Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 3 of 13
Found at i:222925 original size:14 final size:13
Alignment explanation
Indices: 222889--222936 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
222879 ATTAGGCTAA
* *
222889 AAATTTAAAAAAT
1 AAATTTAAATATT
222902 AAATTATAAATATT
1 AAATT-TAAATATT
*
222916 AAGATTTAAATTTT
1 AA-ATTTAAATATT
222930 AAATTTA
1 AAATTTA
222937 TTAAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 10 0.33
14 17 0.57
15 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AAATTTAAATATT
Found at i:228401 original size:23 final size:23
Alignment explanation
Indices: 228347--228401 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
228337 TTTAAAGAAT
* *
228347 AAAATAAAAATATAAGTTAATCA
1 AAAATAAAAATAAAAATTAATCA
* *
228370 AAAAAAAAAATAAAAATT-ATTA
1 AAAATAAAAATAAAAATTAATCA
228392 AACAATAAAA
1 AA-AATAAAA
228402 TAATTCAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAAAATAAAAATTAATCA
Found at i:228448 original size:19 final size:19
Alignment explanation
Indices: 228426--228464 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
228416 ATAAAAAACA
228426 AGAAATAAAAAATAAAAAT
1 AGAAATAAAAAATAAAAAT
**
228445 AGAAATTTAAAATAAAAAT
1 AGAAATAAAAAATAAAAAT
228464 A
1 A
228465 TATTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (19 bp):
AGAAATAAAAAATAAAAAT
Found at i:234004 original size:14 final size:14
Alignment explanation
Indices: 233985--234012 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
233975 AATTAAATAA
233985 TTATTATAATTATT
1 TTATTATAATTATT
233999 TTATTATAATTATT
1 TTATTATAATTATT
234013 ATTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTATAATTATT
Found at i:234004 original size:17 final size:16
Alignment explanation
Indices: 233951--234024 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
233941 GATAATTTAA
233951 ATTTTATAA-TATTTT
1 ATTTTATAATTATTTT
** *
233966 ATTTTATTAAATTAAATA
1 ATTTTA-T-AATTATTTT
233984 ATTATTATAATTATTTT
1 ATT-TTATAATTATTTT
* *
234001 ATTATAATTATTATTTT
1 ATT-TTATAATTATTTT
234018 ATTTTAT
1 ATTTTAT
234025 TTTAATGAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.13
16 4 0.09
17 26 0.57
18 7 0.15
19 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTATAATTATTTT
Found at i:234124 original size:52 final size:52
Alignment explanation
Indices: 234057--234161 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
234047 AAATACATCG
* *
234057 ATGTGCAGTGACAATCACTCAATATAGATTCAAGAGCGATAAAATAATAGTA
1 ATGTGCAGTGACAATCACCCAATATAGATTCAAGAGCGATAAAATAACAGTA
* *
234109 ATGTGCAGTGCCAATCACCCAATATAGATTCAAGAGCGATACAATAACAGTA
1 ATGTGCAGTGACAATCACCCAATATAGATTCAAGAGCGATAAAATAACAGTA
234161 A
1 A
234162 AGACGGTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (52 bp):
ATGTGCAGTGACAATCACCCAATATAGATTCAAGAGCGATAAAATAACAGTA
Found at i:241569 original size:83 final size:84
Alignment explanation
Indices: 241429--241593 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 84
241419 TGTCTGATTC
* *
241429 CACCATTGTCATGAGGAGGTCTAGTCTTAAGTTCTGGATGCCAATGTCGATGTCAATGGCCTACT
1 CACCATTGTCATGAGGAGGTCTAGTCTTAAGTTCTGGATGCCAATGTCGATGTCAATGACCTACA
241494 ATGGAGAACCCGTGACGCG
66 ATGGAGAACCCGTGACGCG
* *
241513 CACCATTGTCATGAGGAGGTGTAGTC-TAGGTTCTGGATGCCAATGTCGATGTCAATGACCTACA
1 CACCATTGTCATGAGGAGGTCTAGTCTTAAGTTCTGGATGCCAATGTCGATGTCAATGACCTACA
*
241577 ATGGAGAATCCGTGACG
66 ATGGAGAACCCGTGACG
241594 GGCTAAGGAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 51 0.67
84 25 0.33
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (84 bp):
CACCATTGTCATGAGGAGGTCTAGTCTTAAGTTCTGGATGCCAATGTCGATGTCAATGACCTACA
ATGGAGAACCCGTGACGCG
Found at i:241865 original size:10 final size:9
Alignment explanation
Indices: 241824--241872 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
241814 CAAATTTTAA
241824 AAAATTAATT
1 AAAA-TAATT
241834 -AAATAATT
1 AAAATAATT
241842 AAAATAATT
1 AAAATAATT
241851 AAAATCAATTT
1 AAAAT-AA-TT
*
241862 AAATTAATT
1 AAAATAATT
241871 AA
1 AA
241873 TTTAATCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 5 0.14
9 20 0.57
10 4 0.11
11 6 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAATAATT
Found at i:241877 original size:9 final size:9
Alignment explanation
Indices: 241860--241903 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
241850 TAAAATCAAT
*
241860 TTAAATTAA
1 TTAATTTAA
241869 TTAATTTAA
1 TTAATTTAA
*
241878 TCAATTTAA
1 TTAATTTAA
*
241887 TTATTTTAA
1 TTAATTTAA
241896 TT-ATTTAA
1 TTAATTTAA
241904 AAAATAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
8 5 0.17
9 25 0.83
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TTAATTTAA
Found at i:241897 original size:23 final size:23
Alignment explanation
Indices: 241826--241886 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 23
241816 AATTTTAAAA
* *
241826 AATTAATTAAAT-AA-TTAAAAT
1 AATTAATTTAATCAATTTAAATT
241847 AATTAA---AATCAATTTAAATT
1 AATTAATTTAATCAATTTAAATT
241867 AATTAATTTAATCAATTTAA
1 AATTAATTTAATCAATTTAA
241887 TTATTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 12 0.35
21 6 0.18
23 11 0.32
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTAATTTAATCAATTTAAATT
Found at i:241969 original size:28 final size:28
Alignment explanation
Indices: 241938--242010 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 28
241928 CATAAATGTT
241938 ATAATATATTATATAATATATAATATAA
1 ATAATATATTATATAATATATAATATAA
** *
241966 ATAACGTATTATAT--TATATAATTTAA
1 ATAATATATTATATAATATATAATATAA
* *
241992 AT-TTATAATATA-AATATAT
1 ATAATATATTATATAATATAT
242011 TTTATTTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
25 6 0.17
26 18 0.50
28 12 0.33
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (28 bp):
ATAATATATTATATAATATATAATATAA
Found at i:242033 original size:27 final size:28
Alignment explanation
Indices: 241986--242041 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
241976 ATATTATATA
*
241986 ATTTAAATTTATAATATAAATATATTTT
1 ATTTAAATTTATAATATAAATATAATTT
*
242014 ATTTATATTATATAA-A-AAATATAATTT
1 ATTTAAATT-TATAATATAAATATAATTT
242041 A
1 A
242042 AAAGAGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTAAATTTATAATATAAATATAATTT
Found at i:243521 original size:43 final size:43
Alignment explanation
Indices: 243460--243541 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
243450 TGTTGGTTAT
*
243460 CCTACAGTTCCAGAGCTTTTTACATTTAAGTCACCATGAGTCA
1 CCTACAATTCCAGAGCTTTTTACATTTAAGTCACCATGAGTCA
*
243503 CCTACAATTCCAGAGCTTTTTGCATTTAAGTCACCATGA
1 CCTACAATTCCAGAGCTTTTTACATTTAAGTCACCATGA
243542 CTTCGTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (43 bp):
CCTACAATTCCAGAGCTTTTTACATTTAAGTCACCATGAGTCA
Found at i:246322 original size:101 final size:101
Alignment explanation
Indices: 246217--246413 Score: 331
Period size: 101 Copynumber: 2.0 Consensus size: 101
246207 CTTATTGTAA
* * *
246217 TTTATATGAAAATTATTTTTTATCCCTTATTTATGTTTATATTTAATCATATCAATTTACCATTT
1 TTTATATGAAAATTAATTTTTATCCCTTATTTATGTTTATATTTAATCATATCAATATACAATTT
*
246282 TATTATTTTTTTAGTAAACCTATATTTAGATACAAT
66 TATAATTTTTTTAGTAAACCTATATTTAGATACAAT
* *
246318 TTTATGTGAAAATTAATTTTTGTCCCTTATTTATGTTTATATTTAATCATATCAATATACAATTT
1 TTTATATGAAAATTAATTTTTATCCCTTATTTATGTTTATATTTAATCATATCAATATACAATTT
*
246383 TCTAATTTTTTTAGTAAACCTATATTTAGAT
66 TATAATTTTTTTAGTAAACCTATATTTAGAT
246414 TGTGATAAGA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (101 bp):
TTTATATGAAAATTAATTTTTATCCCTTATTTATGTTTATATTTAATCATATCAATATACAATTT
TATAATTTTTTTAGTAAACCTATATTTAGATACAAT
Found at i:252304 original size:34 final size:34
Alignment explanation
Indices: 252235--252449 Score: 236
Period size: 34 Copynumber: 6.4 Consensus size: 34
252225 TAAGTTTGAT
* *
252235 TTGTTGATTAAAT-GGTGATTTGATAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * **
252268 TTGTTGATTAAATGGGTGATTTGGTGGTTTGTCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* ***
252302 TTGTTGACTAAATGGAAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
252336 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
252370 TTATTGATTAAATAGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
252404 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
252438 TTGTTGATTAAA
1 TTGTTGATTAAA
252450 CGGTGGTTTT
Statistics
Matches: 153, Mismatches: 27, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
33 16 0.10
34 137 0.90
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:252377 original size:102 final size:101
Alignment explanation
Indices: 252235--252449 Score: 304
Period size: 102 Copynumber: 2.1 Consensus size: 101
252225 TAAGTTTGAT
** * * * * **
252235 TTGTTGATTAAATGGTGATTTGATAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGT
1 TTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTAC
252300 CATTGTTGACTAAATGGAAAATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGAAAATTTGGTAGCTTACCA
*
252336 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
* * * *
252401 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGAAAATTTGGTAGCTTACCA
252438 TTGTTGATTAAA
1 TTGTTGATTAAA
252450 CGGTGGTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 14 0.14
102 86 0.86
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGAAAATTTGGTAGCTTACCA
Found at i:256920 original size:34 final size:34
Alignment explanation
Indices: 256863--257081 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
256853 AAGTGGGAGA
*
256863 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
256896 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
256930 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* ** *
256964 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACT
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
256998 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
257032 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
257066 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
257082 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 142 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:257012 original size:102 final size:101
Alignment explanation
Indices: 256863--257081 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
256853 AAGTGGGAGA
** * * * *
256863 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
256928 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
256964 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACTATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
257029 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
257066 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
257082 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:262627 original size:13 final size:13
Alignment explanation
Indices: 262609--262654 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
262599 TAACTTAATA
262609 TATATTTAATATT
1 TATATTTAATATT
262622 TATATTATAATATT
1 TATATT-TAATATT
262636 ATATATTT-ATATTT
1 -TATATTTAATA-TT
262650 TATAT
1 TATAT
262655 GATAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 14 0.47
14 10 0.33
15 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATATTTAATATT
Found at i:262842 original size:19 final size:18
Alignment explanation
Indices: 262818--262872 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
262808 TACTCAAATT
262818 TTTTTAAATAATAAATAAA
1 TTTTTAAAT-ATAAATAAA
*
262837 TTTTTAAATTTAAATAAA
1 TTTTTAAATATAAATAAA
*
262855 TATTTTAATCTATAAATA
1 T-TTTTAA-ATATAAATA
262873 CCTATAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.29
19 15 0.48
20 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTAAATATAAATAAA
Found at i:263233 original size:2 final size:2
Alignment explanation
Indices: 263226--263259 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
263216 ACACTCCTGC
263226 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
263260 CATTTACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265456 original size:21 final size:21
Alignment explanation
Indices: 265432--265472 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
265422 TATAAGATTA
265432 AGATTTAACAA-ATTAATTATT
1 AGATTTAACAATA-TAATTATT
*
265453 AGATTTAGCAATATAATTAT
1 AGATTTAACAATATAATTAT
265473 ATTTATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
AGATTTAACAATATAATTATT
Found at i:265851 original size:21 final size:21
Alignment explanation
Indices: 265825--265865 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
265815 CATTTAATTT
* *
265825 TTTTATTTATTTAAATATATC
1 TTTTATATATATAAATATATC
*
265846 TTTTATATATATATATATAT
1 TTTTATATATATAAATATAT
265866 ATATAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATATATATAAATATATC
Found at i:268014 original size:31 final size:30
Alignment explanation
Indices: 267976--268052 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 30
267966 TATGATATTT
* * *
267976 TTTTATATTTTAATTATTTTTTATATACAA
1 TTTTATATTTTAATTATATTATATATAAAA
*
268006 TATTTATATTATATAATTATATTATATTTAAAA
1 T-TTTATATT-T-TAATTATATTATATATAAAA
268039 TTATTATATTTTAA
1 TT-TTATATTTTAA
268053 AAATTTTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 1 0.03
31 11 0.28
32 3 0.08
33 24 0.62
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTATATTTTAATTATATTATATATAAAA
Found at i:268017 original size:18 final size:18
Alignment explanation
Indices: 267996--268048 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
267986 TAATTATTTT
267996 TTATATACAATAT-TTATA
1 TTATATA-AATATATTATA
*
268014 TTATATAATTATATTATA
1 TTATATAAATATATTATA
268032 TT-TA-AAAT-TATTATA
1 TTATATAAATATATTATA
268047 TT
1 TT
268049 TTAAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 9 0.28
16 3 0.09
17 6 0.19
18 14 0.44
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATAAATATATTATA
Found at i:268045 original size:15 final size:16
Alignment explanation
Indices: 268025--268054 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
268015 TATATAATTA
268025 TATTATA-TTTAAAAT
1 TATTATATTTTAAAAT
268040 TATTATATTTTAAAA
1 TATTATATTTTAAAA
268055 ATTTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATATTTTAAAAT
Found at i:268760 original size:44 final size:45
Alignment explanation
Indices: 268669--268762 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 45
268659 TTTTAAAAAA
* * * *
268669 TATTCTTAAAAAAGTATCTACTTATTTTTTAAAAAACTTCACGTT
1 TATTCTTAAAAAACTATCCACTTATTATTTAAAAAACTTCACATT
*
268714 TATTCTT-AAAAACTATCCATTTA-TATTTAAAACAACTTTCA-ATT
1 TATTCTTAAAAAACTATCCACTTATTATTTAAAA-AAC-TTCACATT
268758 TATTC
1 TATTC
268763 AGTAACTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
43 8 0.19
44 23 0.55
45 11 0.26
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (45 bp):
TATTCTTAAAAAACTATCCACTTATTATTTAAAAAACTTCACATT
Found at i:269566 original size:18 final size:17
Alignment explanation
Indices: 269543--269590 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
269533 TTTAAAATAA
269543 AATTTATTTTTATTTAAT
1 AATTTATTTTTATTT-AT
*
269561 ATTTTATTTTTATTTAT
1 AATTTATTTTTATTTAT
*
269578 AATTTAATTTTAT
1 AATTTATTTTTAT
269591 GTATTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTATTTTTATTTAT
Found at i:270429 original size:14 final size:16
Alignment explanation
Indices: 270391--270471 Score: 52
Period size: 14 Copynumber: 5.3 Consensus size: 16
270381 TGTTACCTTT
*
270391 ATATTATTTTTATATA
1 ATATTATATTTATATA
270407 ATAATTATATTTA-A-A
1 AT-ATTATATTTATATA
270422 ATATTATATATT-TAT-
1 ATATTATAT-TTATATA
270437 AT-TTAT-TTTA-AT-
1 ATATTATATTTATATA
*
270449 ATATTAATAATTTATATT
1 ATATT-AT-ATTTATATA
270467 ATATT
1 ATATT
270472 TTTATCTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
12 6 0.11
13 3 0.06
14 13 0.25
15 8 0.15
16 7 0.13
17 11 0.21
18 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTATATTTATATA
Found at i:270446 original size:27 final size:27
Alignment explanation
Indices: 270411--270473 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
270401 TATATAATAA
270411 TTATATTTAAAATATT-ATATATTTATAT
1 TTAT-TTTAAAATATTAATA-ATTTATAT
*
270439 TTATTTTAATATATTAATAATTTATAT
1 TTATTTTAAAATATTAATAATTTATAT
270466 TATATTTT
1 T-TATTTT
270474 TATCTATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTTTAAAATATTAATAATTTATAT
Found at i:270451 original size:22 final size:22
Alignment explanation
Indices: 270388--270452 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
270378 TCATGTTACC
*
270388 TTTATA-TTATTTTTATATAATA
1 TTTATATTTATTTTAATAT-ATA
* *** *
270410 ATTATATTTAAAATATTATATA
1 TTTATATTTATTTTAATATATA
270432 TTTATATTTATTTTAATATAT
1 TTTATATTTATTTTAATATAT
270453 TAATAATTTA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATATTTATTTTAATATATA
Found at i:270452 original size:20 final size:20
Alignment explanation
Indices: 270422--270476 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
270412 TATATTTAAA
270422 ATATTATATATTTAT-ATTT
1 ATATTATATATTTATAATTT
* *
270441 ATTTTAATATATTAATAATTT
1 ATATT-ATATATTTATAATTT
*
270462 ATATTATATTTTTAT
1 ATATTATATATTTAT
270477 CTATATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 17 0.59
21 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTATATATTTATAATTT
Found at i:271373 original size:15 final size:16
Alignment explanation
Indices: 271347--271376 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
271337 AACCTAGTAA
271347 ATTTATAGTAAAAATT
1 ATTTATAGTAAAAATT
271363 ATTTA-AGTAAAAAT
1 ATTTATAGTAAAAAT
271377 ATAATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTTATAGTAAAAATT
Found at i:271657 original size:16 final size:16
Alignment explanation
Indices: 271637--271678 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
271627 ACTCAAATAA
* *
271637 AAATTTTATTTAAATT
1 AAATTTAATATAAATT
*
271653 TAATTTAATATAAATT
1 AAATTTAATATAAATT
271669 AAATTTAATA
1 AAATTTAATA
271679 AATAAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTAATATAAATT
Found at i:273578 original size:10 final size:10
Alignment explanation
Indices: 273563--273605 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
273553 CCTTCCATTC
273563 TTCTTTTTCT
1 TTCTTTTTCT
273573 TTC-TTTTCT
1 TTCTTTTTCT
*
273582 TTCTCTTTCT
1 TTCTTTTTCT
*
273592 TTTTTTTTCT
1 TTCTTTTTCT
273602 TTCT
1 TTCT
273606 CTCCTTTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:273583 original size:15 final size:15
Alignment explanation
Indices: 273563--273605 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
273553 CCTTCCATTC
273563 TTCTTTTTCTTTCTT
1 TTCTTTTTCTTTCTT
*
273578 TTCTTTCTCTTTCTT
1 TTCTTTTTCTTTCTT
273593 TT-TTTTTCTTTCT
1 TTCTTTTTCTTTCT
273606 CTCCTTTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCTTTTTCTTTCTT
Found at i:273585 original size:22 final size:22
Alignment explanation
Indices: 273544--273605 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
273534 ACACATAATT
* * *
273544 TTTTTCTTTCCTTCCATTCTTC
1 TTTTTCTTTCTTTTCTTTCTTC
273566 TTTTTCTTTCTTTTCTTTC-TC
1 TTTTTCTTTCTTTTCTTTCTTC
273587 TTTCTT-TTT-TTTTCTTTCT
1 TTT-TTCTTTCTTTTCTTTCT
273606 CTCCTTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.26
21 8 0.23
22 18 0.51
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTCTTTCTTTTCTTTCTTC
Found at i:274121 original size:2 final size:2
Alignment explanation
Indices: 274114--274144 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
274104 CTTCTAAACC
274114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274145 AACTCTCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:277109 original size:27 final size:29
Alignment explanation
Indices: 277077--277144 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
277067 TTTTAAATAA
* *
277077 ATTAAAAAAATTT-AACTATTTATT-TA-
1 ATTAAAAAAATTTAAACCATTAATTATAT
*
277103 ATATAAAAAACTTTAAACCATTAATTATAT
1 AT-TAAAAAAATTTAAACCATTAATTATAT
277133 ATTAAAAAAATT
1 ATTAAAAAAATT
277145 AATATTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.06
27 10 0.29
28 9 0.26
29 11 0.32
30 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTAAAAAAATTTAAACCATTAATTATAT
Found at i:277146 original size:28 final size:26
Alignment explanation
Indices: 277076--277146 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
277066 ATTTTAAATA
* * *
277076 AATTAAAAAAATTTAACTATTTATTT
1 AATTAAAAAAATTAAACCATTAATTT
*
277102 AATATAAAAAACTTTAAACCATTAATTAT
1 AAT-TAAAAAA-ATTAAACCATTAATT-T
277131 ATATTAAAAAAATTAA
1 A-ATTAAAAAAATTAA
277147 TATTCTCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 3 0.08
27 7 0.19
28 15 0.42
29 9 0.25
30 2 0.06
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTAAAAAAATTAAACCATTAATTT
Found at i:278310 original size:17 final size:18
Alignment explanation
Indices: 278284--278338 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
278274 GAAAAAAAAT
*
278284 TAAAATATAATATA-ATA
1 TAAAAAATAATATACATA
278301 TAAAAAATAATA-ACATA
1 TAAAAAATAATATACATA
*
278318 -ATAAAAATACATATATATA
1 TA-AAAAATA-ATATACATA
278337 TA
1 TA
278339 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 2 0.06
17 21 0.68
18 3 0.10
19 4 0.13
20 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAAATAATATACATA
Found at i:278318 original size:20 final size:18
Alignment explanation
Indices: 278285--278324 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
278275 AAAAAAAATT
*
278285 AAAATATAATATAATATAA
1 AAAATATAACATAATA-AA
278304 AAAATAATAACATAATAAA
1 AAAAT-ATAACATAATAAA
278323 AA
1 AA
278325 TACATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATATAACATAATAAA
Found at i:278370 original size:20 final size:19
Alignment explanation
Indices: 278347--278400 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
278337 TATATATATA
278347 TATATATATATATTAAAATT
1 TATATATA-ATATTAAAATT
* * *
278367 TATATATAACCATCAAATTT
1 TATATATAA-TATTAAAATT
278387 TATATATAATATTA
1 TATATATAATATTA
278401 TTATAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATATAATATTAAAATT
Found at i:278374 original size:2 final size:2
Alignment explanation
Indices: 278328--278359 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
278318 ATAAAAATAC
278328 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
278360 TAAAATTTAT
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:278875 original size:21 final size:19
Alignment explanation
Indices: 278850--279010 Score: 103
Period size: 17 Copynumber: 8.7 Consensus size: 19
278840 TAAATAAAAA
278850 ATTTATATATATTTATATCAT
1 ATTTATATATATTTA-AT-AT
278871 ATTTATATAT-TTTAATAT
1 ATTTATATATATTTAATAT
*
278889 ATTATATTTATATTTAA-A-
1 ATT-TATATATATTTAATAT
*
278907 ATTTATATAT-TTAAATA-
1 ATTTATATATATTTAATAT
*
278924 ATTTTTA-ATATATTAATA-
1 ATTTATATATAT-TTAATAT
*
278942 ATTTATAT-TATATAA-AT
1 ATTTATATATATTTAATAT
*
278959 A-TTATA-CTATTT-ATAT
1 ATTTATATATATTTAATAT
*
278975 TTTTATATTATATTTATATTAT
1 ATTTATA-TATATTTA-A-TAT
*
278997 TTTTATATTATATT
1 ATTTATA-TATATT
279011 CACACCTTAC
Statistics
Matches: 115, Mismatches: 10, Indels: 29
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.01
16 18 0.16
17 23 0.20
18 22 0.19
19 14 0.12
20 9 0.08
21 11 0.10
22 17 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTATATATATTTAATAT
Found at i:278898 original size:44 final size:45
Alignment explanation
Indices: 278850--279010 Score: 154
Period size: 44 Copynumber: 3.6 Consensus size: 45
278840 TAAATAAAAA
*
278850 ATTTATA-TATATTTATATCATATTTATATATTTTAATATATTAT
1 ATTTATATTATATTTATATTATATTTATATATTTTAATATATTAT
* * *
278894 ATTTATATTTAAAATT-TA-TATATTTAAATAATTTTTAATATATTAAT
1 ATTTATA-TTATATTTATATTATATTTATAT-A-TTTTAATATATT-AT
**
278941 AATTTATATTATATAAATATTATACTATT-TATATTTT--TATATTAT
1 -ATTTATATTATATTTATATTATA-T-TTATATATTTTAATATATTAT
*
278986 ATTTATATTATTTTTATATTATATT
1 ATTTATATTATATTTATATTATATT
279011 CACACCTTAC
Statistics
Matches: 95, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 36 0.38
45 5 0.05
46 23 0.24
47 6 0.06
48 13 0.14
49 5 0.05
50 3 0.03
51 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (45 bp):
ATTTATATTATATTTATATTATATTTATATATTTTAATATATTAT
Found at i:278902 original size:11 final size:11
Alignment explanation
Indices: 278850--279010 Score: 94
Period size: 11 Copynumber: 15.3 Consensus size: 11
278840 TAAATAAAAA
278850 ATTTATA-TAT
1 ATTTATATTAT
*
278860 ATTTATATCAT
1 ATTTATATTAT
278871 ATTTATA-TAT
1 ATTTATATTAT
*
278881 TTTAATATATTAT
1 ATT--TATATTAT
*
278894 ATTTATATTTAA
1 ATTTATA-TTAT
*
278906 AATT-TA-TAT
1 ATTTATATTAT
*
278915 ATTTA-AATA-
1 ATTTATATTAT
* *
278924 ATTTTTAATAT
1 ATTTATATTAT
278935 A-TTA-A-TA-
1 ATTTATATTAT
278942 ATTTATATTAT
1 ATTTATATTAT
**
278953 ATAAATATTAT
1 ATTTATATTAT
278964 ACTATT-TA-TAT
1 A-T-TTATATTAT
*
278975 TTTTATATTAT
1 ATTTATATTAT
278986 ATTTATATTAT
1 ATTTATATTAT
*
278997 TTTTATATTAT
1 ATTTATATTAT
279008 ATT
1 ATT
279011 CACACCTTAC
Statistics
Matches: 116, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
7 1 0.01
8 5 0.04
9 14 0.12
10 24 0.21
11 54 0.47
12 13 0.11
13 5 0.04
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:278941 original size:18 final size:18
Alignment explanation
Indices: 278906--278959 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
278896 TTATATTTAA
*
278906 AATTTAT-ATATTTAAAT
1 AATTTATAATATATAAAT
* *
278923 AATTTTTAATATATTAAT
1 AATTTATAATATATAAAT
*
278941 AATTTATATTATATAAAT
1 AATTTATAATATATAAAT
278959 A
1 A
278960 TTATACTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTTATAATATATAAAT
Found at i:281599 original size:32 final size:32
Alignment explanation
Indices: 281553--281615 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
281543 GAAAATTGAA
* *
281553 AAGATAGCTCGACAGTTAAGGAAGGAGACTAT
1 AAGATAACTCGACAGTTAAGGAAGAAGACTAT
*
281585 AAGATAACTTGACAGTTAAGGAAGAAGACTA
1 AAGATAACTCGACAGTTAAGGAAGAAGACTA
281616 AGCAAATGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.19
Consensus pattern (32 bp):
AAGATAACTCGACAGTTAAGGAAGAAGACTAT
Found at i:286741 original size:1 final size:1
Alignment explanation
Indices: 286735--286761 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
286725 CACCAATGTT
286735 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
286762 GAGGCTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:288064 original size:22 final size:22
Alignment explanation
Indices: 288038--288108 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
288028 TTAATTTTTA
288038 ATTTTATATTATAAAAATAAAT
1 ATTTTATATTATAAAAATAAAT
*
288060 ATTTTAT-TT-TAAATTAATAAAA
1 ATTTTATATTATAAA--AATAAAT
* * *
288082 AATTTATAATACTATAAA-AAAT
1 ATTTTATATTA-TAAAAATAAAT
288104 ATTTT
1 ATTTT
288109 TTTAATTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 4 0.11
21 2 0.05
22 26 0.68
23 3 0.08
25 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTTATATTATAAAAATAAAT
Found at i:289859 original size:21 final size:22
Alignment explanation
Indices: 289835--289886 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
289825 CACAATCATT
289835 ATTAATTTTAATT-TTATCAA-A
1 ATTAATTTTAATTATTAT-AATA
*
289856 ATTAATTTT-TTTATTATAATA
1 ATTAATTTTAATTATTATAATA
289877 ATTAATTTTA
1 ATTAATTTTA
289887 GTATACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAATTTTAATTATTATAATA
Found at i:290275 original size:2 final size:2
Alignment explanation
Indices: 290270--290294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
290260 GACTGTCATT
290270 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 T
290295 GATTTGCAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:290381 original size:21 final size:22
Alignment explanation
Indices: 290342--290382 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
290332 TTAGCATTAA
290342 TATTTTAACTAATTAATTATTT
1 TATTTTAACTAATTAATTATTT
290364 TATTTT-A-TAATATAATTAT
1 TATTTTAACTAAT-TAATTAT
290383 ATATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTAACTAATTAATTATTT
Found at i:290389 original size:22 final size:22
Alignment explanation
Indices: 290341--290389 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
290331 ATTAGCATTA
290341 ATATTTTAACTAATTAATTATT
1 ATATTTTAACTAATTAATTATT
*
290363 TTATTTT-A-TAATATAATTATAT
1 ATATTTTAACTAAT-TAATTAT-T
290385 ATATT
1 ATATT
290390 ATTTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.17
21 8 0.35
22 11 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTTAACTAATTAATTATT
Found at i:290446 original size:18 final size:18
Alignment explanation
Indices: 290423--290475 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
290413 TTTAATATTT
290423 ATATTATATTAATTAAAA
1 ATATTATATTAATTAAAA
*
290441 ATATTAT-TT--TTAATAT
1 ATATTATATTAATTAA-AA
*
290457 ATATT-TAATAATTAAAA
1 ATATTATATTAATTAAAA
290474 AT
1 AT
290476 TAAATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 5 0.18
18 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTATATTAATTAAAA
Found at i:290498 original size:8 final size:8
Alignment explanation
Indices: 290463--290501 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
290453 ATATATATTT
290463 AATAATTA
1 AATAATTA
290471 AA-AATTA
1 AATAATTA
*
290478 AATTATATA
1 AATAAT-TA
290487 AATAATTA
1 AATAATTA
290495 AATAATT
1 AATAATT
290502 TTAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.26
8 13 0.48
9 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATAATTA
Found at i:290510 original size:27 final size:26
Alignment explanation
Indices: 290448--290515 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
290438 AAAATATTAT
* *
290448 TTTTAATATATATTTAATAATTAAAAA
1 TTTTAATTTATA-TAAATAATTAAAAA
*
290475 --TTAAATTATATAAATAATTAAATAA
1 TTTTAATTTATATAAATAATTAAA-AA
*
290500 TTTTAATTTATTTAAA
1 TTTTAATTTATATAAA
290516 ATTTAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 11 0.33
25 10 0.30
27 12 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTTAATTTATATAAATAATTAAAAA
Found at i:290518 original size:25 final size:25
Alignment explanation
Indices: 290448--290518 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 25
290438 AAAATATTAT
290448 TTTTAATATATATTTAATAATTAAAAA
1 TTTTAAT-T-TATTTAATAATTAAAAA
* *
290475 --TTAAATTATATAAATAATTAAATAA
1 TTTTAATTTAT-TTAATAATTAAA-AA
290500 TTTTAATTTATTTAA-AATT
1 TTTTAATTTATTTAATAATT
290519 TAACATACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
23 3 0.08
24 12 0.33
25 10 0.28
26 3 0.08
27 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTAATTTATTTAATAATTAAAAA
Found at i:290586 original size:9 final size:9
Alignment explanation
Indices: 290574--290610 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
290564 AATTAAATAA
*
290574 ATATAAATT
1 ATATAAAAT
290583 ATATAAAAT
1 ATATAAAAT
290592 ATTATAAAAT
1 A-TATAAAAT
290602 ATATAAAAT
1 ATATAAAAT
290611 TGATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATAAAAT
Found at i:290589 original size:19 final size:19
Alignment explanation
Indices: 290568--290610 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
290558 TAATTAAATT
*
290568 AAATAAATATAAATTATATA
1 AAAT-AATATAAAATATATA
*
290588 AAATATTATAAAATATATA
1 AAATAATATAAAATATATA
290607 AAAT
1 AAAT
290611 TGATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAATATAAAATATATA
Found at i:290654 original size:2 final size:2
Alignment explanation
Indices: 290647--290672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
290637 GAACTTCTTC
290647 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
290673 GCTAAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291388 original size:16 final size:15
Alignment explanation
Indices: 291340--291393 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
291330 AAGATTTAAT
291340 TTTTTATCTAAACTA
1 TTTTTATCTAAACTA
291355 TTTTCTGAGT-TAAA-TA
1 TTTT-T-A-TCTAAACTA
291371 TTTTTATCTAAATCTA
1 TTTTTATCTAAA-CTA
291387 TTTTTAT
1 TTTTTAT
291394 AGATTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 5 0.15
16 16 0.48
17 5 0.15
18 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (15 bp):
TTTTTATCTAAACTA
Found at i:291810 original size:10 final size:10
Alignment explanation
Indices: 291795--291841 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
291785 ATATTAATTT
291795 TTATAATATA
1 TTATAATATA
291805 TTATAATAT-
1 TTATAATATA
291814 TTATATATATA
1 TTATA-ATATA
291825 TTTATAATATA
1 -TTATAATATA
*
291836 ATATAA
1 TTATAA
291842 AATCTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 5 0.15
10 18 0.55
11 5 0.15
12 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTATAATATA
Found at i:291941 original size:14 final size:13
Alignment explanation
Indices: 291908--291942 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
291898 TAACTATTTA
*
291908 ATTAAAATAATTG
1 ATTAAATTAATTG
291921 ATTAAATTAATTG
1 ATTAAATTAATTG
291934 ATTTAAATT
1 A-TTAAATT
291943 TATCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (13 bp):
ATTAAATTAATTG
Found at i:293658 original size:21 final size:22
Alignment explanation
Indices: 293619--293660 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
293609 CAATATTTAT
293619 ATATTTTTATAATTAAATAAAA
1 ATATTTTTATAATTAAATAAAA
293641 ATATTATTT-TAA-TAAATAAA
1 ATATT-TTTATAATTAAATAAA
293661 TAATTCTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTTTTATAATTAAATAAAA
Found at i:294971 original size:40 final size:40
Alignment explanation
Indices: 294920--295006 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
294910 TTGCTATCTG
* * *
294920 GATTGATTTAGCGGCGTTTT-CATGTAAAAT-ACCGCTATAT
1 GATTTATTTAGCGACGTTTTACATG-AAAATGA-CACTATAT
294960 GATTTATTTAGCGACGTTTTACATGAAAATGACACTATAT
1 GATTTATTTAGCGACGTTTTACATGAAAATGACACTATAT
*
295000 GAATTAT
1 GATTTAT
295007 CTTGGGCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (40 bp):
GATTTATTTAGCGACGTTTTACATGAAAATGACACTATAT
Found at i:295206 original size:22 final size:24
Alignment explanation
Indices: 295181--295232 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
295171 TTTTTAAATG
*
295181 ATATTT-ATTCT-TAATATTTATT
1 ATATTTAATTCTATAATATTTATA
*
295203 ATATTTAATTGTAATAATATTTATA
1 ATATTTAATTCT-ATAATATTTATA
295228 ATATT
1 ATATT
295233 CCATGATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 4 0.16
25 15 0.60
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATATTTAATTCTATAATATTTATA
Found at i:295968 original size:2 final size:2
Alignment explanation
Indices: 295961--295992 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
295951 ACAAAAAGCA
295961 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
295993 GTTTGTGAAC
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:297263 original size:19 final size:18
Alignment explanation
Indices: 297239--297276 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
297229 TATTCAATCT
297239 TTTTTAAATATTAAATAAA
1 TTTTTAAAT-TTAAATAAA
297258 TTTTTAAATTTAAATAAA
1 TTTTTAAATTTAAATAAA
297276 T
1 T
297277 ATCTATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAATTTAAATAAA
Found at i:297647 original size:2 final size:2
Alignment explanation
Indices: 297640--297667 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
297630 CACCTCCTAC
297640 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
297668 CATTCACAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:297808 original size:2 final size:2
Alignment explanation
Indices: 297801--297831 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
297791 TAGAATTTCA
*
297801 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
297832 ATGCTAGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:300822 original size:34 final size:35
Alignment explanation
Indices: 300784--300860 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
300774 TGCGGAGATT
*
300784 TTTTATATAATTTATCTTAGTAATTAAA-TA-TAAA
1 TTTTATATAATTTAT-TTAGAAATTAAATTATTAAA
* *
300818 TTTTAAATTTATTTATTTAGAAATTAAATTATTAAA
1 TTTTATA-TAATTTATTTAGAAATTAAATTATTAAA
300854 -TTTATAT
1 TTTTATAT
300861 TTATCATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
34 18 0.50
35 14 0.39
36 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTTATATAATTTATTTAGAAATTAAATTATTAAA
Found at i:300863 original size:35 final size:35
Alignment explanation
Indices: 300784--300864 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
300774 TGCGGAGATT
* *
300784 TTTTATA-TAATTTATCTTAGTAATTAAATATAAA
1 TTTTATATTTATTTATCTTAGAAATTAAATATAAA
*
300818 TTTTAAATTTATTTAT-TTAGAAATTAAATTATTAAA
1 TTTTATATTTATTTATCTTAGAAATTAAA-TA-TAAA
300854 -TTTATATTTAT
1 TTTTATATTTAT
300865 CATATATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 17 0.43
35 19 0.47
36 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTTATATTTATTTATCTTAGAAATTAAATATAAA
Found at i:302852 original size:21 final size:21
Alignment explanation
Indices: 302815--302854 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
302805 CGCAGCCTGT
*
302815 CCTTTAGCTTTAGATTTTTGC
1 CCTTTAGCTTTACATTTTTGC
*
302836 CCTTTAGCTTTTCATTTTT
1 CCTTTAGCTTTACATTTTT
302855 TCTCTCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.57
Consensus pattern (21 bp):
CCTTTAGCTTTACATTTTTGC
Found at i:303229 original size:27 final size:23
Alignment explanation
Indices: 303168--303211 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
303158 AAAAAAAACC
303168 TTCCAATTTATTCATAAAAATAA
1 TTCCAATTTATTCATAAAAATAA
303191 TTCCAATTTATTCATAAAAAT
1 TTCCAATTTATTCATAAAAAT
303212 TACCTTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCCAATTTATTCATAAAAATAA
Found at i:303822 original size:7 final size:7
Alignment explanation
Indices: 303810--303849 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
303800 CTTAATAATG
303810 AAAAATA
1 AAAAATA
303817 AAAAATA
1 AAAAATA
303824 AAAAATA
1 AAAAATA
303831 AAAAATA
1 AAAAATA
303838 AAAAATA
1 AAAAATA
303845 AAAAA
1 AAAAA
303850 AGAAAGAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:305108 original size:27 final size:26
Alignment explanation
Indices: 305042--305139 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 26
305032 TTTGATAATC
305042 TATATATTTATATTATT-TTT--ATAT
1 TATATATTTATATT-TTATTTAAATAT
305066 TAT-TATGTTATAATTTTATTTAAAATAT
1 TATATAT-TTAT-ATTTTATTT-AAATAT
305094 TATATATTTATA-TTTATTTTAATATAT
1 TATATATTTATATTTTA-TTTAA-ATAT
305121 TA-ATAATTTATATTTTATT
1 TATAT-ATTTATATTTTATT
305140 AATGTCTATA
Statistics
Matches: 63, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
23 3 0.05
24 9 0.14
25 6 0.10
26 8 0.13
27 19 0.30
28 15 0.24
29 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (26 bp):
TATATATTTATATTTTATTTAAATAT
Found at i:305123 original size:8 final size:7
Alignment explanation
Indices: 305042--305165 Score: 53
Period size: 6 Copynumber: 19.1 Consensus size: 7
305032 TTTGATAATC
305042 TATATAT
1 TATATAT
305049 T-TATAT
1 TATATAT
305055 TAT-T-T
1 TATATAT
305060 T-TATAT
1 TATATAT
*
305066 TATTATGT
1 TA-TATAT
305074 TATA-AT
1 TATATAT
*
305080 TTTAT-T
1 TATATAT
*
305086 TAAAATAT
1 T-ATATAT
305094 TATATAT
1 TATATAT
305101 T-TATAT
1 TATATAT
*
305107 T-TATTT
1 TATATAT
305113 TAATATAT
1 T-ATATAT
305121 TA-ATAAT
1 TATAT-AT
305128 T-TATAT
1 TATATAT
305134 T-T-TAT
1 TATATAT
*
305139 TA-ATGT
1 TATATAT
305145 CTATATA-
1 -TATATAT
305152 TATATA-
1 TATATAT
305158 TATATAT
1 TATATAT
305165 T
1 T
305166 TTCGCGTCTT
Statistics
Matches: 90, Mismatches: 10, Indels: 34
0.67 0.07 0.25
Matches are distributed among these distances:
4 1 0.01
5 7 0.08
6 46 0.51
7 21 0.23
8 15 0.17
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.60
Consensus pattern (7 bp):
TATATAT
Found at i:305150 original size:52 final size:53
Alignment explanation
Indices: 305039--305167 Score: 135
Period size: 52 Copynumber: 2.5 Consensus size: 53
305029 AAATTTGATA
*
305039 ATCTATATATTTATA-TTATTTTTATATTATTATGTTATAATTTTATTTAAAAT
1 ATCTATATATTTATATTTATTTTTATATTATAATGTTATAATTTTATTT-AAAT
305092 AT-TATATATTTATATTTATTTTAATATATTAATAAT-TTAT-ATTTTA-TT-AAT
1 ATCTATATATTTATATTTATTTT--TATATT-ATAATGTTATAATTTTATTTAAAT
* * *
305143 GTCTATATATATATATATATATTTT
1 ATCTATATATTTATATTTAT-TTTT
305168 CGCGTCTTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
51 5 0.08
52 27 0.41
53 14 0.21
54 6 0.09
55 10 0.15
56 4 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (53 bp):
ATCTATATATTTATATTTATTTTTATATTATAATGTTATAATTTTATTTAAAT
Found at i:305543 original size:24 final size:23
Alignment explanation
Indices: 305476--305545 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
305466 TGCAAATATC
305476 ATAAGATATATT-AATTTTTT-AT
1 ATAA-ATATATTAAATTTTTTAAT
305498 AT-AA-ATATTAAATATATATTTAAT
1 ATAAATATATTAAAT-T-T-TTTAAT
305522 ATAAATATATTTAAATTTTTTAAT
1 ATAAATATA-TTAAATTTTTTAAT
305546 TTTTTTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
19 5 0.12
20 4 0.10
21 2 0.05
22 3 0.08
23 3 0.08
24 10 0.25
25 3 0.08
26 4 0.10
27 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
ATAAATATATTAAATTTTTTAAT
Found at i:306636 original size:20 final size:22
Alignment explanation
Indices: 306597--306640 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
306587 CGTGATATGT
*
306597 AATATAATTATAAAATAATTTA
1 AATATAATTATAAAAAAATTTA
306619 AATATAA-TA-AAAAAAATTTA
1 AATATAATTATAAAAAAATTTA
306639 AA
1 AA
306641 ATTTAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATAATTATAAAAAAATTTA
Found at i:309490 original size:23 final size:21
Alignment explanation
Indices: 309456--309498 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
309446 AATTATATGA
309456 TAAAAACACATAAAAAATAAT
1 TAAAAACACATAAAAAATAAT
309477 TAAAATACAACATAAAAAATAA
1 TAAAA-AC-ACATAAAAAATAA
309499 GATAAACACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAAAACACATAAAAAATAAT
Found at i:310198 original size:19 final size:20
Alignment explanation
Indices: 310176--310224 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
310166 AAAAATTAAA
* *
310176 AATAATTAAAATATAATAC-
1 AATAATAAAAAAATAATACT
310195 AAT-ATAAAAAAATAATACT
1 AATAATAAAAAAATAATACT
310214 AAT-ATAAAAAA
1 AATAATAAAAAA
310225 TATATGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AATAATAAAAAAATAATACT
Found at i:310204 original size:18 final size:20
Alignment explanation
Indices: 310183--310228 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
310173 AAAAATAATT
310183 AAAATATAATAC-AATATAA
1 AAAATATAATACTAATATAA
310202 AAAA-ATAATACTAATATAA
1 AAAATATAATACTAATATAA
310221 AAAATATA
1 AAAATATA
310229 TGTATGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.28
19 15 0.60
20 3 0.12
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATATAATACTAATATAA
Found at i:310753 original size:26 final size:26
Alignment explanation
Indices: 310712--310808 Score: 90
Period size: 26 Copynumber: 3.7 Consensus size: 26
310702 TAGATAACAT
310712 AATTT-ATATATTTATA-TTATAATTA
1 AATTTAATATATTTATATTTAT-ATTA
*
310737 AATTTAATATATTTATATTTATGTTA
1 AATTTAATATATTTATATTTATATTA
* ** *
310763 ATTTTAATATATCAATAATTTATAATA
1 AATTTAATATATTTAT-ATTTATATTA
* *
310790 TATTCTATTATATTTATAT
1 AATT-TAATATATTTATAT
310809 ATTACTTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
25 5 0.09
26 27 0.47
27 16 0.28
28 9 0.16
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (26 bp):
AATTTAATATATTTATATTTATATTA
Found at i:310756 original size:15 final size:14
Alignment explanation
Indices: 310713--310758 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
310703 AGATAACATA
310713 ATTTATATATTTAT
1 ATTTATATATTTAT
*
310727 A-TTATA-A-TTAA
1 ATTTATATATTTAT
310738 ATTTAATATATTTAT
1 ATTT-ATATATTTAT
310753 ATTTAT
1 ATTTAT
310759 GTTAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
11 4 0.15
12 3 0.12
13 8 0.31
14 4 0.15
15 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATATATTTAT
Found at i:310821 original size:19 final size:18
Alignment explanation
Indices: 310787--310823 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
310777 ATAATTTATA
310787 ATATATTCTATTATATTT
1 ATATATTCTATTATATTT
*
310805 ATATATTACTTTTATATTT
1 ATATATT-CTATTATATTT
310824 TATTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATATTCTATTATATTT
Found at i:311584 original size:11 final size:11
Alignment explanation
Indices: 311568--311606 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
311558 TAATACTTTA
311568 AATATAAATAT
1 AATATAAATAT
*
311579 AATATAAAAAT
1 AATATAAATAT
311590 AATATAAATAT
1 AATATAAATAT
*
311601 TATATA
1 AATATA
311607 TTTTAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:311930 original size:5 final size:5
Alignment explanation
Indices: 311920--312051 Score: 52
Period size: 5 Copynumber: 28.4 Consensus size: 5
311910 TTTTATAAAT
* * *
311920 TTATA TTATA TT-TA -TATA TTTTA TTATA TCATAA TTATA TT-TA ATATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA
* * * * * * *
311968 TTTTA -TAT- TTTTA TTA-A TAAT- TTATA TCATA -TAAA TTTTA TAATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * *
312013 TT-TA -TATA TTTTA TTTTA -TATT TTATT TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
312052 TTAATTATTA
Statistics
Matches: 91, Mismatches: 24, Indels: 24
0.65 0.17 0.17
Matches are distributed among these distances:
3 2 0.02
4 25 0.27
5 60 0.66
6 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:311973 original size:16 final size:15
Alignment explanation
Indices: 311925--312045 Score: 65
Period size: 14 Copynumber: 7.8 Consensus size: 15
311915 TAAATTTATA
311925 TTATATTTATATATT
1 TTATATTTATATATT
* *
311940 TTAT-TATATCATA-A
1 TTATATTTAT-ATATT
311954 TTATATTTAATATATT
1 TTATATTT-ATATATT
*
311970 TTATATTTTTATTAATAAT
1 TTATA--TTTA-T-ATATT
* *
311989 TTATATCATATAAATT
1 TTATAT-TTATATATT
312005 TTATAATATT-TATATAT
1 TTAT-AT-TTATATAT-T
312022 TT-TATTT-TATATT
1 TTATATTTATATATT
312035 TTAT-TTTATAT
1 TTATATTTATAT
312046 TATATTTTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 27
0.68 0.09 0.22
Matches are distributed among these distances:
13 6 0.07
14 19 0.23
15 14 0.17
16 19 0.23
17 9 0.11
18 6 0.07
19 9 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:312025 original size:9 final size:9
Alignment explanation
Indices: 311910--312026 Score: 57
Period size: 9 Copynumber: 12.7 Consensus size: 9
311900 TTTGACTTTT
311910 TTTTATA-A
1 TTTTATATA
*
311918 ATTTATATTA
1 TTTTATA-TA
311928 TATTTATATA
1 T-TTTATATA
311938 TTTTATTATA
1 TTTTA-TATA
* *
311948 TCATAATTATA
1 T-TTTA-TATA
*
311959 TTTAATATA
1 TTTTATATA
311968 TTTTATAT-
1 TTTTATATA
311976 TTTTATTAATA
1 TTTTA-T-ATA
*
311987 ATTTATATCA
1 TTTTATAT-A
*
311997 ---TATAAA
1 TTTTATATA
312003 TTTTATA-A
1 TTTTATATA
312011 TATTTATATA
1 T-TTTATATA
312021 TTTTAT
1 TTTTAT
312027 TTTATATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 13 0.15
9 33 0.38
10 18 0.21
11 18 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTATATA
Found at i:312041 original size:17 final size:17
Alignment explanation
Indices: 312019--312064 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
312009 AATATTTATA
312019 TATTTTATTTTATATTT
1 TATTTTATTTTATATTT
*
312036 TATTTTATATTATATTT
1 TATTTTATTTTATATTT
312053 TAATTATTATTT
1 T-ATT-TTATTT
312065 AAATCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 17 0.68
18 3 0.12
19 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTATTTTATATTT
Found at i:312744 original size:11 final size:11
Alignment explanation
Indices: 312721--312878 Score: 70
Period size: 11 Copynumber: 14.7 Consensus size: 11
312711 AAATTTAAAA
312721 ATTTATA-TAT
1 ATTTATATTAT
312731 ATTTATATTAT
1 ATTTATATTAT
312742 ATTTATA-TAT
1 ATTTATATTAT
312752 -TTTATA-TAT
1 ATTTATATTAT
*
312761 -TATA-ATTAT
1 ATTTATATTAT
*
312770 ATTTAAAATTTAT
1 ATTT-ATA-TTAT
* * *
312783 ATATTAAAATAA
1 AT-TTATATTAT
312795 ATTT-TAATGTAAT
1 ATTTAT-AT-T-AT
*
312808 ATATAATATTAT
1 AT-TTATATTAT
* *
312820 A--TAAATTTT
1 ATTTATATTAT
*
312829 A-TCATATTAT
1 ATTTATATTAT
312839 ATTTATATTAT
1 ATTTATATTAT
312850 ATTT-TGATTAT
1 ATTTAT-ATTAT
312861 -TTTATATTAT
1 ATTTATATTAT
*
312871 ATTCATAT
1 ATTTATAT
312879 CTTACCTTAA
Statistics
Matches: 115, Mismatches: 16, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
8 1 0.01
9 21 0.18
10 27 0.23
11 38 0.33
12 9 0.08
13 13 0.11
14 5 0.04
15 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:313348 original size:6 final size:6
Alignment explanation
Indices: 313337--313400 Score: 76
Period size: 6 Copynumber: 10.3 Consensus size: 6
313327 TAGACTCTGA
* *
313337 TAAAAT TAAAAT TAATAT TAAAAT ATATAA- TATAAAT ATAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT -TAAAAT TA-AAAT -TAAAAT TAAAAT
313387 TAAAAT TAAAAT TA
1 TAAAAT TAAAAT TA
313401 TTAATATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 2 0.04
6 38 0.76
7 8 0.16
8 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:313379 original size:32 final size:32
Alignment explanation
Indices: 313339--313411 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
313329 GACTCTGATA
* *
313339 AAAT-TAAAATTAATATTAAAATATATAA-TAT
1 AAATATAAAATTAAAATTAAAAT-TAAAATTAT
313370 AAATATAAAATTAAAATTAAAATTAAAATTAT
1 AAATATAAAATTAAAATTAAAATTAAAATTAT
*
313402 TAATATAAAA
1 AAATATAAAA
313412 CTATATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATATAAAATTAAAATTAAAATTAAAATTAT
Found at i:313387 original size:38 final size:38
Alignment explanation
Indices: 313336--313410 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
313326 CTAGACTCTG
*
313336 ATAAAATTAAAATTAATATTAAAA-TATATAATATAAAT
1 ATAAAATTAAAATTAAAATTAAAATTAT-TAATATAAAT
313374 ATAAAATTAAAATTAAAATTAAAATTATTAATATAAA
1 ATAAAATTAAAATTAAAATTAAAATTATTAATATAAA
313411 ACTATATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 32 0.91
39 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (38 bp):
ATAAAATTAAAATTAAAATTAAAATTATTAATATAAAT
Found at i:313829 original size:2 final size:2
Alignment explanation
Indices: 313822--313850 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
313812 GAAAAAGGAA
313822 AG AG 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 AG AG A
313851 AACGCTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:318489 original size:4 final size:4
Alignment explanation
Indices: 318482--318515 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
318472 TAATTATTTG
318482 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
318516 CCTTTTACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:318976 original size:15 final size:16
Alignment explanation
Indices: 318947--318980 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
318937 ATAAATTATA
*
318947 AATATGCTTTTATAAT
1 AATATGCTTTAATAAT
318963 AATAT-CTTTAATAAT
1 AATATGCTTTAATAAT
318978 AAT
1 AAT
318981 TTTTATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATGCTTTAATAAT
Found at i:319069 original size:22 final size:22
Alignment explanation
Indices: 319023--319076 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
319013 TTATTATCTT
*
319023 TTTTTTTATTTTATTAAAATTA
1 TTTTTTTATATTATTAAAATTA
319045 TTTTTTTA-ATTA-TAATAATTAA
1 TTTTTTTATATTATTAA-AATT-A
*
319067 TTTTATTATA
1 TTTTTTTATA
319077 CATTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.11
21 7 0.26
22 16 0.59
23 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTTTATATTATTAAAATTA
Found at i:319074 original size:18 final size:18
Alignment explanation
Indices: 319030--319090 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
319020 CTTTTTTTTT
*
319030 ATTTTATTAAAATTATT-
1 ATTTTATTATAATTATTA
* *
319047 TTTTTAATTATAATAATTA
1 ATTTT-ATTATAATTATTA
319066 ATTTTATTATACATTATTA
1 ATTTTATTATA-ATTATTA
*
319085 TTTTTA
1 ATTTTA
319091 ATTTAATCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.11
18 16 0.46
19 15 0.43
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATTATAATTATTA
Found at i:319555 original size:21 final size:21
Alignment explanation
Indices: 319514--319557 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
319504 TTAATTAATC
*
319514 AATTATTTTATTTTATAATAT
1 AATTATTTTATTATATAATAT
*
319535 AATTATATTTATTATGT-ATAT
1 AATTAT-TTTATTATATAATAT
319556 AA
1 AA
319558 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AATTATTTTATTATATAATAT
Found at i:319660 original size:16 final size:16
Alignment explanation
Indices: 319621--319692 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 16
319611 ATATATATTT
*
319621 AATA-ATAAAAAATAA
1 AATATATAAATAATAA
*
319636 AATTATATAAATAATTA
1 AA-TATATAAATAATAA
319653 AATATATAAATTATATAA
1 AATATATAAA-TA-ATAA
319671 AATATTATAAAATATATAA
1 AATA-TAT-AAATA-ATAA
319690 AAT
1 AAT
319693 TAATTTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.04
16 10 0.21
17 13 0.27
18 7 0.15
19 13 0.27
20 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATATAAATAATAA
Found at i:319681 original size:19 final size:18
Alignment explanation
Indices: 319632--319692 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
319622 ATAATAAAAA
319632 ATAAAAT-TATATAAATA-
1 ATAAAATAT-TATAAATAT
*
319649 ATTAAATA-TATAAATTAT
1 ATAAAATATTATAAA-TAT
319667 ATAAAATATTATAAAATAT
1 ATAAAATATTAT-AAATAT
319686 ATAAAAT
1 ATAAAAT
319693 TAATTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 6 0.16
17 8 0.22
18 7 0.19
19 13 0.35
20 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAATATTATAAATAT
Found at i:319691 original size:9 final size:9
Alignment explanation
Indices: 319621--319692 Score: 73
Period size: 9 Copynumber: 8.3 Consensus size: 9
319611 ATATATATTT
319621 AATA-ATAA
1 AATATATAA
319629 AA-A-ATAA
1 AATATATAA
319636 AAT-TATATA
1 AATATATA-A
*
319645 AATA-ATTA
1 AATATATAA
319653 AATATATAA
1 AATATATAA
*
319662 ATTATATAA
1 AATATATAA
319671 AATATTATAA
1 AATA-TATAA
319681 AATATATAA
1 AATATATAA
319690 AAT
1 AAT
319693 TAATTTAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
7 7 0.13
8 10 0.19
9 28 0.52
10 9 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AATATATAA
Found at i:320878 original size:18 final size:18
Alignment explanation
Indices: 320850--320900 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
320840 ATATTAATTC
320850 TTATAATATATTATATTAT
1 TTAT-ATATATTATATTAT
*
320869 TTATATATA-TAAATTTAT
1 TTATATATATTATA-TTAT
*
320887 TTATA-ATATAATAT
1 TTATATATATTATAT
320901 AAAATCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATATATTATATTAT
Found at i:320978 original size:17 final size:18
Alignment explanation
Indices: 320958--320991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
320948 CACAATTGAG
*
320958 ATAATT-ATTTAATTAAA
1 ATAATTAATTAAATTAAA
320975 ATAATTAATTAAATTAA
1 ATAATTAATTAAATTAA
320992 TTGATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAATTAAATTAAA
Found at i:321940 original size:19 final size:19
Alignment explanation
Indices: 321916--321961 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
321906 TTTAATGATT
*
321916 ATATTAA-ATAAATATATAA
1 ATATTAATATAAA-AAATAA
321935 ATATTAATATAAAAAATAA
1 ATATTAATATAAAAAATAA
321954 ATATTAAT
1 ATATTAAT
321962 TATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATTAATATAAAAAATAA
Found at i:326127 original size:11 final size:11
Alignment explanation
Indices: 326111--326177 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 11
326101 TTTAAATATT
326111 ATATAATTATA
1 ATATAATTATA
326122 ATATAA-TA-A
1 ATATAATTATA
*
326131 AAATAATTA-A
1 ATATAATTATA
326141 ATATAA--ATA
1 ATATAATTATA
326150 ATATAA-TATA
1 ATATAATTATA
326160 A-AT-ATT-TA
1 ATATAATTATA
326168 ATA-AATTATA
1 ATATAATTATA
326178 TAATATAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
8 5 0.11
9 20 0.43
10 16 0.34
11 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAATTATA
Found at i:326139 original size:28 final size:28
Alignment explanation
Indices: 326104--326177 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
326094 CAATAATTTT
326104 AAAT-ATTATATAATTATAATATAATAA
1 AAATAATTATATAATTATAATATAATAA
*
326131 AAATAATTAAATATAA--ATAATATAATAT
1 AAATAATT--ATATAATTATAATATAATAA
*
326159 AAATATTTA-ATAAATTATA
1 AAATAATTATAT-AATTATA
326178 TAATATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
25 2 0.05
26 3 0.08
27 4 0.10
28 24 0.62
30 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATAATTATATAATTATAATATAATAA
Found at i:326149 original size:20 final size:18
Alignment explanation
Indices: 326113--326197 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 18
326103 TAAATATTAT
326113 ATAATTATAATATAATAAAA
1 ATAATTA-AATATAAT-AAA
*
326133 ATAATTAAATATAAATAAT
1 ATAATTAAATAT-AATAAA
* *
326152 ATAATATAAATAT-TTAAT
1 ATAAT-TAAATATAATAAA
326170 A-AATT--ATATAATATAA
1 ATAATTAAATATAATA-AA
*
326186 ATTATTAAATAT
1 ATAATTAAATAT
326198 TAAAATTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
14 4 0.08
15 2 0.04
16 3 0.06
17 6 0.11
18 5 0.09
19 16 0.30
20 17 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATTAAATATAATAAA
Found at i:326171 original size:25 final size:25
Alignment explanation
Indices: 326103--326227 Score: 101
Period size: 25 Copynumber: 4.7 Consensus size: 25
326093 ACAATAATTT
*
326103 TAAATATTATATAATTATAATATAATA
1 TAAATATTAAATAA--ATAATATAATA
*
326130 AAAATAATTAAATATAAATAATATAATA
1 TAAAT-ATT-AA-ATAAATAATATAATA
* *
326158 TAAATATTTAATAAATTATATAATA
1 TAAATATTAAATAAATAATATAATA
*
326183 TAAATTATTAAATATTAA-AATTTAA-A
1 TAAA-TATTAAATA--AATAATATAATA
326209 TAAATATATAATATAAATA
1 TAAATAT-TAA-ATAAATA
326228 GTCTGATCTA
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
25 23 0.28
26 18 0.22
27 15 0.19
28 20 0.25
29 1 0.01
30 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAATATTAAATAAATAATATAATA
Found at i:326183 original size:39 final size:39
Alignment explanation
Indices: 326140--326227 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
326130 AAAATAATTA
326140 AATATAAATAA-TATAATA-TAAATATTT-AATAAATTATAT
1 AATATAAATAATTA-AATATTAAA-ATTTAAATAAA-TATAT
*
326179 AATATAAATTATTAAATATTAAAATTTAAATAAATATAT
1 AATATAAATAATTAAATATTAAAATTTAAATAAATATAT
326218 AATATAAATA
1 AATATAAATA
326228 GTCTGATCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
39 32 0.73
40 12 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (39 bp):
AATATAAATAATTAAATATTAAAATTTAAATAAATATAT
Found at i:326185 original size:14 final size:14
Alignment explanation
Indices: 326122--326226 Score: 75
Period size: 14 Copynumber: 7.9 Consensus size: 14
326112 TATAATTATA
* *
326122 ATATAATAAAAATA
1 ATATAATATAAATT
*
326136 AT-TAAATATAAATA
1 ATAT-AATATAAATT
326150 ATATAATATAAA-T
1 ATATAATATAAATT
*
326163 AT-TTA-ATAAATT
1 ATATAATATAAATT
326175 ATATAATATAAATT
1 ATATAATATAAATT
326189 AT-TAAATATTAAA--
1 ATAT-AATA-TAAATT
*
326202 ATTTAA-ATAAA-T
1 ATATAATATAAATT
326214 ATATAATATAAAT
1 ATATAATATAAAT
326227 AGTCTGATCT
Statistics
Matches: 75, Mismatches: 5, Indels: 22
0.74 0.05 0.22
Matches are distributed among these distances:
11 9 0.12
12 11 0.15
13 15 0.20
14 35 0.47
15 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:326492 original size:22 final size:23
Alignment explanation
Indices: 326454--326542 Score: 80
Period size: 22 Copynumber: 4.0 Consensus size: 23
326444 TCTTTGAAAC
* *
326454 TATATTTAT-TATATTTTATTTT
1 TATATTTATATATATTTTAATAT
326476 TATATTTATATAT-TTTTAATAT
1 TATATTTATATATATTTTAATAT
* *
326498 TATAATTATATATA---AAATAT
1 TATATTTATATATATTTTAATAT
*
326518 TATAAATTTATATAAATTTTAATAT
1 TAT--ATTTATATATATTTTAATAT
326543 ATTAATCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
20 8 0.15
22 37 0.70
23 3 0.06
25 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTTATATATATTTTAATAT
Found at i:326500 original size:16 final size:15
Alignment explanation
Indices: 326454--326501 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
326444 TCTTTGAAAC
326454 TATATTTATTATATT-
1 TATATTT-TTATATTA
326469 T-TATTTTTATATTTA
1 TATATTTTTATA-TTA
326484 TATATTTTTAATATTA
1 TATATTTTT-ATATTA
326500 TA
1 TA
326502 ATTATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.17
14 7 0.24
15 2 0.07
16 12 0.41
17 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTTATATTA
Found at i:326510 original size:30 final size:30
Alignment explanation
Indices: 326454--326510 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
326444 TCTTTGAAAC
* * *
326454 TATATTTATTATATTTTATTTTTATATTTA
1 TATATTTATTATATTATAATTATATATTTA
326484 TATATTT-TTAATATTATAATTATATAT
1 TATATTTATT-ATATTATAATTATATAT
326511 AAAATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TATATTTATTATATTATAATTATATATTTA
Found at i:326516 original size:20 final size:20
Alignment explanation
Indices: 326493--326533 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
326483 ATATATTTTT
326493 AATATTAT-AATTATATATAA
1 AATATTATAAATT-TATATAA
326513 AATATTATAAATTTATATAA
1 AATATTATAAATTTATATAA
326533 A
1 A
326534 TTTTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTATAAATTTATATAA
Found at i:326543 original size:22 final size:23
Alignment explanation
Indices: 326479--326544 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 23
326469 TTATTTTTAT
*
326479 ATTTATAT-ATTTTTAATATTATA
1 ATTTATATAAATTTTAATA-TATA
* *
326502 ATTATATATAAA--ATATTATA-A
1 ATT-TATATAAATTTTAATATATA
326523 ATTTATATAAATTTTAATATAT
1 ATTTATATAAATTTTAATATAT
326545 TAATCATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
20 8 0.24
21 4 0.12
22 8 0.24
23 7 0.21
24 5 0.15
25 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATATAAATTTTAATATATA
Done.