATTATTTATTATTATT
*
29195395 TTTTATATTATTTATTTTTATT
1 TTTTATATTATTTATTATTATT
*
29195417 TTACTAATATTTATTTATTTATTA-T
1 TT--TTATA-TTATTTA-TTATTATT
*
29195442 TCTTATATT
1 TTTTATATT
29195451 TAGATTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 24 0.52
23 4 0.09
24 4 0.09
25 9 0.20
26 5 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTATATTATTTATTATTATT
Found at i:29195440 original size:36 final size:36
Alignment explanation
Indices: 29195369--29195442 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
29195359 AGCCACCCAT
* * *
29195369 TTTATTTTATTTTATTTATTATTATTTTTTATATTA
1 TTTATTTTATTTTACTAATTATTATTTATTATATTA
29195405 TTTATTTTTATTTTACTAA-TATTTATTTATT-TATTA
1 TTTA-TTTTATTTTACTAATTA-TTATTTATTATATTA
29195441 TT
1 TT
29195443 CTTATATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (36 bp):
TTTATTTTATTTTACTAATTATTATTTATTATATTA
Found at i:29195956 original size:15 final size:15
Alignment explanation
Indices: 29195932--29196010 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
29195922 AGCCACCCAT
29195932 TTTATT-TTATTTTA
1 TTTATTATTATTTTA
29195946 TTTATTATTATTTT-
1 TTTATTATTATTTTA
29195960 TTATATTATTTATTTTTA
1 TT-TATTA-TTA-TTTTA
* *
29195978 TTTTACTAATA-TTTA
1 -TTTATTATTATTTTA
29195993 TTTATTTATTATTCTTA
1 TTTA-TTATTATT-TTA
29196010 T
1 T
29196011 ACCTTGATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
14 12 0.23
15 20 0.38
16 4 0.08
17 10 0.19
18 4 0.08
19 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATTATTTTA
Found at i:29195968 original size:22 final size:22
Alignment explanation
Indices: 29195936--29196005 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
29195926 ACCCATTTTA
*
29195936 TTTTATTTTATTTATTATTATT
1 TTTTATATTATTTATTATTATT
*
29195958 TTTTATATTATTTATTTTTATT
1 TTTTATATTATTTATTATTATT
*
29195980 TTACTAATATTTATTTATTTATTATT
1 TT--TTATA-TTATTTA-TTATTATT
29196006 CTTATACCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 22 0.55
24 4 0.10
25 7 0.17
26 7 0.17
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATATTATTTATTATTATT
Found at i:29195977 original size:32 final size:32
Alignment explanation
Indices: 29195932--29196010 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
29195922 AGCCACCCAT
* *
29195932 TTTATTT-TATTTTATTTATTATTATTT-TTTA
1 TTTATTTAT-TTTTATTTACTAATATTTATTTA
29195963 TATTATTTATTTTTATTTTACTAATATTTATTTA
1 T-TTATTTATTTTTA-TTTACTAATATTTATTTA
*
29195997 TTTA-TTATTCTTAT
1 TTTATTTATTTTTAT
29196011 ACCTTGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
31 2 0.05
32 19 0.46
33 15 0.37
34 5 0.12
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (32 bp):
TTTATTTATTTTTATTTACTAATATTTATTTA
Found at i:29196003 original size:36 final size:36
Alignment explanation
Indices: 29195932--29196005 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
29195922 AGCCACCCAT
* * *
29195932 TTTATTTTATTTTATTTATTATTATTTTTTATATTA
1 TTTATTTTATTTTACTAATTATTATTTATTATATTA
29195968 TTTATTTTTATTTTACTAA-TATTTATTTATT-TATTA
1 TTTA-TTTTATTTTACTAATTA-TTATTTATTATATTA
29196004 TT
1 TT
29196006 CTTATACCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (36 bp):
TTTATTTTATTTTACTAATTATTATTTATTATATTA
Found at i:29196141 original size:15 final size:15
Alignment explanation
Indices: 29196121--29196181 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
29196111 GAGTTTATTG
29196121 TTATTATTTTTCGTT
1 TTATTATTTTTCGTT
29196136 TTATTA-TTTTCG-T
1 TTATTATTTTTCGTT
* *
29196149 TTATTTATTTATCTTT
1 TTA-TTATTTTTCGTT
* *
29196165 TTTTTAATTTT-GTT
1 TTATTATTTTTCGTT
29196179 TTA
1 TTA
29196182 GTTGCTTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
13 4 0.11
14 13 0.36
15 16 0.44
16 3 0.08
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (15 bp):
TTATTATTTTTCGTT
Found at i:29196153 original size:13 final size:14
Alignment explanation
Indices: 29196121--29196181 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
29196111 GAGTTTATTG
29196121 TTATTATTTTTCGTT
1 TTATTA-TTTTCGTT
29196136 TTATTATTTTCG-T
1 TTATTATTTTCGTT
*
29196149 TTATTTATTTATCTTT
1 TTA-TTATTT-TCGTT
*
29196165 TTTTTAATTTT-GTT
1 TTATT-ATTTTCGTT
29196179 TTA
1 TTA
29196182 GTTGCTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 4 0.11
14 16 0.42
15 11 0.29
16 7 0.18
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (14 bp):
TTATTATTTTCGTT
Found at i:29196166 original size:29 final size:29
Alignment explanation
Indices: 29196124--29196179 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
29196114 TTTATTGTTA
*
29196124 TTATTTTTCGTTTTATT-ATTTTCGTTTAT
1 TTATTTATCGTTTTATTAATTTT-GTTTAT
* *
29196153 TTATTTATCTTTTTTTTAATTTTGTTT
1 TTATTTATCGTTTTATTAATTTTGTTT
29196180 TAGTTGCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.75
Consensus pattern (29 bp):
TTATTTATCGTTTTATTAATTTTGTTTAT
Found at i:29198929 original size:14 final size:14
Alignment explanation
Indices: 29198910--29198939 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29198900 GTTGCGTTCG
29198910 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
29198924 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
29198938 TA
1 TA
29198940 AAAACAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:29205392 original size:73 final size:73
Alignment explanation
Indices: 29205267--29205414 Score: 201
Period size: 73 Copynumber: 2.0 Consensus size: 73
29205257 TAAAGCATGA
*
29205267 CTTCTAATTATCTTTGTAAAATTTATGGTGAATTTCCAAAGTCAGAACAGGGGATCCAGAAATCG
1 CTTCTAATTATCTTTGTAAAATTTATGGCGAATTTCCAAAGTCAGAACAGGGGATCCAGAAATCG
*
29205332 CTCTGGCC
66 CTCTGACC
* * * * *
29205340 CTTCTAATTAGT-TTTGTACAATTTATGGCGAATTTCCGAAGT-TGAAATAGGGGATTCAGAAAT
1 CTTCTAATTA-TCTTTGTAAAATTTATGGCGAATTTCCAAAGTCAG-AACAGGGGATCCAGAAAT
29205403 CGCTCTGACC
64 CGCTCTGACC
29205413 CT
1 CT
29205415 GTTTCACTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
72 1 0.02
73 64 0.97
74 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (73 bp):
CTTCTAATTATCTTTGTAAAATTTATGGCGAATTTCCAAAGTCAGAACAGGGGATCCAGAAATCG
CTCTGACC
Done.