Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold385
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: 58113
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3328 original size:12 final size:12
Alignment explanation
Indices: 3311--3337 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3301 ATTCCGAAGT
3311 ATATATATATAC
1 ATATATATATAC
3323 ATATATATATAC
1 ATATATATATAC
3335 ATA
1 ATA
3338 AGTATGCCCA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:3870 original size:27 final size:28
Alignment explanation
Indices: 3786--3883 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
3776 CATGAGATTG
* * * *
3786 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
3815 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
3843 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
3870 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
3884 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:3894 original size:27 final size:27
Alignment explanation
Indices: 3814--3896 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
3804 TAAATTGTAC
* *
3814 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
3842 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
3869 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
3896 A
1 A
3897 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:7648 original size:93 final size:93
Alignment explanation
Indices: 7540--7710 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
7530 GCCCATAAGT
* * *
7540 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
7605 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * *
7633 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
7698 CGAGTTCGGATGC
66 CGAGTTCGGATGC
7711 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:7707 original size:46 final size:46
Alignment explanation
Indices: 7532--7707 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
7522 TGTAACCCGC
* * *
7532 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
7578 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * * *
7628 --TTCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
7671 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
7708 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:8165 original size:30 final size:30
Alignment explanation
Indices: 8131--8190 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
8121 ATTTAATACG
8131 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
8161 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
8191 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:12398 original size:37 final size:37
Alignment explanation
Indices: 12345--12447 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
12335 CGAATAGTCC
*
12345 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
* *
12382 CCACACGTAGTCATCGGGTCTTACCCAGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
12419 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
12448 ATATATTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:12645 original size:48 final size:48
Alignment explanation
Indices: 12587--13011 Score: 751
Period size: 48 Copynumber: 8.9 Consensus size: 48
12577 ATATACACAC
* * *
12587 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12635 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12683 ATCTCATACATTTTTCACACTAGCCATTCGACTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12731 ATCTCATACATTTTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12779 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
12827 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
12875 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
12923 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
12971 ATCTCATACATATTTCACACTAGTCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA
13012 CATATTTATA
Statistics
Matches: 361, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 361 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:17048 original size:40 final size:40
Alignment explanation
Indices: 17016--17207 Score: 276
Period size: 40 Copynumber: 4.8 Consensus size: 40
17006 CCAGCATGAT
* *
17016 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAACACTAGCACGAA
* * * *
17056 TGCTCTTCGGGACTTAACCCTGATATAACTCTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATATAACACTAGCACGAA
* * *
17096 TGCTCTTCGAGACTTAGCCCGGGTATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAACACTAGCACGAA
* *
17136 TGCTCTACGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATAACACTAGCACGAA
*
17176 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATAACACT
17208 CTCAATTCTC
Statistics
Matches: 135, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATAACACTAGCACGAA
Found at i:18540 original size:37 final size:37
Alignment explanation
Indices: 18487--18589 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
18477 CGAATAGTCC
*
18487 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
18524 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
18561 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
18590 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:18788 original size:48 final size:48
Alignment explanation
Indices: 18730--19307 Score: 985
Period size: 48 Copynumber: 12.0 Consensus size: 48
18720 ATATACACAC
* * *
18730 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
18778 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
18826 ATCTCATACATATTTCACACTAGCCATTTGACTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
18874 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
18922 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
18970 ATCTCATACATATTTCACACTAGCCATTCGCCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
19018 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
19066 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
19114 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
19162 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
19210 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
19258 ATCTCATACATATTTCACACTAGTCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
19306 AT
1 AT
19308 ATTTATCTTG
Statistics
Matches: 502, Mismatches: 28, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 502 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:28131 original size:43 final size:43
Alignment explanation
Indices: 28081--28234 Score: 195
Period size: 43 Copynumber: 3.6 Consensus size: 43
28071 TAGCCTAGAT
* * *
28081 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACATGTAATCACATATCAATGCCAATGTCCCAGAC
* * * *
28124 AGGGTCTTACATGGAATCGA-TTAACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATC-ACATATCAATGCCAATGTCCCAGAC
* *
28167 ATGGTCTTACACGTAATCACA-ATACAATGCCAATGTGCCAGAC
1 ATGGTCTTACATGTAATCACATAT-CAATGCCAATGTCCCAGAC
28210 ATGGTCTTACATGTAATCACATATC
1 ATGGTCTTACATGTAATCACATATC
28235 GATAACCTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 2 0.02
43 88 0.95
44 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCAATGCCAATGTCCCAGAC
Found at i:29036 original size:30 final size:30
Alignment explanation
Indices: 29002--29098 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
28992 AGCTCACTCC
29002 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
29032 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
29062 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
29092 TAGCTCA
1 TAGCTCA
29099 TTTTAGCTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:31579 original size:30 final size:30
Alignment explanation
Indices: 31494--31590 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31484 TAAACTAAAA
* *
31494 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
31524 TGAGCTGAGGCTAAACTCTTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
31554 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
31583 ATGAGCTA
1 -TGAGCTA
31591 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:40437 original size:18 final size:18
Alignment explanation
Indices: 40416--40478 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
40406 ATACTCACTC
40416 TCTTTTTCAATTTTCTTT
1 TCTTTTTCAATTTTCTTT
**
40434 TCTTAATCAA-TTTCTTTT
1 TCTTTTTCAATTTTC-TTT
*
40452 TCTTTTTCAATTTCACTTT
1 TCTTTTTCAATTT-TCTTT
40471 TCTTTTTC
1 TCTTTTTC
40479 TCACTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.11
18 19 0.51
19 13 0.35
20 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTTCAATTTTCTTT
Found at i:40525 original size:15 final size:16
Alignment explanation
Indices: 40495--40530 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
40485 TCTTTTGCTC
40495 TCTTTCACTCTCTTTT
1 TCTTTCACTCTCTTTT
*
40511 TCTTTCA-TTTCTTTT
1 TCTTTCACTCTCTTTT
40526 TCTTT
1 TCTTT
40531 TTAAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTTTCACTCTCTTTT
Found at i:40966 original size:63 final size:64
Alignment explanation
Indices: 40886--41017 Score: 230
Period size: 63 Copynumber: 2.1 Consensus size: 64
40876 TCTTGTTGGG
* *
40886 CTCTTGCTAGATGATCGCGCTTTTCTTGGATAGGCTTGATTTTTCGGTTGAGCATGCACTCTAT
1 CTCTTGCTAGATGATCGCACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
*
40950 -TCTTGCTCGATGATCGCACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
1 CTCTTGCTAGATGATCGCACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
41013 CTCTT
1 CTCTT
41018 TCAAAAAATA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 60 0.94
64 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (64 bp):
CTCTTGCTAGATGATCGCACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
Found at i:42833 original size:54 final size:53
Alignment explanation
Indices: 42716--42891 Score: 194
Period size: 54 Copynumber: 3.3 Consensus size: 53
42706 GAATACTTTA
* * * *
42716 GTTTACCAAATTACTGAAATATCCTC-AGTTGTAAAATTACCAAAGTACCCTC
1 GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATCAAAGTACCCTC
* * *
42768 GGTTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTATCGAAA-TACCCTC
1 -GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATC-AAAGTACCCTC
* ** * *
42822 AGTTTGCAAAATTATTGAAATACCCTCGACATGTAAAATTATCAAAGTACCCTC
1 -GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATCAAAGTACCCTC
42876 GATTTACAAAATTACC
1 G-TTTACAAAATTACC
42892 ATTTTACCCT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
53 26 0.26
54 72 0.71
55 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (53 bp):
GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATCAAAGTACCCTC
Found at i:42859 original size:27 final size:27
Alignment explanation
Indices: 42723--42889 Score: 117
Period size: 27 Copynumber: 6.2 Consensus size: 27
42713 TTAGTTTACC
* * *
42723 AAATTACTGAAATATCCTC-AGTTGTA
1 AAATTATTGAAATACCCTCGATTTGTA
** * *
42749 AAATTA-CCAAAGTACCCTCGGTTTATA
1 AAATTATTGAAA-TACCCTCGATTTGTA
*** *
42776 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTATTGAAATACCCTCGATTTGTA
* *
42803 AAATTATCGAAATACCCTC-AGTTTGCA
1 AAATTATTGAAATACCCTCGA-TTTGTA
**
42830 AAATTATTGAAATACCCTCGACATGTA
1 AAATTATTGAAATACCCTCGATTTGTA
* **
42857 AAATTA-TCAAAGTACCCTCGATTTACA
1 AAATTATTGAAA-TACCCTCGATTTGTA
42884 AAATTA
1 AAATTA
42890 CCATTTTACC
Statistics
Matches: 113, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.03
26 17 0.15
27 87 0.77
28 6 0.05
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTATTGAAATACCCTCGATTTGTA
Found at i:42899 original size:27 final size:27
Alignment explanation
Indices: 42869--43259 Score: 320
Period size: 27 Copynumber: 14.4 Consensus size: 27
42859 ATTATCAAAG
*
42869 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
42896 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
42923 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
42950 TACCCTCGATTTACAGAGTTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * *
42977 TACCCTTGAATTACAAAATTATTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
43004 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * * *
43031 TACCCTCAATTTAGAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* * * * ***
43058 CACCCTTGATTTAGAAAATTACAAAAA
1 TACCCTCGATTTACAAAATTACTATTT
* ** ***
43085 TACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTACAAAATTACTATTT
* ** **
43112 TACCCCCTGATTTGTAAAATTACTGA-AA
1 TACCCTC-GATTTACAAAATTACT-ATTT
* * ***
43140 TACCCTCGACTGGTA-AAAATTACCAAAG
1 TACCCTCGA-T-TTACAAAATTACTATTT
* * *
43168 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
43195 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
43222 TACCCTTGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
43249 TACCCTCGATT
1 TACCCTCGATT
43260 GTGAAATTAC
Statistics
Matches: 305, Mismatches: 52, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 257 0.84
28 44 0.14
29 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTATTT
Found at i:42927 original size:81 final size:81
Alignment explanation
Indices: 42842--43079 Score: 199
Period size: 81 Copynumber: 2.9 Consensus size: 81
42832 ATTATTGAAA
** *
42842 TACCCTCGACATGTAAAATTA-TCAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAT
1 TACCCTCGACATACAAAATTACT-AAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAA
* *
42906 TTACAGAATTACTGTTT
65 TTACAAAATTACTATTT
** *** * * * *
42923 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAGTTACTATTTTACCCTTGAAT
1 TACCCTCGACATACAAAATTACTAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAAT
*
42988 TACAAAATTATTATTT
66 TACAAAATTACTATTT
** * * *** * * * * * *
43004 TACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTAGAGAATTACCATTTCACCCTTGATT
1 TACCCTCGACATACAAAATTACTAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAAT
*
43069 TAGAAAATTAC
66 TACAAAATTAC
43080 AAAAATACCC
Statistics
Matches: 131, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
81 130 0.99
82 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (81 bp):
TACCCTCGACATACAAAATTACTAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAAT
TACAAAATTACTATTT
Found at i:43118 original size:28 final size:28
Alignment explanation
Indices: 43064--43144 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
43054 ATTTCACCCT
*
43064 TGATTTAG-AAAATTACAAAAATA-CCCC
1 TGATTT-GTAAAATTACTAAAATACCCCC
*
43091 TGGTTTGTAAAATTACTAAAATACCCCC
1 TGATTTGTAAAATTACTAAAATACCCCC
*
43119 TGATTTGTAAAATTACTGAAATACCC
1 TGATTTGTAAAATTACTAAAATACCC
43145 TCGACTGGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 19 0.40
28 28 0.58
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (28 bp):
TGATTTGTAAAATTACTAAAATACCCCC
Found at i:43158 original size:28 final size:27
Alignment explanation
Indices: 43097--43176 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
43087 CCCCTGGTTT
* * *
43097 GTAAAATTACTAAAATACCCCCTGATTT
1 GTAAAATTACTAAAATACCCTC-GACTG
*
43125 GTAAAATTACTGAAATACCCTCGACTG
1 GTAAAATTACTAAAATACCCTCGACTG
* *
43152 GTAAAAATTACCAAAGTACCCTCGA
1 GT-AAAATTACTAAAATACCCTCGA
43177 TTTATAGAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 5 0.11
28 39 0.89
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (27 bp):
GTAAAATTACTAAAATACCCTCGACTG
Found at i:43294 original size:27 final size:27
Alignment explanation
Indices: 43264--43754 Score: 648
Period size: 27 Copynumber: 18.3 Consensus size: 27
43254 TCGATTGTGA
* *
43264 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * ** *
43291 AATTACCAAAACACCCCTAGT-TTGTAA
1 AATTACCGAAATACCCCT-GTAGGGTAG
* *
43318 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
43345 AATTACTAAAATA-CCCTAGTAAGGTAG
1 AATTACCGAAATACCCCT-GTAGGGTAG
*
43372 AATTACCG-AATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
43398 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
43425 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43452 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43479 AATTACCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
43506 AACTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43533 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43560 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
43587 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
43614 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
43641 AATTATCGTAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
43668 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
43695 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
43722 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
43748 AATTACC
1 AATTACC
43755 ATTTTGCCCC
Statistics
Matches: 405, Mismatches: 54, Indels: 11
0.86 0.11 0.02
Matches are distributed among these distances:
26 41 0.10
27 363 0.90
28 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:44033 original size:27 final size:26
Alignment explanation
Indices: 43995--44046 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
43985 CTCGCTGCAA
*
43995 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
44022 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACTTCGCCACAATATCTG
44047 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:44084 original size:67 final size:67
Alignment explanation
Indices: 43976--44129 Score: 299
Period size: 67 Copynumber: 2.3 Consensus size: 67
43966 GAGGAAGTGT
43976 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
44041 TA
66 TA
*
44043 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCATAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
44108 TA
66 TA
44110 TCTGGCAGCCTCGCTGCAAT
1 TCTGGCAGCCTCGCTGCAAT
44130 TTCTGTGGTG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 86 1.00
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
TA
Found at i:44241 original size:6 final size:6
Alignment explanation
Indices: 44232--44415 Score: 137
Period size: 6 Copynumber: 29.8 Consensus size: 6
44222 TTGCATTCAC
*
44232 ATTCTG ATTCTG ATTCTG -TTACCTG ATAT-TG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG AT-TCTG ATTCTG ATTCTG ATT--CTG
* * *
44282 ATTCTA ATTCTG GTTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * * * *
44331 ATTCTG -TTACCTA ATTCTA ATTCTG GTTCTG ATTTTG ATTCTG -TCACCTG
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG
*
44381 ATTCTG ATTCTG ATTCTG ATTCTG ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
44416 AGTTATGATA
Statistics
Matches: 145, Mismatches: 16, Indels: 34
0.74 0.08 0.17
Matches are distributed among these distances:
5 10 0.07
6 114 0.79
7 13 0.09
8 7 0.05
9 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:44291 original size:25 final size:25
Alignment explanation
Indices: 44232--44299 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
44222 TTGCATTCAC
*
44232 ATTCTGATTCTGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTA
44257 ATAT-TGATTCTGATTCTGTTACCTA
1 AT-TCTGATTCTGATTCTGTTACCTA
* *
44282 ATTCTAATTCTGGTTCTG
1 ATTCTGATTCTGATTCTG
44300 ATTCTGATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.49
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTA
Found at i:44302 original size:37 final size:37
Alignment explanation
Indices: 44261--44336 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
44251 TACCTGATAT
* *
44261 TGATTCTGATTCTGTTACCTAATTCTAATTCTGGTTC
1 TGATTCTGATTCTGTTACCTAATACTAATTCTGATTC
* *
44298 TGATTCTGATTCTGTTACCTGATACTGATTCTGATTC
1 TGATTCTGATTCTGTTACCTAATACTAATTCTGATTC
44335 TG
1 TG
44337 TTACCTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (37 bp):
TGATTCTGATTCTGTTACCTAATACTAATTCTGATTC
Found at i:44326 original size:25 final size:25
Alignment explanation
Indices: 44297--44361 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
44287 AATTCTGGTT
*
44297 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTAATA
*
44322 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTAATA
* *
44347 CTAATTCTGGTTCTG
1 CTGATTCTGATTCTG
44362 ATTTTGATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTAATA
Found at i:44330 original size:62 final size:62
Alignment explanation
Indices: 44233--44398 Score: 296
Period size: 62 Copynumber: 2.7 Consensus size: 62
44223 TGCATTCACA
*
44233 TTCTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTGTTACCTAATTCTAATTCTGG
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGG
44295 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGG
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGG
* * *
44357 TTCTGATTTTGATTCTGTCACCTGATTCTGATTCTGATTCTG
1 TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTG
44399 ATTCTGATTT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 100 1.00
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (62 bp):
TTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTGG
Found at i:44363 original size:37 final size:37
Alignment explanation
Indices: 44316--44407 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 37
44306 ATTCTGTTAC
* *
44316 CTGATACTGATTCTGATTCTGTTACCTAATTCTAATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTAATT
* * * *
44353 CTGGTTCTGATTTTGATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTAATT
44390 CTGATTCTGATTCTGATT
1 CTGATTCTGATTCTGATT
44408 TTGATTCTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTCACCTAATTCTAATT
Found at i:44424 original size:18 final size:18
Alignment explanation
Indices: 44232--44415 Score: 83
Period size: 19 Copynumber: 9.9 Consensus size: 18
44222 TTGCATTCAC
*
44232 ATTCTGATTCTGATTCTG
1 ATTCTGATTATGATTCTG
44250 -TTACCTGA-TATTGATTCTG
1 ATT--CTGATTA-TGATTCTG
* *
44269 ATTCTG-TTACCTAATTCTA
1 ATTCTGATTA--TGATTCTG
* *
44288 ATTCTGGTTCTGATTCTG
1 ATTCTGATTATGATTCTG
*
44306 ATTCTG-TTACCTGATACTG
1 ATTCTGATTA--TGATTCTG
* *
44325 ATTCTGATTCTG-TTACCTA
1 ATTCTGATTATGATT--CTG
* * *
44344 ATTCTAATTCTGGTTCTG
1 ATTCTGATTATGATTCTG
* * *
44362 ATTTTGATTCTG-TCACCTG
1 ATTCTGATTATGAT--TCTG
*
44381 ATTCTGATTCTGATTCTG
1 ATTCTGATTATGATTCTG
*
44399 ATTCTGATTTTGATTCT
1 ATTCTGATTATGATTCT
44416 AGTTATGATA
Statistics
Matches: 130, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
17 6 0.05
18 51 0.39
19 64 0.49
20 9 0.07
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (18 bp):
ATTCTGATTATGATTCTG
Found at i:48194 original size:46 final size:46
Alignment explanation
Indices: 48144--48315 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
48134 TGAGCATCCA
*
48144 AACTCGTTGAGTTGAGTCCGAGTTCACTTCTGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * *
48190 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
*
48237 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-G
* * * *
48283 AGCTCATTGAGTTGAGTCCAAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
48316 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 55 0.53
47 29 0.28
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:48296 original size:93 final size:93
Alignment explanation
Indices: 48137--48308 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
48127 GGATGGTTGA
* * *
48137 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTCTGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAGT
*
48202 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* *
48230 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCATTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCATTGAG
48294 TTGAGTCCAAGTTCG
65 TTGAGTCCAAGTTCG
48309 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:53239 original size:27 final size:28
Alignment explanation
Indices: 53155--53252 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
53145 CATGAGATTG
* * * *
53155 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
53184 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
53212 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
53239 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
53253 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:53263 original size:27 final size:27
Alignment explanation
Indices: 53183--53265 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
53173 TAAATTGTAC
* *
53183 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
53211 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
53238 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
53265 A
1 A
53266 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:53266 original size:29 final size:27
Alignment explanation
Indices: 53155--53266 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
53145 CATGAGATTG
** * *
53155 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
53184 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
53212 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
53239 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
53267 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Done.