Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 42741
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:2184 original size:47 final size:46
Alignment explanation
Indices: 2115--2509 Score: 413
Period size: 47 Copynumber: 8.6 Consensus size: 46
2105 ATATTTGAAA
2115 AATGTGAAAGTGTATATATGTGATAAGCCTAAT-GCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGCCTAATGGCCGATGTGATG
* * *
2160 AATGTGGAAAGTGTAGTATATGTGATAAGGCGAAT-GCCAATG-GATG
1 AATGT-GAAAGTGTA-TATATGTGATAAGCCTAATGGCCGATGTGATG
2206 AATGTGAAAGTGTATATATACTGTGATAAGCCTAATGG-CGATGTGATG
1 AATGTGAAAGTG--TATATA-TGTGATAAGCCTAATGGCCGATGTGATG
*
2254 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAA-GCCTAATGGCCGATGTGATG
*
2301 AAT-TGAAAGTGTATATATGTGATTAAGGCCTAATGGCTGATGTGATG
1 AATGTGAAAGTGTATATATGTGA-TAA-GCCTAATGGCCGATGTGATG
* * *
2348 -ATGTGAAAGTGTATATTATGTGATAAGTCGAATGGCCGATGGATTGTTG
1 AATGTGAAAGTGTATA-TATGTGATAAGCCTAATGGCCGAT-G--TGATG
* * *
2397 AATGTG-AAGTG--TATAT-TGATAGGCCGAATGGCC-AAGTGA-G
1 AATGTGAAAGTGTATATATGTGATAAGCCTAATGGCCGATGTGATG
* * * *
2437 -ATGTGAAAGTGTATATATGTGATAGGTC-AAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGCCTAA-TGGCCGATGTGATG
* *
2482 GATGTGAAAGTGTTTGATATGTGATAAG
1 AATGTGAAAGTGTAT-ATATGTGATAAG
2510 TCCCGAAGGG
Statistics
Matches: 304, Mismatches: 21, Indels: 48
0.82 0.06 0.13
Matches are distributed among these distances:
39 5 0.02
40 6 0.02
41 2 0.01
42 7 0.02
43 14 0.05
44 6 0.02
45 36 0.12
46 84 0.28
47 106 0.35
48 24 0.08
49 9 0.03
50 5 0.02
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (46 bp):
AATGTGAAAGTGTATATATGTGATAAGCCTAATGGCCGATGTGATG
Found at i:2309 original size:139 final size:141
Alignment explanation
Indices: 2115--2509 Score: 459
Period size: 139 Copynumber: 2.9 Consensus size: 141
2105 ATATTTGAAA
2115 AATGTGAAAGTGTATATATGTGATAA-GCCTAATGCCGATGTGATGAATGTGGAAAGTGTAGTAT
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGCCGATGTGATGAATGT-GAAAGTGTA-TAT
* *
2179 ATGTGATAAGGCGAAT-GCCAATG-GATGAATGTGAAAGTGTATATATACTGTGATAAGCCTAAT
64 ATGTGATAAGGCCAATGGCCAATGTGATG-ATGTGAAAGTGTATATATA-TGTGATAAGCCGAAT
2242 GG-CGAT-G-TGATG
127 GGCCGATGGATGATG
2254 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT-TGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATA
** *
2318 TGTGATTAAGGCCTAATGGCTGATGTGATGATGTGAAAGTGTATAT-TATGTGATAAGTCGAATG
65 TGTGA-TAAGGCC-AATGGCCAATGTGATGATGTGAAAGTGTATATATATGTGATAAGCCGAATG
*
2382 GCCGATGGATTGTTG
128 GCCGATGGA-TGATG
* *
2397 AATGTG-AAGTG--TATAT-TGAT-AGGCCGAATGGCC-AAGTGA-G-ATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATA
* *
2454 TGTGAT-AGGTCAAGTGGCCAACGTGATGGATGTGAAAGTGT-T-TGATATGTGATAAG
65 TGTGATAAGGCCAA-TGGCCAATGTGAT-GATGTGAAAGTGTATAT-ATATGTGATAAG
2510 TCCCGAAGGG
Statistics
Matches: 228, Mismatches: 13, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
133 3 0.01
134 15 0.07
135 27 0.12
136 20 0.09
137 5 0.02
138 20 0.09
139 60 0.26
140 22 0.10
141 37 0.16
142 9 0.04
143 10 0.04
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (141 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCAATGGCCAATGTGATGATGTGAAAGTGTATATATATGTGATAAGCCGAATGGCC
GATGGATGATG
Found at i:4153 original size:120 final size:120
Alignment explanation
Indices: 3933--4216 Score: 377
Period size: 120 Copynumber: 2.4 Consensus size: 120
3923 AGAGTGAATA
* * *
3933 GTAT-CGGGCTAAGTCCCGAAGAGCA-TCGTGCTAGTGATGTATCTGGGCTAACTTCCCGGAAGA
1 GTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAACGTCCCGGAAGA
*
3996 GTATTCGTGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCATAGCTAATGAT
66 GCATTCGTGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCAT-GCT-ATGAT
*
4053 -TATCCGGGCTAAAGTCTCGAAGGAGCGATTCGTGCTAGTGATGTATCCGGGCTAA-GTCTC-GA
1 GTATCCGGGCT-AAGTCTCGAA-GAGC-ATTCGTGCTAGTGATGTATCCGGGCTAACGTCCCGGA
* *
4115 AGAGCA-TCGTGCTA-TGATGTATCCGGCTAAGTCTCGAAGAGCCTTCATGCTATGAT
63 AGAGCATTCGTGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCATGCTATGAT
* * *
4171 GTATTCGGACTAAGT-TCGAAGAGCATTCGTGCTAGTGATATATCCG
1 GTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCG
4217 CTGGCCCTTA
Statistics
Matches: 148, Mismatches: 10, Indels: 17
0.85 0.06 0.10
Matches are distributed among these distances:
115 21 0.14
116 4 0.03
117 5 0.03
118 9 0.06
119 14 0.09
120 38 0.26
121 17 0.11
122 11 0.07
123 4 0.03
124 25 0.17
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (120 bp):
GTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAACGTCCCGGAAGA
GCATTCGTGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCATGCTATGAT
Found at i:4166 original size:38 final size:39
Alignment explanation
Indices: 3933--4216 Score: 319
Period size: 38 Copynumber: 7.2 Consensus size: 39
3923 AGAGTGAATA
* *
3933 GTATCGGGCTAAGTCCCGAAGAGCA-TCGTGCTAGTGAT
1 GTATCCGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGAT
* * * *
3971 GTATCTGGGCTAACTTCCCGGAAGAGTATTCGTGCTAGTGAT
1 GTATC-CGGCTAA-GTCTC-GAAGAGCATTCGTGCTAGTGAT
* * *
4013 GTATCCGGCTAAGTCCCGAAGAGCATTCATAGCTAATGAT
1 GTATCCGGCTAAGTCTCGAAGAGCATTCGT-GCTAGTGAT
4053 -TATCCGGGCTAAAGTCTCGAAGGAGCGATTCGTGCTAGTGAT
1 GTATCC-GGCT-AAGTCTCGAA-GAGC-ATTCGTGCTAGTGAT
4095 GTATCCGGGCTAAGTCTCGAAGAGCA-TCGTGCTA-TGAT
1 GTATCC-GGCTAAGTCTCGAAGAGCATTCGTGCTAGTGAT
* *
4133 GTATCCGGCTAAGTCTCGAAGAGCCTTCATGCTA-TGAT
1 GTATCCGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGAT
*
4171 GTATTCGGACTAAGT-TCGAAGAGCATTCGTGCTAGTGAT
1 GTATCCGG-CTAAGTCTCGAAGAGCATTCGTGCTAGTGAT
*
4210 ATATCCG
1 GTATCCG
4217 CTGGCCCTTA
Statistics
Matches: 216, Mismatches: 17, Indels: 25
0.84 0.07 0.10
Matches are distributed among these distances:
37 18 0.08
38 50 0.23
39 46 0.21
40 21 0.10
41 26 0.12
42 40 0.19
43 15 0.07
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (39 bp):
GTATCCGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGAT
Found at i:8359 original size:47 final size:47
Alignment explanation
Indices: 8304--8708 Score: 659
Period size: 47 Copynumber: 8.6 Consensus size: 47
8294 TATTTGAATA
8304 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
8351 GATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
8398 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
8447 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
8494 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
8541 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
8588 AATGTGAAAGTGTATATATGTGATAAGG-CTAAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTGATG
* * * * *
8635 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
8682 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
8709 TCCCGAAGGG
Statistics
Matches: 336, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 289 0.86
48 1 0.00
49 45 0.13
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:11197 original size:47 final size:47
Alignment explanation
Indices: 11132--11248 Score: 227
Period size: 47 Copynumber: 2.5 Consensus size: 47
11122 TTTGTGTGCT
11132 AGTGTAAGA-CATGTCTGGGACATGCATGGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATGGGCCACATTATGAGAGCC
11178 AGTGTAAGACCATGTCTGGGACATGCATGGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATGGGCCACATTATGAGAGCC
11225 AGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGACCATGTCTGGGACAT
11249 AGCAACGACA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
46 9 0.13
47 61 0.87
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATGGGCCACATTATGAGAGCC
Found at i:11359 original size:46 final size:47
Alignment explanation
Indices: 11132--11437 Score: 188
Period size: 47 Copynumber: 6.5 Consensus size: 47
11122 TTTGTGTGCT
* * * *
11132 AGTGTAAGA-CATGTCTGGGACATGCATGGGCCAC-ATTATG-AGAGCC
1 AGTGTAAGACCATGTTTGGGACATGCATCGGCTACGA-GATGTA-AGCC
* * * *
11178 AGTGTAAGACCATGTCTGGGACATGCATGGGCCAC-ATTATG-AGAGCC
1 AGTGTAAGACCATGTTTGGGACATGCATCGGCTACGA-GATGTA-AGCC
* * * * ** *
11225 AGTGTAAGACCATGTCTGGGACATAGCAACGAC-ATTGAGA-CAAACGCT
1 AGTGTAAGACCATGTTTGGGACAT-GCATCGGCTA-CGAGATGTAA-GCC
* * * *
11273 GGTGTAAGA-CATGTCTAGGACATGCATCGGCCT-CGAGATGTAACCC
1 AGTGTAAGACCATGTTTGGGACATGCATCGG-CTACGAGATGTAAGCC
*
11319 AGTGTAAGA-CATGTTTGGGACATGCATCGGCTACGAGATGT--GTC
1 AGTGTAAGACCATGTTTGGGACATGCATCGGCTACGAGATGTAAGCC
* * * *
11363 AGTGTCAGACCATGTTTGGGACATGGCATTGGC-ACGGATATGTGAGAGCT
1 AGTGTAAGACCATGTTTGGGACAT-GCATCGGCTAC-GAGATGT-A-AGCC
*
11413 AGGGTAAGACCATGTTTGGGACATG
1 AGTGTAAGACCATGTTTGGGACATG
11438 GCGTCGGCCT
Statistics
Matches: 215, Mismatches: 28, Indels: 31
0.78 0.10 0.11
Matches are distributed among these distances:
44 9 0.04
45 18 0.08
46 67 0.31
47 79 0.37
48 17 0.08
49 2 0.01
50 23 0.11
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTTTGGGACATGCATCGGCTACGAGATGTAAGCC
Found at i:11525 original size:47 final size:46
Alignment explanation
Indices: 11132--11538 Score: 175
Period size: 47 Copynumber: 8.6 Consensus size: 46
11122 TTTGTGTGCT
*
11132 AGTGTAAGA-CATGTCTGGGACATGCATGGGCCACATT-AT-GA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGCAT---CGAC-TTGATAGATGAGCC
*
11178 AGTGTAAGACCATGTCTGGGACATGCATGGGCCACATT-AT-GA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGCAT---CGAC-TTGATAGATGAGCC
* * * * *
11225 AGTGTAAGACCATGTCTGGGACATAGCAACGACATTGAGACA-AACGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGAC-TTGATAGATGA-GCC
* * * * *
11273 GGTGTAAGA-CATGTCTAGGACATGCATCGGCCTCG--AGATGTAACCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GACTTGATAGATG--AGCC
* * * * *
11319 AGTGTAAGA-CATGTTTGGGACATGCATCGGC-T-ACGAGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGACTTGA-TAGATGAGCC
* * * * *
11363 AGTGTCAGACCATGTTTGGGACATGGCATTGGCAC-GGATATG-TGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCA-TCG-ACTTGATA-GAT--GAGCC
* * * * * *
11413 AGGGTAAGACCATGTTTGGGACATGGCGTCGGCCTTGATTTCGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATC-GACTTGA--TAGATGAGCC
*
11462 AATGTAA-AGCCATGTCTGGGACATGGCATCGACTTGATAGATGAGCC
1 AGTGTAAGA-CCATGTCTGGGACAT-GCATCGACTTGATAGATGAGCC
11509 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACAT-GCATC
11539 ACCATTATAC
Statistics
Matches: 285, Mismatches: 48, Indels: 55
0.73 0.12 0.14
Matches are distributed among these distances:
44 11 0.04
45 22 0.08
46 54 0.19
47 111 0.39
48 24 0.08
49 30 0.11
50 30 0.11
51 1 0.00
52 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGACTTGATAGATGAGCC
Found at i:26450 original size:13 final size:13
Alignment explanation
Indices: 26432--26460 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26422 GCTCAGTAGG
26432 GACACGACCGTGT
1 GACACGACCGTGT
26445 GACACGACCGTGT
1 GACACGACCGTGT
26458 GAC
1 GAC
26461 GTGATTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.14
Consensus pattern (13 bp):
GACACGACCGTGT
Found at i:33628 original size:27 final size:27
Alignment explanation
Indices: 33595--33801 Score: 281
Period size: 27 Copynumber: 7.6 Consensus size: 27
33585 TAAATTGTGC
33595 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
33622 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
33650 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
33677 AGCACTAAGTGTGTGAGTTTAACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
*
33705 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
33732 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
33760 AGCACTAAGTGTGC-AAGTTGATTATAT
1 AGCACTAAGTGTGCGAA-TTGACTATGT
*
33787 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
33802 GACTTAATAT
Statistics
Matches: 162, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
27 89 0.55
28 73 0.45
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:33659 original size:55 final size:55
Alignment explanation
Indices: 33595--33801 Score: 335
Period size: 55 Copynumber: 3.8 Consensus size: 55
33585 TAAATTGTGC
33595 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
33650 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGTGAGTTTAACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
33705 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
33760 AGCACTAAGTGTGC-AAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAA-TTGACTATGTAGCACTAAGTGTGCG
33802 GACTTAATAT
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
54 1 0.01
55 140 0.99
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:41664 original size:18 final size:18
Alignment explanation
Indices: 41634--41726 Score: 56
Period size: 18 Copynumber: 5.5 Consensus size: 18
41624 AAACACCCCA
41634 AACACA-ACA-AAACCAC
1 AACACACACACAAACCAC
41650 AACACACACACAAA-CACC
1 AACACACACACAAACCA-C
* * *
41668 ACCAAAAACACAAACCAC
1 AACACACACACAAACCAC
** *
41686 CCCACACA-ACAAACAAC
1 AACACACACACAAACCAC
*
41703 -AC-CA-ACACAACCCAC
1 AACACACACACAAACCAC
*
41718 ACCACACAC
1 AACACACAC
41727 CCACCCAACA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.02
15 9 0.16
16 8 0.14
17 15 0.26
18 23 0.40
19 2 0.03
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (18 bp):
AACACACACACAAACCAC
Found at i:41668 original size:20 final size:19
Alignment explanation
Indices: 41606--41711 Score: 75
Period size: 18 Copynumber: 5.8 Consensus size: 19
41596 ATCGCTGTCC
*
41606 AACACC-CAAACACCCACGA
1 AACACCACAAACACACAC-A
*
41625 AACACCCCAAACACA-ACA
1 AACACCACAAACACACACA
41643 AA-ACCACAACACACACACA
1 AACACCACAA-ACACACACA
41662 AACACCACCAAA-A-ACACA
1 AACACCA-CAAACACACACA
*
41680 AACCACC-C-CACACA-ACA
1 AA-CACCACAAACACACACA
* *
41697 AACAACACCAACACA
1 AACACCACAAACACA
41712 ACCCACACCA
Statistics
Matches: 72, Mismatches: 5, Indels: 21
0.73 0.05 0.21
Matches are distributed among these distances:
16 4 0.06
17 14 0.19
18 21 0.29
19 18 0.25
20 12 0.17
21 3 0.04
ACGTcount: A:0.55, C:0.44, G:0.01, T:0.00
Consensus pattern (19 bp):
AACACCACAAACACACACA
Found at i:41692 original size:36 final size:38
Alignment explanation
Indices: 41615--41707 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
41605 CAACACCCAA
* *
41615 ACACCCACGAAACACC-CCAAACACAACAAAACCACAAC
1 ACACACAC-AAACACCACCAAAAACAACAAAACCACAAC
**
41653 ACACACACAAACACCACCAAAAAC-AC-AAACCACCCC
1 ACACACACAAACACCACCAAAAACAACAAAACCACAAC
*
41689 ACACA-ACAAACAACACCAA
1 ACACACACAAACACCACCAA
41708 CACAACCCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
35 13 0.27
36 13 0.27
37 9 0.18
38 14 0.29
ACGTcount: A:0.55, C:0.44, G:0.01, T:0.00
Consensus pattern (38 bp):
ACACACACAAACACCACCAAAAACAACAAAACCACAAC
Found at i:41706 original size:35 final size:35
Alignment explanation
Indices: 41639--41707 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
41629 CCCCAAACAC
*
41639 AACAAAACCACAACACACACACAAACACCACCAAA
1 AACAAAACCACAACACACACACAAACAACACCAAA
**
41674 AACACAAACCACCCCACACA-ACAAACAACACCAA
1 AACA-AAACCACAACACACACACAAACAACACCAA
41708 CACAACCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (35 bp):
AACAAAACCACAACACACACACAAACAACACCAAA
Found at i:41710 original size:32 final size:33
Alignment explanation
Indices: 41634--41726 Score: 102
Period size: 32 Copynumber: 2.8 Consensus size: 33
41624 AAACACCCCA
*
41634 AACA-CAACA-AAACCACAACACACACACAAAC
1 AACACCAACACAAACCACACCACACACACAAAC
* *
41665 ACCACCAAAAACACAAACCACCCCACACA-ACAAAC
1 AACACC---AACACAAACCACACCACACACACAAAC
*
41700 AACACCAACACAACCCACACCACACAC
1 AACACCAACACAAACCACACCACACAC
41727 CCACCCAACA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
31 3 0.06
32 19 0.38
35 15 0.30
36 13 0.26
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (33 bp):
AACACCAACACAAACCACACCACACACACAAAC
Found at i:41728 original size:13 final size:14
Alignment explanation
Indices: 41701--41739 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
41691 ACAACAAACA
41701 ACACCAACACAACCC
1 ACACCAACAC-ACCC
41716 ACACC-ACACACCC
1 ACACCAACACACCC
41729 AC-CCAACACAC
1 ACACCAACACAC
41740 AACGTAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 12 0.52
14 4 0.17
15 5 0.22
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (14 bp):
ACACCAACACACCC
Found at i:41734 original size:27 final size:28
Alignment explanation
Indices: 41686--41773 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 28
41676 CACAAACCAC
* *
41686 CCCACACAACAAA-CAACACCAACACAA
1 CCCACACCACAAACCCACACCAACACAA
*
41713 CCCACACCACACACCCAC-CCAACACACAA
1 CCCACACCACAAACCCACACC-A-ACACAA
** *
41742 CGTA-ACCACAAACCCACACCCACACAA
1 CCCACACCACAAACCCACACCAACACAA
41769 CCCAC
1 CCCAC
41774 CAAACAAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
27 21 0.45
28 16 0.34
29 10 0.21
ACGTcount: A:0.45, C:0.52, G:0.01, T:0.01
Consensus pattern (28 bp):
CCCACACCACAAACCCACACCAACACAA
Found at i:41736 original size:40 final size:41
Alignment explanation
Indices: 41686--41781 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 41
41676 CACAAACCAC
*
41686 CCCACACAACAAACAAC-ACCAACACAACCCACA-CCACAC-A
1 CCCACCCAACAAACAACAACC-ACA-AACCCACACCCACACAA
*
41726 CCCACCCAACACACAACGTAACCACAAACCCACACCCACACAA
1 CCCACCCAACAAACAAC--AACCACAAACCCACACCCACACAA
*
41769 CCCACCAAACAAA
1 CCCACCCAACAAA
41782 ACACCAGCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 15 0.32
41 8 0.17
42 9 0.19
43 15 0.32
ACGTcount: A:0.48, C:0.50, G:0.01, T:0.01
Consensus pattern (41 bp):
CCCACCCAACAAACAACAACCACAAACCCACACCCACACAA
Found at i:41817 original size:3 final size:3
Alignment explanation
Indices: 41809--41908 Score: 58
Period size: 3 Copynumber: 30.7 Consensus size: 3
41799 ACCCAACCAC
* * *
41809 ACA ACA ACA ACA CACA CCAA ACA CCCA CCA ACA ACA CACA ACAA ACA
1 ACA ACA ACA ACA -ACA AC-A ACA -ACA ACA ACA ACA -ACA AC-A ACA
* * *
41856 AAA ACC AC- ACAA ACA CACA ACA ACA ACA ACA ACA ACCC ACA ACCA ACA
1 ACA ACA ACA AC-A ACA -ACA ACA ACA ACA ACA ACA A-CA ACA A-CA ACA
41904 ACA AC
1 ACA AC
41909 CCTACAAAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
2 2 0.03
3 53 0.68
4 23 0.29
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:41821 original size:11 final size:11
Alignment explanation
Indices: 41802--41906 Score: 62
Period size: 11 Copynumber: 9.7 Consensus size: 11
41792 ACAAAAAACC
*
41802 CAACCACACAA
1 CAACAACACAA
41813 CAACAACACACA
1 CAACAACACA-A
* *
41825 CCAA-ACACCCAC
1 -CAACA-ACACAA
41837 CAACAACAC-A
1 CAACAACACAA
41847 CAACAA-ACAA
1 CAACAACACAA
* *
41857 AAACCACAC-A
1 CAACAACACAA
41867 -AAC-ACACAA
1 CAACAACACAA
41876 CAACAACAACAA
1 CAACAAC-ACAA
*
41888 CAAC-CCACAA
1 CAACAACACAA
41898 CCAACAACA
1 -CAACAACA
41907 ACCCTACAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 23
0.70 0.09 0.22
Matches are distributed among these distances:
8 4 0.05
9 6 0.08
10 19 0.26
11 24 0.33
12 13 0.18
13 7 0.10
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (11 bp):
CAACAACACAA
Found at i:41828 original size:24 final size:23
Alignment explanation
Indices: 41809--41908 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 23
41799 ACCCAACCAC
41809 ACAACAACAACACACACCAAACA
1 ACAACAACAACACACACCAAACA
* * *
41832 CCCACCAACAACACACAACAAACA
1 -ACAACAACAACACACACCAAACA
* *
41856 AAAACCACACAA-ACACACAACAACA
1 ACAA-CA-ACAACACACACCA-AACA
*
41881 ACAACAACAACCCACAACC-AACA
1 ACAACAACAACACAC-ACCAAACA
41904 ACAAC
1 ACAAC
41909 CCTACAAAGC
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
23 14 0.23
24 33 0.55
25 13 0.22
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (23 bp):
ACAACAACAACACACACCAAACA
Found at i:41905 original size:55 final size:55
Alignment explanation
Indices: 41803--41907 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 55
41793 CAAAAAACCC
* * *
41803 AACCACACAACAACAACACACACCAAACACCCACCAACAACACACAACAAACAAA
1 AACCACACAACAACAACACACAACAAACAACAACCAACAACACACAACAAACAAA
*
41858 AACCACACAAACACACAACA-ACAAC-AACAACAACCCACAAC-CAACAACAA
1 AACCACAC-AACA-ACAACACACAACAAACAACAACCAACAACAC-ACAACAA
41908 CCCTACAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.02
55 28 0.65
56 8 0.19
57 6 0.14
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (55 bp):
AACCACACAACAACAACACACAACAAACAACAACCAACAACACACAACAAACAAA
Found at i:41972 original size:14 final size:14
Alignment explanation
Indices: 41953--42015 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 14
41943 CCAACAAACC
41953 CACACACAACCAAA
1 CACACACAACCAAA
41967 CACACACAACACAAA
1 CACACACAAC-CAAA
*
41982 CCAAACCCCACAACCACAA
1 -C--A-CACACAACCA-AA
42001 CACACACAA-CAAA
1 CACACACAACCAAA
42014 CA
1 CA
42016 ACCAACACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 4 0.10
14 12 0.29
15 10 0.24
16 2 0.05
18 4 0.10
19 9 0.22
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (14 bp):
CACACACAACCAAA
Found at i:41975 original size:39 final size:37
Alignment explanation
Indices: 41921--42022 Score: 113
Period size: 34 Copynumber: 2.7 Consensus size: 37
41911 TACAAAGCCG
*
41921 CCACAACATCCCACAACAAAAACCAACAAACCCACACACAA
1 CCACAACA-CACACAACAAAAACCAACAAA-CC-C-CACAA
*
41962 CCA-AACACACACAACACAAA-C--CAAACCCCACAA
1 CCACAACACACACAACAAAAACCAACAAACCCCACAA
41995 CCACAACACACACAACAAACAACCAACA
1 CCACAACACACACAACAAA-AACCAACA
42023 CCCAACACCC
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
33 8 0.15
34 15 0.28
35 4 0.08
36 5 0.09
38 3 0.06
39 11 0.21
40 4 0.08
41 3 0.06
ACGTcount: A:0.55, C:0.44, G:0.00, T:0.01
Consensus pattern (37 bp):
CCACAACACACACAACAAAAACCAACAAACCCCACAA
Found at i:42023 original size:20 final size:20
Alignment explanation
Indices: 41932--42023 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
41922 CACAACATCC
*
41932 CACAACAAA-AACCAACAAA
1 CACAACAAACAACCAACACA
* *
41951 C-CCACACACAACCAAACACA
1 CACAACAAACAACC-AACACA
*
41971 CACAACACA-AACCAA-AC-
1 CACAACAAACAACCAACACA
* *
41988 C-CCAC-AACCA-CAACACA
1 CACAACAAACAACCAACACA
42005 CACAACAAACAACCAACAC
1 CACAACAAACAACCAACAC
42024 CCAACACCCC
Statistics
Matches: 55, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
15 4 0.07
16 6 0.11
17 2 0.04
18 10 0.18
19 11 0.20
20 16 0.29
21 6 0.11
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (20 bp):
CACAACAAACAACCAACACA
Found at i:42038 original size:23 final size:21
Alignment explanation
Indices: 42012--42056 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
42002 ACACACAACA
*
42012 AACAACCAACACCCAACACCCCC
1 AACAA-CAA-ACCCAACAACCCC
*
42035 AACAACAAACCCACCAACCCC
1 AACAACAAACCCAACAACCCC
42056 A
1 A
42057 CACCAAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (21 bp):
AACAACAAACCCAACAACCCC
Found at i:42038 original size:36 final size:36
Alignment explanation
Indices: 41932--42038 Score: 96
Period size: 36 Copynumber: 2.9 Consensus size: 36
41922 CACAACATCC
**
41932 CACAACAAA-AACCAACAAACCCACACACAACCAA-ACA
1 CACAACAAACAACCAAC--ACCCA-ACACCCCCAACACA
* * *
41969 CAC-ACAACACAAACCAA-ACCCCACAACCACAACACA
1 CACAACAA-AC-AACCAACACCCAACACCCCCAACACA
42005 CACAACAAACAACCAACACCCAACACCCCCAACA
1 CACAACAAACAACCAACACCCAACACCCCCAACA
42039 ACAAACCCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
35 12 0.21
36 30 0.54
37 8 0.14
39 6 0.11
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (36 bp):
CACAACAAACAACCAACACCCAACACCCCCAACACA
Found at i:42347 original size:26 final size:26
Alignment explanation
Indices: 42261--42352 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
42251 AACTCAACAC
42261 CTTA-TGCTACATAGT-CATCGCACA
1 CTTAGTGCTACATAGTACATCGCACA
*
42285 C-TAGTGCAACTTACATAGTCCAAACTCGCACCA
1 CTTAGTG---C-TACATAGT--ACA-TCGCA-CA
42318 CTTAGTGCTACATAGTACATCGCACA
1 CTTAGTGCTACATAGTACATCGCACA
42344 CTTAGTGCT
1 CTTAGTGCT
42353 CACAATTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
23 2 0.04
24 3 0.05
26 11 0.20
27 6 0.11
28 10 0.18
30 8 0.15
31 2 0.04
32 5 0.09
33 3 0.05
34 5 0.09
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.27
Consensus pattern (26 bp):
CTTAGTGCTACATAGTACATCGCACA
Done.