Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold648
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: 25319
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:683 original size:42 final size:42
Alignment explanation
Indices: 636--1076 Score: 302
Period size: 42 Copynumber: 10.3 Consensus size: 42
626 TTTGAACAGA
* * * *
636 AAACGCCGCTAAAAGTAGATACCTTTAGCGACGCTTTACCAT
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTTACCAC
* * *
678 AAACGCCGCTAATAGTATAGACCTTTAGCGGCGC-TTAGCAAAC
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTTA-C-CAC
* * * * *
721 AAACGCCACTAAAAGCACATACCTTTAGCGG-GCTTTGCAAAC
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTTAC-CAC
** *
763 AAACGCCGCT-AAAGCTGTAGACCTTTAGCGGCGTTTTACCAC
1 AAACGCCGCTAAAAG-TACAGACCTTTAGCGGCGCTTTACCAC
* * * **
805 AAACGCCACTAAAGGTATAGACCTTTAGC-GCG-TTT-CCGGGG
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTTACC--AC
* * ****
846 AAAGCGCCGCTAAAAGTGCAGACCTTTAGCGACG-TTTGTTTGC
1 AAA-CGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTT-ACCAC
* * * *
889 AAACGCCGCTAAAAGTACAGACCTTTAGCAGAGCTTTTGCCCAAA
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGC-TTT-ACC-AC
* ** * * *
934 AAAGGGCCGCTAAATTTACAGACCTATAGCGGCGCTTACACCAA
1 AAA-CGCCGCTAAAAGTACAGACCTTTAGCGGCGCTT-TACCAC
* *
978 AAACGCCGCCAAAAGTACAGACCTTTTAGCGGCGCTTTCTCCAC
1 AAACGCCGCTAAAAGTACAGACC-TTTAGCGGCGCTTT-ACCAC
* * * * *
1022 AAATGCCGCCAAAAGTAGAGTCCTTTAGCGGCGCTTTCCCAC
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTTACCAC
*
1064 AAATGCCGCTAAA
1 AAACGCCGCTAAA
1077 TTTATAGATT
Statistics
Matches: 317, Mismatches: 63, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.01
40 3 0.01
41 13 0.04
42 147 0.46
43 76 0.24
44 44 0.14
45 7 0.02
46 25 0.08
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGCTTTACCAC
Found at i:767 original size:85 final size:84
Alignment explanation
Indices: 636--817 Score: 217
Period size: 85 Copynumber: 2.2 Consensus size: 84
626 TTTGAACAGA
* * * * *
636 AAACGCCGCTAAAAGTAGATACCTTTAGCGACGCTTTACCATAAACGCCGCTAATAG-TATAGAC
1 AAACGCCACTAAAAGCACATACCTTTAGCGACGCTTTACAACAAACGCCGCTAA-AGCTATAGAC
700 CTTTAGCGGCG-CTTAGCAAAC
65 CTTTAGCGGCGTCTTA-C-AAC
* * *
721 AAACGCCACTAAAAGCACATACCTTTAGCG-GGCTTTGCAAACAAACGCCGCTAAAGCTGTAGAC
1 AAACGCCACTAAAAGCACATACCTTTAGCGACGCTTTAC-AACAAACGCCGCTAAAGCTATAGAC
* *
785 CTTTAGCGGCGTTTTACCAC
65 CTTTAGCGGCGTCTTACAAC
805 AAACGCCACTAAA
1 AAACGCCACTAAA
818 GGTATAGACC
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
84 23 0.27
85 58 0.69
86 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (84 bp):
AAACGCCACTAAAAGCACATACCTTTAGCGACGCTTTACAACAAACGCCGCTAAAGCTATAGACC
TTTAGCGGCGTCTTACAAC
Found at i:7023 original size:9 final size:9
Alignment explanation
Indices: 7009--7139 Score: 109
Period size: 9 Copynumber: 13.9 Consensus size: 9
6999 ATGTATTAGT
7009 TAAGTTATG
1 TAAGTTATG
7018 TAAGTTATG
1 TAAGTTATG
*
7027 TGAGTTATG
1 TAAGTTATG
*
7036 TAAGTTGTTATA
1 TAA---GTTATG
*
7048 TACGTTATG
1 TAAGTTATG
* *
7057 TGAGTTATA
1 TAAGTTATG
*
7066 TAAATTATG
1 TAAGTTATG
7075 TAAGTTATG
1 TAAGTTATG
7084 TAAGTTATG
1 TAAGTTATG
*
7093 TAGGTTGTTATG
1 TA---AGTTATG
*
7105 TAAATTATG
1 TAAGTTATG
*
7114 TAAGTTACG
1 TAAGTTATG
*
7123 TGAGTTATG
1 TAAGTTATG
*
7132 TAACTTAT
1 TAAGTTAT
7140 TTATTTAATG
Statistics
Matches: 95, Mismatches: 21, Indels: 12
0.74 0.16 0.09
Matches are distributed among these distances:
9 80 0.84
12 15 0.16
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:7103 original size:48 final size:48
Alignment explanation
Indices: 7009--7140 Score: 149
Period size: 48 Copynumber: 2.8 Consensus size: 48
6999 ATGTATTAGT
* *
7009 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTGTTATATACGTTATG
1 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATTAGATACGTTATG
* * * * * *
7057 TGAGTTATATAAATTATGTAAGTTATGTAAGTTATGTAGGT-TGTTATG
1 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTAT-TAGATACGTTATG
* * *
7105 TAAATTATGTAAGTTACGTGAGTTATGTAACTTATT
1 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATT
7141 TATTTAATGA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 64 0.94
49 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (48 bp):
TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATTAGATACGTTATG
Found at i:7131 original size:57 final size:57
Alignment explanation
Indices: 7009--7139 Score: 163
Period size: 57 Copynumber: 2.3 Consensus size: 57
6999 ATGTATTAGT
* ** * *
7009 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTGTTATATACGTTATGTGAGTTATA
1 TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTGTTATATAAATTATGTAAGTTACA
* * * *
7066 TAAATTATGTAAGTTATGTAAGTTATGTAGGTTGTTATGTAAATTATGTAAGTTACG
1 TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTGTTATATAAATTATGTAAGTTACA
* *
7123 TGAGTTATGTAACTTAT
1 TAAGTTATGTAAGTTAT
7140 TTATTTAATG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (57 bp):
TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTGTTATATAAATTATGTAAGTTACA
Found at i:8841 original size:46 final size:45
Alignment explanation
Indices: 8791--8965 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 45
8781 TGGTTGAGCA
8791 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
8837 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
8883 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
8929 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8966 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 99 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:8945 original size:92 final size:92
Alignment explanation
Indices: 8788--8957 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
8778 GGATGGTTGA
* *
8788 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
8853 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
8880 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
8945 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
8958 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:11847 original size:15 final size:15
Alignment explanation
Indices: 11827--11895 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
11817 GTATCTTGGG
11827 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
11842 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
11857 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
11872 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
11887 TTTCTTTAT
1 TTTCTTTAT
11896 TCGGTTTCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:11896 original size:30 final size:30
Alignment explanation
Indices: 11818--11904 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
11808 CATAGTATCG
* * * * *
11818 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGGTTTCTC
11848 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGGTTTCTC
11878 TATCTTGGATTTCTTTATTC--GGTTTCT
1 TATCTTGGATTTCTTTATTCTGGGTTTCT
11905 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.14
29 1 0.02
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGGTTTCTC
Found at i:14321 original size:46 final size:46
Alignment explanation
Indices: 14271--14446 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
14261 TGGTTGAGCA
14271 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
14317 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
14362 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
14410 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
14447 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 65 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:14427 original size:93 final size:93
Alignment explanation
Indices: 14268--14438 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
14258 GGATGGTTGA
* *
14268 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
14333 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
14361 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
14426 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
14439 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:17332 original size:24 final size:25
Alignment explanation
Indices: 17279--17332 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
17269 TTATAATTAA
* *
17279 ATTAATATAATATATAAAATTTAGG
1 ATTAATATAAGATAAAAAATTTAGG
* *
17304 A-TAATATTAGATAAAAAATTT-TG
1 ATTAATATAAGATAAAAAATTTAGG
17327 ATTAAT
1 ATTAAT
17333 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 2 0.08
24 21 0.88
25 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (25 bp):
ATTAATATAAGATAAAAAATTTAGG
Found at i:19844 original size:47 final size:47
Alignment explanation
Indices: 19787--20090 Score: 437
Period size: 47 Copynumber: 6.4 Consensus size: 47
19777 ATTGATGTAC
* * *
19787 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
19834 AAGTATATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAG--TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * * *
19883 AAGTGTATATATGTGATAGGGTCGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
19930 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
19977 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
20024 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
20071 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
20091 TCCCGAAGGG
Statistics
Matches: 238, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 192 0.81
49 46 0.19
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:23271 original size:7 final size:7
Alignment explanation
Indices: 23259--23304 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
23249 ACAAAATCAG
23259 ACCCTAA
1 ACCCTAA
23266 ACCCTAA
1 ACCCTAA
* *
23273 ATCTTAA
1 ACCCTAA
23280 ACCCTAA
1 ACCCTAA
*
23287 ACTCTAA
1 ACCCTAA
*
23294 ACCATAA
1 ACCCTAA
23301 ACCC
1 ACCC
23305 CTAACCTTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:23284 original size:21 final size:21
Alignment explanation
Indices: 23259--23331 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
23249 ACAAAATCAG
*
23259 ACCCTAAACCCTAAATCTTAA
1 ACCCTAAACCCTAAAACTTAA
* * *
23280 ACCCTAAACTCTAAACCATAA
1 ACCCTAAACCCTAAAACTTAA
*
23301 ACCCCT-AACCTTATAAACATTAA
1 A-CCCTAAACCCTA-AAAC-TTAA
23324 ACCCTAAA
1 ACCCTAAA
23332 TTCTAGATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 24 0.59
22 11 0.27
23 6 0.15
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
ACCCTAAACCCTAAAACTTAA
Found at i:24591 original size:15 final size:15
Alignment explanation
Indices: 24564--24697 Score: 54
Period size: 15 Copynumber: 9.1 Consensus size: 15
24554 AACACGAAAC
24564 CCCT-AACCACT-AA
1 CCCTAAACCACTAAA
*
24577 CCCTTAAACCCCTAAA
1 CCC-TAAACCACTAAA
24593 CCCTAAACCA-TAAAA
1 CCCTAAACCACT-AAA
* * *
24608 ACATAAACCA-TGAA
1 CCCTAAACCACTAAA
24622 CCCTTAAA-C-CTAAA
1 CCC-TAAACCACTAAA
*
24636 CCATAAACC-CTTAATA
1 CCCTAAACCAC-TAA-A
*
24652 CCGCTAAA-CATTAAGA
1 CC-CTAAACCACTAA-A
* *
24668 TCATAAA-CACTAAA
1 CCCTAAACCACTAAA
*
24682 CACTAAA-CACTAAA
1 CCCTAAACCACTAAA
24696 CC
1 CC
24698 TCAAACCCAA
Statistics
Matches: 91, Mismatches: 19, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
13 7 0.08
14 26 0.29
15 40 0.44
16 14 0.15
17 4 0.04
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (15 bp):
CCCTAAACCACTAAA
Found at i:24599 original size:7 final size:7
Alignment explanation
Indices: 24575--24697 Score: 50
Period size: 7 Copynumber: 16.6 Consensus size: 7
24565 CCTAACCACT
24575 AACCCTTA
1 AACCC-TA
24583 AACCCCTA
1 AA-CCCTA
24591 AACCCTA
1 AACCCTA
*
24598 AACCATAA
1 AACCCT-A
* *
24606 AAACATA
1 AACCCTA
* *
24613 AACCATG
1 AACCCTA
24620 AACCCTTA
1 AACCC-TA
24628 AA-CCTA
1 AACCCTA
*
24634 AACCATA
1 AACCCTA
24641 AACCCTTA
1 AACCC-TA
24649 ATACCGCTA
1 A-ACC-CTA
**
24658 AACATTA
1 AACCCTA
* *
24665 AGATCATA
1 A-ACCCTA
*
24673 AACACTA
1 AACCCTA
*
24680 AACACTA
1 AACCCTA
*
24687 AACACTA
1 AACCCTA
24694 AACC
1 AACC
24698 TCAAACCCAA
Statistics
Matches: 90, Mismatches: 17, Indels: 17
0.73 0.14 0.14
Matches are distributed among these distances:
6 4 0.04
7 52 0.58
8 24 0.27
9 9 0.10
10 1 0.01
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:24635 original size:21 final size:21
Alignment explanation
Indices: 24606--24649 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
24596 TAAACCATAA
*
24606 AAACATAAACCATGAACCCTT
1 AAACATAAACCATAAACCCTT
*
24627 AAACCTAAACCATAAACCCTT
1 AAACATAAACCATAAACCCTT
24648 AA
1 AA
24650 TACCGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (21 bp):
AAACATAAACCATAAACCCTT
Found at i:24637 original size:6 final size:7
Alignment explanation
Indices: 24589--24644 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
24579 CTTAAACCCC
*
24589 TAAACCC
1 TAAACCA
24596 TAAACCA
1 TAAACCA
*
24603 TAAAAACA
1 T-AAACCA
24611 TAAACCA
1 TAAACCA
* *
24618 TGAACCCT
1 T-AAACCA
24626 TAAACC-
1 TAAACCA
24632 TAAACCA
1 TAAACCA
24639 TAAACC
1 TAAACC
24645 CTTAATACCG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 6 0.15
7 23 0.57
8 11 0.28
ACGTcount: A:0.52, C:0.30, G:0.02, T:0.16
Consensus pattern (7 bp):
TAAACCA
Found at i:24902 original size:41 final size:40
Alignment explanation
Indices: 24847--25316 Score: 518
Period size: 41 Copynumber: 11.5 Consensus size: 40
24837 AATTCAAAAA
* * * * *
24847 AGACGTTTAGCGGCGTTTCTCCAAAAATGCTGCTAATTCTC
1 AGACTTTTGGCGGCGTTT-TCCAAAAACGCCGCTAATGCTC
* *
24888 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCGAATACTC
1 AGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTAATGCTC
24929 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATGACTC
1 AGACTTTTGGCGGCGTTTT-CCAAAAACGCCGCTAATG-CTC
* *
24971 AGACTTTTGGCGGTGTTTTCCCAAAAACACCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTT-CCAAAAACGCCGCTAATGCTC
*
25012 AGTA-TTATAATGGCGGCGTTTTCCGAAAAACCGCCGCTAATTCTC
1 AG-ACTT-T--TGGCGGCGTTTTCC-AAAAA-CGCCGCTAATGCTC
* * *
25057 -GACTTTTAGCGGCGCTTTCCAAAAACGCCGCAAATGCTC
1 AGACTTTTGGCGGCGTTTTCCAAAAACGCCGCTAATGCTC
* * * *
25096 AGACTTTTTGCGGCGTTTTTTCAACAACGCCGCTAATTCTC
1 AGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTAATGCTC
* *
25137 AGAC-TTTAGCGG-GTTTTTCCAACAACGCCGCTAATGCTC
1 AGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTAATGCTC
* *
25176 AGACTTTTAGCGGCGCTTTTCCAAAAAAGCCGCTAATGCTC
1 AGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTAATGCTC
* *
25217 AGACTTTTAGCGGCG-TTTCCAAAAACGCCGCTAATTCTC
1 AGACTTTTGGCGGCGTTTTCCAAAAACGCCGCTAATGCTC
** * *
25256 AGACTTTTGGCGGCGTGTTTAATAAAAACTCCGCTAACGCTC
1 AGACTTTTGGCGGCGT-TTT-CCAAAAACGCCGCTAATGCTC
25298 AGACTTTTGGCGGCGTTTT
1 AGACTTTTGGCGGCGTTTT
25317 GGT
Statistics
Matches: 375, Mismatches: 37, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
39 77 0.21
40 37 0.10
41 150 0.40
42 76 0.20
43 4 0.01
44 19 0.05
45 12 0.03
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (40 bp):
AGACTTTTGGCGGCGTTTTCCAAAAACGCCGCTAATGCTC
Found at i:25145 original size:80 final size:81
Alignment explanation
Indices: 24847--25316 Score: 520
Period size: 80 Copynumber: 5.7 Consensus size: 81
24837 AATTCAAAAA
* * * * * *
24847 AGACGTTTAGCGGCGTTTCTCCAAAAATGCTGCTAATTCTCAGACTTTTGGCGGCGTTTTTCCAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATTCTCAGACTTTTAGCGGCG-TTTTCCAA
* *
24912 AAACGCCGCGAATACTC
65 AAACGCCGCTAATGCTC
* * * *
24929 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATGACTCAGACTTTTGGCGGTGTTTTCCCA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAAT-TCTCAGACTTTTAGCGGCGTTTT-CCA
*
24994 AAAACACCGCTAATGCTC
64 AAAACGCCGCTAATGCTC
*
25012 AGTA-TTATAATGGCGGCG-TTTTCCGAAAAACCGCCGCTAATTCTC-GACTTTTAGCGGCGCTT
1 AG-ACTT-T--TGGCGGCGTTTTTCC-AAAAA-CGCCGCTAATTCTCAGACTTTTAGCGGCGTTT
*
25074 TCCAAAAACGCCGCAAATGCTC
60 TCCAAAAACGCCGCTAATGCTC
* * *
25096 AGACTTTTTGCGGCGTTTTTTCAACAACGCCGCTAATTCTCAGAC-TTTAGCGG-GTTTTTCCAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATTCTCAGACTTTTAGCGGCG-TTTTCCAA
*
25159 CAACGCCGCTAATGCTC
65 AAACGCCGCTAATGCTC
* * * *
25176 AGACTTTTAGCGGCGCTTTTCCAAAAAAGCCGCTAATGCTCAGACTTTTAGCGGCG-TTTCCAAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATTCTCAGACTTTTAGCGGCGTTTTCCAAA
*
25240 AACGCCGCTAATTCTC
66 AACGCCGCTAATGCTC
*** * ** *
25256 AGACTTTTGGCGGCGTGTTTAATAAAAACTCCGCTAACGCTCAGACTTTTGGCGGCGTTTT
1 AGACTTTTGGCGGCGT-TTTTCCAAAAACGCCGCTAATTCTCAGACTTTTAGCGGCGTTTT
25317 GGT
Statistics
Matches: 331, Mismatches: 41, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
79 1 0.00
80 119 0.36
81 55 0.17
82 44 0.13
83 41 0.12
84 25 0.08
85 20 0.06
86 16 0.05
87 10 0.03
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (81 bp):
AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATTCTCAGACTTTTAGCGGCGTTTTCCAAA
AACGCCGCTAATGCTC
Done.