Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold481
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1334154
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 122349 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:733776 original size:31 final size:30
Alignment explanation
Indices: 733730--733823 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
733720 AAGAAACTCA
*
733730 ACCTTATTCCTATAGCTAGTCTGTAATCTG
1 ACCTTATTCCTATAGCTAGTCTTTAATCTG
*
733760 ACCTTATTCCCTATAGCTAATCTTTAATCTG
1 ACCTTATT-CCTATAGCTAGTCTTTAATCTG
*
733791 ATCTTATTCCTATAGCTAGTCTTTAATCTG
1 ACCTTATTCCTATAGCTAGTCTTTAATCTG
733821 ACC
1 ACC
733824 AAAAAAAACC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 31 0.53
31 27 0.47
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (30 bp):
ACCTTATTCCTATAGCTAGTCTTTAATCTG
Found at i:735133 original size:35 final size:35
Alignment explanation
Indices: 735093--735342 Score: 227
Period size: 35 Copynumber: 7.1 Consensus size: 35
735083 CAGAAAACCT
735093 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
* * * * *
735128 ATGTAGGTCAAGGTTAGATGCTGGACAGAAAACCT-
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAA-TTG
* * *
735163 TTGTAGGTCAAGGTAAGACTCTTGATAGGAAATTG
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
* * * * * *
735198 TTATAGGTCAAAGTTAGATGCTGGACAG-AAATCAG
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAAT-TG
735233 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
* * * * * * * *
735268 ATATAGGTTAAAGTTAGATGCTGGACAG-AAATCAG
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAAT-TG
* * *
735303 TTGTTGGTCAAGGTAAGATTCTGGATAGGAAACTG
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
735338 TTGTA
1 TTGTA
735343 CATCAGGGTT
Statistics
Matches: 163, Mismatches: 46, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
34 9 0.06
35 146 0.90
36 8 0.05
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (35 bp):
TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTG
Found at i:735354 original size:140 final size:141
Alignment explanation
Indices: 735093--735368 Score: 410
Period size: 140 Copynumber: 2.0 Consensus size: 141
735083 CAGAAAACCT
* *
735093 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATGTAGGTCAAGGTTAGATGCTGGACAGAA
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
** * * **
735158 AACCTTTGTAGGTCAAGGTAAGACTCTTGATAGGAAATTGTTATAGGTCAAAGTTAGATGCTGGA
66 AACAGTTGTAGGTCAAGGTAAGACTCTGGATAGGAAACTGTTATACATCAAAGTTAGATGCTGGA
735223 -CAGAAATCAG
131 GCAGAAATCAG
*
735233 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTTAAAGTTAGATGCTGGACAGAA
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
* * * * **
735298 ATCAGTTGTTGGTCAAGGTAAGATTCTGGATAGGAAACTGTTGTACATCAGGGTTAGATGCTGGA
66 AACAGTTGTAGGTCAAGGTAAGACTCTGGATAGGAAACTGTTATACATCAAAGTTAGATGCTGGA
735363 GCAGAA
131 GCAGAA
735369 GATGTAGGTC
Statistics
Matches: 120, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
140 115 0.96
141 5 0.04
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (141 bp):
TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
AACAGTTGTAGGTCAAGGTAAGACTCTGGATAGGAAACTGTTATACATCAAAGTTAGATGCTGGA
GCAGAAATCAG
Found at i:735362 original size:70 final size:70
Alignment explanation
Indices: 735093--735330 Score: 377
Period size: 70 Copynumber: 3.4 Consensus size: 70
735083 CAGAAAACCT
* *
735093 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATGTAGGTCAAGGTTAGATGCTGGACAGAA
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
* **
735158 AACCT
66 ATCAG
* * * *
735163 TTGTAGGTCAAGGTAAGACTCTTGATAGGAAATTGTTATAGGTCAAAGTTAGATGCTGGACAGAA
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
735228 ATCAG
66 ATCAG
*
735233 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTTAAAGTTAGATGCTGGACAGAA
1 TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
735298 ATCAG
66 ATCAG
*
735303 TTGTTGGTCAAGGTAAGATTCTGGATAG
1 TTGTAGGTCAAGGTAAGATTCTGGATAG
735331 GAAACTGTTG
Statistics
Matches: 153, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 153 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (70 bp):
TTGTAGGTCAAGGTAAGATTCTGGATAGAAAATTGATATAGGTCAAAGTTAGATGCTGGACAGAA
ATCAG
Found at i:740649 original size:21 final size:21
Alignment explanation
Indices: 740604--740649 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
740594 TGCCAAATTT
**
740604 TATTGAATAACCCCCTTACTT
1 TATTGAATAACCCCCTTACAA
740625 TATTGAATAACCCCC-TATCAA
1 TATTGAATAACCCCCTTA-CAA
740646 TATT
1 TATT
740650 TGCATCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (21 bp):
TATTGAATAACCCCCTTACAA
Found at i:750197 original size:2 final size:2
Alignment explanation
Indices: 750190--750248 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
750180 AAATTCGTGT
750190 TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
750231 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
750249 ATTTCTTGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:757891 original size:2 final size:2
Alignment explanation
Indices: 757884--757929 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
757874 AGTAAAATAC
757884 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
757926 AG AG
1 AG AG
757930 TCTTTTTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:763421 original size:4 final size:4
Alignment explanation
Indices: 763412--763474 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
763402 TATAAAACAC
763412 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
763460 CTAT CTAT CTAT CTA
1 CTAT CTAT CTAT CTA
763475 CAGTAAAACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (4 bp):
CTAT
Found at i:763492 original size:20 final size:20
Alignment explanation
Indices: 763469--763511 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
763459 TCTATCTATC
763469 TATCTACAGTAAAACTCGGT
1 TATCTACAGTAAAACTCGGT
763489 TATCTACAGTAAAACTCGGT
1 TATCTACAGTAAAACTCGGT
763509 TAT
1 TAT
763512 AGAGAATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCTACAGTAAAACTCGGT
Found at i:763562 original size:16 final size:16
Alignment explanation
Indices: 763541--763571 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
763531 ATGGATTTAC
763541 TTCGTTATATCCGTAA
1 TTCGTTATATCCGTAA
763557 TTCGTTATATCCGTA
1 TTCGTTATATCCGTA
763572 TAACGAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (16 bp):
TTCGTTATATCCGTAA
Found at i:764003 original size:4 final size:4
Alignment explanation
Indices: 763994--764061 Score: 136
Period size: 4 Copynumber: 17.0 Consensus size: 4
763984 CGAGTTTTAC
763994 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
764042 TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA
764062 CTGATATATC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TCTA
Found at i:771018 original size:2 final size:2
Alignment explanation
Indices: 771011--771057 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
771001 TCTTGGTAAG
771011 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
771053 TC TC T
1 TC TC T
771058 TTTCAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:771558 original size:20 final size:20
Alignment explanation
Indices: 771533--771580 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
771523 CACATGTTGG
*
771533 TATGTAAATTGTATATATTT
1 TATGTAAATTGTATATATTA
771553 TATGTAAATTGTATATATTA
1 TATGTAAATTGTATATATTA
771573 TATGTAAA
1 TATGTAAA
771581 ACTTAATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
TATGTAAATTGTATATATTA
Found at i:779630 original size:2 final size:2
Alignment explanation
Indices: 779623--779647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
779613 TGGTATGTAA
779623 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 A
779648 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:793032 original size:2 final size:2
Alignment explanation
Indices: 793025--793064 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
793015 NNNNNNNNNN
793025 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
793065 GAGAAAGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:796934 original size:21 final size:21
Alignment explanation
Indices: 796891--796934 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
796881 TTGATTCGAT
* * * *
796891 TTTATTCGCGATTGTTTCTCG
1 TTTATTCGCAATAGTTACGCG
796912 TTTATTCGCAATAGTTACGCG
1 TTTATTCGCAATAGTTACGCG
796933 TT
1 TT
796935 CATTTGCGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (21 bp):
TTTATTCGCAATAGTTACGCG
Found at i:797082 original size:21 final size:22
Alignment explanation
Indices: 797053--797106 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
797043 ACGTTATGCT
* * *
797053 TTTACTCGCGAAT-GTTTCTCG
1 TTTATTCGCGAATAGTTGCGCG
797074 TTTATTCGC-AATAGTTGCGCG
1 TTTATTCGCGAATAGTTGCGCG
*
797095 TTTATTTGCGAA
1 TTTATTCGCGAA
797107 ACTAACGCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTATTCGCGAATAGTTGCGCG
Found at i:797106 original size:42 final size:42
Alignment explanation
Indices: 797005--797107 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
796995 GTATGCAAAG
* *
797005 TGCGCGTTTATTTGTGAAAGTTTCGGGTTTATCCGCAAACGT
1 TGCGCGTTTATTTGCGAAAGTTTCGCGTTTATCCGCAAACGT
** * * * * * *
797047 TATGCTTTTACTCGCGAATGTTTCTCGTTTATTCGCAATA-GT
1 TGCGCGTTTATTTGCGAAAGTTTCGCGTTTATCCGCAA-ACGT
797089 TGCGCGTTTATTTGCGAAA
1 TGCGCGTTTATTTGCGAAA
797108 CTAACGCGTT
Statistics
Matches: 44, Mismatches: 16, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.41
Consensus pattern (42 bp):
TGCGCGTTTATTTGCGAAAGTTTCGCGTTTATCCGCAAACGT
Found at i:799498 original size:2 final size:2
Alignment explanation
Indices: 799491--799521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
799481 TATAACATAA
799491 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
799522 ACCTGAAATA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:801025 original size:2 final size:2
Alignment explanation
Indices: 801018--801103 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
801008 TGCGTTGCAA
801018 CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
801059 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
801101 CT C
1 CT C
801104 GTTGCCTTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 82 0.99
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:803095 original size:21 final size:21
Alignment explanation
Indices: 803049--803095 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
803039 AAAAACCCCA
*
803049 AAAAACACCAAACAAACAAAC
1 AAAAACAACAAACAAACAAAC
* * *
803070 GAAAACAACAAACAAACCAAT
1 AAAAACAACAAACAAACAAAC
803091 AAAAA
1 AAAAA
803096 AAACTCGTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.72, C:0.23, G:0.02, T:0.02
Consensus pattern (21 bp):
AAAAACAACAAACAAACAAAC
Found at i:805718 original size:22 final size:22
Alignment explanation
Indices: 805694--805814 Score: 163
Period size: 22 Copynumber: 5.5 Consensus size: 22
805684 ACGCATTCAA
*
805694 ATGTAGGGACTGAAGCATAG-G
1 ATGTAGGGACTGAGGCATAGAG
*
805715 AATGTAGGAACTGAGGCATAGAG
1 -ATGTAGGGACTGAGGCATAGAG
* *
805738 ATGTAGAGACTGAGGCATAAAG
1 ATGTAGGGACTGAGGCATAGAG
805760 ATGTAGGGACTGAGGCATAGAG
1 ATGTAGGGACTGAGGCATAGAG
* *
805782 ATGCAGGGACTGAGGCATAGAA
1 ATGTAGGGACTGAGGCATAGAG
*
805804 ATATAGGGACT
1 ATGTAGGGACT
805815 ATTGCTAAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
22 86 0.99
23 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.18
Consensus pattern (22 bp):
ATGTAGGGACTGAGGCATAGAG
Found at i:806047 original size:2 final size:2
Alignment explanation
Indices: 806040--806080 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
806030 TTATGTACAT
806040 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
806081 TTTTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:808342 original size:4 final size:4
Alignment explanation
Indices: 808333--808374 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
808323 AATAGTGCTT
*
808333 TTTG TTTG TTTG TTTG TTTG TTGG TTTG TTTG TTT- TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
808375 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:808376 original size:1 final size:1
Alignment explanation
Indices: 808365--808399 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
808355 GGTTTGTTTG
*
808365 TTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
808400 GGGGGGGGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:808376 original size:8 final size:8
Alignment explanation
Indices: 808332--808400 Score: 65
Period size: 7 Copynumber: 9.0 Consensus size: 8
808322 AAATAGTGCT
808332 TTTTGTTTG
1 TTTT-TTTG
*
808341 TTTGTTTG
1 TTTTTTTG
* *
808349 TTTGTTGG
1 TTTTTTTG
*
808357 TTTGTTTG
1 TTTTTTTG
808365 -TTTTTTG
1 TTTTTTTG
808372 TTTTTTT-
1 TTTTTTTG
808379 TTTTTTT-
1 TTTTTTTG
808386 TTTTTTT-
1 TTTTTTTG
808393 TTTTTTTG
1 TTTTTTTG
808401 GGGGGGGGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
7 27 0.50
8 24 0.44
9 3 0.06
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:808380 original size:12 final size:12
Alignment explanation
Indices: 808331--808399 Score: 63
Period size: 12 Copynumber: 6.0 Consensus size: 12
808321 TAAATAGTGC
*
808331 TTTTTGTTTGTT
1 TTTTTGTTTTTT
* *
808343 TGTTTGTTTGTT
1 TTTTTGTTTTTT
** *
808355 GGTTTG-TTTGT
1 TTTTTGTTTTTT
808366 TTTTTGTTTTTT
1 TTTTTGTTTTTT
808378 TTTTT-TTTTTT
1 TTTTTGTTTTTT
808389 TTTTT-TTTTTT
1 TTTTTGTTTTTT
808400 GGGGGGGGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
11 24 0.49
12 25 0.51
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:813594 original size:21 final size:21
Alignment explanation
Indices: 813570--813611 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
813560 ATCAATTCAC
813570 TATTTAAATTATTAATTTTAA
1 TATTTAAATTATTAATTTTAA
* * *
813591 TATTTAACTTTTTACTTTTAA
1 TATTTAAATTATTAATTTTAA
813612 CCATTTTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTAAATTATTAATTTTAA
Found at i:820667 original size:2 final size:2
Alignment explanation
Indices: 820660--820706 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
820650 GTCAATCATT
*
820660 AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
820702 AG AG A
1 AG AG A
820707 TTCCATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:830209 original size:2 final size:2
Alignment explanation
Indices: 830202--830253 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
830192 TTGTGCATTT
830202 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
830244 GA GA GA GA GA
1 GA GA GA GA GA
830254 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:830595 original size:167 final size:167
Alignment explanation
Indices: 830319--830653 Score: 670
Period size: 167 Copynumber: 2.0 Consensus size: 167
830309 NNNNNNCCCC
830319 CCTCCGATGCTAAGTGCCTGTTGTTTTCCTGTAACATTGATTTTGATTGTTCTCTCAATTATTTA
1 CCTCCGATGCTAAGTGCCTGTTGTTTTCCTGTAACATTGATTTTGATTGTTCTCTCAATTATTTA
830384 TTAAATTTTTTGGTGTAAAATCTAATGTACATAACATTTTTATCACTTCTGATCATATTTTTCAT
66 TTAAATTTTTTGGTGTAAAATCTAATGTACATAACATTTTTATCACTTCTGATCATATTTTTCAT
830449 ATAAAAATCGCATTTTTAAATTGCACATATATCAGTT
131 ATAAAAATCGCATTTTTAAATTGCACATATATCAGTT
830486 CCTCCGATGCTAAGTGCCTGTTGTTTTCCTGTAACATTGATTTTGATTGTTCTCTCAATTATTTA
1 CCTCCGATGCTAAGTGCCTGTTGTTTTCCTGTAACATTGATTTTGATTGTTCTCTCAATTATTTA
830551 TTAAATTTTTTGGTGTAAAATCTAATGTACATAACATTTTTATCACTTCTGATCATATTTTTCAT
66 TTAAATTTTTTGGTGTAAAATCTAATGTACATAACATTTTTATCACTTCTGATCATATTTTTCAT
830616 ATAAAAATCGCATTTTTAAATTGCACATATATCAGTT
131 ATAAAAATCGCATTTTTAAATTGCACATATATCAGTT
830653 C
1 C
830654 GAAGTTCCTC
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 168 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (167 bp):
CCTCCGATGCTAAGTGCCTGTTGTTTTCCTGTAACATTGATTTTGATTGTTCTCTCAATTATTTA
TTAAATTTTTTGGTGTAAAATCTAATGTACATAACATTTTTATCACTTCTGATCATATTTTTCAT
ATAAAAATCGCATTTTTAAATTGCACATATATCAGTT
Found at i:835281 original size:2 final size:2
Alignment explanation
Indices: 835274--835310 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
835264 TGAGAAATTA
*
835274 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
835311 TTCTCGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:843382 original size:19 final size:19
Alignment explanation
Indices: 843358--843415 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
843348 AGATGCTGAG
843358 AAGGGGAAAAATAAAAGAC
1 AAGGGGAAAAATAAAAGAC
843377 AAGGGGAAAAATAAAAGAC
1 AAGGGGAAAAATAAAAGAC
843396 AAGGGGAAAAATAAAAGAC
1 AAGGGGAAAAATAAAAGAC
843415 A
1 A
843416 TTGCAAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.64, C:0.05, G:0.26, T:0.05
Consensus pattern (19 bp):
AAGGGGAAAAATAAAAGAC
Found at i:844440 original size:15 final size:15
Alignment explanation
Indices: 844420--844450 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
844410 TTAGGTTTCA
844420 TAAATGATGATTGTC
1 TAAATGATGATTGTC
844435 TAAATGATGATTGTC
1 TAAATGATGATTGTC
844450 T
1 T
844451 GCACAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TAAATGATGATTGTC
Found at i:850631 original size:41 final size:42
Alignment explanation
Indices: 850568--850649 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
850558 CAAATTTTTA
850568 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
1 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
* * *
850610 ATTATTAAGTATA-AAAAGAAAATTACATTTTAACAATGTA
1 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTA
850650 AACAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 26 0.70
42 11 0.30
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (42 bp):
ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
Found at i:861554 original size:32 final size:32
Alignment explanation
Indices: 861508--861571 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
861498 GCTTCGCGTC
861508 GGTTCACAATGGTTTCCTCGGGGTGTCAATTT
1 GGTTCACAATGGTTTCCTCGGGGTGTCAATTT
*
861540 GGTTGACAATGGTTTCCTCGGGGTGTCAATTT
1 GGTTCACAATGGTTTCCTCGGGGTGTCAATTT
861572 CAACTGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.17, G:0.30, T:0.38
Consensus pattern (32 bp):
GGTTCACAATGGTTTCCTCGGGGTGTCAATTT
Found at i:863265 original size:19 final size:20
Alignment explanation
Indices: 863235--863272 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
863225 TCACTGTAAA
863235 ATTTATTCTTTATCTTGTGT
1 ATTTATTCTTTATCTTGTGT
863255 ATTTA-TCTTTATCTTGTG
1 ATTTATTCTTTATCTTGTG
863273 CACTTATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.63
Consensus pattern (20 bp):
ATTTATTCTTTATCTTGTGT
Found at i:863279 original size:19 final size:19
Alignment explanation
Indices: 863241--863279 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
863231 TAAAATTTAT
* *
863241 TCTTTATCTTGTGTATTTA
1 TCTTTATCTTGTGCACTTA
863260 TCTTTATCTTGTGCACTTA
1 TCTTTATCTTGTGCACTTA
863279 T
1 T
863280 TGCCAGTTAC
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:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (19 bp):
TCTTTATCTTGTGCACTTA
Found at i:864658 original size:31 final size:31
Alignment explanation
Indices: 864620--864812 Score: 89
Period size: 32 Copynumber: 5.8 Consensus size: 31
864610 AATGATAGGC
864620 TTACTTTTGAACTGCTCAAGTAAACGTTAAG
1 TTACTTTTGAACTGCTCAAGTAAACGTTAAG
* * ** * *
864651 TTACTTTTGAAATGTTTTAGTAAAAGGTTGGCAGATACA
1 TTACTTTTGAACTGCTCAAGT-AAACGTT-----A-A-G
* * * *
864690 TGTACTTTTGAACTGCTCAAGAAAAAGTTGAT
1 T-TACTTTTGAACTGCTCAAGTAAACGTTAAG
* **
864722 TTACTTTTGAACTACTCAAGAATAAACGTTTGG
1 TTACTTTTGAACTGCTCAAG--TAAACGTTAAG
* * * * **
864755 CCTACTTTTGAACAGTTAAAGTAAACGTTTGG
1 -TTACTTTTGAACTGCTCAAGTAAACGTTAAG
*
864787 TCTACTTTTGTACTGCTCAAGTAAAC
1 T-TACTTTTGAACTGCTCAAGTAAAC
864813 TTTTGAACAG
Statistics
Matches: 119, Mismatches: 30, Indels: 25
0.68 0.17 0.14
Matches are distributed among these distances:
31 35 0.29
32 38 0.32
33 7 0.06
34 15 0.13
37 1 0.01
38 1 0.01
39 7 0.06
40 15 0.13
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (31 bp):
TTACTTTTGAACTGCTCAAGTAAACGTTAAG
Found at i:864809 original size:32 final size:32
Alignment explanation
Indices: 864692--864817 Score: 128
Period size: 32 Copynumber: 3.9 Consensus size: 32
864682 CAGATACATG
* * * *
864692 TACTTTTGAACTGCTCAAGAAAAAG-TTGATT
1 TACTTTTGAACTGCTCAAGTAAACGTTTGGTC
* *
864723 TACTTTTGAACTACTCAAGAATAAACGTTTGGCC
1 TACTTTTGAACTGCTCAAG--TAAACGTTTGGTC
* * *
864757 TACTTTTGAACAGTTAAAGTAAACGTTTGGTC
1 TACTTTTGAACTGCTCAAGTAAACGTTTGGTC
* *
864789 TACTTTTGTACTGCTCAAGTAAACTTTTG
1 TACTTTTGAACTGCTCAAGTAAACGTTTG
864818 AACAGTTAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
31 18 0.24
32 36 0.47
33 4 0.05
34 18 0.24
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (32 bp):
TACTTTTGAACTGCTCAAGTAAACGTTTGGTC
Found at i:864821 original size:53 final size:53
Alignment explanation
Indices: 864758--864907 Score: 264
Period size: 53 Copynumber: 2.8 Consensus size: 53
864748 CGTTTGGCCT
864758 ACTTTTGAACAGTTAAAGTAAACGTTTGGTCTACTTTTGTACTGCTCAAGTAA
1 ACTTTTGAACAGTTAAAGTAAACGTTTGGTCTACTTTTGTACTGCTCAAGTAA
*
864811 ACTTTTGAACAGTTAAAGTAAACGTTTGGTCTTCTTTTGTACTGCTCAAGTAA
1 ACTTTTGAACAGTTAAAGTAAACGTTTGGTCTACTTTTGTACTGCTCAAGTAA
* * *
864864 ACTTTTGAACTGTTAAAGTAAACGTTGGGTCTACTTTTGAACTG
1 ACTTTTGAACAGTTAAAGTAAACGTTTGGTCTACTTTTGTACTG
864908 TAAATGTACA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (53 bp):
ACTTTTGAACAGTTAAAGTAAACGTTTGGTCTACTTTTGTACTGCTCAAGTAA
Found at i:864870 original size:21 final size:21
Alignment explanation
Indices: 864844--864886 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
864834 GTTTGGTCTT
* *
864844 CTTTTGTACTGCTCAAGTAAA
1 CTTTTGAACTGCTAAAGTAAA
*
864865 CTTTTGAACTGTTAAAGTAAA
1 CTTTTGAACTGCTAAAGTAAA
864886 C
1 C
864887 GTTGGGTCTA
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:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
CTTTTGAACTGCTAAAGTAAA
Found at i:864905 original size:32 final size:32
Alignment explanation
Indices: 864864--864935 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
864854 GCTCAAGTAA
864864 ACTTTTGAACTGTTAAA-GTAAACGT-TGGGTCT
1 ACTTTTGAACTG-TAAATGTAAACGTAT-GGTCT
* *
864896 ACTTTTGAACTGTAAATGTACATGTATGGTCT
1 ACTTTTGAACTGTAAATGTAAACGTATGGTCT
864928 ACTTTTGA
1 ACTTTTGA
864936 GCCGCAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 4 0.11
32 31 0.86
33 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (32 bp):
ACTTTTGAACTGTAAATGTAAACGTATGGTCT
Found at i:866018 original size:2 final size:2
Alignment explanation
Indices: 866011--866071 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
866001 GCGTATAGGA
866011 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
866053 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
866072 TGGTACATGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:872062 original size:8 final size:8
Alignment explanation
Indices: 872051--872101 Score: 84
Period size: 8 Copynumber: 6.4 Consensus size: 8
872041 TAAAAAGTTT
872051 ACAGACGG
1 ACAGACGG
*
872059 ACAGACAG
1 ACAGACGG
872067 ACAGACGG
1 ACAGACGG
*
872075 ACAGACAG
1 ACAGACGG
872083 ACAGACGG
1 ACAGACGG
872091 ACAGACGG
1 ACAGACGG
872099 ACA
1 ACA
872102 AAATGTGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.43, C:0.25, G:0.31, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:872067 original size:4 final size:4
Alignment explanation
Indices: 872051--872101 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
872041 TAAAAAGTTT
* * * *
872051 ACAG ACGG ACAG ACAG ACAG ACGG ACAG ACAG ACAG ACGG ACAG ACGG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
872099 ACA
1 ACA
872102 AAATGTGATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.43, C:0.25, G:0.31, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:872072 original size:16 final size:16
Alignment explanation
Indices: 872051--872101 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
872041 TAAAAAGTTT
872051 ACAGACGGACAGACAG
1 ACAGACGGACAGACAG
872067 ACAGACGGACAGACAG
1 ACAGACGGACAGACAG
*
872083 ACAGACGGACAGACGG
1 ACAGACGGACAGACAG
872099 ACA
1 ACA
872102 AAATGTGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.43, C:0.25, G:0.31, T:0.00
Consensus pattern (16 bp):
ACAGACGGACAGACAG
Found at i:877929 original size:13 final size:13
Alignment explanation
Indices: 877911--877937 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
877901 AAACAACACC
877911 TAACGTAAGAATG
1 TAACGTAAGAATG
877924 TAACGTAAGAATG
1 TAACGTAAGAATG
877937 T
1 T
877938 TCAGTTTAGT
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:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (13 bp):
TAACGTAAGAATG
Found at i:878915 original size:10 final size:10
Alignment explanation
Indices: 878900--878924 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
878890 ATTTTTTTTA
878900 AAATTAAATC
1 AAATTAAATC
878910 AAATTAAATC
1 AAATTAAATC
878920 AAATT
1 AAATT
878925 TTTGCTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAATC
Found at i:890310 original size:53 final size:52
Alignment explanation
Indices: 890243--890405 Score: 260
Period size: 53 Copynumber: 3.1 Consensus size: 52
890233 ATCATCTATA
890243 TTTATTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
1 TTTA-TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
890296 TCTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATG--
1 T-TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
* *
890347 TTT-TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT
1 TTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATG-TT
890399 TTTATTA
1 TTTATTA
890406 TTATTTTTTT
Statistics
Matches: 103, Mismatches: 2, Indels: 10
0.90 0.02 0.09
Matches are distributed among these distances:
49 44 0.43
50 2 0.02
51 1 0.01
52 3 0.03
53 50 0.49
54 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (52 bp):
TTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
Found at i:890373 original size:49 final size:49
Alignment explanation
Indices: 890247--890400 Score: 254
Period size: 49 Copynumber: 3.1 Consensus size: 49
890237 TCTATATTTA
890247 TTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTCT
1 TTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATG--T-T
890299 TATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
1 T-TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
* *
890349 TTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTT
1 TTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
890398 TTT
1 TTT
890401 TATTATTATT
Statistics
Matches: 99, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
49 49 0.49
50 2 0.02
51 1 0.01
52 1 0.01
53 46 0.46
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (49 bp):
TTTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTT
Found at i:894536 original size:2 final size:2
Alignment explanation
Indices: 894529--894560 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
894519 AACCATGATG
894529 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
894561 AAATTTGCTC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:901308 original size:2 final size:2
Alignment explanation
Indices: 901301--901350 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
901291 AATTCATTCT
901301 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
901343 GA GA GA GA
1 GA GA GA GA
901351 TTCATATACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:904632 original size:10 final size:9
Alignment explanation
Indices: 904609--904635 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
904599 CAGCTTTAAA
904609 TAAAAATTT
1 TAAAAATTT
904618 TAAAAATTT
1 TAAAAATTT
904627 TAAAAATTT
1 TAAAAATTT
904636 AAATCGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAAAATTT
Found at i:905272 original size:2 final size:2
Alignment explanation
Indices: 905265--905298 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
905255 AAGAAAACAT
905265 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
905299 AAGTTATGTG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:913108 original size:9 final size:9
Alignment explanation
Indices: 913080--913150 Score: 69
Period size: 9 Copynumber: 8.0 Consensus size: 9
913070 ATGAAAATTG
913080 CAAAAAAA-
1 CAAAAAAAC
913088 -AAAAAAGA-
1 CAAAAAA-AC
913096 CAAAAAAAC
1 CAAAAAAAC
913105 C-AAAAAAC
1 CAAAAAAAC
* *
913113 CCAAATAAC
1 CAAAAAAAC
913122 CAAAAAAAAC
1 C-AAAAAAAC
913132 CAAAAAAAC
1 CAAAAAAAC
913141 CAAAATAAAC
1 CAAAA-AAAC
913151 TGACAATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
7 6 0.11
8 10 0.19
9 27 0.50
10 11 0.20
ACGTcount: A:0.76, C:0.20, G:0.01, T:0.03
Consensus pattern (9 bp):
CAAAAAAAC
Found at i:913150 original size:19 final size:18
Alignment explanation
Indices: 913080--913150 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 18
913070 ATGAAAATTG
913080 CAAAAAAA--AAAAAAGA-
1 CAAAAAAACCAAAAAA-AC
913096 CAAAAAAACC-AAAAAAC
1 CAAAAAAACCAAAAAAAC
* *
913113 CCAAATAACCAAAAAAAAC
1 CAAAAAAACC-AAAAAAAC
913132 CAAAAAAACCAAAATAAAC
1 CAAAAAAACCAAAA-AAAC
913151 TGACAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
16 9 0.20
17 13 0.29
18 4 0.09
19 19 0.42
ACGTcount: A:0.76, C:0.20, G:0.01, T:0.03
Consensus pattern (18 bp):
CAAAAAAACCAAAAAAAC
Found at i:916705 original size:174 final size:173
Alignment explanation
Indices: 916415--916757 Score: 634
Period size: 174 Copynumber: 2.0 Consensus size: 173
916405 ACTAAATAAA
916415 ATTTGTTCATCATTTTAAATCAGCTCAGGTTTAAATAATATAAACGAGCATCTTATACAGTAAGA
1 ATTTGTTCATCATTTTAAATCAGCTCAGGTTTAAATAATATAAACGAGCATCTTATACAGTAAGA
916480 AAGACCAAAGGTTAATTGTCTTCGATCAGGTTCGTTTGATATATAAAACAAATGGCAAATTAGCG
66 AAGACCAAAGGTTAATTGTCTTCGATCAGGTTCGTTTGATATATAAAACAAATGGCAAATTAGCG
* *
916545 TTTAATCAGGAAAGTGCTCCTGTGCTTATACATATATATATAT
131 TTTAATCAGGAAAGTGCTCCTCTGCTTATACATAAATATATAT
916588 NATTTGTTCATCATTTTAAATCAGCTCAGGTTTAAATAATATAAACGAGCATCTTATACAGTAAG
1 -ATTTGTTCATCATTTTAAATCAGCTCAGGTTTAAATAATATAAACGAGCATCTTATACAGTAAG
*
916653 -AAGACCAAAGGTTAATTGTCTTCGATCGGGTTCGTTTGATATCATAAAACAAATGGCAAATTAG
65 AAAGACCAAAGGTTAATTGTCTTCGATCAGGTTCGTTTGATAT-ATAAAACAAATGGCAAATTAG
916717 CGTTTAATCAGGAAAGTGCTCCTCTGCTTATACATAAATAT
129 CGTTTAATCAGGAAAGTGCTCCTCTGCTTATACATAAATAT
916758 GTAGCTAGCT
Statistics
Matches: 165, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
173 41 0.25
174 124 0.75
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (173 bp):
ATTTGTTCATCATTTTAAATCAGCTCAGGTTTAAATAATATAAACGAGCATCTTATACAGTAAGA
AAGACCAAAGGTTAATTGTCTTCGATCAGGTTCGTTTGATATATAAAACAAATGGCAAATTAGCG
TTTAATCAGGAAAGTGCTCCTCTGCTTATACATAAATATATAT
Found at i:917336 original size:4 final size:4
Alignment explanation
Indices: 917327--917362 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
917317 AATAATTTCT
917327 GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA
917363 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:921322 original size:18 final size:18
Alignment explanation
Indices: 921299--921450 Score: 270
Period size: 18 Copynumber: 8.4 Consensus size: 18
921289 AAAAACTTAT
921299 ACTTGAGGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
921317 ACTTGAGGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
*
921335 ACTTAAGGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
921353 ACTT-AGGGCTGAGTATTG
1 ACTTGA-GGCTGAGTATTG
921371 ACTTGAGGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
*
921389 ACTTGAAGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
921407 ACTTGAGGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
921425 ACTTGAGGCTGAGTATTG
1 ACTTGAGGCTGAGTATTG
921443 ACTTGAGG
1 ACTTGAGG
921451 AAAGCTGGTG
Statistics
Matches: 129, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
17 1 0.01
18 127 0.98
19 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (18 bp):
ACTTGAGGCTGAGTATTG
Found at i:922145 original size:18 final size:19
Alignment explanation
Indices: 922119--922155 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
922109 TTGAACTGAT
*
922119 ACAAGATCTT-TAAATGTA
1 ACAAAATCTTATAAATGTA
922137 ACAAAATCTTATAAATGTA
1 ACAAAATCTTATAAATGTA
922156 TACCTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
ACAAAATCTTATAAATGTA
Found at i:926044 original size:2 final size:2
Alignment explanation
Indices: 926037--926062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
926027 CATTTGAGTC
926037 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
926063 ATAAATAAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:937059 original size:2 final size:2
Alignment explanation
Indices: 937052--937090 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
937042 ATGTTTGTTT
* *
937052 GA GA GA GA GA AA GA GA GA GA GA GA GA GA -A GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
937091 TTTAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:937688 original size:12 final size:12
Alignment explanation
Indices: 937671--937695 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
937661 TGTATTTGCT
937671 TGATTATCAATA
1 TGATTATCAATA
937683 TGATTATCAATA
1 TGATTATCAATA
937695 T
1 T
937696 TACAAGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGATTATCAATA
Found at i:944885 original size:36 final size:36
Alignment explanation
Indices: 944801--944888 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
944791 TTCCAACTTG
* * *
944801 CGCCAGAGTTCGATTGTACCAAACCAAGCAAACTTC
1 CGCCAGAGTTCGTTTGTACCAAACCAAACAAACCTC
* *
944837 CACCAGAGTTCGTTTGTACCAAACTAAACAAACCTC
1 CGCCAGAGTTCGTTTGTACCAAACCAAACAAACCTC
*
944873 CGCCTGAGTTCGTTTG
1 CGCCAGAGTTCGTTTG
944889 ACGTACTACC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (36 bp):
CGCCAGAGTTCGTTTGTACCAAACCAAACAAACCTC
Found at i:947068 original size:2 final size:2
Alignment explanation
Indices: 947061--947095 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
947051 GGTATAACGG
*
947061 CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
947096 GTTAACTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:953394 original size:437 final size:436
Alignment explanation
Indices: 952549--953918 Score: 2118
Period size: 437 Copynumber: 3.1 Consensus size: 436
952539 ATATTTACAA
* *
952549 GACCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTAAAGTTAGGGAACCACAGGTCTCTAA
1 GACCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTAAAATTAGGGAACCAAAGG-CTCTAA
* * * *
952614 AGTCTTTAATTTGTAGCTCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATATGTTT
65 AGTCTTTAATCTGTAGCCCTTTACTGAAAGATATTTTGTAAAATGTTATAGAAGCAAATATGTTT
*
952679 ATCTCACAGTTATGTATCCAAGCAGTGTAATGATTTTGTCATGTATTACGTAATTAAGGGTTTTT
130 ATCTCACAGTTATGTATCCAAGCAATGTAATGATTTTGTCATGTATTACGTAATTAAGGGTTTTT
*
952744 AGGGGCCAAAAGTCCAAAATTTCAATCACCCATATCTCAGAAAGGAAAAATATTTTGGT-ATGCA
195 AGGGGCCAAAAGTCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTT-GTAATGCA
* *
952808 ACACAGAAGAAAAGTTGTTCAAATTAATGTTCTTAACAATATGAAACCTTCAAAATTTCGTTAAA
259 ATACAGAAGAAAAGTTGTTCAAATTAATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAA
*
952873 CGGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAATGG
324 CGGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGG
* * * * *
952938 TAACAAATTTCTAAACACTTGTTGAATAAAATTTGTTTAGAATTAGAT
389 TAACGATTTTCTAAACACTTGTTGAACAAAATTTGTTAAGAATTAAAT
* *
952986 GACCTTTCATTTGATATCAAGAAAAAGGGGCTGGCCCCTAAAATTAGGGAACCAAATGGCTTTAA
1 GACCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTAAAATTAGGGAACCAAA-GGCTCTAA
* *
953051 AGTCTTTAATCTGTAGCCCTTTAATGAAAGGTATTTTGTAAAATGTTATAGAAGCAAATATGTTT
65 AGTCTTTAATCTGTAGCCCTTTACTGAAAGATATTTTGTAAAATGTTATAGAAGCAAATATGTTT
* * *
953116 ATCTCACAGTTATGTATGCAAGCAATGTAACGATTTTGTCATGTATTACGTAATAAAGGGTTTTT
130 ATCTCACAGTTATGTATCCAAGCAATGTAATGATTTTGTCATGTATTACGTAATTAAGGGTTTTT
*
953181 AGGGGCCAAAAGTCCAAAATTTCGATCACCCATATCTCAGAAAGGAGAAATATTTTGTAATGCAA
195 AGGGGCCAAAAGTCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAA
* * *
953246 TACAGAAGAAAAGTTGTTTAAATTAATGTTCTAAACAATATGCAACCTTCAAAATTTCGTTCAAC
260 TACAGAAGAAAAGTTGTTCAAATTAATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAAC
* * *
953311 GGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTAATATTTCTTCAGAACGGT
325 GGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGT
* *
953376 AACGATTTTCTGAACACTTGTTGAACAAAATTTGTTAAGAAATAAAT
390 AACGATTTTCTAAACACTTGTTGAACAAAATTTGTTAAGAATTAAAT
* * * *
953423 GACCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTTAACTAAGGGGACCAAAGGGCTCTAA
1 GACCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTAAAATTAGGGAACCAAA-GGCTCTAA
* * *
953488 AGTCTTTAATCTGTACCCCTTTACTGTAAGATATTTTGTAAAAGGTTATAGAAGCAAATATGTTT
65 AGTCTTTAATCTGTAGCCCTTTACTGAAAGATATTTTGTAAAATGTTATAGAAGCAAATATGTTT
* * *
953553 ATCTCACAGTTATGTATCCAAGCAATGTAATGATTTTATTATGTGTTACGTAATTAAGGGTTTTT
130 ATCTCACAGTTATGTATCCAAGCAATGTAATGATTTTGTCATGTATTACGTAATTAAGGGTTTTT
* * *
953618 GGGGGCCAAAAGTCCAAAATTTCGGTCCCCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAA
195 AGGGGCCAAAAGTCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAA
* * * *
953683 TACAGAAGAAAAGGTGTTCAAATTTATGTTCTTAACAATATGCAACCTTCAATATGTCGTTAAAC
260 TACAGAAGAAAAGTTGTTCAAATTAATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAAC
*
953748 GGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATGTATCTCCAGAACGGT
325 GGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGT
* *
953813 AACGAATTTT-TAAACACTTGTTG-ACAAAATGTGTTCAGAATTAAAT
390 AACG-ATTTTCTAAACACTTGTTGAACAAAATTTGTTAAGAATTAAAT
* * * * * *
953859 GTCCTTTTATTTGAT-TCAAAGAAAAAAGGGGACTGGCCCCTTAAATTAGGGGATCAAAGG
1 GACCTTTCATTTAATATC-AAG-AAAAAGGGG-CTGGCCCCTAAAATTAGGGAACCAAAGG
953919 GCACTAAAAA
Statistics
Matches: 852, Mismatches: 75, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
435 2 0.00
436 37 0.04
437 783 0.92
438 30 0.04
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (436 bp):
GACCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTAAAATTAGGGAACCAAAGGCTCTAAA
GTCTTTAATCTGTAGCCCTTTACTGAAAGATATTTTGTAAAATGTTATAGAAGCAAATATGTTTA
TCTCACAGTTATGTATCCAAGCAATGTAATGATTTTGTCATGTATTACGTAATTAAGGGTTTTTA
GGGGCCAAAAGTCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAAT
ACAGAAGAAAAGTTGTTCAAATTAATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAACG
GCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTA
ACGATTTTCTAAACACTTGTTGAACAAAATTTGTTAAGAATTAAAT
Found at i:961585 original size:16 final size:16
Alignment explanation
Indices: 961564--961594 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
961554 ATGAATTTAC
961564 TTCGTTATATCCGTAA
1 TTCGTTATATCCGTAA
961580 TTCGTTATATCCGTA
1 TTCGTTATATCCGTA
961595 TAACGAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (16 bp):
TTCGTTATATCCGTAA
Found at i:961889 original size:17 final size:17
Alignment explanation
Indices: 961864--961915 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
961854 TCAAAATCAG
*
961864 TTCGCTATAACCGTAAA
1 TTCGTTATAACCGTAAA
**
961881 TTCGTTATATTCG--AA
1 TTCGTTATAACCGTAAA
961896 TTCGTTATAACCGTGAAA
1 TTCGTTATAACCGT-AAA
961914 TT
1 TT
961916 TTGCAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 13 0.48
17 10 0.37
18 4 0.15
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (17 bp):
TTCGTTATAACCGTAAA
Found at i:965953 original size:165 final size:165
Alignment explanation
Indices: 965681--966212 Score: 752
Period size: 165 Copynumber: 3.2 Consensus size: 165
965671 AGAAATTTTC
* *
965681 AAAAATCTTCTTCTCAAGAACCATAA--AGCCAGGAAAGCTGAAACTTTTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTC-AGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
965744 GGTAGTGTAGATTCAAAGTTATGAAAATCATGACCCCTGGGGGTAGGGTTGGGCCACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTTGGGCCACAATGGGGG
*
965809 TCGAAGTTTTATATAGGAATATATAGAGTAAATCTTT
129 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
965846 AAAAATCTTCTTCTCAGAAACTAATCAGCTAGGTAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
965911 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGG-TGGGGCACAATGGAGGCT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTTGGGCCACAATGG-GGGT
*
965975 CGAAGTTTTACATAGGAATATATAGAGTAAATATTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
966011 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGTAAGTATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
966076 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGTGGGTAGGGTGGGGCCACATTGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTTGGGCCACAAT-------
** *
966141 GGGGGGTTTAAGTTTTACATAGGAATATATAAAGTAAATCTTT
124 -GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
966184 TAAAA---TCTTCTCAGAAACTAATCAGCCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
966213 ATGATTCTTT
Statistics
Matches: 331, Mismatches: 24, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
163 3 0.01
164 17 0.05
165 238 0.72
166 8 0.02
170 24 0.07
173 39 0.12
174 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTTGGGCCACAATGGGGGTC
GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:973317 original size:2 final size:2
Alignment explanation
Indices: 973310--973360 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
973300 TTTTTCCCCA
*
973310 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC -C TC TC TC TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
973350 T- TC -C TC TC TC T
1 TC TC TC TC TC TC T
973361 TTTCCGTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:975380 original size:11 final size:11
Alignment explanation
Indices: 975364--975411 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
975354 ATCGTCGGTG
*
975364 AAAAAAACCCC
1 AAAAAAACCCA
*
975375 AAAAAAACCAA
1 AAAAAAACCCA
975386 AAAAAAACCCA
1 AAAAAAACCCA
* *
975397 ACAACAA-CCA
1 AAAAAAACCCA
975407 AAAAA
1 AAAAA
975412 CCAAATGCCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 6 0.20
11 24 0.80
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACCCA
Found at i:975392 original size:22 final size:22
Alignment explanation
Indices: 975364--975411 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
975354 ATCGTCGGTG
*
975364 AAAAAAACCCCAA-AAAAACCA
1 AAAAAAAACCCAACAAAAACCA
*
975385 AAAAAAAACCCAACAACAACCA
1 AAAAAAAACCCAACAAAAACCA
975407 AAAAA
1 AAAAA
975412 CCAAATGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAAAACCCAACAAAAACCA
Found at i:997614 original size:2 final size:2
Alignment explanation
Indices: 997607--997632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
997597 GTGTNTTCCC
997607 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
997633 GTCTGTGTGT
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:998035 original size:18 final size:18
Alignment explanation
Indices: 997993--998036 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
997983 GGGGTGACTT
*
997993 TACAGTCAAGGGCGACTC
1 TACAGTCAAGGGCGACCC
998011 TACAGTCAAGAGG-GACCC
1 TACAGTCAAG-GGCGACCC
*
998029 TAGAGTCA
1 TACAGTCA
998037 CTGTCACTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (18 bp):
TACAGTCAAGGGCGACCC
Found at i:998845 original size:21 final size:21
Alignment explanation
Indices: 998816--998867 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
998806 TAGTACCGCT
**
998816 GGACTGTACTCCGGTGATGCC
1 GGACTGTACTCCGGTGACACC
* *
998837 GGGCTGTACTCTGGTGACACC
1 GGACTGTACTCCGGTGACACC
998858 GGACTGTACT
1 GGACTGTACT
998868 TCGTCGTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (21 bp):
GGACTGTACTCCGGTGACACC
Found at i:1000348 original size:17 final size:17
Alignment explanation
Indices: 1000326--1000359 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1000316 TCAAAAGCAA
1000326 GGGGTGACTCGACAGTC
1 GGGGTGACTCGACAGTC
*
1000343 GGGGTGACTCTACAGTC
1 GGGGTGACTCGACAGTC
1000360 AAGTACATTA
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:0.18, C:0.24, G:0.38, T:0.21
Consensus pattern (17 bp):
GGGGTGACTCGACAGTC
Found at i:1004512 original size:13 final size:13
Alignment explanation
Indices: 1004494--1004521 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1004484 CCCCGCCTGT
1004494 GCAGTTCAATGAC
1 GCAGTTCAATGAC
1004507 GCAGTTCAATGAC
1 GCAGTTCAATGAC
1004520 GC
1 GC
1004522 GACAACGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (13 bp):
GCAGTTCAATGAC
Found at i:1011565 original size:2 final size:2
Alignment explanation
Indices: 1011560--1011604 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
1011550 ACATTTTTTT
*
1011560 TC TC TC TC TC TC TC TT TC TC TC TC TC TC ATC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC
1011603 TC
1 TC
1011605 ATTGTGACGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1021761 original size:2 final size:2
Alignment explanation
Indices: 1021743--1021786 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1021733 GTGTATACCC
* *
1021743 CT CT GT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1021785 CT
1 CT
1021787 GCGTTTACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1023658 original size:32 final size:32
Alignment explanation
Indices: 1023617--1023710 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
1023607 TTCAGACAAA
**
1023617 GGGGTCATTTTTCTACGTAGAATAATGACTGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCAG
*
1023649 GGGGTCATTTTTCTGCGTAGAATAATGACCAG
1 GGGGTCATTTTTCTACGTAGAATAATGACCAG
* * * *
1023681 GGGGTCATTATTCAACGTCGAAAAATGACC
1 GGGGTCATTTTTCTACGTAGAATAATGACC
1023711 CCCGGTCATT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (32 bp):
GGGGTCATTTTTCTACGTAGAATAATGACCAG
Found at i:1026284 original size:43 final size:43
Alignment explanation
Indices: 1026223--1026308 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1026213 ATAAATACAC
*
1026223 ATAGACATATTACTCTACTATCACATAAACCTGCTCTTTTTTT
1 ATAGACATATTACCCTACTATCACATAAACCTGCTCTTTTTTT
1026266 ATAGACATATTACCCTACTATCACATAAACCTGCTCTTTTTTT
1 ATAGACATATTACCCTACTATCACATAAACCTGCTCTTTTTTT
1026309 TCCGACACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (43 bp):
ATAGACATATTACCCTACTATCACATAAACCTGCTCTTTTTTT
Found at i:1030384 original size:2 final size:2
Alignment explanation
Indices: 1030377--1030438 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
1030367 TATGACATAT
1030377 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
1030419 TC TA TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
1030439 ATTGTAACGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1043077 original size:62 final size:63
Alignment explanation
Indices: 1043001--1043234 Score: 305
Period size: 62 Copynumber: 3.6 Consensus size: 63
1042991 ACCTCTGTTT
1043001 ACCCTGTTTCAGAACAGAGATTTA-TATAGACACAAGGGTCTGTAACCCTCGTAACCCTTGTA
1 ACCCTGTTTCAGAACAGAGATTTAGTATAGACACAAGGGTCTGTAACCCTCGTAACCCTTGTA
1043063 ACCCTGTTTCAGAACAGAGATTTA-TATAGACACAAGGGTCTGTAACCCTCGTAACCCTCGTAAC
1 ACCCTGTTTCAGAACAGAGATTTAGTATAGACACAA-GG---GT----CT-GTAACCCTCGTAAC
1043127 CCTTGTA
57 CCTTGTA
* * *
1043134 ACCCTGTTTCAGAACAGAG-TTTAGTATATAAATAAGGGTCTGTAACCCTCGTAACCCTTGTA
1 ACCCTGTTTCAGAACAGAGATTTAGTATAGACACAAGGGTCTGTAACCCTCGTAACCCTTGTA
* * *
1043196 ACCCTGTTTCAGACCAGAGA-TTAGTATAGAGACATGGGT
1 ACCCTGTTTCAGAACAGAGATTTAGTATAGACACAAGGGT
1043235 TAGTTAGTAT
Statistics
Matches: 153, Mismatches: 8, Indels: 22
0.84 0.04 0.12
Matches are distributed among these distances:
62 89 0.58
63 4 0.03
66 2 0.01
67 2 0.01
70 8 0.05
71 48 0.31
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
ACCCTGTTTCAGAACAGAGATTTAGTATAGACACAAGGGTCTGTAACCCTCGTAACCCTTGTA
Found at i:1043118 original size:9 final size:9
Alignment explanation
Indices: 1043104--1043138 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
1043094 ACAAGGGTCT
1043104 GTAACCCTC
1 GTAACCCTC
1043113 GTAACCCTC
1 GTAACCCTC
*
1043122 GTAACCCTT
1 GTAACCCTC
1043131 GTAACCCT
1 GTAACCCT
1043139 GTTTCAGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.23, C:0.40, G:0.11, T:0.26
Consensus pattern (9 bp):
GTAACCCTC
Found at i:1043130 original size:71 final size:71
Alignment explanation
Indices: 1043042--1043200 Score: 266
Period size: 71 Copynumber: 2.2 Consensus size: 71
1043032 ACAAGGGTCT
*
1043042 GTAACCCTCGTAACCCTTGTAACCCTGTTTCAGAACAGAGATTTA-TATAGACACAAGGGTCTGT
1 GTAACCCTCGTAACCCTTGTAACCCTGTTTCAGAACAGAG-TTTAGTATAGAAACAAGGGTCTGT
1043106 AACCCTC
65 AACCCTC
* *
1043113 GTAACCCTCGTAACCCTTGTAACCCTGTTTCAGAACAGAGTTTAGTATATAAATAAGGGTCTGTA
1 GTAACCCTCGTAACCCTTGTAACCCTGTTTCAGAACAGAGTTTAGTATAGAAACAAGGGTCTGTA
1043178 ACCCTC
66 ACCCTC
*
1043184 GTAACCCTTGTAACCCT
1 GTAACCCTCGTAACCCT
1043201 GTTTCAGACC
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
70 4 0.05
71 79 0.95
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (71 bp):
GTAACCCTCGTAACCCTTGTAACCCTGTTTCAGAACAGAGTTTAGTATAGAAACAAGGGTCTGTA
ACCCTC
Found at i:1043414 original size:2 final size:2
Alignment explanation
Indices: 1043407--1043445 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1043397 GACTCGCGCT
1043407 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1043446 TTCATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1049502 original size:119 final size:119
Alignment explanation
Indices: 1049291--1049512 Score: 399
Period size: 119 Copynumber: 1.9 Consensus size: 119
1049281 TGTTTTGAGG
*
1049291 TATTTCATTTTTTAACTTAGACTTAAATATAGACTTCTAAACCCTTGTATCACTTTCTAAAAGTG
1 TATTTCATTTTTTAACTTAGACTAAAATATAGACTTCTAAACCCTTGTATCACTTTCTAAAAGTG
1049356 TTGTAACCTACCCGTATCCAAGTGTACCCTTTGTACCCTTTCCTTCAGCTCATT
66 TTGTAACCTACCCGTATCCAAGTGTACCCTTTGTACCCTTTCCTTCAGCTCATT
* *
1049410 TATTTGATTTTTTAACTTAGACTAAAATATAGACTTCTAAACCCTTGTATCACTTTCTAATAGTG
1 TATTTCATTTTTTAACTTAGACTAAAATATAGACTTCTAAACCCTTGTATCACTTTCTAAAAGTG
* *
1049475 TTGTAACCTACCTGTTTCCAAGTGTACCCTTTGTACCC
66 TTGTAACCTACCCGTATCCAAGTGTACCCTTTGTACCC
1049513 ACTGTACCCT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 98 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.41
Consensus pattern (119 bp):
TATTTCATTTTTTAACTTAGACTAAAATATAGACTTCTAAACCCTTGTATCACTTTCTAAAAGTG
TTGTAACCTACCCGTATCCAAGTGTACCCTTTGTACCCTTTCCTTCAGCTCATT
Found at i:1054692 original size:10 final size:10
Alignment explanation
Indices: 1054669--1054749 Score: 135
Period size: 10 Copynumber: 7.8 Consensus size: 10
1054659 ATTTCTGTCA
1054669 TTGGGGTATCC
1 TTGGGGT-TCC
1054680 TTGGGGTTCC
1 TTGGGGTTCC
1054690 TTGGGGTGTCC
1 TTGGGGT-TCC
1054701 TTGGGGTTCC
1 TTGGGGTTCC
1054711 TTGGGGTTTCC
1 TTGGGG-TTCC
1054722 TTGGGGTTCC
1 TTGGGGTTCC
1054732 TTGGGGTTCC
1 TTGGGGTTCC
1054742 TTGGGGTT
1 TTGGGGTT
1054750 AAAAGACGTG
Statistics
Matches: 68, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
10 41 0.60
11 27 0.40
ACGTcount: A:0.01, C:0.17, G:0.41, T:0.41
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:1054695 original size:21 final size:20
Alignment explanation
Indices: 1054669--1054749 Score: 135
Period size: 21 Copynumber: 3.9 Consensus size: 20
1054659 ATTTCTGTCA
1054669 TTGGGGTATCCTTGGGGTTCC
1 TTGGGGT-TCCTTGGGGTTCC
1054690 TTGGGGTGTCCTTGGGGTTCC
1 TTGGGGT-TCCTTGGGGTTCC
1054711 TTGGGGTTTCCTTGGGGTTCC
1 TTGGGG-TTCCTTGGGGTTCC
1054732 TTGGGGTTCCTTGGGGTT
1 TTGGGGTTCCTTGGGGTT
1054750 AAAAGACGTG
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
20 12 0.21
21 45 0.78
22 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.41, T:0.41
Consensus pattern (20 bp):
TTGGGGTTCCTTGGGGTTCC
Found at i:1054714 original size:31 final size:31
Alignment explanation
Indices: 1054664--1054749 Score: 138
Period size: 31 Copynumber: 2.7 Consensus size: 31
1054654 TATTCATTTC
*
1054664 TGTCATTGGGGTATCCTTGGGGTTCCTTGGGG
1 TGTCCTTGGGGT-TCCTTGGGGTTCCTTGGGG
1054696 TGTCCTTGGGGTTCCTTGGGGTTTCCTTGGGG
1 TGTCCTTGGGGTTCCTTGGGG-TTCCTTGGGG
1054728 T-TCCTTGGGGTTCCTTGGGGTT
1 TGTCCTTGGGGTTCCTTGGGGTT
1054750 AAAAGACGTG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
30 2 0.04
31 28 0.54
32 22 0.42
ACGTcount: A:0.02, C:0.17, G:0.40, T:0.41
Consensus pattern (31 bp):
TGTCCTTGGGGTTCCTTGGGGTTCCTTGGGG
Found at i:1059105 original size:14 final size:14
Alignment explanation
Indices: 1059083--1059115 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1059073 AAAATGGATG
*
1059083 TAAAAGGCTGGTAA
1 TAAAGGGCTGGTAA
1059097 TAAAGGGCTGGTAA
1 TAAAGGGCTGGTAA
1059111 TAAAG
1 TAAAG
1059116 CTGTAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.30, T:0.21
Consensus pattern (14 bp):
TAAAGGGCTGGTAA
Found at i:1060933 original size:2 final size:2
Alignment explanation
Indices: 1060926--1060951 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1060916 AGTGAAGGGA
1060926 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
1060952 TTAAGGGGGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1062539 original size:162 final size:161
Alignment explanation
Indices: 1062180--1062683 Score: 692
Period size: 162 Copynumber: 3.1 Consensus size: 161
1062170 GAAACATCCA
* ** * *
1062180 CAAAGAAAATGAACGTAAACTGCAAATATTTGGAATTTTGCTAA-GTCCAAGGGTCATAACTCTG
1 CAAAGAAAATGAACGGAAACTGCAAATAACTGGAATTTT-TTAACGTCCAAGGGCCATAACTCTG
* * * ** *
1062244 TCAAAAATTGCTCTATCATACCCAA-ATCAAA-TTGACCTCTATATTATTAAGATAAACCTGTAT
65 TCGAAAATGGCTCGATCATACCCAATATCAAACTTGACCTAGATATTATCAAGATAAACCTGTAT
** *
1062307 ACCAAATTTCACATCAATATGTGCA-CCCTCTG
130 ACCAAATTTCATTTCAATATGTTCATCCC-CTG
*
1062339 CAAAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTTAACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAACGGAAACTGCAAATAACTGGAATTTTTTAACGTCCAAGGGCCATAACTCTGT
* * *
1062404 CGAAAATGGCTCGATCATACCCAATATCAAACTTGACCTAGATAATATCATGATTAACCTGTATA
66 CGAAAATGGCTCGATCATACCCAATATCAAACTTGACCTAGATATTATCAAGATAAACCTGTATA
* *
1062469 ACAAATTTCATTTCAAAAATGTTCATCCCCTG
131 CCAAATTTCATTTC-AATATGTTCATCCCCTG
** * *
1062501 TGAAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCAACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAACGGAAACTGCAAATAACTGGAATTTTTTAACGTCCAAGGGCCATAACTCTGT
* * *
1062566 CGAAAATGGCTAGATCGTACCCAATATCGAACTTGACCTAGATATTATCAAGATAAACCTGTATA
66 CGAAAATGGCTCGATCATACCCAATATCAAACTTGACCTAGATATTATCAAGATAAACCTGTATA
* *
1062631 CCAAAATTCATTTCAATATGTTCATCCTCTG
131 CCAAATTTCATTTCAATATGTTCATCCCCTG
1062662 CAAAGAAAATGAACGGAAACTG
1 CAAAGAAAATGAACGGAAACTG
1062684 TTGGTGGACT
Statistics
Matches: 304, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
158 3 0.01
159 76 0.25
160 6 0.02
161 72 0.24
162 144 0.47
163 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27
Consensus pattern (161 bp):
CAAAGAAAATGAACGGAAACTGCAAATAACTGGAATTTTTTAACGTCCAAGGGCCATAACTCTGT
CGAAAATGGCTCGATCATACCCAATATCAAACTTGACCTAGATATTATCAAGATAAACCTGTATA
CCAAATTTCATTTCAATATGTTCATCCCCTG
Found at i:1079060 original size:32 final size:32
Alignment explanation
Indices: 1079019--1079084 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
1079009 AAAAATCCAG
* *
1079019 TTATTTGCAGTTTCCGTTCGCAGATGTTTCAA
1 TTATTTGCAGTTTCCATTAGCAGATGTTTCAA
*
1079051 TTATTTGCAGTTTCCATTAGCAGATGTTTGAA
1 TTATTTGCAGTTTCCATTAGCAGATGTTTCAA
1079083 TT
1 TT
1079085 TGCATTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (32 bp):
TTATTTGCAGTTTCCATTAGCAGATGTTTCAA
Found at i:1090109 original size:2 final size:2
Alignment explanation
Indices: 1090102--1090154 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1090092 TGAAAAGGAA
1090102 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1090144 CT CT CT CT CT C
1 CT CT CT CT CT C
1090155 GTAATATCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1096246 original size:28 final size:28
Alignment explanation
Indices: 1096214--1096269 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1096204 TCATTTAATA
1096214 GAAGAACATGCATAATTATGGATCAAGT
1 GAAGAACATGCATAATTATGGATCAAGT
*
1096242 GAAGAACATGTATAATTATGGATCAAGT
1 GAAGAACATGCATAATTATGGATCAAGT
1096270 TGTATAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (28 bp):
GAAGAACATGCATAATTATGGATCAAGT
Found at i:1101477 original size:2 final size:2
Alignment explanation
Indices: 1101470--1101521 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1101460 TCAAGTTAGA
1101470 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1101512 AG AG AG AG AG
1 AG AG AG AG AG
1101522 TCTTGCAGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1104018 original size:31 final size:31
Alignment explanation
Indices: 1103983--1104045 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1103973 CATCCTTTCC
*
1103983 ATCGGTTTCTACAAAAACACTCGATTTTAAA
1 ATCGGTTTCTACAAAAACACTCGATCTTAAA
1104014 ATCGGTTTCTACAAAAACACTCGATCTTAAA
1 ATCGGTTTCTACAAAAACACTCGATCTTAAA
1104045 A
1 A
1104046 ACCCATCTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (31 bp):
ATCGGTTTCTACAAAAACACTCGATCTTAAA
Found at i:1119034 original size:105 final size:104
Alignment explanation
Indices: 1118833--1119041 Score: 364
Period size: 105 Copynumber: 2.0 Consensus size: 104
1118823 GAGGCAAGTA
* * *
1118833 AAGTTACGATATCTGTTGTAATTTGCCTGAAAAAGTCAATGGTACTAATTTTTTCACAGAAATTT
1 AAGTTACGATATCTGTCGTAATTTGCCTGAAAAAATCAATGGTACTAATTTTTTCACAGAAATTG
* *
1118898 AGTGGAAATAAGATTAATCAGTCTAAAACTAGGACAATT
66 AGTGGAAATAAGATTAATCAGTCCAAAACTAGCACAATT
1118937 AAGTTACGATATCTGTCGTAATTTGCCTGAAAAAATCAATGGTACTAATTTTTTTCACAGAAATT
1 AAGTTACGATATCTGTCGTAATTTGCCTGAAAAAATCAATGGTACTAA-TTTTTTCACAGAAATT
1119002 GAGTGGAAATAAGATTAATCAGTCCAAAACTAGCACAATT
65 GAGTGGAAATAAGATTAATCAGTCCAAAACTAGCACAATT
1119042 TTTTATGTGC
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
104 46 0.46
105 53 0.54
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (104 bp):
AAGTTACGATATCTGTCGTAATTTGCCTGAAAAAATCAATGGTACTAATTTTTTCACAGAAATTG
AGTGGAAATAAGATTAATCAGTCCAAAACTAGCACAATT
Found at i:1121649 original size:2 final size:2
Alignment explanation
Indices: 1121644--1121684 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1121634 TAACAAAGAA
1121644 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1121685 GCATAAGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1133897 original size:33 final size:33
Alignment explanation
Indices: 1133851--1133932 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
1133841 TTTTGATACC
* *
1133851 GCGAAATATTGAACCCGGGTTCAATATATCGCA
1 GCGATATATTGAACCCGGGTTCAAAATATCGCA
*
1133884 GCGATAT-TATGAACCCGGGTTCAAAATATCGCT
1 GCGATATAT-TGAACCCGGGTTCAAAATATCGCA
1133917 GCGATATATTGAACCC
1 GCGATATATTGAACCC
1133933 CCCCCTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 1 0.02
33 42 0.95
34 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (33 bp):
GCGATATATTGAACCCGGGTTCAAAATATCGCA
Found at i:1134079 original size:65 final size:65
Alignment explanation
Indices: 1133955--1134838 Score: 1088
Period size: 65 Copynumber: 13.6 Consensus size: 65
1133945 TTGAACCCCT
* * * * *
1133955 GGTTCAAAATATTATGGCCGCGATATTTTGAAACCCCCT-CGAATTTTC-ATTGCTCTTGGAGAG
1 GGTTCAAAATATTATGGCTGCGATATTTTG-AACCCCCTAC-TATTTCCAATTCCTTTTGGAGAG
1134018 GG
64 GG
* * *
1134020 GGTTCAAAATATTATGGCCGCGATATATTGAACCCCCTACTGTTTCCAATTCCTTTTGGAGAGGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
** * * *
1134085 GGTTCAAAATATTATGGCCACGATA-TATGTAACCCCCTACTGTTTCCAATTCCTTTTGGAGAAG
1 GGTTCAAAATATTATGGCTGCGATATTTTG-AACCCCCTACTATTTCCAATTCCTTTTGGAGAGG
1134149 G
65 G
** * * *
1134150 GGTTCAAAATATTATGGCCACGATATATTGAACCCCCTTCTATTTCCAATTCCTTTTAGAGAGGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
* * * * * *
1134215 GGTTCAAAAT-TATATGGCTGCAATATTTTGAAACCCCCT-CAATTTTTC-ATTGCTATTGGAAA
1 GGTTCAAAATAT-TATGGCTGCGATATTTTG-AACCCCCTACTA-TTTCCAATTCCTTTTGGAGA
*
1134277 TGG
63 GGG
* * **
1134280 GGTTCAAAATATTATGGCTGCGATATATAGAACCCCCTACCTATTTCCAATTCCCATTGGAGAGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTA-CTATTTCCAATTCCTTTTGGAGAGG
1134345 G
65 G
* * *
1134346 GGTTCAAAATATTATGGCTGGGATATTTTGAACCCCCTCCTATTTCCAATTCCTTTTTGACGAGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGA-GAGG
1134411 G
65 G
* * *
1134412 GG-TCAAAATATTATGGCTGGGATATTTTGAACCCCCTCCTATTTCCAATTCCTTTGGGAGAGGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
*
1134476 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTTCTTTTGGAGAGGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
***
1134541 GGTTCAAAATATTATGGCCATGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
* * * * *
1134606 GGTTCAAAATATTATGGCTGCGATATTTTGAAACTCCCT-CGAATTTTC-ATTGCTCTTGGAGAG
1 GGTTCAAAATATTATGGCTGCGATATTTTG-AACCCCCTAC-TATTTCCAATTCCTTTTGGAGAG
1134669 GG
64 GG
* * * * * *
1134671 GGTTCAAAATATTATGGCAGCGATATTTTGAACCCCCCT-CAATGTTTC-ATTGCTATTGGAGAA
1 GGTTCAAAATATTATGGCTGCGATATTTTGAA-CCCCCTACTAT-TTCCAATTCCTTTTGGAGAG
1134734 GG
64 GG
* * *
1134736 GGTTCAAAATATTATGGCTGCGATATATAGAGCCCCCTACCTATTTCCAATTCCTTTTGGAGAGG
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTA-CTATTTCCAATTCCTTTTGGAGAGG
1134801 G
65 G
*
1134802 GGTTCAAAATATTATGGCCGCGATATTTTGAACCCCC
1 GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCC
1134839 CTCAATTTTT
Statistics
Matches: 721, Mismatches: 78, Indels: 39
0.86 0.09 0.05
Matches are distributed among these distances:
64 41 0.06
65 546 0.76
66 134 0.19
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (65 bp):
GGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTACTATTTCCAATTCCTTTTGGAGAGGG
Found at i:1152698 original size:13 final size:14
Alignment explanation
Indices: 1152682--1152715 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1152672 AAAAAAAAAA
1152682 AAAAAAAATGT-GG
1 AAAAAAAATGTCGG
*
1152695 AAAAAAAATTTCGG
1 AAAAAAAATGTCGG
1152709 AAAAAAA
1 AAAAAAA
1152716 TCGGGCTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.68, C:0.03, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAAAAATGTCGG
Found at i:1152702 original size:1 final size:1
Alignment explanation
Indices: 1152664--1152689 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1152654 TTTTGTATTT
1152664 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1152690 TGTGGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1153388 original size:14 final size:14
Alignment explanation
Indices: 1153369--1153396 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1153359 TAGTATAGAA
1153369 GTTTGTATCTATAT
1 GTTTGTATCTATAT
1153383 GTTTGTATCTATAT
1 GTTTGTATCTATAT
1153397 CAGTTGACAT
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:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTTGTATCTATAT
Found at i:1155842 original size:21 final size:21
Alignment explanation
Indices: 1155816--1156004 Score: 278
Period size: 21 Copynumber: 9.1 Consensus size: 21
1155806 TTAGATGATT
1155816 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
1155837 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
*
1155858 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
1155879 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
1155900 TTATTATATGCTGTGGATCTA
1 TTATTATATGCTGTGGGTCTA
1155921 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
1155942 --ATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
*
1155961 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
1155982 TTATTATATGTTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
1156003 TT
1 TT
1156005 NTTCAGTAAA
Statistics
Matches: 156, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
19 19 0.12
20 1 0.01
21 135 0.87
22 1 0.01
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (21 bp):
TTATTATATGCTGTGGGTCTA
Found at i:1155978 original size:82 final size:82
Alignment explanation
Indices: 1155816--1156004 Score: 310
Period size: 82 Copynumber: 2.3 Consensus size: 82
1155806 TTAGATGATT
1155816 TTATTATATGCTGTGGGTCTATTATTATATGCTGTGGTTCTATAATTATATGCTGTGGGTCTATA
1 TTATTATATGCTGTGGGTCTATTATTATATGCTGTGGTTC--TAATTATATGCTGTGGGTCTATA
1155881 ATTATATGCTGTGGGTCTA
64 ATTATATGCTGTGGGTCTA
*
1155900 TTATTATATGCTGTGGATCTATTATTATATGCTGTGGGTTC-AATTATATGCTGTGGGT-TCATA
1 TTATTATATGCTGTGGGTCTATTATTATATGCTGT-GGTTCTAATTATATGCTGTGGGTCT-ATA
1155963 ATTATATGCTGTGGGTCTA
64 ATTATATGCTGTGGGTCTA
*
1155982 TTATTATATGTTGTGGGTCTATT
1 TTATTATATGCTGTGGGTCTATT
1156005 NTTCAGTAAA
Statistics
Matches: 100, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
81 1 0.01
82 60 0.60
84 34 0.34
85 5 0.05
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (82 bp):
TTATTATATGCTGTGGGTCTATTATTATATGCTGTGGTTCTAATTATATGCTGTGGGTCTATAAT
TATATGCTGTGGGTCTA
Found at i:1156404 original size:33 final size:33
Alignment explanation
Indices: 1156362--1156442 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
1156352 GCCCTCTAAG
1156362 GGGACACAGGTAGACTTTACCTGTATATACTTT
1 GGGACACAGGTAGACTTTACCTGTATATACTTT
1156395 GGGACACAGGTAGACTTTACCTGTATATACTTT
1 GGGACACAGGTAGACTTTACCTGTATATACTTT
*
1156428 GGGACACAGTTAGAC
1 GGGACACAGGTAGAC
1156443 GACATTGTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (33 bp):
GGGACACAGGTAGACTTTACCTGTATATACTTT
Found at i:1161246 original size:18 final size:19
Alignment explanation
Indices: 1161211--1161246 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1161201 AGTCTAAATA
1161211 TGTTCAACATTCAGGGATG
1 TGTTCAACATTCAGGGATG
*
1161230 TGTTCATCATT-AGGGAT
1 TGTTCAACATTCAGGGAT
1161247 CAAACCCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (19 bp):
TGTTCAACATTCAGGGATG
Found at i:1165009 original size:2 final size:2
Alignment explanation
Indices: 1165002--1165030 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1164992 TGAATAGTTG
1165002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1165031 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1176025 original size:2 final size:2
Alignment explanation
Indices: 1176018--1176074 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1176008 ACAAAAGTAC
1176018 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1176060 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
1176075 TATTTTACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1176410 original size:2 final size:2
Alignment explanation
Indices: 1176403--1176451 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1176393 ATACTGGTAT
1176403 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1176445 TC TC TC T
1 TC TC TC T
1176452 TATATATGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1185775 original size:201 final size:202
Alignment explanation
Indices: 1185429--1185834 Score: 708
Period size: 201 Copynumber: 2.0 Consensus size: 202
1185419 GTTGGCATGT
* *
1185429 TTTTCATTTAGATATAGTAGTCCCATCTTTTTTGCCATTCCTTAGTCATGTGTTTTTTATTGTGT
1 TTTTCATATAGATATAGTAGTCCCATCTTGTTTGCCATTCCTTAGTCATGTGTTTTTTATTGTGT
* *
1185494 GTGTACAATTTATATGTTCATGATACTGTCTCTTTTTGGTTGTTTTATGTTTCATTGTGACAGGT
66 ATGTACAATTTATATATTCATGATACTGTCTCTTTTTGGTTGTTTTATGTTTCATTGTGACAGGT
* *
1185559 GTAACGTACAGTTTGATAGCGGACAATGCCGCTACATTTACATTGGCATTTGTAATAAAATGCTC
131 GTAACGTACAGTTTGATAGCGGACAATACCGCTACATTTACATTGGCATTTGTAATAAAATCCTC
1185624 TTTTCAA
196 TTTTCAA
*
1185631 TTTTCATATAGATATAGTAGTCCCATCTTGTTTGCCATTCGTTAGTCATGTG-TTTTTATTGTGT
1 TTTTCATATAGATATAGTAGTCCCATCTTGTTTGCCATTCCTTAGTCATGTGTTTTTTATTGTGT
* *
1185695 ATGTACAATTTTTATATTCATGATACTGTCT-TTTGTTGGTTGTTTTATTTTTCATTGTGACAGG
66 ATGTACAATTTATATATTCATGATACTGTCTCTTT-TTGGTTGTTTTATGTTTCATTGTGACAGG
1185759 TGTAACGTACAGTTTGATAGCGGACAATACCGCTACATTTACATTGGCATTTGTAATAAAATCCT
130 TGTAACGTACAGTTTGATAGCGGACAATACCGCTACATTTACATTGGCATTTGTAATAAAATCCT
1185824 CTTTTCAA
195 CTTTTCAA
1185832 TTT
1 TTT
1185835 AGACTCTGGT
Statistics
Matches: 194, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
200 3 0.02
201 142 0.73
202 49 0.25
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.46
Consensus pattern (202 bp):
TTTTCATATAGATATAGTAGTCCCATCTTGTTTGCCATTCCTTAGTCATGTGTTTTTTATTGTGT
ATGTACAATTTATATATTCATGATACTGTCTCTTTTTGGTTGTTTTATGTTTCATTGTGACAGGT
GTAACGTACAGTTTGATAGCGGACAATACCGCTACATTTACATTGGCATTTGTAATAAAATCCTC
TTTTCAA
Found at i:1185904 original size:3 final size:3
Alignment explanation
Indices: 1185890--1185924 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1185880 GGACGATGGT
* *
1185890 ATA ATG ATA ATA ATA ATA ATA ATA ATT ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1185925 TTGCTGGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1187360 original size:2 final size:2
Alignment explanation
Indices: 1187353--1187385 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1187343 CGCCTAAAAC
*
1187353 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1187386 GTTTAGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1190835 original size:115 final size:115
Alignment explanation
Indices: 1190633--1190861 Score: 413
Period size: 115 Copynumber: 2.0 Consensus size: 115
1190623 TTATTTATTT
* *
1190633 AAACAAGAGAGATTATTGCAAAACTGTTTGATATGTAATGCTTTTGTTTCATTTGCTGTCTATAG
1 AAACAAGAGAGATTATTGCAAAAATGTTTGATATGTAATGCTTTTGTTTAATTTGCTGTCTATAG
1190698 GAAGTACATGTGCTTGTTACAAGTTTGAAGAGAAAATATACTTTAATATA
66 GAAGTACATGTGCTTGTTACAAGTTTGAAGAGAAAATATACTTTAATATA
*
1190748 AAACAAGAGAGATTATTGTAAAAATGTTTGATATGTAATGCTTTTGTTTAATTTGCTGTCTATAG
1 AAACAAGAGAGATTATTGCAAAAATGTTTGATATGTAATGCTTTTGTTTAATTTGCTGTCTATAG
* *
1190813 GAAGTGCATGTGCTTGTTACAAGTTTGAAGAGAAAATATACTTTGATAT
66 GAAGTACATGTGCTTGTTACAAGTTTGAAGAGAAAATATACTTTAATAT
1190862 TCAATTATCG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 109 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.38
Consensus pattern (115 bp):
AAACAAGAGAGATTATTGCAAAAATGTTTGATATGTAATGCTTTTGTTTAATTTGCTGTCTATAG
GAAGTACATGTGCTTGTTACAAGTTTGAAGAGAAAATATACTTTAATATA
Found at i:1193867 original size:12 final size:13
Alignment explanation
Indices: 1193841--1193871 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1193831 CAGAAATTTA
1193841 AGATTTGAGGCTG
1 AGATTTGAGGCTG
1193854 AGATTTGA-GCTG
1 AGATTTGAGGCTG
1193866 AGATTT
1 AGATTT
1193872 TTACATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (13 bp):
AGATTTGAGGCTG
Found at i:1203818 original size:21 final size:21
Alignment explanation
Indices: 1203780--1203823 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1203770 GTTCATCCCT
*
1203780 TCCTATCGTGAATTAATCCTA
1 TCCTATCGTGAATGAATCCTA
**
1203801 TCCTATCGTGTGTGAATCCTA
1 TCCTATCGTGAATGAATCCTA
1203822 TC
1 TC
1203824 GTTTAGCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (21 bp):
TCCTATCGTGAATGAATCCTA
Found at i:1208340 original size:42 final size:42
Alignment explanation
Indices: 1208221--1208342 Score: 199
Period size: 42 Copynumber: 2.9 Consensus size: 42
1208211 CATCAAGTTT
* * * *
1208221 ACTTTTCAACCGACAGGCAAGACAGAGAAAAAAAGAAGGATC
1 ACTTTTCAACTGATAGGCAAGACAAAGAAAAAAAGGAGGATC
1208263 ACTTTTCAACTGATAGGCAAGACAAAGAAAAAAAGGAGGATC
1 ACTTTTCAACTGATAGGCAAGACAAAGAAAAAAAGGAGGATC
*
1208305 ACTTTTCAACTGATAGGCGAGACAAAGAAAAAAAGGAG
1 ACTTTTCAACTGATAGGCAAGACAAAGAAAAAAAGGAG
1208343 AACCATATAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.15
Consensus pattern (42 bp):
ACTTTTCAACTGATAGGCAAGACAAAGAAAAAAAGGAGGATC
Done.