Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold224
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: 480342
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 3 of 3
Found at i:434263 original size:85 final size:84
Alignment explanation
Indices: 433940--434263 Score: 261
Period size: 85 Copynumber: 3.8 Consensus size: 84
433930 GTTGGTGACA
* * * * * * *
433940 CCCTTTAGTCCTCAAATAGAAGGACGC-CTT-TTTCTTTTCTCTTTTGTCCTCAAAGCGCAGGAC
1 CCCTTT-GTCCTCAAAGAGCAGAATGCACTTATTTCCTTTCTCCTTTGTCCTCAAAGAGCAGGAC
*
434003 ACATTTCATTTCCTTCTTTTTTT
65 ACATTTCATTT-C-T-TTATTTT
* * *
434026 ACTTTTGTCCTCAAAGAGCATGACA--CACTTGATTTCCTTTTTCCTTTGTCCTCAAAGAGCATG
1 CCCTTTGTCCTCAAAGAGCA-GA-ATGCACTT-ATTTCCTTTCTCCTTTGTCCTCAAAGAGCA-G
* * *
434089 G-CGCACCTT-ATTTCCTTATTTT
62 GACACA-TTTCATTTCTTTATTTT
* * * * *
434111 CTCTTAGTCCTCAAAGAGCAAAATG--CTT-TTTCCTTTTTTCCTTTGTCCTCAAAGAGTAGGAC
1 CCCTTTGTCCTCAAAGAGCAGAATGCACTTATTTCC-TTTCTCCTTTGTCCTCAAAGAGCAGGAC
*
434173 ACATTTCATTTCTTTCTTTT
65 ACATTTCATTTCTTTATTTT
* * * *
434193 CCCTTTGTCCTCAAAAAGCAGAATGCACTATATTTCCTTTCTCCTTTGTCCTTAAAAAGTAGGAC
1 CCCTTTGTCCTCAAAGAGCAGAATGCACT-TATTTCCTTTCTCCTTTGTCCTCAAAGAGCAGGAC
*
434258 GCATTT
65 ACATTT
434264 TCCTTTTCAA
Statistics
Matches: 191, Mismatches: 31, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
81 9 0.05
82 58 0.30
83 4 0.02
84 3 0.02
85 66 0.35
86 13 0.07
87 2 0.01
88 32 0.17
89 4 0.02
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (84 bp):
CCCTTTGTCCTCAAAGAGCAGAATGCACTTATTTCCTTTCTCCTTTGTCCTCAAAGAGCAGGACA
CATTTCATTTCTTTATTTT
Found at i:434347 original size:62 final size:62
Alignment explanation
Indices: 434253--434587 Score: 422
Period size: 62 Copynumber: 5.3 Consensus size: 62
434243 CTTAAAAAGT
* * *
434253 AGGACGCATTTTCCTTTTCAAAGCCCACACAAGTAGGTGGCACCTTTTTAGTCCTCAAAGAGC
1 AGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACC-TTTTAGTCCTCAAAGAGC
* * * **
434316 AGAACGCCTTTTTCTTTTC-AAGCCCACACAAGTTTATGGCATCCTTTT-GTCCTCAAAGAGC
1 AGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGAGC
* *
434377 AGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTTGTCCTCAAAGAGC
1 AGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGC
* * *
434439 AGGACACATTTTCCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGC
1 AGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGC
* * *
434501 AAGATGCCTTTTTCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAG
1 AGGACG-C-----CTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAG
434566 AGC
60 AGC
* *
434569 AGGATGCCTTTTTCTTTTC
1 AGGACGCCTTTTCCTTTTC
434588 TCATTTATCC
Statistics
Matches: 238, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
61 35 0.15
62 126 0.53
63 19 0.08
67 1 0.00
68 57 0.24
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (62 bp):
AGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGC
Found at i:434732 original size:168 final size:166
Alignment explanation
Indices: 434553--435029 Score: 587
Period size: 168 Copynumber: 2.8 Consensus size: 166
434543 GTGGCACCCT
*
434553 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCTCATTTATCCTCAAAGAGCATGACACATTT
1 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCTCCTTTATCCTCAAAGAGCATGACACATTT
*
434618 CATTTCTTTCTTTTTCCTTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCTTTTATC
66 CATTTCTTTC-TTTTCC-TTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCCTTTATC
* * *
434683 CTCAAAGAGTAGGGCGCACCTTATTTCCTTATTGTCCA
129 CTCAAAGAGCAGGACGCACCTTATTTACTTATTGTCCA
* * *
434721 TTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTTTCCTTTATCCTCAAAGAGCATGACACATTT
1 TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCTCCTTTATCCTCAAAGAGCATGACACATTT
* *
434786 CATTTCTTTCTTTTCCCTTTGTCCTCAAAGAGCTA-GATGCACTTTTTTTCCTTTTCTCCTTTGT
66 CATTTCTTTCTTTT-CCTTTGTCCTCAAAGAGC-AGGATGCACTTTATTTCCTTTT-TCCTTTAT
* * * * *
434850 CCTCAAAGAGCAGGACGCACTTTATTTATTTCTTTTCCC
128 CCTCAAAGAGCAGGACGCACCTTATTTACTTATTGTCCA
* * * * * *
434889 TTTGTCCTTAAATAGCAGGATACACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCAAGACGC
1 TTAGTCCTCAAAGAGCAGGATGC-C-TT-TTT-CTTTTCTCCTTTATCCTCAAAGAGCATGACAC
* * * ** **
434954 ACTTCTTTTCCTTCTTTTCCTTTGTCCTCAAAGAGGGGGACACACTTTATTTCCTTTTTTCCTTT
62 ATTTCATTTCTTTCTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCC-TTTTTCCTTT
* *
435019 GTCCTTAAAGA
126 ATCCTCAAAGA
435030 ACATGACACA
Statistics
Matches: 267, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
167 39 0.15
168 129 0.48
169 1 0.00
170 2 0.01
171 48 0.18
172 48 0.18
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (166 bp):
TTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCTCCTTTATCCTCAAAGAGCATGACACATTT
CATTTCTTTCTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCCTTTATCCT
CAAAGAGCAGGACGCACCTTATTTACTTATTGTCCA
Found at i:434855 original size:42 final size:42
Alignment explanation
Indices: 434550--435206 Score: 426
Period size: 42 Copynumber: 15.8 Consensus size: 42
434540 TTGGTGGCAC
434550 CCTTTAGTCCTCAAAGAGCAGGATGC-C--TTTTT-CTTTTCT
1 CCTTT-GTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
* * * ** * *
434589 CATTTATCCTCAAAGAGCATGACACATTTCATTTCTTTCTTTT-T
1 CCTTTGTCCTCAAAGAGCAGGATGCACTT--TTT-TTCCTTTTCT
*
434633 CCTTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTT-T
1 CC-TTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
* * * ** * * *
434675 CTTTTATCCTCAAAGAGTAGGGCGCACCTTATTTCCTTATTGT
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTT-TTCT
* * *
434718 CCATTAGTCCTCAAAGAGTAGGATGC-C---TTTTCCTTTTTT
1 CC-TTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
* * ** * *
434757 CCTTTATCCTCAAAGAGCATGACACATTTCATTTCTTTCTTTTC-
1 CCTTTGTCCTCAAAGAGCAGGATGCACTT--TTT-TTCCTTTTCT
434801 CCTTTGTCCTCAAAGAGCTA-GATGCACTTTTTTTCCTTTTCT
1 CCTTTGTCCTCAAAGAGC-AGGATGCACTTTTTTTCCTTTTCT
* *
434843 CCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTATTTCTTTTC-
1 CCTTTGTCCTCAAAGAGCAGGATGCAC-TT-TTT-TTCCTTTTCT
* * * *
434887 CCTTTGTCCTTAAATAGCAGGATACACTTTATTTCCTTTTCT
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
* * * * *
434929 CCTTTATCCTCAAAGAGCAAGACGCACTTCTTTTCCTTCTTTT
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTT-TTCT
** ** * *
434972 CCTTTGTCCTCAAAGAGGGGGACACACTTTATTTCCTTTTTT
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
* * * * *
435014 CCTTTGTCCTTAAAGAACATGA--CACATTTCATTTCCTTTTTT
1 CCTTTGTCCTCAAAGAGCAGGATGCAC-TTT-TTTTCCTTTTCT
** * * **
435056 CCTTTGTTTTCAAAGAGTAGGACGCACTTCATTTCCTTTT-T
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
** * *
435097 CCTTTGTCCTTGAAGAGCAGGGTGCA------TTCTTTTTCT
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
** * *
435133 -CTTTGTCCTCAAAGAGCAGGATGCACTTCATTTCTTTTTTT
1 CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
*
435174 CCTTTGTCCTTC-AAGAGCAGGATGCACTATTTT
1 CCTTTGTCC-TCAAAGAGCAGGATGCACTTTTTT
435207 CCCTCTGTCC
Statistics
Matches: 487, Mismatches: 92, Indels: 75
0.74 0.14 0.11
Matches are distributed among these distances:
35 29 0.06
36 1 0.00
38 33 0.07
39 9 0.02
40 10 0.02
41 80 0.16
42 155 0.32
43 50 0.10
44 77 0.16
45 43 0.09
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (42 bp):
CCTTTGTCCTCAAAGAGCAGGATGCACTTTTTTTCCTTTTCT
Found at i:434855 original size:86 final size:86
Alignment explanation
Indices: 434549--435192 Score: 575
Period size: 86 Copynumber: 7.7 Consensus size: 86
434539 GTTGGTGGCA
*
434549 CCCTTTAGTCCTCAAAGAGCAGGATGC-C-TT-TTT-CTTTTCTCATTTATCCTCAAAGAGCATG
1 CCCTTT-GTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATG
*
434610 ACACATTTCATTTCTTTCTTTTT
65 ACACATTTCATTTCCTTC-TTTT
* * * * *
434633 CCTTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTT-TCTTTTATCCTCAAAGAGTAGGG
1 CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATGA
* * * *
434697 CGCACCTT-ATTTCCTTATTGT
66 CACA-TTTCATTTCCTTCTTTT
* * * *
434718 CCATTAGTCCTCAAAGAGTAGGATGC-C--T-TTTCCTTTTTTCCTTTATCCTCAAAGAGCATGA
1 CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATGA
*
434779 CACATTTCATTTCTTTCTTTT
66 CACATTTCATTTCCTTCTTTT
* * *
434800 CCCTTTGTCCTCAAAGAGCTA-GATGCACTTTTTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGG
1 CCCTTTGTCCTCAAAGAGC-AGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATG
* **
434864 ACGCACTTT-ATTTATTTCTTTT
65 ACACA-TTTCATTTCCTTCTTTT
* * * *
434886 CCCTTTGTCCTTAAATAGCAGGATACACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCAAGA
1 CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATGA
* * *
434951 CGCACTTCTTTTCCTTCTTTT
66 CACATTTCATTTCCTTCTTTT
** ** * * * *
434972 -CCTTTGTCCTCAAAGAGGGGGACACACTTTATTTCCTTTTTTCCTTTGTCCTTAAAGAACATGA
1 CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATGA
435036 CACATTTCATTTCCTT-TTTT
66 CACATTTCATTTCCTTCTTTT
** * * * * **
435056 -CCTTTGTTTTCAAAGAGTAGGACGCACTTCATTTCCTTTT-TCCTTTGTCCTTGAAGAGCA-G-
1 CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATGA
** *
435117 ---GGTGCA-TT-C-T-TTTT
66 CACATTTCATTTCCTTCTTTT
* * * * *
435131 CTCTTTGTCCTCAAAGAGCAGGATGCACTTCATTTCTTTTTTTCCTTTGTCCTTC-AAGAGCA
1 CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCC-TCAAAGAGCA
435193 GGATGCACTA
Statistics
Matches: 471, Mismatches: 71, Indels: 43
0.81 0.12 0.07
Matches are distributed among these distances:
75 5 0.01
76 35 0.07
77 19 0.04
78 4 0.01
81 11 0.02
82 55 0.12
83 40 0.08
84 45 0.10
85 99 0.21
86 148 0.31
87 10 0.02
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (86 bp):
CCCTTTGTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCATGA
CACATTTCATTTCCTTCTTTT
Found at i:435137 original size:76 final size:76
Alignment explanation
Indices: 435051--435227 Score: 230
Period size: 76 Copynumber: 2.3 Consensus size: 76
435041 TTCATTTCCT
** * *
435051 TTTTTCCTTTGTTTTCAAAGAGTAGGACGCACTTCATTTC-CTTTTTCCTTTGTCCTTGAAGAGC
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTCTTTTTCCTTTGTCCTTCAAGAGC
*
435115 AGGGTGCATTC
66 AGGATGCATTC
* *
435126 TTTTTCTCTTTGTCCTCAAAGAGCAGGATGCACTTCATTTCTTTTTTTCCTTTGTCCTTCAAGAG
1 TTTTTC-CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTCTTTTTCCTTTGTCCTTCAAGAG
* *
435191 CAGGATGCACTA
65 CAGGATGCATTC
* * *
435203 TTTTCCCTCTGTCCTCAAGGAGCAG
1 TTTTTCCTTTGTCCTCAAAGAGCAG
435228 TACACTTTCC
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
75 6 0.07
76 47 0.53
77 35 0.40
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (76 bp):
TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTCTTTTTCCTTTGTCCTTCAAGAGC
AGGATGCATTC
Found at i:435139 original size:35 final size:34
Alignment explanation
Indices: 435091--435227 Score: 105
Period size: 34 Copynumber: 3.8 Consensus size: 34
435081 ACTTCATTTC
** *
435091 CTTTTTCCTTTGTCCTTGAAGAGCAGGGTGCATT
1 CTTTTTCCTTTGTCCTCAAAGAGCAGGATGCATT
435125 CTTTTTCTCTTTGTCCTCAAAGAGCAGGATGCACTTCATTT
1 CTTTTTC-CTTTGTCCTCAAAGAGCAGGATG-----CA-TT
*
435166 CTTTTTTTCCTTTGTCCTTC-AAGAGCAGGATGCACT
1 C--TTTTTCCTTTGTCC-TCAAAGAGCAGGATGCATT
* * * *
435202 ATTTTCCCTCTGTCCTCAAGGAGCAG
1 CTTTTTCCTTTGTCCTCAAAGAGCAG
435228 TACACTTTCC
Statistics
Matches: 84, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
33 2 0.02
34 26 0.31
35 20 0.24
36 1 0.01
37 2 0.02
40 2 0.02
41 3 0.04
42 20 0.24
43 8 0.10
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (34 bp):
CTTTTTCCTTTGTCCTCAAAGAGCAGGATGCATT
Found at i:436747 original size:11 final size:11
Alignment explanation
Indices: 436731--436767 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
436721 TATGAGTTTC
436731 AAAATTATGTA
1 AAAATTATGTA
436742 AAAATTATGTA
1 AAAATTATGTA
*
436753 ACAATTATGTA
1 AAAATTATGTA
436764 AAAA
1 AAAA
436768 ACCAAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (11 bp):
AAAATTATGTA
Found at i:437711 original size:80 final size:79
Alignment explanation
Indices: 437479--437722 Score: 274
Period size: 79 Copynumber: 3.1 Consensus size: 79
437469 TCATTCATGT
* * * * * *
437479 TTTTATTTCTAAAATACCGATTTTTCGCCATCGGAGATGCTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTTTAAAATATCAATTTTTCACCATCGGAGATACTCCAACCCCGTTATTTCTGAGGGGA
* *
437544 TACTCCAACCACAA
66 TACTCCAACCCCGA
* * ** * * *
437558 TTTTATTTTCAAAACATCAATTTTTCATAATC-AATGATACTCCAACCCTGTTATTTTTGAGGGG
1 TTTTATTTTTAAAATATCAATTTTTCACCATCGGA-GATACTCCAACCCCGTTATTTCTGAGGGG
437622 ATACTCCAACCCCGA
65 ATACTCCAACCCCGA
* * * *
437637 TTTTATTTTTAAAATATCAATTTTCCACCATCGGGGGATACTCCAACCCCATTATTTCTGAAGGG
1 TTTTATTTTTAAAATATCAATTTTTCACCATC-GGAGATACTCCAACCCCGTTATTTCTGAGGGG
* *
437702 ATACTCCAACCCTGT
65 ATACTCCAACCCCGA
437717 TTTTAT
1 TTTTAT
437723 CTCCAAAATA
Statistics
Matches: 134, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
78 1 0.01
79 89 0.66
80 44 0.33
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTTATTTTTAAAATATCAATTTTTCACCATCGGAGATACTCCAACCCCGTTATTTCTGAGGGGA
TACTCCAACCCCGA
Found at i:440175 original size:34 final size:34
Alignment explanation
Indices: 440132--440200 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
440122 TGTCGATGCT
*
440132 TCTTGGACTCTTTGAATAGCCATTGAAGAAAAAC
1 TCTTGGACTCTTTGAACAGCCATTGAAGAAAAAC
*
440166 TCTTGGACTCTTTGAACCGCCATTGAAGAAAAAC
1 TCTTGGACTCTTTGAACAGCCATTGAAGAAAAAC
440200 T
1 T
440201 TTACAGGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (34 bp):
TCTTGGACTCTTTGAACAGCCATTGAAGAAAAAC
Found at i:440388 original size:2 final size:2
Alignment explanation
Indices: 440381--440423 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
440371 ACAATCAAGA
440381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
440423 A
1 A
440424 ATCGATTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:440793 original size:25 final size:25
Alignment explanation
Indices: 440764--440826 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
440754 AAACCAACTT
440764 AATTAAGTATATTAT-ATAAAAATCA
1 AATTAAGTATATTATAAT-AAAATCA
*
440789 AATTAAAGT-TATAATAATAAAATCA
1 AATT-AAGTATATTATAATAAAATCA
440814 AATTTAAG-ATATT
1 AA-TTAAGTATATT
440827 TAAGTATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
25 24 0.75
26 8 0.25
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (25 bp):
AATTAAGTATATTATAATAAAATCA
Found at i:442308 original size:16 final size:16
Alignment explanation
Indices: 442274--442306 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
442264 AAATAATTCG
442274 AATCTAAAATGACCTA
1 AATCTAAAATGACCTA
*
442290 AATCTAAGATGA-CTA
1 AATCTAAAATGACCTA
442305 AA
1 AA
442307 ATTTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (16 bp):
AATCTAAAATGACCTA
Found at i:442333 original size:16 final size:16
Alignment explanation
Indices: 442312--442372 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
442302 CTAAAATTTG
442312 AAACAACTTGAATCTA
1 AAACAACTTGAATCTA
* *
442328 AAACAACTGGAATTTA
1 AAACAACTTGAATCTA
*
442344 AAATGAAC-T-AATCTCA
1 AAA-CAACTTGAATCT-A
*
442360 AAATAACTTGAAT
1 AAACAACTTGAAT
442373 AATTAACACT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
15 7 0.20
16 22 0.63
17 6 0.17
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (16 bp):
AAACAACTTGAATCTA
Found at i:443634 original size:17 final size:16
Alignment explanation
Indices: 443612--443645 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
443602 GAGTATATAA
*
443612 TTAATTAGTTTAATTCT
1 TTAATTACTTT-ATTCT
443629 TTAATTACTTTATTCT
1 TTAATTACTTTATTCT
443645 T
1 T
443646 AAGGAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAATTACTTTATTCT
Found at i:445710 original size:29 final size:29
Alignment explanation
Indices: 445673--445736 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
445663 ATATTCTCTA
*
445673 CTTTAAGATCTTGTTGTCTTTCTATTTTT
1 CTTTCAGATCTTGTTGTCTTTCTATTTTT
*
445702 CTTTCAGATCTTGTTGTCTTTTTATTTTT
1 CTTTCAGATCTTGTTGTCTTTCTATTTTT
445731 CTTTCA
1 CTTTCA
445737 TCATTCAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.09, T:0.62
Consensus pattern (29 bp):
CTTTCAGATCTTGTTGTCTTTCTATTTTT
Found at i:447767 original size:47 final size:47
Alignment explanation
Indices: 447715--447812 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
447705 TAAAAGGAAA
** *
447715 ATGAAAGAAAATGGAAATGGCCTAAGTGAAGTACATATATTTAAAAG
1 ATGAAAGAAAATAAAAATAGCCTAAGTGAAGTACATATATTTAAAAG
* *
447762 ATGAAAGAAAATAAAAATAGCTTAAGTGAAGTACGTATATTTAAAAG
1 ATGAAAGAAAATAAAAATAGCCTAAGTGAAGTACATATATTTAAAAG
447809 ATGA
1 ATGA
447813 TCTTTTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (47 bp):
ATGAAAGAAAATAAAAATAGCCTAAGTGAAGTACATATATTTAAAAG
Found at i:457620 original size:2 final size:2
Alignment explanation
Indices: 457613--457639 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
457603 GTAATAAAGA
457613 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 A
457640 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:459019 original size:16 final size:16
Alignment explanation
Indices: 458998--459071 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
458988 TCAAAAACCT
458998 GAACCCGAAATTA-TCC
1 GAACCCGAAA-TAGTCC
459014 GAACCCGAAATAGTCC
1 GAACCCGAAATAGTCC
* * * *
459030 GAACTCGAGACAGCCC
1 GAACCCGAAATAGTCC
* * *
459046 GAACCTGAAAAAGCCC
1 GAACCCGAAATAGTCC
*
459062 GAACTCGAAA
1 GAACCCGAAA
459072 AAACTCGAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 2 0.04
16 45 0.96
ACGTcount: A:0.39, C:0.31, G:0.19, T:0.11
Consensus pattern (16 bp):
GAACCCGAAATAGTCC
Found at i:459072 original size:16 final size:16
Alignment explanation
Indices: 459012--459073 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
459002 CCGAAATTAT
* * *
459012 CCGAACCCGAAATAGT
1 CCGAACTCGAAAAAGC
* *
459028 CCGAACTCGAGACAGC
1 CCGAACTCGAAAAAGC
459044 CCGAAC-CTGAAAAAGC
1 CCGAACTC-GAAAAAGC
459060 CCGAACTCGAAAAA
1 CCGAACTCGAAAAA
459074 ACTCGAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 1 0.03
16 36 0.95
17 1 0.03
ACGTcount: A:0.40, C:0.32, G:0.19, T:0.08
Consensus pattern (16 bp):
CCGAACTCGAAAAAGC
Found at i:459081 original size:32 final size:32
Alignment explanation
Indices: 459012--459081 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
459002 CCGAAATTAT
* * * * *
459012 CCGAACCCGAAATAGTCCGAACTCGAGACAGC
1 CCGAACCCGAAAAAGCCCGAACTCGAAAAAAC
*
459044 CCGAACCTGAAAAAGCCCGAACTCGAAAAAAC
1 CCGAACCCGAAAAAGCCCGAACTCGAAAAAAC
*
459076 TCGAAC
1 CCGAAC
459082 TTAAAAGAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.33, G:0.19, T:0.09
Consensus pattern (32 bp):
CCGAACCCGAAAAAGCCCGAACTCGAAAAAAC
Found at i:459096 original size:16 final size:16
Alignment explanation
Indices: 459059--459109 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
459049 CCTGAAAAAG
*
459059 CCCGAACTCGAAAA-AA
1 CCCGAACT-TAAAAGAA
*
459075 CTCGAACTTAAAAGAA
1 CCCGAACTTAAAAGAA
* *
459091 CCCGAACCTGAAAGAA
1 CCCGAACTTAAAAGAA
459107 CCC
1 CCC
459110 AAACCTAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.45, C:0.31, G:0.14, T:0.10
Consensus pattern (16 bp):
CCCGAACTTAAAAGAA
Found at i:459114 original size:16 final size:16
Alignment explanation
Indices: 459085--459133 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
459075 CTCGAACTTA
*
459085 AAAGAACCCGAACCTG
1 AAAGAACCCAAACCTG
459101 AAAGAACCCAAACCT-
1 AAAGAACCCAAACCTG
* *
459116 AAGAAAATCCAAACCTG
1 AA-AGAACCCAAACCTG
459133 A
1 A
459134 GACTGACCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 25 0.89
17 1 0.04
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.08
Consensus pattern (16 bp):
AAAGAACCCAAACCTG
Found at i:459585 original size:16 final size:15
Alignment explanation
Indices: 459564--459593 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
459554 ATGTTACACT
459564 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
459580 TAGAATAGAATATA
1 TAGAATAGAATATA
459594 AATTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:460541 original size:16 final size:16
Alignment explanation
Indices: 460519--460590 Score: 90
Period size: 16 Copynumber: 4.5 Consensus size: 16
460509 AAGCCTGAAA
*
460519 TCGAATGAGCTCAAAC
1 TCGAATGAGCCCAAAC
* *
460535 CCGAATGAGCCCGAAC
1 TCGAATGAGCCCAAAC
* *
460551 TCGAACGAGCCCGAAC
1 TCGAATGAGCCCAAAC
*
460567 TCAAATGAGCCCAAAC
1 TCGAATGAGCCCAAAC
460583 TCGAATGA
1 TCGAATGA
460591 ACTTGAACCC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.36, C:0.31, G:0.21, T:0.12
Consensus pattern (16 bp):
TCGAATGAGCCCAAAC
Found at i:460555 original size:32 final size:32
Alignment explanation
Indices: 460500--460590 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
460490 TATAAGTCCG
* * * *
460500 AACCCAAATAAGCCTGAAATCGAATGAGCTCA
1 AACCCAAATGAGCCCGAACTCGAATGAGCCCA
* * *
460532 AACCCGAATGAGCCCGAACTCGAACGAGCCCG
1 AACCCAAATGAGCCCGAACTCGAATGAGCCCA
* *
460564 AACTCAAATGAGCCCAAACTCGAATGA
1 AACCCAAATGAGCCCGAACTCGAATGA
460591 ACTTGAACCC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.40, C:0.30, G:0.19, T:0.12
Consensus pattern (32 bp):
AACCCAAATGAGCCCGAACTCGAATGAGCCCA
Found at i:460604 original size:48 final size:48
Alignment explanation
Indices: 460522--460614 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
460512 CCTGAAATCG
* * *
460522 AATGAGCTCAAACCCGAATGAGCCCGAACTCGAACGAGCCCGAACTCA
1 AATGAGCCCAAACCCGAATGAACCCGAACCCGAACGAGCCCGAACTCA
* ** **
460570 AATGAGCCCAAACTCGAATGAACTTGAACCCGAACTTGCCCGAAC
1 AATGAGCCCAAACCCGAATGAACCCGAACCCGAACGAGCCCGAAC
460615 CCGCCCAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.13
Consensus pattern (48 bp):
AATGAGCCCAAACCCGAATGAACCCGAACCCGAACGAGCCCGAACTCA
Found at i:461840 original size:3 final size:3
Alignment explanation
Indices: 461832--461859 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
461822 TTTTCTACCT
461832 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
461860 CTTTTATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:462852 original size:21 final size:21
Alignment explanation
Indices: 462827--462866 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
462817 TTTGAAATAT
462827 ATTTATTATTAACAAACATTA
1 ATTTATTATTAACAAACATTA
* *
462848 ATTTATTGTTAATAAACAT
1 ATTTATTATTAACAAACAT
462867 GTCATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTTATTATTAACAAACATTA
Found at i:469024 original size:14 final size:14
Alignment explanation
Indices: 469005--469048 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
468995 TAAATATTAG
469005 ATTTTTAAAAAAAT
1 ATTTTTAAAAAAAT
*
469019 ATTTTTTAAAAAAT
1 ATTTTTAAAAAAAT
*
469033 A-TATTAAAAATAAT
1 ATTTTTAAAAA-AAT
469047 AT
1 AT
469049 AAACAGACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTTTAAAAAAAT
Found at i:469767 original size:15 final size:16
Alignment explanation
Indices: 469747--469807 Score: 72
Period size: 15 Copynumber: 3.8 Consensus size: 16
469737 ATTTATATAT
469747 TATATATTAT-ATTTA
1 TATATATTATAATTTA
469762 TATATATTATGAATTTA
1 TATATATTAT-AATTTA
* *
469779 TATCATATTAAAATATA
1 TAT-ATATTATAATTTA
469796 TA-ATATTATAAT
1 TATATATTATAAT
469808 ATAAATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 19 0.47
17 15 0.38
18 6 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TATATATTATAATTTA
Found at i:469808 original size:15 final size:15
Alignment explanation
Indices: 469750--469817 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
469740 TATATATTAT
*
469750 ATATTAT-ATTTATA
1 ATATTATAATATATA
*
469764 TATATTATGAATTTATATC
1 -ATATTAT-AA--TATATA
*
469783 ATATTAAAATATATA
1 ATATTATAATATATA
469798 ATATTATAATATA-A
1 ATATTATAATATATA
469812 ATATTA
1 ATATTA
469818 AAAAATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
14 7 0.16
15 24 0.55
17 3 0.07
18 6 0.14
19 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (15 bp):
ATATTATAATATATA
Done.