Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 423 of 427
Found at i:123191335 original size:53 final size:53
Alignment explanation
Indices: 123191263--123191368 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
123191253 CTTCTTTCGT
* *
123191263 TCCACCCTTCTCCCTCTTTTCAGTCTGGTTCCTATTTCGTTCCACCCTTCTCC
1 TCCACCCTTCTCCCTCTTTTCAGTCTGATTCCCATTTCGTTCCACCCTTCTCC
* * *
123191316 TCCACCCTTCTCCCTCTTTTCAGTCTTATTCCCATTTCGTTTCATCCTTCTCC
1 TCCACCCTTCTCCCTCTTTTCAGTCTGATTCCCATTTCGTTCCACCCTTCTCC
123191369 CTCTTTTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.08, C:0.42, G:0.06, T:0.43
Consensus pattern (53 bp):
TCCACCCTTCTCCCTCTTTTCAGTCTGATTCCCATTTCGTTCCACCCTTCTCC
Found at i:123193255 original size:2 final size:2
Alignment explanation
Indices: 123193248--123193272 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
123193238 AAGATGCGTG
123193248 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
123193273 GTAAGATTCT
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:123194382 original size:12 final size:12
Alignment explanation
Indices: 123194365--123194391 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
123194355 ACAATAATTA
123194365 TTGGGTATTGTT
1 TTGGGTATTGTT
123194377 TTGGGTATTGTT
1 TTGGGTATTGTT
123194389 TTG
1 TTG
123194392 CATAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (12 bp):
TTGGGTATTGTT
Found at i:123194634 original size:32 final size:32
Alignment explanation
Indices: 123194593--123194657 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
123194583 CAAGATGACG
123194593 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
1 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
* *
123194625 AGATAGATGTAAAGGCTAAGGGCAAATATAAA
1 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
123194657 A
1 A
123194658 CAAATTGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (32 bp):
AGATAGATGTAAAAGCCAAGGGCAAATATAAA
Found at i:123195012 original size:2 final size:2
Alignment explanation
Indices: 123195007--123195039 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
123194997 GTGAAACAGT
123195007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
123195040 TATTAGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123198877 original size:17 final size:17
Alignment explanation
Indices: 123198857--123198889 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
123198847 ATTAAGAATG
123198857 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
123198874 TTATTAAATTATATTT
1 TTATTAAATTATATTT
123198890 AATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:123199154 original size:46 final size:44
Alignment explanation
Indices: 123199061--123199154 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
123199051 ATTACAACAT
*
123199061 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
***
123199105 CATTCCATTCAACCAAACAGTTGAATTACTTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAA-TAC-TATTACAGCTCTATTC
123199151 CATT
1 CATT
123199155 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 22 0.50
45 3 0.07
46 19 0.43
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:123199157 original size:16 final size:16
Alignment explanation
Indices: 123199136--123199191 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
123199126 TGAATTACTT
123199136 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
123199152 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
123199168 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
123199184 ATTACAGC
1 ATTACAGC
123199192 CAACCAAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:123199600 original size:1 final size:1
Alignment explanation
Indices: 123199594--123199619 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
123199584 ATGGCATGTC
123199594 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
123199620 GCAAACTTCT
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:123208610 original size:30 final size:30
Alignment explanation
Indices: 123208574--123208634 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
123208564 ATAACCGGCT
123208574 TTCATGATCCATGACTTGGTTTCCTTTATA
1 TTCATGATCCATGACTTGGTTTCCTTTATA
*
123208604 TTCATGATCCATTACTTGGTTTCCTTTATA
1 TTCATGATCCATGACTTGGTTTCCTTTATA
123208634 T
1 T
123208635 CCTGTTGGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (30 bp):
TTCATGATCCATGACTTGGTTTCCTTTATA
Found at i:123214542 original size:21 final size:21
Alignment explanation
Indices: 123214499--123214549 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
123214489 CTTTCATTTT
*
123214499 TATAATTAATTATTGAGTAAA
1 TATAATTAATTATTAAGTAAA
* * *
123214520 TATAATTAATTGTTAATTTAA
1 TATAATTAATTATTAAGTAAA
123214541 TATTAATTA
1 TA-TAATTA
123214550 TAAAATGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (21 bp):
TATAATTAATTATTAAGTAAA
Found at i:123214912 original size:11 final size:12
Alignment explanation
Indices: 123214896--123214924 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
123214886 AGATTGGAGG
123214896 AAAAGAAAAA-A
1 AAAAGAAAAAGA
123214907 AAAAGAAAAAGA
1 AAAAGAAAAAGA
123214919 AAAAGA
1 AAAAGA
123214925 TGAAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:123214923 original size:6 final size:6
Alignment explanation
Indices: 123214896--123214924 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
123214886 AGATTGGAGG
123214896 AAAAGA AAAA-A AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
123214925 TGAAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:123229982 original size:21 final size:21
Alignment explanation
Indices: 123229956--123229996 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
123229946 ATCTGCTCAA
* *
123229956 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
123229977 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
123229997 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:123237621 original size:20 final size:20
Alignment explanation
Indices: 123237596--123237643 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
123237586 TTGCCTGAGC
123237596 ATCGATACCCTGGGACAAGT
1 ATCGATACCCTGGGACAAGT
* * *
123237616 ATCGATATCTTGGGGCAAGT
1 ATCGATACCCTGGGACAAGT
*
123237636 ATTGATAC
1 ATCGATAC
123237644 TATAAGCTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
ATCGATACCCTGGGACAAGT
Found at i:123240871 original size:31 final size:31
Alignment explanation
Indices: 123240826--123240896 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
123240816 ACAAAAGTCT
* * * *
123240826 AATAATTCAGTAACTTAAATAAAAATTTTTG
1 AATAATTTAATAACTTAAATAAAAACTTTTA
*
123240857 AATAGTTTAATAACTTAAATAAAAACTTTTA
1 AATAATTTAATAACTTAAATAAAAACTTTTA
123240888 AATAATTTA
1 AATAATTTA
123240897 GTGACTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (31 bp):
AATAATTTAATAACTTAAATAAAAACTTTTA
Found at i:123245270 original size:20 final size:20
Alignment explanation
Indices: 123245234--123245277 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
123245224 TCAAAAGCCA
*
123245234 TAAAATAAAATTTATTTTAT
1 TAAAATAAAATTAATTTTAT
*
123245254 TAAAAT-AAATCTAATTTTTT
1 TAAAATAAAAT-TAATTTTAT
123245274 TAAA
1 TAAA
123245278 TTTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATAAAATTAATTTTAT
Found at i:123246178 original size:77 final size:77
Alignment explanation
Indices: 123246083--123246240 Score: 280
Period size: 77 Copynumber: 2.1 Consensus size: 77
123246073 TACTATAATA
*
123246083 AAATCACATTTTAAACATTTCCAAATTATATATAAACTTATCAATCTAACCAATTATTTTTTTAT
1 AAATCACATTTTAAACATTTCCAAATTATATATAAACTTATCAATCTAACCAATTACTTTTTTAT
123246148 CGATTAAATTTT
66 CGATTAAATTTT
* * *
123246160 AAATCCCATTTTAGACATTTCCAAATTTTATATAAACTTATCAATCTAACCAATTACTTTTTTAT
1 AAATCACATTTTAAACATTTCCAAATTATATATAAACTTATCAATCTAACCAATTACTTTTTTAT
123246225 CGATTAAATTTT
66 CGATTAAATTTT
123246237 AAAT
1 AAAT
123246241 AAGTTGACAC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.44
Consensus pattern (77 bp):
AAATCACATTTTAAACATTTCCAAATTATATATAAACTTATCAATCTAACCAATTACTTTTTTAT
CGATTAAATTTT
Found at i:123246970 original size:41 final size:41
Alignment explanation
Indices: 123246912--123246995 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
123246902 CAAGAGAATG
**
123246912 TGAGCATCATGTTTTTGGTAGGGTTCGATCTAGAGTGATCA
1 TGAGCATCATGCGTTTGGTAGGGTTCGATCTAGAGTGATCA
123246953 TGAGCATCATGCGTTTGGTAGGGTTCGATCTAGAGTGATCA
1 TGAGCATCATGCGTTTGGTAGGGTTCGATCTAGAGTGATCA
123246994 TG
1 TG
123246996 GGTTGGATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (41 bp):
TGAGCATCATGCGTTTGGTAGGGTTCGATCTAGAGTGATCA
Found at i:123247136 original size:16 final size:17
Alignment explanation
Indices: 123247109--123247141 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
123247099 CCAGCCTGCC
*
123247109 TTATTAATTTTTTTATA
1 TTATTAATTTTTATATA
123247126 TTATT-ATTTTTATATA
1 TTATTAATTTTTATATA
123247142 AAAATAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTAATTTTTATATA
Found at i:123256563 original size:23 final size:24
Alignment explanation
Indices: 123256537--123256585 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
123256527 AAATGATTTG
123256537 AATTTAAAATAAATCAAAT-AAAT
1 AATTTAAAATAAATCAAATCAAAT
* * *
123256560 AATTTGAAATAACTTAAATCAAAT
1 AATTTAAAATAAATCAAATCAAAT
123256584 AA
1 AA
123256586 CCCGACTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (24 bp):
AATTTAAAATAAATCAAATCAAAT
Found at i:123259321 original size:5 final size:5
Alignment explanation
Indices: 123259311--123259338 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
123259301 AATAATTAAG
123259311 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
123259339 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:123262666 original size:21 final size:21
Alignment explanation
Indices: 123262642--123262718 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
123262632 GACGCTCGAA
*
123262642 AGCTGAGCAAAAGCTCATAAG
1 AGCTGAACAAAAGCTCATAAG
*
123262663 AGCTGAACAAAAACTCATAAG
1 AGCTGAACAAAAGCTCATAAG
* *
123262684 AGTTGAACAGAAGCTCGA-AAG
1 AGCTGAACAAAAGCTC-ATAAG
*
123262705 AGCTAAACAGAAAG
1 AGCTGAACA-AAAG
123262719 TAAAACACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 42 0.91
22 4 0.09
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
AGCTGAACAAAAGCTCATAAG
Found at i:123267966 original size:16 final size:16
Alignment explanation
Indices: 123267945--123267978 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
123267935 GGCCAAAGTC
123267945 AATTTTAATTAATTTT
1 AATTTTAATTAATTTT
* *
123267961 AATTTTTATTATTTTT
1 AATTTTAATTAATTTT
123267977 AA
1 AA
123267979 AAGGACTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTTAATTAATTTT
Found at i:123267998 original size:78 final size:78
Alignment explanation
Indices: 123267865--123268009 Score: 179
Period size: 78 Copynumber: 1.8 Consensus size: 78
123267855 ATAAAAATGT
* *
123267865 AATTTTATTATTAATTTATAATTCTATCATTTTTTAAAGGACTAAATATATTTTTTTTTCATATT
1 AATTTTA-TATTAATTTATAATTCTATCATTTTTAAAAGGACTAAATATA-ATTTTTTTCATATT
123267930 TAAAAGGCCAAAGTC
64 TAAAAGGCCAAAGTC
* * * *
123267945 AATTTTA-ATTAATTT-TAATTTTTATTATTTTTAAAAGGACTGAAT-TGAATTTTTTTCATTTT
1 AATTTTATATTAATTTATAA-TTCTATCATTTTTAAAAGGACTAAATAT-AATTTTTTTCATATT
123268007 TAA
64 TAA
123268010 GGCGGGCTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
77 19 0.33
78 31 0.54
80 7 0.12
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (78 bp):
AATTTTATATTAATTTATAATTCTATCATTTTTAAAAGGACTAAATATAATTTTTTTCATATTTA
AAAGGCCAAAGTC
Found at i:123269435 original size:16 final size:17
Alignment explanation
Indices: 123269414--123269445 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
123269404 AATGACACTA
123269414 GAAAAAG-AAAAGAAAG
1 GAAAAAGCAAAAGAAAG
123269430 GAAAAAGCAAAAGAAA
1 GAAAAAGCAAAAGAAA
123269446 CCAATGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (17 bp):
GAAAAAGCAAAAGAAAG
Found at i:123271539 original size:24 final size:27
Alignment explanation
Indices: 123271507--123271563 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 27
123271497 CTTTATTAAA
* *
123271507 TTAATTTTTA-TAAA-ATATTTTA-TC
1 TTAAATTTTAGTAAATATATTCTATTC
*
123271531 TTAAATTTTAGTAAATTTATTCTATTC
1 TTAAATTTTAGTAAATATATTCTATTC
123271558 TTAAAT
1 TTAAAT
123271564 GAATCTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.33
25 4 0.15
26 6 0.22
27 8 0.30
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAATTTTAGTAAATATATTCTATTC
Found at i:123280657 original size:21 final size:22
Alignment explanation
Indices: 123280631--123280680 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
123280621 ATATAAGAGA
*
123280631 ACAATGG-TAAGTATTTTATTG
1 ACAATGGTTAAGTACTTTATTG
123280652 ACAATGGTTAAGTACTTTATTG
1 ACAATGGTTAAGTACTTTATTG
*
123280674 ACCATGG
1 ACAATGG
123280681 ACGAATTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
ACAATGGTTAAGTACTTTATTG
Found at i:123295750 original size:40 final size:40
Alignment explanation
Indices: 123295695--123295775 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
123295685 TTATTATTTG
123295695 ACCTTTTCAAAGTCTCATCTATTATTTATATAAATTTTTA
1 ACCTTTTCAAAGTCTCATCTATTATTTATATAAATTTTTA
123295735 ACCTTTTCAAAGTCTCATCTATTATTTATATAAATTTTTA
1 ACCTTTTCAAAGTCTCATCTATTATTTATATAAATTTTTA
123295775 A
1 A
123295776 TATATACATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.49
Consensus pattern (40 bp):
ACCTTTTCAAAGTCTCATCTATTATTTATATAAATTTTTA
Found at i:123296415 original size:19 final size:18
Alignment explanation
Indices: 123296367--123296426 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
123296357 AAAAATATAA
123296367 TTACAATTAT-AAATTCT
1 TTACAATTATAAAATTCT
* *
123296384 TTA-AACTTTTAAAATATGT
1 TTACAA-TTATAAAAT-TCT
*
123296403 TTACAATTATAAATTTCT
1 TTACAATTATAAAATTCT
123296421 TCTACA
1 T-TACA
123296427 TTGGTAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
18 7 0.21
19 16 0.48
20 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (18 bp):
TTACAATTATAAAATTCT
Found at i:123298583 original size:2 final size:2
Alignment explanation
Indices: 123298576--123298602 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
123298566 AAAATCATTT
123298576 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
123298603 TTAATTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123306840 original size:27 final size:26
Alignment explanation
Indices: 123306800--123306850 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
123306790 ATTATTTTTA
* *
123306800 TTAAAAAAATAATATTTGAATTTGTT
1 TTAAAAAAATAATAATTAAATTTGTT
*
123306826 TTAAAAATATAAATAATTAAATTTG
1 TTAAAAAAAT-AATAATTAAATTTG
123306851 GTTATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (26 bp):
TTAAAAAAATAATAATTAAATTTGTT
Found at i:123313172 original size:26 final size:26
Alignment explanation
Indices: 123313136--123313191 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
123313126 GCTAAATCTA
*
123313136 TTCAAGTTTGGCCTTATTTGGTTCTT
1 TTCAAGTTTGGCCTTATTTGATTCTT
* *
123313162 TTCAATTTTGGCTTTATTTGATTCTT
1 TTCAAGTTTGGCCTTATTTGATTCTT
123313188 TTCA
1 TTCA
123313192 TTAGTATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (26 bp):
TTCAAGTTTGGCCTTATTTGATTCTT
Found at i:123314466 original size:27 final size:27
Alignment explanation
Indices: 123314428--123314481 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
123314418 ATTAAACAAA
123314428 ATTAAATGATCGTTATGATGTCTCTGT
1 ATTAAATGATCGTTATGATGTCTCTGT
123314455 ATTAAATGATCGTTATGATGTCTCTGT
1 ATTAAATGATCGTTATGATGTCTCTGT
123314482 CATGCTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTAAATGATCGTTATGATGTCTCTGT
Found at i:123315537 original size:241 final size:239
Alignment explanation
Indices: 123315012--123315701 Score: 1154
Period size: 238 Copynumber: 2.9 Consensus size: 239
123315002 TTTTCACTAC
* * *
123315012 TACGGTCCGCTGTTTGCACCATTGGAATTTAAAAACGAAAATCCTCTTGAAACTTTTCCATCAAG
1 TACGGTCCTCTGTTTGCACCATTGGAATTTAAAAACG-AAATCCTC-TAAAACTTTGCCATCAAG
*
123315077 TAAAATAGGG-AGATAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCATTTTTTTTT-
64 TAAAACAGGGAAG-TAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCATTTTTTTTTC
*
123315140 TCCTTACGTTTTTCTCGGCAACCAAACAACGTTCTTCACAGTATTGCTACTAACATTTTCTAATC
128 TCCTTACGTTTTTCTCGGCAACCAAACAACGTTCTTCACCGTATTGCTACTAACATTTTCTAATC
* *
123315205 GTATATAACTGAAAAAAGTCAGGCAAATCATTACTGCATATAGACAT
193 GTATATAACTAAAAAAAGTCAGACAAATCATTACTGCATATAGACAT
* * *
123315252 TACGGTCCTCTGTTTGCACCATTGGAATTTAAAAACTAAATCCTCTAAAACCTTGCCATCAGGTA
1 TACGGTCCTCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTAAAACTTTGCCATCAAGTA
123315317 AAACAGGGAAGTAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCATTTTTTTTTTCTC
66 AAACAGGGAAGTAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCA-TTTTTTTTTCTC
123315382 CTTACGTTTTTCTCGGCAACCAAACAACGTTCTTCACCGTATTGCTACTAACATTTTCTAATCGT
130 CTTACGTTTTTCTCGGCAACCAAACAACGTTCTTCACCGTATTGCTACTAACATTTTCTAATCGT
*
123315447 ATATAACCAAAAACAAGTCAGACAAATCATTACTGCATATAGACAT
195 ATATAACTAAAAA-AAGTCAGACAAATCATTACTGCATATAGACAT
*
123315493 TACGGTCCTCTGTTTGCACCATTGGAATATAAAAACGAAATCCTCTAAAACTTTGCCATCAAGTA
1 TACGGTCCTCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTAAAACTTTGCCATCAAGTA
*
123315558 AAACAGGGAAGTAGTTGCATGGAGTTCATAAAC--ATCACTCATTCACTTCATTTTTTTTTCTCC
66 AAACAGGGAAGTAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCATTTTTTTTTCTCC
* * * *
123315621 TTACGTTTTCCTCGGCAACCAAACAACGTTCTTAACCGTATTGCTTCTAACATTTTCAAATCGTA
131 TTACGTTTTTCTCGGCAACCAAACAACGTTCTTCACCGTATTGCTACTAACATTTTCTAATCGTA
123315686 TATAACTAAAAAAAGT
196 TATAACTAAAAAAAGT
123315702 GCAAAAAAAA
Statistics
Matches: 425, Mismatches: 21, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
237 4 0.01
238 149 0.35
239 35 0.08
240 112 0.26
241 125 0.29
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (239 bp):
TACGGTCCTCTGTTTGCACCATTGGAATTTAAAAACGAAATCCTCTAAAACTTTGCCATCAAGTA
AAACAGGGAAGTAGTTGCATGGAGTTCATAAACATATCACTCATTCACTCCATTTTTTTTTCTCC
TTACGTTTTTCTCGGCAACCAAACAACGTTCTTCACCGTATTGCTACTAACATTTTCTAATCGTA
TATAACTAAAAAAAGTCAGACAAATCATTACTGCATATAGACAT
Found at i:123315817 original size:24 final size:24
Alignment explanation
Indices: 123315785--123315832 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
123315775 AAAATTACTT
123315785 GTGAAAATCACGAGTTGTATCCTC
1 GTGAAAATCACGAGTTGTATCCTC
123315809 GTGAAAATCACGAGTTGTATCCTC
1 GTGAAAATCACGAGTTGTATCCTC
123315833 CGATTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
GTGAAAATCACGAGTTGTATCCTC
Found at i:123324760 original size:2 final size:2
Alignment explanation
Indices: 123324753--123324785 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
123324743 AACAAATGTT
123324753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
123324786 TATTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123327263 original size:23 final size:23
Alignment explanation
Indices: 123327237--123327280 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
123327227 TAAATTTTAA
123327237 AATT-TGAAAAATAAAGAGATTGG
1 AATTCTGAAAAATAAA-AGATTGG
* *
123327260 AATTCTTATAAATAAAAGATT
1 AATTCTGAAAAATAAAAGATT
123327281 AGGTGCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (23 bp):
AATTCTGAAAAATAAAAGATTGG
Found at i:123354045 original size:2 final size:2
Alignment explanation
Indices: 123354038--123354070 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
123354028 AACTAACCCC
123354038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
123354071 TTAAAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123354731 original size:24 final size:24
Alignment explanation
Indices: 123354698--123354771 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 24
123354688 TATGTTTAAA
123354698 AAATATAAATTATATTTATTATTTT
1 AAATA-AAATTATATTTATTATTTT
*
123354723 AAATAAAATTAT-TTATATTTTTTT
1 AAATAAAATTATATT-TATTATTTT
* *
123354747 ATATAAATAATATTATGTTATTATT
1 AAATAAA-ATTA-TAT-TTATTATT
123354772 AACAGATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 21 0.52
25 8 0.20
26 1 0.03
27 7 0.17
28 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
AAATAAAATTATATTTATTATTTT
Found at i:123360766 original size:18 final size:19
Alignment explanation
Indices: 123360743--123360780 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
123360733 GAAAAGAATA
*
123360743 AAAATTTTAATTTA-TATT
1 AAAATTTTAACTTATTATT
123360761 AAAATTTTAACTTATTATT
1 AAAATTTTAACTTATTATT
123360780 A
1 A
123360781 TTAAGATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAATTTTAACTTATTATT
Found at i:123362186 original size:23 final size:23
Alignment explanation
Indices: 123362161--123362215 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
123362151 ATATTTATGA
*
123362161 TTTATATTATTATAAATAAATTAT
1 TTTA-ATTATTAAAAATAAATTAT
**
123362185 TTTAATTATTAAAAATTTATTAT
1 TTTAATTATTAAAAATAAATTAT
123362208 TTGTAATT
1 TT-TAATT
123362216 TATATTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAATTATTAAAAATAAATTAT
Found at i:123367736 original size:110 final size:110
Alignment explanation
Indices: 123367591--123367810 Score: 440
Period size: 110 Copynumber: 2.0 Consensus size: 110
123367581 TCTATGTGTG
123367591 AAGGAACATAATTAAAAATCTCAACAATTTTATAGAAATTGCTGCTCTTATGCTCTATTTTAAAA
1 AAGGAACATAATTAAAAATCTCAACAATTTTATAGAAATTGCTGCTCTTATGCTCTATTTTAAAA
123367656 ATAAAAAAAATGTCACCTTAATTATACAAAGTGCATTCATTGCAT
66 ATAAAAAAAATGTCACCTTAATTATACAAAGTGCATTCATTGCAT
123367701 AAGGAACATAATTAAAAATCTCAACAATTTTATAGAAATTGCTGCTCTTATGCTCTATTTTAAAA
1 AAGGAACATAATTAAAAATCTCAACAATTTTATAGAAATTGCTGCTCTTATGCTCTATTTTAAAA
123367766 ATAAAAAAAATGTCACCTTAATTATACAAAGTGCATTCATTGCAT
66 ATAAAAAAAATGTCACCTTAATTATACAAAGTGCATTCATTGCAT
123367811 GTTTTATATT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (110 bp):
AAGGAACATAATTAAAAATCTCAACAATTTTATAGAAATTGCTGCTCTTATGCTCTATTTTAAAA
ATAAAAAAAATGTCACCTTAATTATACAAAGTGCATTCATTGCAT
Found at i:123368859 original size:2 final size:2
Alignment explanation
Indices: 123368852--123368880 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123368842 TATTTCAAGA
123368852 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
123368881 AAAGATGATT
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:123369266 original size:30 final size:30
Alignment explanation
Indices: 123369205--123369266 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
123369195 ATTTAAATAT
* * *
123369205 AAATATTTAAATTAGAATAATTTTCTTTTA
1 AAATATTTAAAATAGAATAATTTTATGTTA
123369235 AAATATTTAAAATAGAA-AATTTTATAGTTA
1 AAATATTTAAAATAGAATAATTTTAT-GTTA
123369265 AA
1 AA
123369267 TTACTATCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
AAATATTTAAAATAGAATAATTTTATGTTA
Found at i:123372011 original size:15 final size:16
Alignment explanation
Indices: 123371985--123372015 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
123371975 AATATTATAT
123371985 TTTTATAATTAAATTA
1 TTTTATAATTAAATTA
123372001 TTTTA-AATTAAATTA
1 TTTTATAATTAAATTA
123372016 GGAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTATAATTAAATTA
Found at i:123374960 original size:218 final size:219
Alignment explanation
Indices: 123374641--123375070 Score: 736
Period size: 218 Copynumber: 2.0 Consensus size: 219
123374631 TTATTAGAGT
* * *
123374641 ATTGAAGAAAGAATGAAGAAACACATTTTTTTATACTTCCATACAAACCGAAGTTGTGAACTATG
1 ATTGAAGAAAGAATGAAGAAACACATTTTTTCATACTTCAATACAAACCAAAGTTGTGAACTATG
*
123374706 TAAAATTGATCACTTAATGCTTGCATCAGAAACTCGAGTTAGCATCACCCATGATGTCTTGAAGG
66 TAAAATTGATCACTTAATGCTTGCATCAGAAACTCGAGTTAGCATCACCCATGAAGTCTTGAAGG
* * * *
123374771 GGAATCCGAGTAGAGTTCATCGTATGCATATAATAGGAGGGAAAAACAACCAAAACCAATGCAAA
131 GGAATCCGAGTAGAGTTCATCATATGAATACAATAGGAAGGAAAAACAACCAAAACCAATGCAAA
*
123374836 TAGGAAGGCAAATCAACAAACTGA
196 TAGGAAAGCAAATCAACAAACTGA
* * *
123374860 ATTGAAGAAAGAATGAAGAAACACA-TTTTTCATACTTTAATACAAATCAAATTTGTGAACTATG
1 ATTGAAGAAAGAATGAAGAAACACATTTTTTCATACTTCAATACAAACCAAAGTTGTGAACTATG
*
123374924 TAAAATTGATCACTTAATGTTTGCATCAGAAACTCGAGTTAGCATCACCCATGAAGTCTTGAAGG
66 TAAAATTGATCACTTAATGCTTGCATCAGAAACTCGAGTTAGCATCACCCATGAAGTCTTGAAGG
123374989 GGAATCCGAGTAGAGTTCATCATATGAATACAATAGGAAGGAAAAACAACCAAAACCAATGCAAA
131 GGAATCCGAGTAGAGTTCATCATATGAATACAATAGGAAGGAAAAACAACCAAAACCAATGCAAA
123375054 TAGGAAAGCAAATCAAC
196 TAGGAAAGCAAATCAAC
123375071 CAAAAGCAAT
Statistics
Matches: 198, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
218 173 0.87
219 25 0.13
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (219 bp):
ATTGAAGAAAGAATGAAGAAACACATTTTTTCATACTTCAATACAAACCAAAGTTGTGAACTATG
TAAAATTGATCACTTAATGCTTGCATCAGAAACTCGAGTTAGCATCACCCATGAAGTCTTGAAGG
GGAATCCGAGTAGAGTTCATCATATGAATACAATAGGAAGGAAAAACAACCAAAACCAATGCAAA
TAGGAAAGCAAATCAACAAACTGA
Found at i:123375071 original size:32 final size:32
Alignment explanation
Indices: 123375020--123375083 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
123375010 ATATGAATAC
*
123375020 AATAGGAAGGAAAAACAACCAAAACCAATGCA
1 AATAGGAAAGAAAAACAACCAAAACCAATGCA
* * *
123375052 AATAGGAAAGCAAATCAACCAAAAGCAATGCA
1 AATAGGAAAGAAAAACAACCAAAACCAATGCA
123375084 GGCAAGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.58, C:0.19, G:0.16, T:0.08
Consensus pattern (32 bp):
AATAGGAAAGAAAAACAACCAAAACCAATGCA
Found at i:123376809 original size:18 final size:18
Alignment explanation
Indices: 123376775--123376809 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
123376765 TTATAATGTT
**
123376775 TTATATATTATGTAATTC
1 TTATATATTATAAAATTC
123376793 TTATATATTATAAAATT
1 TTATATATTATAAAATT
123376810 TATAACACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATATATTATAAAATTC
Found at i:123377843 original size:14 final size:15
Alignment explanation
Indices: 123377826--123377862 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
123377816 TAAAATTACA
123377826 TAATTTTAA-TTAAT
1 TAATTTTAATTTAAT
*
123377840 TAATTGTAATTTAAT
1 TAATTTTAATTTAAT
123377855 T-ATTTTAA
1 TAATTTTAA
123377863 ACTACATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TAATTTTAATTTAAT
Found at i:123379205 original size:24 final size:24
Alignment explanation
Indices: 123379169--123379224 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
123379159 TCATATGCAC
* * *
123379169 CTCCTTCACCGGCACCGTATGGGG
1 CTCCTCCAGCGGCACCATATGGGG
* *
123379193 CTGCTCCAGCGGCAGCATATGGGG
1 CTCCTCCAGCGGCACCATATGGGG
123379217 CTCCTCCA
1 CTCCTCCA
123379225 CCAAGTTCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.20
Consensus pattern (24 bp):
CTCCTCCAGCGGCACCATATGGGG
Found at i:123379792 original size:21 final size:21
Alignment explanation
Indices: 123379768--123379810 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
123379758 CAAAATTTAA
123379768 TTTTTTTAGAATACAAATAAT
1 TTTTTTTAGAATACAAATAAT
123379789 TTTTTTTAGAATACAAATAAT
1 TTTTTTTAGAATACAAATAAT
123379810 T
1 T
123379811 AACTTGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTTTTTAGAATACAAATAAT
Found at i:123382446 original size:19 final size:19
Alignment explanation
Indices: 123382410--123382449 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
123382400 ATACTCTTTT
*
123382410 TATTTTTTTCTAATATCAA
1 TATTTATTTCTAATATCAA
123382429 TATTTATTT-TAATAATCAA
1 TATTTATTTCTAAT-ATCAA
123382448 TA
1 TA
123382450 ATACGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTATTTCTAATATCAA
Found at i:123383896 original size:23 final size:23
Alignment explanation
Indices: 123383870--123383913 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
123383860 ATATTATCCT
123383870 TCCATATATTACAATCTTTTGAG
1 TCCATATATTACAATCTTTTGAG
123383893 TCCATATATTACAATCTTTTG
1 TCCATATATTACAATCTTTTG
123383914 CTGCTCAAAG
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:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (23 bp):
TCCATATATTACAATCTTTTGAG
Found at i:123395333 original size:53 final size:53
Alignment explanation
Indices: 123395252--123395402 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
123395242 CTTACACGGT
* *
123395252 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
123395307 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
123395360 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
123395403 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:123402770 original size:53 final size:53
Alignment explanation
Indices: 123402689--123402839 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
123402679 CTTACACGGT
* *
123402689 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
123402744 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
123402797 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
123402840 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:123404697 original size:92 final size:92
Alignment explanation
Indices: 123404532--123404702 Score: 238
Period size: 92 Copynumber: 1.9 Consensus size: 92
123404522 TGCCATAGTG
* * * * *
123404532 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTTTTG
1 TCTTTCAACCATGGTCTTACACATTTTCTATCAGGCTGCCATGGTATCTTTCAACCATGGTTTTG
** *
123404597 TTCTTTTCATATCACGTTTCCATGGTA
66 CACATTTCATATCACGTTTCCATGGTA
123404624 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTT
1 TCTTTCAACCATGGTCTTACACATTTTC-TATCAGGCTGCCATGGTATCTTTCAACCATGGT-TT
123404688 T-CACATTTCATATCA
64 TGCACATTTCATATCA
123404703 GAGAGCACAC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 4 0.06
92 62 0.90
93 3 0.04
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (92 bp):
TCTTTCAACCATGGTCTTACACATTTTCTATCAGGCTGCCATGGTATCTTTCAACCATGGTTTTG
CACATTTCATATCACGTTTCCATGGTA
Found at i:123404703 original size:46 final size:46
Alignment explanation
Indices: 123404522--123404703 Score: 213
Period size: 46 Copynumber: 4.0 Consensus size: 46
123404512 TTTGACATGA
* * * * * *
123404522 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *** * *
123404568 TGCCATGGTATCTTTCAACCATGGTTTTGTTCTTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
123404614 TTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
123404660 TGCCATGGTATCTTTCAACCATGGTCTTTCACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
123404704 AGAGCACACT
Statistics
Matches: 116, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
45 4 0.03
46 112 0.97
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:123408079 original size:20 final size:21
Alignment explanation
Indices: 123408041--123408079 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
123408031 AGAATAGAAA
* *
123408041 TGTAAAGTATATATTAAAATT
1 TGTAAAGTAGATATAAAAATT
123408062 TGTAAA-TAGATATAAAAA
1 TGTAAAGTAGATATAAAAA
123408080 AGAGAGAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
TGTAAAGTAGATATAAAAATT
Found at i:123413328 original size:42 final size:42
Alignment explanation
Indices: 123413282--123413362 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
123413272 TAGAAAAGTT
*
123413282 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGATAGAAAGACTA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
*
123413324 ACAGAGAGCAAACGTGAGAAAGAAAGAAGGAAAGAAAGA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGA
123413363 AAGAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.05
Consensus pattern (42 bp):
ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
Found at i:123414185 original size:47 final size:47
Alignment explanation
Indices: 123414146--123414278 Score: 239
Period size: 47 Copynumber: 2.8 Consensus size: 47
123414136 TGTCAACTAC
123414146 TGTTAAAGTTCCGGATTTGTTCCGATGAAGTACTTTGTGTACTATAA
1 TGTTAAAGTTCCGGATTTGTTCCGATGAAGTACTTTGTGTACTATAA
*
123414193 TGTTAAAGTTCCAGATTTGTTCCGATGAAGTACTTTGTGTACTATAA
1 TGTTAAAGTTCCGGATTTGTTCCGATGAAGTACTTTGTGTACTATAA
* *
123414240 TGTTAAAGTTCCGGATTTGTTCCGATGAAGCACTATGTG
1 TGTTAAAGTTCCGGATTTGTTCCGATGAAGTACTTTGTG
123414279 CTTATCCCGG
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 82 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (47 bp):
TGTTAAAGTTCCGGATTTGTTCCGATGAAGTACTTTGTGTACTATAA
Found at i:123417990 original size:38 final size:38
Alignment explanation
Indices: 123417939--123418015 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
123417929 TTAAAGAGAT
123417939 AGTGGGATATGATGGCTTGGCATTTGGTGTAATAAATA
1 AGTGGGATATGATGGCTTGGCATTTGGTGTAATAAATA
123417977 AGTGGGATATGATGGCTTGGCATTTGGTGTAATAAATA
1 AGTGGGATATGATGGCTTGGCATTTGGTGTAATAAATA
123418015 A
1 A
123418016 AGTGTGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (38 bp):
AGTGGGATATGATGGCTTGGCATTTGGTGTAATAAATA
Found at i:123419095 original size:28 final size:28
Alignment explanation
Indices: 123419034--123419095 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
123419024 TCAGTGTACG
*
123419034 AAATATTGAGAATGGCACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAGTGTGCA
*
123419062 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAGTGTGCA
123419090 AAATAT
1 AAATAT
123419096 CGAATGATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAGTGTGCA
Found at i:123420625 original size:13 final size:14
Alignment explanation
Indices: 123420609--123420644 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
123420599 CAATCTCATA
123420609 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
123420622 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
123420635 TCTC-ATTTCA
1 TCTCAATTTCA
123420645 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:123420634 original size:18 final size:19
Alignment explanation
Indices: 123420596--123420636 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
123420586 TGGTTCATGT
123420596 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
123420615 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
123420633 TTTC
1 TTTC
123420637 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:123420826 original size:39 final size:38
Alignment explanation
Indices: 123420759--123420893 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
123420749 ACCAATATGG
* * *
123420759 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
123420798 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
123420836 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
123420877 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
123420894 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:123421159 original size:18 final size:19
Alignment explanation
Indices: 123421133--123421171 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
123421123 TTTCAATTCA
123421133 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
123421152 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
123421170 AT
1 AT
123421172 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:123421535 original size:5 final size:5
Alignment explanation
Indices: 123421525--123421581 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
123421515 TTACTTATTT
* *
123421525 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
123421573 ATAT- ATATA
1 ATATA ATATA
123421582 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:123421541 original size:12 final size:12
Alignment explanation
Indices: 123421524--123421579 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
123421514 TTTACTTATT
123421524 TATATAATATAA
1 TATATAATATAA
123421536 TATATAATATAATA
1 TATATAATAT-A-A
123421550 TACTATAATATAA
1 TA-TATAATATAA
*
123421563 TA-ATAATTTAA
1 TATATAATATAA
123421574 TATATA
1 TATATA
123421580 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:123421594 original size:26 final size:26
Alignment explanation
Indices: 123421526--123421581 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
123421516 TACTTATTTA
*
123421526 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
123421553 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
123421578 TATA
1 TATA
123421582 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:123423568 original size:18 final size:18
Alignment explanation
Indices: 123423545--123423618 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
123423535 TTTTAGTTAA
*
123423545 TATTTTATTATAATATAT
1 TATTATATTATAATATAT
* * *
123423563 TATTTTATTATTATATCAA
1 TATTATATTATAATAT-AT
* * *
123423582 TATTACATTATATTAAAT
1 TATTATATTATAATATAT
123423600 TATTATATTATATATATAT
1 TATTATATTATA-ATATAT
123423619 AACAAAAGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
18 27 0.63
19 16 0.37
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATTATAATATAT
Found at i:123423596 original size:5 final size:5
Alignment explanation
Indices: 123423544--123423618 Score: 55
Period size: 5 Copynumber: 14.8 Consensus size: 5
123423534 TTTTTAGTTA
* * * * *
123423544 ATATT TTATT ATAAT ATATT ATTTT ATTATT ATATCA ATATT ACATT ATATT
1 ATATT ATATT ATATT ATATT ATATT A-TATT ATAT-T ATATT ATATT ATATT
*
123423596 A-AAT -TATT ATATT ATATAT ATAT
1 ATATT ATATT ATATT ATAT-T ATAT
123423619 AACAAAAGAA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
4 4 0.08
5 36 0.68
6 13 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:123424424 original size:23 final size:24
Alignment explanation
Indices: 123424398--123424443 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
123424388 TATCATTCAT
*
123424398 TTCATTATATCAATAT-TTTATGC
1 TTCATCATATCAATATATTTATGC
* *
123424421 TTCATCATTTCCATATATTTATG
1 TTCATCATATCAATATATTTATG
123424444 TATATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.52
Consensus pattern (24 bp):
TTCATCATATCAATATATTTATGC
Found at i:123424764 original size:46 final size:47
Alignment explanation
Indices: 123424704--123425012 Score: 414
Period size: 46 Copynumber: 6.7 Consensus size: 47
123424694 TTTGACGTGA
* * * * *
123424704 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
**
123424750 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
* **
123424796 TGCCATGGTATCTTTCAACCACGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
**
123424842 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
* * *
123424888 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
* * *
123424934 TGCCATGGTATCTATCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
123424980 TGCCATGGTATCTTTCAACCATGGTCTTACACA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA
123425013 CAGGTTCCCA
Statistics
Matches: 245, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.02
46 240 0.98
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
Found at i:123424822 original size:92 final size:93
Alignment explanation
Indices: 123424704--123425107 Score: 501
Period size: 92 Copynumber: 4.5 Consensus size: 93
123424694 TTTGACGTGA
* * * * *
123424704 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCAAGTTGCCATGGTATCTTTCAA
** * *
123424768 CCATGGTCTTATTCTTTTCATGTCACGT
66 CCATGGTCTTACACATTTCATATCACGT
* ** *
123424796 TGCCATGGTATCTTTCAACCACGGTCTTATTC-TTTTCATGTCACGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCAAGTTGCCATGGTATCTTTCAA
** * *
123424860 CCATGGTCTTATTCTTTTCATGTCACGT
66 CCATGGTCTTACACATTTCATATCACGT
* * *
123424888 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATCAAGTTGCCATGGTATCTATCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCAAGTTGCCATGGTATCTTTCAA
*
123424952 CCATGGTCTTACACATTTCATATCAGGT
66 CCATGGTCTTACACATTTCATATCACGT
*
123424980 TGCCATGGTATCTTTCAACCATGGTCTTACACA----CA-G----GTTCCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCAAGTTGCCATGGTATCTTTCAA
*
123425036 CCATGGTCTTACACATTTCATATCAGGT
66 CCATGGTCTTACACATTTCATATCACGT
*
123425064 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCAA
123425108 AGAGCACACT
Statistics
Matches: 280, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
84 79 0.28
87 2 0.01
89 2 0.01
91 5 0.02
92 192 0.69
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (93 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCAAGTTGCCATGGTATCTTTCAA
CCATGGTCTTACACATTTCATATCACGT
Found at i:123424858 original size:25 final size:25
Alignment explanation
Indices: 123424783--123424858 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
123424773 GTCTTATTCT
123424783 TTTCATGTCACGTTGCCATGGTATC
1 TTTCATGTCACGTTGCCATGGTATC
** *
123424808 TTTCA-ACCACG--GTC-T--TATTC
1 TTTCATGTCACGTTGCCATGGTA-TC
123424828 TTTTCATGTCACGTTGCCATGGTATC
1 -TTTCATGTCACGTTGCCATGGTATC
123424854 TTTCA
1 TTTCA
123424859 ACCATGGTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 6 0.16
22 6 0.16
24 6 0.16
25 11 0.30
26 2 0.05
27 2 0.05
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (25 bp):
TTTCATGTCACGTTGCCATGGTATC
Found at i:123424952 original size:138 final size:137
Alignment explanation
Indices: 123424704--123425106 Score: 534
Period size: 138 Copynumber: 3.0 Consensus size: 137
123424694 TTTGACGTGA
* * * *
123424704 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTA-TC-TTTTCATGTCACGTTGCCATGGTATCTTTCAA
** * * * * ** *
123424768 CCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCACGGTCTTATTCTTTTC
64 CCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
*
123424833 ATGTCACGT
129 ATATCACGT
123424842 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTA-TCTTTTCATGTCACGTTGCCATGGTATCTTTCAAC
* *
123424907 CATGGTCTTACACATCTCATATCAAGTTGCCATGGTATCTATCAACCATGGTCTTACACATTTCA
65 CATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
*
123424972 TATCAGGT
130 TATCACGT
* * *
123424980 TGCCATGGTATCTTTCAACCATGGTCTTA-C---ACA---CAGGTTCCCATGGTATCTTTCAACC
1 TGCCATGGTATCTTTCAACCATGGTCTTATCTTTTCATGTCACGTTGCCATGGTATCTTTCAACC
*
123425038 ATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
66 ATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
123425103 ATCA
131 ATCA
123425107 AAGAGCACAC
Statistics
Matches: 240, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
130 89 0.37
133 2 0.01
136 1 0.00
137 5 0.02
138 143 0.60
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (137 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATCTTTTCATGTCACGTTGCCATGGTATCTTTCAACC
ATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
ATCACGT
Found at i:123425026 original size:38 final size:39
Alignment explanation
Indices: 123424973--123425097 Score: 171
Period size: 38 Copynumber: 3.1 Consensus size: 39
123424963 CACATTTCAT
123424973 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
123425012 A-CAGGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C
123425055 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 --ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
123425096 AT
1 AT
123425098 TTCATATCAA
Statistics
Matches: 76, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
38 32 0.42
39 3 0.04
40 3 0.04
41 1 0.01
43 1 0.01
44 3 0.04
45 1 0.01
46 32 0.42
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (39 bp):
ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:123425077 original size:84 final size:84
Alignment explanation
Indices: 123424936--123425096 Score: 313
Period size: 84 Copynumber: 1.9 Consensus size: 84
123424926 TATCAAGTTG
123424936 CCATGGTATCTATCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
1 CCATGGTATCTATCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
123425001 TGGTCTTACACACAGGTTC
66 TGGTCTTACACACAGGTTC
*
123425020 CCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
1 CCATGGTATCTATCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
123425085 TGGTCTTACACA
66 TGGTCTTACACA
123425097 TTTCATATCA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (84 bp):
CCATGGTATCTATCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
TGGTCTTACACACAGGTTC
Found at i:123425080 original size:46 final size:46
Alignment explanation
Indices: 123425013--123425106 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
123425003 GTCTTACACA
123425013 CAGGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CAGGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
123425059 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CAGGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
123425105 CA
1 CA
123425107 AAGAGCACAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (46 bp):
CAGGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:123427209 original size:23 final size:24
Alignment explanation
Indices: 123427174--123427223 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
123427164 TTCTTTCTTT
123427174 ATATACTAATAAAATAATAATAAA
1 ATATACTAATAAAATAATAATAAA
* * *
123427198 ATAT-CTATTAAAGTATTAATAAA
1 ATATACTAATAAAATAATAATAAA
123427221 ATA
1 ATA
123427224 ATATTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
ATATACTAATAAAATAATAATAAA
Found at i:123429524 original size:44 final size:45
Alignment explanation
Indices: 123429434--123429562 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
123429424 GACAGAACGA
*
123429434 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
123429480 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
123429524 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
123429563 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:123434570 original size:47 final size:46
Alignment explanation
Indices: 123434456--123434635 Score: 207
Period size: 46 Copynumber: 3.9 Consensus size: 46
123434446 ATCTGATAGA
* * * * *
123434456 AAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
* * *
123434502 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGG
* * * *
123434549 AAATGAATAAGACCATGGTTGAATGATACCATGGCAATATGACAGA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
* * * *
123434595 AAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
123434636 TCGAAGATAA
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
46 75 0.66
47 39 0.34
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG
Found at i:123437248 original size:18 final size:17
Alignment explanation
Indices: 123437225--123437266 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
123437215 ATTAAATTAT
123437225 TATTAAA-TTATTTAGAGA
1 TATTAAAGTTA-TTAGA-A
123437243 TATTAAAGTTATTAGAA
1 TATTAAAGTTATTAGAA
123437260 TATTAAA
1 TATTAAA
123437267 AACGCTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 12 0.52
19 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (17 bp):
TATTAAAGTTATTAGAA
Found at i:123443312 original size:20 final size:20
Alignment explanation
Indices: 123443287--123443332 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
123443277 GTCGCTGGTT
123443287 TTTTGGTCCCAAGAGTTAGG
1 TTTTGGTCCCAAGAGTTAGG
123443307 TTTTGGTCCCAAGAGTTAGG
1 TTTTGGTCCCAAGAGTTAGG
*
123443327 TCTTGG
1 TTTTGG
123443333 CTGTATGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.37
Consensus pattern (20 bp):
TTTTGGTCCCAAGAGTTAGG
Found at i:123443646 original size:25 final size:25
Alignment explanation
Indices: 123443628--123443678 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
123443618 AAATATATAC
123443628 ACCTCATCTATGTATAAATTATCAA
1 ACCTCATCTATGTATAAATTATCAA
123443653 ACCTCATCTATGTATAAATTATCAA
1 ACCTCATCTATGTATAAATTATCAA
123443678 A
1 A
123443679 TTTATCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (25 bp):
ACCTCATCTATGTATAAATTATCAA
Found at i:123443920 original size:30 final size:31
Alignment explanation
Indices: 123443886--123443946 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
123443876 AAAAAAAGAA
*
123443886 TTTAATAATTTAATAAC-TTAAATAATTTTT
1 TTTAATAATTCAATAACATTAAATAATTTTT
**
123443916 TTTAATAATTCAATAACATTTTATAATTTTT
1 TTTAATAATTCAATAACATTAAATAATTTTT
123443947 AAAATTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTAATAATTCAATAACATTAAATAATTTTT
Found at i:123443937 original size:21 final size:22
Alignment explanation
Indices: 123443894--123443942 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
123443884 AATTTAATAA
**
123443894 TTTAATAACTTAAATAATTTTT
1 TTTAATAACTTAAATAACATTT
*
123443916 TTTAATAA-TTCAATAACATTT
1 TTTAATAACTTAAATAACATTT
*
123443937 TATAAT
1 TTTAAT
123443943 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAATAACTTAAATAACATTT
Found at i:123443937 original size:22 final size:22
Alignment explanation
Indices: 123443894--123443937 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
123443884 AATTTAATAA
*
123443894 TTTAATAACTTAAATAATTTTT
1 TTTAATAACTTAAATAAATTTT
*
123443916 TTTAATAA-TTCAATAACATTTT
1 TTTAATAACTTAAATAA-ATTTT
123443938 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAATAACTTAAATAAATTTT
Found at i:123446955 original size:20 final size:20
Alignment explanation
Indices: 123446903--123446956 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
123446893 CTTTTTTGTA
*
123446903 AACTTAAAATTTAGTAATTT
1 AACTTAAAATTTAGGAATTT
* **
123446923 -ACTTTTATTTTTAGGAATTT
1 AAC-TTAAAATTTAGGAATTT
123446943 AACTTAAAATTTAG
1 AACTTAAAATTTAG
123446957 ATACACTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (20 bp):
AACTTAAAATTTAGGAATTT
Found at i:123448905 original size:56 final size:56
Alignment explanation
Indices: 123448819--123448997 Score: 351
Period size: 56 Copynumber: 3.2 Consensus size: 56
123448809 ATAAACAAGC
123448819 CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
1 CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
123448875 CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
1 CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
123448931 CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
1 CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
123448987 CTTTAT-ATATT
1 CTTTATGATATT
123448998 GAAAGTAATT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
55 5 0.04
56 118 0.96
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (56 bp):
CTTTATGATATTTTTATATAAATTTAAATTATTAATATATGTAAAATATATATCAT
Found at i:123456667 original size:23 final size:23
Alignment explanation
Indices: 123456641--123456686 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
123456631 CCACAATCCC
123456641 TAACTCTGCACACAAAACAAAGA
1 TAACTCTGCACACAAAACAAAGA
123456664 TAACTCTGCACACAAAACAAAGA
1 TAACTCTGCACACAAAACAAAGA
123456687 ACCCACCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.09, T:0.13
Consensus pattern (23 bp):
TAACTCTGCACACAAAACAAAGA
Found at i:123464163 original size:154 final size:152
Alignment explanation
Indices: 123463934--123464367 Score: 414
Period size: 154 Copynumber: 2.8 Consensus size: 152
123463924 CATTGATAAA
* * *
123463934 TAAATAAAAATTTCATGTAAAATTTT-AAAATTCATTGTTAAACATTAAAAAAATGCA-TATTTT
1 TAAATAAAAATTT-ATGTATAATTTTAAAAATTC--T-TTAAAAATT-AAAAAATGTATTATTTT
* * * * * *
123463997 GTAAAAATTCTAAATCAAAGTGAGAAACTAACTCTTGTTGAAATATCTATACTA-TAATAAAATT
61 ATAAAAGTTCTAAATCAAAGTGAGAAA-TAATTCTTATTAAAATATCTATACTATTAATAAAATC
*
123464061 ATTAACCGAGTTGGTATATAAAATTACATAT
125 A-TAACCGAATTGG--TATAAAATTACATAT
*
123464092 TAAATTAAAATTTATGTATAATTTTAAAAATTCTTTAAAAATT-AAAAATGTATTATTTTATAAA
1 TAAATAAAAATTTATGTATAATTTTAAAAATTCTTTAAAAATTAAAAAATGTATTATTTTATAAA
* * * * * * *
123464156 AGTTCTAAATTGACA-TCAGAAAT--TTTTTCTTAAAATATCTATACTATTAATAGAACTCATGA
66 AGTTCTAAA-TCAAAGTGAGAAATAATTCTTATTAAAATATCTATACTATTAATA-AAATCATAA
**
123464218 TTGAATTGGTATAAAATTACATAT
129 CCGAATTGGTATAAAATTACATAT
* * * * * * *
123464242 TAAATCAAAATTAATATATAACTTTAAAACTTGTCCTTAAATATTAAAAAAATGTATTATTTTAT
1 TAAATAAAAATTTATGTATAATTTTAAAA-AT-TCTTTAAAAATT-AAAAAATGTATTATTTTAT
* * *
123464307 AAAAGTTCTAAATCAAAGTGAGAAGTTAATTCCTATCAAAATATCTATACTATTAATAAAA
63 AAAAGTTCTAAATCAAAGTGAGAA-ATAATTCTTATTAAAATATCTATACTATTAATAAAA
123464368 CTCCTAATTT
Statistics
Matches: 228, Mismatches: 35, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
150 40 0.18
151 20 0.09
152 23 0.10
153 16 0.07
154 59 0.26
155 12 0.05
156 3 0.01
157 36 0.16
158 19 0.08
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (152 bp):
TAAATAAAAATTTATGTATAATTTTAAAAATTCTTTAAAAATTAAAAAATGTATTATTTTATAAA
AGTTCTAAATCAAAGTGAGAAATAATTCTTATTAAAATATCTATACTATTAATAAAATCATAACC
GAATTGGTATAAAATTACATAT
Found at i:123466003 original size:16 final size:18
Alignment explanation
Indices: 123465982--123466021 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
123465972 AAAATAGAAA
*
123465982 AAAATAATACT-T-AAAT
1 AAAATAATAATGTCAAAT
123465998 AAAATAATAATGTCAAAT
1 AAAATAATAATGTCAAAT
123466016 AAAATA
1 AAAATA
123466022 GTGATAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 1 0.05
18 10 0.48
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATAATAATGTCAAAT
Found at i:123466006 original size:19 final size:18
Alignment explanation
Indices: 123465979--123466021 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
123465969 TTAAAAATAG
* *
123465979 AAAAAAATAATACTTAAAT
1 AAAATAATAAT-CTCAAAT
*
123465998 AAAATAATAATGTCAAAT
1 AAAATAATAATCTCAAAT
123466016 AAAATA
1 AAAATA
123466022 GTGATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATAATAATCTCAAAT
Found at i:123489807 original size:30 final size:30
Alignment explanation
Indices: 123489771--123489839 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
123489761 CTAGCCTTTG
123489771 CCACCACCAACTCCACTAGCCACAATTGCT
1 CCACCACCAACTCCACTAGCCACAATTGCT
*
123489801 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACAATTGCT
*
123489831 CCACTACCA
1 CCACCACCA
123489840 CTTGTACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.29, C:0.49, G:0.06, T:0.16
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACAATTGCT
Found at i:123491724 original size:5 final size:5
Alignment explanation
Indices: 123491703--123491755 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
123491693 TGTTAAAATA
* *
123491703 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
123491751 TATAT
1 TATAT
123491756 AAATAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:123491734 original size:10 final size:9
Alignment explanation
Indices: 123491700--123491756 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
123491690 ATGTGTTAAA
123491700 ATATATATT
1 ATATATATT
*
123491709 AAAT-TATT
1 ATATATATT
123491717 AT-TATATT
1 ATATATATT
123491725 ATAGTATATT
1 ATA-TATATT
123491735 ATAT-TA-T
1 ATATATATT
123491742 ATATTATATT
1 ATA-TATATT
123491752 ATATA
1 ATATA
123491757 AATAGTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:123491746 original size:12 final size:12
Alignment explanation
Indices: 123491701--123491756 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
123491691 TGTGTTAAAA
*
123491701 TATATATTAAAT
1 TATATATTATAT
123491713 TAT-TATTATATT
1 TATATATTATA-T
123491725 ATAGTATATTATAT
1 -TA-TATATTATAT
123491739 TATATATTATAT
1 TATATATTATAT
123491751 TATATA
1 TATATA
123491757 AATAGTAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:123493093 original size:18 final size:19
Alignment explanation
Indices: 123493072--123493110 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
123493062 ATATATAGAT
123493072 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
123493090 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
123493109 AT
1 AT
123493111 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:123493459 original size:39 final size:39
Alignment explanation
Indices: 123493349--123493483 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
123493339 GACCTCGAGT
* * * *
123493349 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
123493390 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
123493428 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
123493467 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
123493484 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:123493627 original size:18 final size:19
Alignment explanation
Indices: 123493606--123493646 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
123493596 AATGAAATGA
123493606 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
123493624 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
123493643 GAAA
1 GAAA
123493647 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:123498174 original size:5 final size:5
Alignment explanation
Indices: 123498153--123498205 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
123498143 TGTTAAAATA
* *
123498153 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
123498201 TATAT
1 TATAT
123498206 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:123498184 original size:10 final size:9
Alignment explanation
Indices: 123498150--123498206 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
123498140 ATGTGTTAAA
123498150 ATATATATT
1 ATATATATT
*
123498159 AAAT-TATT
1 ATATATATT
123498167 AT-TATATT
1 ATATATATT
123498175 ATAGTATATT
1 ATA-TATATT
123498185 ATAT-TA-T
1 ATATATATT
123498192 ATATTATATT
1 ATA-TATATT
123498202 ATATA
1 ATATA
123498207 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:123498196 original size:12 final size:12
Alignment explanation
Indices: 123498151--123498206 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
123498141 TGTGTTAAAA
*
123498151 TATATATTAAAT
1 TATATATTATAT
123498163 TAT-TATTATATT
1 TATATATTATA-T
123498175 ATAGTATATTATAT
1 -TA-TATATTATAT
123498189 TATATATTATAT
1 TATATATTATAT
123498201 TATATA
1 TATATA
123498207 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:123499544 original size:18 final size:19
Alignment explanation
Indices: 123499523--123499561 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
123499513 ATATATAGAT
123499523 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
123499541 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
123499560 AT
1 AT
123499562 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:123499910 original size:39 final size:39
Alignment explanation
Indices: 123499800--123499934 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
123499790 GACCTCGAGT
* * * *
123499800 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
123499841 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
123499879 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
123499918 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
123499935 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:123500078 original size:18 final size:19
Alignment explanation
Indices: 123500057--123500097 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
123500047 AATGAAATGA
123500057 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
123500075 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
123500094 GAAA
1 GAAA
123500098 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:123502585 original size:30 final size:30
Alignment explanation
Indices: 123502495--123502585 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
123502485 TAGGTACAAG
123502495 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
* *
123502525 AGGTAGTAGAGCAAGTGTGGCTAGTGGAGT
1 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
123502555 TGGTGGTGGAGCAATTGTGGCTAATGGAGT
1 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
123502585 T
1 T
123502586 TGTGGTGGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.22, C:0.07, G:0.44, T:0.27
Consensus pattern (30 bp):
TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:123503493 original size:30 final size:30
Alignment explanation
Indices: 123503457--123503518 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
123503447 TTTTGAAAAA
** *
123503457 CAGAAATTAAATGGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAAATCACCTCTCG
123503487 CAGAAATTAAAAAGCTCAAATCACCTCTCG
1 CAGAAATTAAAAAGCTCAAATCACCTCTCG
123503517 CA
1 CA
123503519 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAAATCACCTCTCG
Found at i:123503522 original size:84 final size:83
Alignment explanation
Indices: 123503416--123503571 Score: 258
Period size: 84 Copynumber: 1.9 Consensus size: 83
123503406 GTGACTCGAG
* * *
123503416 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTAAATGGCTCAACTCAC
1 GCTCAAATCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTAAAAGGCTCAACTCAC
123503481 CTCTCGCAGAAATTAAAAA
65 CTCTCGCAGAAATTAAAAA
* *
123503500 GCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTAAAAGGCTTAACTCACT
1 GCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTAAAAGGCTCAACTCACC
123503565 TCTCGCA
66 TCTCGCA
123503572 ATATGAGTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 33 0.49
84 34 0.51
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
GCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTAAAAGGCTCAACTCACC
TCTCGCAGAAATTAAAAA
Found at i:123503569 original size:53 final size:53
Alignment explanation
Indices: 123503487--123503606 Score: 186
Period size: 53 Copynumber: 2.2 Consensus size: 53
123503477 TCACCTCTCG
123503487 CAGAAATTAAAAAGCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 CAGAAATTAAAAAGCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * * *
123503540 CAGAAATTAAAAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
1 CAGAAATTAAAAAGCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAA
*
123503593 CAGAATTTGAAAAA
1 CAGAAATT-AAAAA
123503607 CAGATTTTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 56 0.93
54 4 0.07
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (53 bp):
CAGAAATTAAAAAGCTCAAATCACCTCTCGCAATATGAGTTGATTTTTGAAAA
Found at i:123503608 original size:14 final size:14
Alignment explanation
Indices: 123503585--123503619 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
123503575 TGAGTTGATT
123503585 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
123503598 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
123503612 TTTGAAAA
1 TTTGAAAA
123503620 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:123503970 original size:72 final size:73
Alignment explanation
Indices: 123503638--123504879 Score: 1235
Period size: 72 Copynumber: 16.6 Consensus size: 73
123503628 CATGTGACCC
* * * * * *
123503638 GAGGCTCAACTCACATTTCTCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG---AAAATAC
* *
123503703 CTCAGTGTGTGATCT
61 CTCAGCGTGT-CT-T
* *
123503718 GAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAATTGAAAATAGCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAA-ACAGAAATTGAAAATACCT
* *
123503783 CAGCGCGTGAGC-C
63 CA--GCGTG-TCTT
* * *
123503796 AAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTGAAAGGCAGAAATTGAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAA-ACAGAAATTGAAAATACC
* *
123503861 TCAGCATGTGAAC-C
62 TCAGC--GTG-TCTT
* * *
123503875 GAGGCTCAACTTACCTCTGGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAAATACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
*
123503939 CTTGTCTT
66 CGTGTCTT
* * *
123503947 GAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTGGACAACAGAAATT-AAAATTACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-GAAAACAGAAATTGAAAA-TACCTC
* *
123504011 AACGTGTCCT
64 AGCGTGTCTT
123504021 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTC
*
123504086 AGCATGTCTT
64 AGCGTGTCTT
**
123504096 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTGAAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTG-AAAACAGAAATTGAAAATAC
*
123504161 CTCAGCATGTCTT
61 CTCAGCGTGTCTT
** *
123504174 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATT-AAAATTACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAA-TACCTCA
*
123504237 ACGTGTCTT
65 GCGTGTCTT
**
123504246 GAGGCTCAACTCATTTCTCGCAATATGAGTTGGA--TTTTGAAAACAGAAATTGAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
123504309 ACGTGTCTT
65 GCGTGTCTT
** * * *
123504318 GAGGCTCAACTCATTTCTCGC---A--AGTTGATTTTTTTGACAACAGAAATTGAAATTACTTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCA
*
123504378 GCGTGTCCT
65 GCGTGTCTT
* *
123504387 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTC
*
123504452 AGCATGTCTT
64 AGCGTGTCTT
** *
123504462 GAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTTTTTTTGAAAAACAGAAATTGAAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTG-AAAACAGAAATTGAAAATA
*
123504527 CCTCAGCATGTCTT
60 CCTCAGCGTGTCTT
* ** * * *
123504541 GACGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTAAAAACAGAAATTGAAAATACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
*
123504605 TGTGTCTT
66 CGTGTCTT
** ** *
123504613 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAGGTAGAAATTGAAAATGCCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTC
* * *
123504678 AGTATGTGAAC-C
64 AG--CGTG-TCTT
* *
123504690 GAGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAAATACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
123504754 CGTGTCTT
66 CGTGTCTT
* ** * * *
123504762 GAAGCTCAACTCATTTATCGCAATATGAGTTGA-ATTTTGAAAATAGAAATTGAAAATACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
* *
123504826 CATGTGAAC-C
66 C--GTG-TCTT
*
123504836 GAGGCTCCACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAC
123504880 GGAAGTAACA
Statistics
Matches: 1009, Mismatches: 107, Indels: 98
0.83 0.09 0.08
Matches are distributed among these distances:
66 2 0.00
67 4 0.00
69 52 0.05
71 6 0.01
72 265 0.26
73 24 0.02
74 162 0.16
75 150 0.15
76 4 0.00
77 36 0.04
78 112 0.11
79 138 0.14
80 38 0.04
81 16 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (73 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
CGTGTCTT
Found at i:123504421 original size:366 final size:367
Alignment explanation
Indices: 123503638--123504873 Score: 1487
Period size: 366 Copynumber: 3.3 Consensus size: 367
123503628 CATGTGACCC
* * * * * *
123503638 GAGGCTCAACTCACATTTCTCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAAATAC
1 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG---AAAATAC
** * *
123503703 CTCAGTGTGTGA-TCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTGAAAGA
63 CTCAGCATGT-ACT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAA
* * * ** ** *
123503765 CAGAAATTGAAAATAGCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGTCGA
126 CAGAAATTGAAAATACCTCA--GCATG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
* * * * * **
123503829 TTTTTTTTTGAAAGGCAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTTACCTCT
188 ----ATTTTGAAA-ACAGAAATTGAAAATACCTCA--ATGTG-TCTTGAGGCTCAACTCATTTCT
* *
123503893 GGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAACTTGTCTTGAGGCTCAACT
245 CGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACT
* * *
123503958 CGCCTCTCGCAATACGAGTTGATTTTTTGGACAACAGAAATTAAAATTACCTCAACGTGTCCT
310 CACCTCTCGC---A--AGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAACGTGTCCT
*
123504021 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTC
**
123504086 AGCATGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAA
66 AGCATGTACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAA
123504150 ATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAA
131 ATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAA
*
123504215 AACAGAAATT-AAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGG
196 AACAGAAATTGAAAA-TACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT-G
**
123504279 A-TTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAGT
259 ATTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAAGT
* *
123504343 TGATTTTTTTGACAACAGAAATTGAAATTACTTCAGCGTGTCCT
324 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAACGTGTCCT
*
123504387 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTT
1 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTC
** *
123504452 AGCATGT-CTTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTTTTTTTGAAAAACAGA
66 AGCATGTACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTTGAAAAACAGA
* *
123504516 AATTGAAAATACCTCAGCATGTCTTGACGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTAA
130 AATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA
123504581 AAACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
195 AAACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
** * * * * *
123504646 TTTTTTTGAAAGGTAGAAATTGAAAATGCCTCAGTATGTGAAC-CGAGGCTCAACTCACCTCTTG
260 --TTTTTGAAA-ACAGAAATTGAAAATACCTCA--ACGTG-TCTTGAGGCTCAACTCACCTCTCG
* * *
123504710 CAA-TATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTT
319 CAAGT-TGA-TT--TTTTTGACAACAGAAATTGAAATTACCTCAACGTGTCCT
* * * *
123504762 GAAGCTCAACTCA-TTTATCGCAATATGAGTTGA--ATTTTGAAA-ATAGAAATTGAAAATACCT
1 GAGGCTCAACTCACCTT-TCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCT
* *
123504823 CAGCATGTGAAC-CGAGGCTCCACTCACCTCTCGCAATATGAGTTGATTTTT
65 CAGCATGT--ACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
123504874 GAAAACGGAA
Statistics
Matches: 761, Mismatches: 68, Indels: 58
0.86 0.08 0.07
Matches are distributed among these distances:
366 150 0.20
367 140 0.18
368 5 0.01
369 8 0.01
370 19 0.02
371 87 0.11
372 58 0.08
373 31 0.04
374 39 0.05
375 63 0.08
377 1 0.00
378 64 0.08
379 1 0.00
380 47 0.06
383 48 0.06
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (367 bp):
GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTC
AGCATGTACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAA
ATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAA
AACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
TTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAAGTTG
ATTTTTTTGACAACAGAAATTGAAATTACCTCAACGTGTCCT
Found at i:123512334 original size:30 final size:30
Alignment explanation
Indices: 123512299--123512361 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
123512289 ACAAGTGGTA
* *
123512299 GTGGAGCAAGTGTGGCTAGTAAAGTTAGTG
1 GTGGAGCAAGTGTGACTAATAAAGTTAGTG
* * *
123512329 GTGGAGCAATTGTGACTAATGAAGTTGGTG
1 GTGGAGCAAGTGTGACTAATAAAGTTAGTG
123512359 GTG
1 GTG
123512362 ACAAAAGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.06, G:0.40, T:0.29
Consensus pattern (30 bp):
GTGGAGCAAGTGTGACTAATAAAGTTAGTG
Found at i:123513316 original size:26 final size:26
Alignment explanation
Indices: 123513280--123513332 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
123513270 AACTTTGATT
123513280 AGTAAAGCACAAACCTACAATAGCTA
1 AGTAAAGCACAAACCTACAATAGCTA
123513306 AGTAAAGCACAAACCTACAATAGCTA
1 AGTAAAGCACAAACCTACAATAGCTA
123513332 A
1 A
123513333 CATATTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.15
Consensus pattern (26 bp):
AGTAAAGCACAAACCTACAATAGCTA
Found at i:123514279 original size:180 final size:171
Alignment explanation
Indices: 123513974--123514558 Score: 646
Period size: 174 Copynumber: 3.4 Consensus size: 171
123513964 ACAAGACTTC
** * *
123513974 GCTCGTT--AACCCTAAACCTTGTTTTAATCATGGCTGCGA-TTACTACAAAACAACATTCAAAA
1 GCTCGTTACAACCCTAAACCTCATTTTAATCATCGCTGC-ACTTACTACAAAACAACACTCAAAA
* * **
123514036 A-CAAACAATTGTTTGAAAATCTTGAAC-TTCAAATTGAAAAAACACCGTAAAAAAGACTAACGG
65 ACCAAACAATTGTTT-AAAATCTTGAACATTC-AATCGGAAAAACGTCGTAAAAAAGA-TAACGG
* * * * * *
123514099 CACCTAATTAGTGATTATATTGGGAACATAGCTTAGGCACATCCTT
127 CAGCTCATTAGAGATTATATT-GTAACATAGCTTAGGCAAAACCTT
* * *
123514145 CGCTCGTTACAACCCTACACCTCAATTTATTTTAAATCATCGCTGCGCTTACCACAAAACAACAC
1 -GCTCGTTACAACCCTAAACCTC-----ATTTT-AATCATCGCTGCACTTACTACAAAACAACAC
* ** *
123514210 TCAAAAAACCAAACAATTGTTTAAAATTTTGAACATTCGGTCGGAAAAACGTTGTAAAAAAGATA
59 TC-AAAAACCAAACAATTGTTTAAAATCTTGAACATTCAATCGGAAAAACGTCGTAAAAAAGATA
* * *
123514275 ACGGCAGCTCATTAGAGATTATATTGTATTCATGGCTTAGGCAAAAACTT
123 ACGGCAGCTCATTAGAGATTATATTGTA-ACATAGCTTAGGCAAAACCTT
* *
123514325 GGCTCGTTACAACCCTAAACCTCATTTTAATCATCGCTGCAAC-CACTACAAAACAACACTCGAA
1 -GCTCGTTACAACCCTAAACCTCATTTTAATCATCGCTGC-ACTTACTACAAAACAACACTCAAA
* * *
123514389 AACCAAACATTTGTTTATAAATCTTGAACATTCAATCGGAAAAACGTCGTAAGAAAGATAAAGGC
64 AACCAAACAATTGTTTA-AAATCTTGAACATTCAATCGGAAAAACGTCGTAAAAAAGATAACGGC
* * * *
123514454 AGCTCATTAGGGATTATATTGTAATCAAAGCTAAGGCAAAGCCTT
128 AGCTCATTAGAGATTATATTGTAA-CATAGCTTAGGCAAAACCTT
123514499 GCCTCGTT--AACCCTAAACCTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCA
1 G-CTCGTTACAACCCTAAACCTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCA
123514559 TATTCCAAAC
Statistics
Matches: 349, Mismatches: 46, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
171 2 0.01
172 54 0.15
173 19 0.05
174 123 0.35
175 6 0.02
179 6 0.02
180 89 0.26
181 34 0.10
182 16 0.05
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (171 bp):
GCTCGTTACAACCCTAAACCTCATTTTAATCATCGCTGCACTTACTACAAAACAACACTCAAAAA
CCAAACAATTGTTTAAAATCTTGAACATTCAATCGGAAAAACGTCGTAAAAAAGATAACGGCAGC
TCATTAGAGATTATATTGTAACATAGCTTAGGCAAAACCTT
Found at i:123519612 original size:28 final size:29
Alignment explanation
Indices: 123519581--123519639 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
123519571 GCCCCCCAAA
123519581 AAAAACCTAACCCAAAAAAAAA-AAAAAG
1 AAAAACCTAACCCAAAAAAAAAGAAAAAG
123519609 AAAAACCTAACCCAAAAAAAAAGAAAAAG
1 AAAAACCTAACCCAAAAAAAAAGAAAAAG
123519638 AA
1 AA
123519640 GAAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.75, C:0.17, G:0.05, T:0.03
Consensus pattern (29 bp):
AAAAACCTAACCCAAAAAAAAAGAAAAAG
Found at i:123519636 original size:38 final size:35
Alignment explanation
Indices: 123519594--123519679 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 35
123519584 AACCTAACCC
123519594 AAAAAAAAAAAAAAGAAAAACCTAACCCAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAACCTAA--CAAAAAAAAA
* * *
123519631 GAAAAAGAAGAAAAAGAAAAACCTAACAAAAAAATA
1 -AAAAAAAAAAAAAAGAAAAACCTAACAAAAAAAAA
*
123519667 AAAAATAAAAAAA
1 AAAAAAAAAAAAA
123519680 CCTAGCCACC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 11 0.26
36 9 0.21
38 23 0.53
ACGTcount: A:0.80, C:0.09, G:0.06, T:0.05
Consensus pattern (35 bp):
AAAAAAAAAAAAAAGAAAAACCTAACAAAAAAAAA
Done.