Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold452
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: 589716
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 5 of 5
Found at i:531462 original size:22 final size:22
Alignment explanation
Indices: 531395--531462 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
531385 GCACCTTTAT
*
531395 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* ** *
531417 CTTGAA-T-CAGCATA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
531438 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
531460 CTT
1 CTT
531463 GAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:531474 original size:22 final size:22
Alignment explanation
Indices: 531409--531474 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
531399 AAGTCCAATG
531409 TAGCTGGCCTTGAATCAGCATA
1 TAGCTGGCCTTGAATCAGCATA
*
531431 T---TGGCACCTTTAAGTC--CAATA
1 TAGCTGG--CCTTGAA-TCAGC-ATA
531452 TAGCTGGCCTTGAATCAGCATA
1 TAGCTGGCCTTGAATCAGCATA
531474 T
1 T
531475 TGACACCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 12 0.36
22 13 0.39
23 1 0.03
24 3 0.09
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (22 bp):
TAGCTGGCCTTGAATCAGCATA
Found at i:531716 original size:49 final size:49
Alignment explanation
Indices: 531225--531878 Score: 552
Period size: 43 Copynumber: 13.8 Consensus size: 49
531215 AAGCCTAATA
* * *
531225 TCGCTGGCCTTGAATTAACATATTGGCACCTTTATCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
531274 TAGCTGACCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * * *
531317 TAGCTGACCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
531360 TAGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
531409 TAGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
531452 TAGCTGGCCTTGAATCAGCATATTGACACCTTTATCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
531501 TCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
531544 TCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * * *
531592 TCGCTGGCCTTGAATCAGCACATTGACACC-T--TC---AAGTCTAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
531635 TCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * * * *
531684 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCAACTTGAAGCCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* ** * ** ** *
531733 TCGCTAGCC--GCATATTGGC-TCTT-TTATCCTTTTTCTCATCTTTAAACCCAATA
1 TCGCTGGCCTTG-A-ATCAGCATATTGGCA-CC----T-TCATCTTTAAGTCCAATG
* * *
531786 TCGCTGGCCTTGAATCACCATATTGGCGCCTTTGTCATCTTTCAA-ACCAATG
1 TCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTT-AAGTCCAATG
*
531838 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
531879 CATTCCTAAG
Statistics
Matches: 502, Mismatches: 66, Indels: 75
0.78 0.10 0.12
Matches are distributed among these distances:
43 194 0.39
44 1 0.00
46 4 0.01
47 3 0.01
48 47 0.09
49 173 0.34
50 1 0.00
52 44 0.09
53 28 0.06
54 6 0.01
55 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
Found at i:531842 original size:52 final size:52
Alignment explanation
Indices: 531768--531869 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
531758 ATCCTTTTTC
* *
531768 TCATCTTTAAACCCAATATCGCTGGCCTTGAATCACCATATTGGCGCCTTTG
1 TCATCTTTAAACCCAATATCGCTGGCCTTGAATCACCACATTGGCACCTTTG
* *
531820 TCATCTTTCAAA-CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TCATCTTT-AAACCCAATATCGCTGGCCTTGAATCACCACATTGGCACCTT
531870 CATCTTTAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 42 0.93
53 3 0.07
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (52 bp):
TCATCTTTAAACCCAATATCGCTGGCCTTGAATCACCACATTGGCACCTTTG
Found at i:532725 original size:19 final size:19
Alignment explanation
Indices: 532701--532764 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
532691 TTTCAACGAT
532701 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
532720 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
532734 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
* *
532752 TTATATTGATACA
1 TTGTATCGATACA
532765 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:532738 original size:32 final size:32
Alignment explanation
Indices: 532702--532811 Score: 139
Period size: 32 Copynumber: 3.4 Consensus size: 32
532692 TTCAACGATT
532702 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
532734 TGTATCGATACATAAGTGTTATATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* * ** *
532766 TGTATCGATACATCACTCAAATGTATCGATACAT
1 TGTATCGATACATAAGT--GTTGTATCGATACAA
532800 TGTATCGATACA
1 TGTATCGATACA
532812 CTGATCTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
32 45 0.67
34 22 0.33
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:532739 original size:13 final size:13
Alignment explanation
Indices: 532721--532777 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
532711 ACATAAGTGT
532721 TGTATCGATACAA
1 TGTATCGATACAA
532734 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
532749 GTGTTATATTGATACAA
1 -TG---TATCGATACAA
532766 TGTATCGATACA
1 TGTATCGATACA
532778 TCACTCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
15 2 0.06
16 4 0.11
17 2 0.06
19 8 0.22
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:532805 original size:13 final size:13
Alignment explanation
Indices: 532787--532811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532777 ATCACTCAAA
532787 TGTATCGATACAT
1 TGTATCGATACAT
532800 TGTATCGATACA
1 TGTATCGATACA
532812 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:536211 original size:16 final size:16
Alignment explanation
Indices: 536187--536225 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
536177 ATTCATGTAT
536187 TTATATTATATTTATA
1 TTATATTATATTTATA
*
536203 TTATTTTATATTTATA
1 TTATATTATATTTATA
*
536219 TTTTATT
1 TTATATT
536226 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTATATTTATA
Found at i:536226 original size:11 final size:11
Alignment explanation
Indices: 536184--536225 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
536174 TAAATTCATG
536184 TATTTATATTA
1 TATTTATATTA
536195 TATTTATATTA
1 TATTTATATTA
536206 T-TTTATATTTA
1 TATTTATA-TTA
536217 TATTT-TATT
1 TATTTATATT
536226 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.28
11 18 0.62
12 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTTATATTA
Found at i:537970 original size:38 final size:38
Alignment explanation
Indices: 537918--538043 Score: 126
Period size: 38 Copynumber: 3.3 Consensus size: 38
537908 TTCAATTTGA
* * *
537918 AATTCTCTAGCCGTCAGCCACCATCTAATTCCAAATTG
1 AATTCTCTAACCGTCAGCCACCAACAAATTCCAAATTG
* * * * *
537956 AATTCTTTAACCGTCAGTCGCTAACAAATTTCAAATTG
1 AATTCTCTAACCGTCAGCCACCAACAAATTCCAAATTG
* * * * *
537994 AATTCTCTAACCGTCAACCGCCAACCAATTTCAAATTA
1 AATTCTCTAACCGTCAGCCACCAACAAATTCCAAATTG
*
538032 AATTTTCTAACC
1 AATTCTCTAACC
538044 TCAACTAATT
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (38 bp):
AATTCTCTAACCGTCAGCCACCAACAAATTCCAAATTG
Found at i:539846 original size:19 final size:18
Alignment explanation
Indices: 539822--539866 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
539812 TGAGGTGAAA
539822 AATTAAAATCATATATTAC
1 AATTAAAATCATA-ATTAC
* *
539841 AATTAAAAATTATAATTAT
1 AATT-AAAATCATAATTAC
539860 AATTAAA
1 AATTAAA
539867 TAATTATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 12 0.52
20 8 0.35
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAATCATAATTAC
Found at i:540944 original size:113 final size:115
Alignment explanation
Indices: 540718--540991 Score: 387
Period size: 113 Copynumber: 2.4 Consensus size: 115
540708 AAAAAAAAAT
* * *
540718 AAAAATAAAAACTATAA-CTGCAATGATTCTTTTTGGATG-AAAAAAAAAATTTCAAGAACAAAA
1 AAAATTAAAAACTACAACCAGCAATGATTCTTTTTGGATGAAAAAAAAAAATTTCAAGAACAAAA
* *
540781 TGATCGAAAAAATCGAGGGAGACAAAGGGAAAACAGGTGGCAGTAAAATTC
66 TGATC-AAAAAATCAAGGGAGACAAAGGGAAAACAGGTAGCAGTAAAATTC
540832 AAAATTAAAAACTACAACCAGCAATGATTCTTTTTGGATGAAAAAAAAAAATTT-AAGAAC-AAA
1 AAAATTAAAAACTACAACCAGCAATGATTCTTTTTGGATGAAAAAAAAAAATTTCAAGAACAAAA
* * * * *
540895 TGAT-AAAAATTTCAATGGTGACAATGGGAAAACATGTAGCAGTAAAATTC
66 TGATCAAAAA-ATCAAGGGAGACAAAGGGAAAACAGGTAGCAGTAAAATTC
* *
540945 AAAATTAAAAACTTCAACCAGCAATGATTCTATTTGGATGAAAAAAA
1 AAAATTAAAAACTACAACCAGCAATGATTCTTTTTGGATGAAAAAAA
540992 TTCAAAAACA
Statistics
Matches: 145, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
112 5 0.03
113 78 0.54
114 22 0.15
115 27 0.19
116 13 0.09
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (115 bp):
AAAATTAAAAACTACAACCAGCAATGATTCTTTTTGGATGAAAAAAAAAAATTTCAAGAACAAAA
TGATCAAAAAATCAAGGGAGACAAAGGGAAAACAGGTAGCAGTAAAATTC
Found at i:541064 original size:5 final size:5
Alignment explanation
Indices: 541054--541096 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
541044 ATTTTAAAAG
541054 TTTAA TTTAA TTTAA TTT-A TTTAAA TTTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTT-AA -TTTAA TTTAA TTTAA TT
541097 AAAAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.11
5 25 0.71
6 3 0.09
7 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:541068 original size:26 final size:27
Alignment explanation
Indices: 541039--541094 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
541029 TTAATTTTGA
541039 TTAAAATT-TTAAAAGTTTAATTTAAT
1 TTAAAATTATTAAAAGTTTAATTTAAT
* * *
541065 TT-AATTTATTTAAATTTTAATTTAAT
1 TTAAAATTATTAAAAGTTTAATTTAAT
541091 TTAA
1 TTAA
541095 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 20 0.80
27 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTAAAATTATTAAAAGTTTAATTTAAT
Found at i:541083 original size:21 final size:21
Alignment explanation
Indices: 541059--541099 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
541049 AAAAGTTTAA
*
541059 TTTAATTTAATTTATTTAAAT
1 TTTAATTTAATTTAATTAAAT
541080 TTTAATTTAATTTAATTAAA
1 TTTAATTTAATTTAATTAAA
541100 AAAAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAATTTAATTTAATTAAAT
Found at i:541105 original size:26 final size:26
Alignment explanation
Indices: 541049--541105 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
541039 TTAAAATTTT
* * **
541049 AAAAGTTTAATTTAATTTAATTTATT
1 AAAATTTTAATTTAATTTAATTAAAA
*
541075 TAAATTTTAATTTAATTTAATTAAAA
1 AAAATTTTAATTTAATTTAATTAAAA
541101 AAAAT
1 AAAAT
541106 AACAATTCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
AAAATTTTAATTTAATTTAATTAAAA
Found at i:541170 original size:15 final size:15
Alignment explanation
Indices: 541150--541202 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
541140 TATTCTAATC
*
541150 TAAAATGTTAAAACT
1 TAAAATGTTAAAATT
*
541165 TAAAATAACTT-AAATT
1 TAAAAT--GTTAAAATT
541181 TAAAATGATTAAAATT
1 TAAAATG-TTAAAATT
541197 TAAAAT
1 TAAAAT
541203 AATCTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 8 0.26
16 21 0.68
17 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (15 bp):
TAAAATGTTAAAATT
Found at i:541185 original size:16 final size:16
Alignment explanation
Indices: 541157--541210 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
541147 ATCTAAAATG
*
541157 TTAAAACTTAAAATAA
1 TTAAAATTTAAAATAA
*
541173 CTT-AAATTTAAAATGA
1 -TTAAAATTTAAAATAA
541189 TTAAAATTTAAAATAA
1 TTAAAATTTAAAATAA
541205 TCTAAA
1 T-TAAA
541211 TAATTAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 24 0.75
17 6 0.19
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (16 bp):
TTAAAATTTAAAATAA
Found at i:541211 original size:32 final size:31
Alignment explanation
Indices: 541131--541211 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
541121 ATCGATCTGG
*
541131 ACTTAAAATTATTCT-AATCTAAAATGTTAAA
1 ACTTAAAA-TAATCTAAATCTAAAATGTTAAA
*
541162 ACTTAAAATAA-CTTAAATTTAAAATGATTAAA
1 ACTTAAAATAATC-TAAATCTAAAATG-TTAAA
*
541194 ATTTAAAATAATCTAAAT
1 ACTTAAAATAATCTAAAT
541212 AATTAACTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.02
30 3 0.07
31 18 0.42
32 20 0.47
33 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (31 bp):
ACTTAAAATAATCTAAATCTAAAATGTTAAA
Found at i:541331 original size:16 final size:16
Alignment explanation
Indices: 541312--541364 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
541302 ACTTGAACAA
*
541312 AAAATGACTTAAAATC
1 AAAATGACTTAAAATT
* * **
541328 AAAATAATTTAATTTT
1 AAAATGACTTAAAATT
541344 AAAATGACTTAAAATT
1 AAAATGACTTAAAATT
541360 AAAAT
1 AAAAT
541365 AATCTGAATT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (16 bp):
AAAATGACTTAAAATT
Found at i:541353 original size:32 final size:30
Alignment explanation
Indices: 541312--541412 Score: 114
Period size: 32 Copynumber: 3.2 Consensus size: 30
541302 ACTTGAACAA
541312 AAAATGACTTAAAATCAAAATAATTTAATTTT
1 AAAATGACTTAAAAT-AAAATAATTTAA-TTT
*
541344 AAAATGACTTAAAATTAAAATAATCTGAATTT
1 AAAATGACTTAAAA-TAAAATAAT-TTAATTT
*
541376 AAAAT-AATTCAAAAATAAAATAATTTAAATTT
1 AAAATGACTT--AAAATAAAATAATTT-AATTT
541408 AAAAT
1 AAAAT
541413 TTTAAAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
31 4 0.07
32 49 0.80
33 8 0.13
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATGACTTAAAATAAAATAATTTAATTT
Found at i:541410 original size:16 final size:16
Alignment explanation
Indices: 541328--541426 Score: 94
Period size: 16 Copynumber: 6.2 Consensus size: 16
541318 ACTTAAAATC
*
541328 AAAATAATTTAATTTT
1 AAAATAATTTAAATTT
* * *
541344 AAAATGACTTAAAATT
1 AAAATAATTTAAATTT
* *
541360 AAAATAATCTGAATTT
1 AAAATAATTTAAATTT
* **
541376 AAAATAATTCAAAAAT
1 AAAATAATTTAAATTT
541392 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
541408 AAAAT--TTTAAAATTT
1 AAAATAATTT-AAATTT
541423 AAAA
1 AAAA
541427 GTTAAAAAAT
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
14 3 0.05
15 10 0.15
16 52 0.80
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:541687 original size:19 final size:20
Alignment explanation
Indices: 541625--541690 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 20
541615 TTTATATAAA
*
541625 ATTTA-ATAAATTAATAATTT
1 ATTTATATAAA-TATTAATTT
* *
541645 ATATTATATAAATTTTAATGT
1 AT-TTATATAAATATTAATTT
*
541666 ATTTATAT-AATATTATTTT
1 ATTTATATAAATATTAATTT
541685 ATTTAT
1 ATTTAT
541691 TATTTTAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 14 0.37
20 8 0.21
21 11 0.29
22 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTATATAAATATTAATTT
Found at i:542157 original size:29 final size:29
Alignment explanation
Indices: 542112--542198 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
542102 CCACAATAAG
*
542112 GCTCCACTCTTCTGTTGTTCAAGAAATTA
1 GCTCCACTCTTCAGTTGTTCAAGAAATTA
*
542141 GCTCCACTCTGT-AGTTGTTCAAGAAGTTA
1 GCTCCACTCT-TCAGTTGTTCAAGAAATTA
* *
542170 GCTTCACTGTTCAGTTGTTCAAGAAATTA
1 GCTCCACTCTTCAGTTGTTCAAGAAATTA
542199 CCAGGTGATT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
28 1 0.02
29 49 0.96
30 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (29 bp):
GCTCCACTCTTCAGTTGTTCAAGAAATTA
Found at i:544909 original size:20 final size:20
Alignment explanation
Indices: 544884--544922 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
544874 TCTTTGATAC
544884 TCTGCACTGCGCAGTTAGGT
1 TCTGCACTGCGCAGTTAGGT
*
544904 TCTGCACTGTGCAGTTAGG
1 TCTGCACTGCGCAGTTAGG
544923 ATTAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (20 bp):
TCTGCACTGCGCAGTTAGGT
Found at i:555095 original size:2 final size:2
Alignment explanation
Indices: 555088--555128 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
555078 GATGAGATAC
555088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
555129 AAGGACAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:555389 original size:10 final size:10
Alignment explanation
Indices: 555374--555398 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
555364 CAAATATATC
555374 TATATCTATA
1 TATATCTATA
555384 TATATCTATA
1 TATATCTATA
555394 TATAT
1 TATAT
555399 TATTTTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATCTATA
Found at i:558040 original size:23 final size:25
Alignment explanation
Indices: 558004--558049 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
557994 ATTTGATATT
*
558004 TTTTTAAACACTAA-AATTAAAAAG
1 TTTTTAAACACTAAGAAATAAAAAG
*
558028 TTTTTAAA-GCTAAGAAATAAAA
1 TTTTTAAACACTAAGAAATAAAA
558050 CTAAAGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (25 bp):
TTTTTAAACACTAAGAAATAAAAAG
Found at i:561588 original size:22 final size:23
Alignment explanation
Indices: 561541--561588 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
561531 ACAATATAAT
* *
561541 TATATAGGTTAATATTGGAGATA
1 TATATAGGTTAATATTGGAAAAA
561564 TATATA-GTTAAT-TTGGAAACAA
1 TATATAGGTTAATATTGGAAA-AA
561586 TAT
1 TAT
561589 GATTTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 10 0.45
23 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (23 bp):
TATATAGGTTAATATTGGAAAAA
Found at i:564417 original size:4 final size:4
Alignment explanation
Indices: 564408--564438 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
564398 AATCTTTGAA
564408 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
564439 ACAAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:573116 original size:13 final size:13
Alignment explanation
Indices: 573098--573147 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
573088 TTTTCATAAT
573098 TTGTATCGATACA
1 TTGTATCGATACA
*
573111 TTGTATCGATACG
1 TTGTATCGATACA
*
573124 TTCTA--GAT-CA
1 TTGTATCGATACA
*
573134 ATGTATCGATACA
1 TTGTATCGATACA
573147 T
1 T
573148 CCAAGCATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
10 4 0.14
11 3 0.11
12 3 0.11
13 18 0.64
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:575399 original size:79 final size:79
Alignment explanation
Indices: 575277--575806 Score: 485
Period size: 79 Copynumber: 6.7 Consensus size: 79
575267 AAAACACTGA
* *
575277 TTTTCTACAATCGGGGATACTCCAATCCC-GTTATCGTC-AAGGGGATACTCCAACCCCGGTTTT
1 TTTTC-ACAATCGGGGATACTCCAA-CCCTGTTAT-TTCTGAGGGGATACTCCAACCCCGGTTTT
* * *
575340 ATTTTCAAAATACTAAT
63 ATTTCCAAAACACCAAT
* *** * * *
575357 TTTTCATAATTAAGGATACTCTAA-CCTCGTTATTTCTGAGGGGATACTTCAACCTCGGTTTTAT
1 TTTTCACAATCGGGGATACTCCAACCCT-GTTATTTCTGAGGGGATACTCCAACCCCGGTTTTAT
575421 TTCCAAAACACCAAT
65 TTCCAAAACACCAAT
* * * * ** * * *
575436 TTTTCACAATCGGAGATACTCTAACCCCGTTATCTCCAAAGGGATACTTCAACCCTGGTTTTATT
1 TTTTCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
* * *
575501 TCCGAAATACCAAA
66 TCCAAAACACCAAT
** * *
575515 TTTTCACAATCGGGGATACTCCAACCCCATTATTTCTGAGGGAATACTCTAACCCCGGTTTTATT
1 TTTTCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
** *
575580 TCCAAAACATTAGT
66 TCCAAAACACCAAT
* * * *
575594 TTTTCACAATCGGGGATACTCCAACCCTGTCATTT-TCGAGAGGATACTCTAACCCCGATTTTAT
1 TTTTCACAATCGGGGATACTCCAACCCTGTTATTTCT-GAGGGGATACTCCAACCCCGGTTTTAT
* * *
575658 TTCTAAAATACCGAT
65 TTCCAAAACACCAAT
* * * * * * * *
575673 TTTTCACAATCGAGGATACTCCAGCCCTATTATTT-TCAAGGGATACTCTAACCTCGATTTTATT
1 TTTTCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
* *
575737 TTCAAAACATCAAT
66 TCCAAAACACCAAT
* * * * * **
575751 TTTCCATAGTTGGGGATACTCCAACCCTGTTATTTTTGAAAGGATACTCCAACCCC
1 TTTTCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCC
575807 ATCTTTATCT
Statistics
Matches: 364, Mismatches: 80, Indels: 13
0.80 0.18 0.03
Matches are distributed among these distances:
77 2 0.01
78 64 0.18
79 291 0.80
80 7 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
TTTTCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
TCCAAAACACCAAT
Found at i:575555 original size:158 final size:157
Alignment explanation
Indices: 575277--575783 Score: 563
Period size: 158 Copynumber: 3.2 Consensus size: 157
575267 AAAACACTGA
* * *
575277 TTTTCTACAATCGGGGATACTCCAATCCCGTTATCGTCAAGGGGATACTCCAACCCCGGTTTTAT
1 TTTTC-ACAATCGGGGATACTCCAACCCCGTTATC-TCAAAGGGATACTTCAACCCCGGTTTTAT
* * * ** * * *
575342 TTTCAAAATACTAATTTTTCATAATTAAGGATACTCTAACCTCGTTATTTCTGAGGGGATACT-T
64 TTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCCCATTATTTCTGAGGGGATACTCT
*
575406 CAACCTCGGTTTTATTTCCAAAACACCAAT
129 -AACCTCGGTTTTATTTCCAAAACATCAAT
* * *
575436 TTTTCACAATCGGAGATACTCTAACCCCGTTATCTCCAAAGGGATACTTCAACCCTGGTTTTATT
1 TTTTCACAATCGGGGATACTCCAACCCCGTTATCT-CAAAGGGATACTTCAACCCCGGTTTTATT
* * * *
575501 TCCGAAATACCAAATTTTCACAATCGGGGATACTCCAACCCCATTATTTCTGAGGGAATACTCTA
65 TCCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCCCATTATTTCTGAGGGGATACTCTA
* * *
575566 ACCCCGGTTTTATTTCCAAAACATTAGT
130 ACCTCGGTTTTATTTCCAAAACATCAAT
* * * * *
575594 TTTTCACAATCGGGGATACTCCAACCCTGTCATTTTC-GAGAGGATAC-TCTAACCCCGATTTTA
1 TTTTCACAATCGGGGATACTCCAACCCCGTTA-TCTCAAAG-GGATACTTC-AACCCCGGTTTTA
* * * * * *
575657 TTTCTAAAATACCGATTTTTCACAATCGAGGATACTCCAGCCCTATTATTT-TCAAGGGATACTC
63 TTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCCCATTATTTCTGAGGGGATACTC
* *
575721 TAACCTCGATTTTATTTTCAAAACATCAAT
128 TAACCTCGGTTTTATTTCCAAAACATCAAT
* * * * *
575751 TTTCCATAGTTGGGGATACTCCAACCCTGTTAT
1 TTTTCACAATCGGGGATACTCCAACCCCGTTAT
575784 TTTTGAAAGG
Statistics
Matches: 293, Mismatches: 50, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
156 1 0.00
157 67 0.23
158 217 0.74
159 8 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (157 bp):
TTTTCACAATCGGGGATACTCCAACCCCGTTATCTCAAAGGGATACTTCAACCCCGGTTTTATTT
CCAAAATACCAATTTTTCACAATCGAGGATACTCCAACCCCATTATTTCTGAGGGGATACTCTAA
CCTCGGTTTTATTTCCAAAACATCAAT
Found at i:581119 original size:158 final size:158
Alignment explanation
Indices: 580813--581363 Score: 586
Period size: 158 Copynumber: 3.5 Consensus size: 158
580803 AATCATTCAT
* * * * * * *
580813 GTTTTTATTTCTAAAACATCGA-TTTTCTACAATTGAGGATGCTACAATCCCGTTATTTTC-GAG
1 GTTTTTTTTTC-AAAACATCAATTTTTC-ACAATCGGGGATACTCCAACCCCGTTATTTTCTGAG
**
580876 -GAGATACTCCAACCCTGGTTTTATTTTCAAAACACTAATTTTTCACAATCAAGGATACTCCAAC
64 AG-GATACTCCAACCCTGGTTTTATTTT-AAAACACTAATTTTTCACAATCGGGGATACTCCAAC
* * * * *
580940 CTCGTTATTTTTGAAGAGATACTCCAACCCCA
127 CTCATTATTTTCGAGGGGATACTCAAACCCCA
* * * * *
580972 GTTTTTTTTTCAAAACA-CTAATTTTTTATAATCGGGGATACTTCAACCTCGTT-TTTTCTGAGG
1 GTTTTTTTTTCAAAACATC-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCTGAGA
* *
581035 GGATACTCCAATCCC-GGTTTTATTTCTAAAACACTAATTTTTTACAATTGGGGATACTCCAACC
65 GGATACTCCAA-CCCTGGTTTTATTT-TAAAACACTAATTTTTCACAATCGGGGATACTCCAACC
* *
581099 TCATTATTTTCGAGGGGATACTCTAACCCTA
128 TCATTATTTTCGAGGGGATACTCAAACCCCA
* * * *
581130 GTTTTATTTCCAAAACATCACTTTTTCACAATCGGAGATACTCCAACCCCGTTA-TTTCTGAGAG
1 GTTTTTTTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCTGAGAG
* * * *
581194 GATACTCTAACCCTGATTTTATTTTTAAAATA-TCAA-TTTTCACAATCGGGGATACTTCAACC-
66 GATACTCCAACCCTGGTTTTA-TTTTAAAACACT-AATTTTTCACAATCGGGGATACTCCAACCT
581256 CTATTATTTTCGAGGGGATACTCAAACCCC-
129 C-ATTATTTTCGAGGGGATACTCAAACCCCA
* * * * * *
581286 GATTTTATTTCTAAAACATCGATTTTCCACAATCGGGGATACTCCAGCCCCGTTATTTT-TGAAA
1 GTTTTTTTTTC-AAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCTGAGA
581350 GGATACTCCAACCC
65 GGATACTCCAACCC
581364 CGTCTTTATC
Statistics
Matches: 330, Mismatches: 48, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
156 8 0.02
157 114 0.35
158 185 0.56
159 23 0.07
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (158 bp):
GTTTTTTTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCTGAGAG
GATACTCCAACCCTGGTTTTATTTTAAAACACTAATTTTTCACAATCGGGGATACTCCAACCTCA
TTATTTTCGAGGGGATACTCAAACCCCA
Found at i:581364 original size:79 final size:79
Alignment explanation
Indices: 580815--581414 Score: 529
Period size: 79 Copynumber: 7.6 Consensus size: 79
580805 TCATTCATGT
* * * * * * * *
580815 TTTTATTTCTAAAACATCGA-TTTTCTACAATTGAGGATGCTACAATCCCGTTATTTTCGAGGAG
1 TTTTATTTCTAAAACATCAATTTTTC-ACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGG
* *
580879 ATACTCCAACCCTGG
65 ATACTCCAACCCCGA
** * * *
580894 TTTTATTT-TCAAAACA-CTAATTTTTCACAATCAAGGATACTCCAACCTCGTTATTTTTGAAGA
1 TTTTATTTCT-AAAACATC-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGG
*
580957 GATACTCCAACCCCAGT
64 GATACTCCAACCCC-GA
* * * * *
580974 TTTTTTTTC-AAAACA-CTAATTTTTTATAATCGGGGATACTTCAACCTCGTT-TTTTCTGAGGG
1 TTTTATTTCTAAAACATC-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTT-TGAGGG
* *
581036 GATACTCCAATCCCGG
64 GATACTCCAACCCCGA
* * * * *
581052 TTTTATTTCTAAAACA-CTAATTTTTTACAATTGGGGATACTCCAACCTCATTATTTTCGAGGGG
1 TTTTATTTCTAAAACATC-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGG
* *
581116 ATACTCTAA-CCCTA
65 ATACTCCAACCCCGA
* * * * *
581130 GTTTTATTTCCAAAACATCACTTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCTGAGAGG
1 -TTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGG
* *
581195 ATACTCTAACCCTGA
65 ATACTCCAACCCCGA
* * * ** *
581210 TTTTATTTTTAAAATATCAA-TTTTCACAATCGGGGATACTTCAACCCTATTATTTTCGAGGGGA
1 TTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
*
581274 TACTCAAACCCCGA
66 TACTCCAACCCCGA
* * * **
581288 TTTTATTTCTAAAACATCGATTTTCCACAATCGGGGATACTCCAGCCCCGTTATTTTTGAAAGGA
1 TTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
581353 TACTCCAACCCCG-
66 TACTCCAACCCCGA
* * * * * *
581366 TCTTTATCTCCAAAATATTAAATTTTTCATCAA-CGAGTATACTCCAACC
1 T-TTTATTTCTAAAACA-TCAATTTTTCA-CAATCGGGGATACTCCAACC
581415 GCGTGCCTCG
Statistics
Matches: 430, Mismatches: 76, Indels: 29
0.80 0.14 0.05
Matches are distributed among these distances:
78 85 0.20
79 300 0.70
80 42 0.10
81 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
TACTCCAACCCCGA
Found at i:583729 original size:79 final size:79
Alignment explanation
Indices: 583598--583837 Score: 480
Period size: 79 Copynumber: 3.0 Consensus size: 79
583588 TGGCCAACAT
583598 CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
1 CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
583663 TTCTACCACCTTGA
66 TTCTACCACCTTGA
583677 CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
1 CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
583742 TTCTACCACCTTGA
66 TTCTACCACCTTGA
583756 CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
1 CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
583821 TTCTACCACCTTGA
66 TTCTACCACCTTGA
583835 CTG
1 CTG
583838 AGAATGGCTC
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 161 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (79 bp):
CTGCTTTTCATATATGGAAAGGGCTTGATGTTTGGGTGAAAATGCCTTACTAAAAAAGGCAATTG
TTCTACCACCTTGA
Found at i:585796 original size:79 final size:79
Alignment explanation
Indices: 585537--585803 Score: 299
Period size: 79 Copynumber: 3.4 Consensus size: 79
585527 AAATTTAATA
* ** * *
585537 TTTTAGAGATAAAAA-AGGGGGTTGGAGTATTCCCTTGGAAATGACGGGGTTGGAGTATCTCCGA
1 TTTTAGAAATAAAAACA--GGGTTGGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCCGA
** *
585601 TGGTGGAAAATCGATG
64 TTATGAAAAATCGATG
* * *
585617 TTTTGGAAAT-CAAACCGAGGTTGGAGTA-TCCCTTCAGAAATAACGGGGTTGGAGTATCCCCGA
1 TTTTAGAAATAAAAACAG-GGTTGGAGTATTCCC-TCAGAAATAACGGGGTTGGAGTATCCCCGA
585680 TTATGAAAAATCGATG
64 TTATGAAAAATCGATG
* * * * *
585696 TTTTAGAAA-ATAAGCTGGGGTTGGAGTATTCTCTCAGAAATAACGGAGTTGGAGTATCCCCGAT
1 TTTTAGAAATAAAAAC-AGGGTTGGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
585760 TATGAAAAATCGATG
65 TATGAAAAATCGATG
* *
585775 TTCTAGAAATAAAAACAGGGTTAGAGTAT
1 TTTTAGAAATAAAAACAGGGTTGGAGTAT
585804 CATCGATTGT
Statistics
Matches: 158, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
78 5 0.03
79 137 0.87
80 16 0.10
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (79 bp):
TTTTAGAAATAAAAACAGGGTTGGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATT
ATGAAAAATCGATG
Found at i:585811 original size:51 final size:51
Alignment explanation
Indices: 585747--585855 Score: 132
Period size: 51 Copynumber: 2.1 Consensus size: 51
585737 AACGGAGTTG
* *
585747 GAGTATCCCCGATTATGAAAAATCGAT-GTTCTAGAAATAAAAACAGGG-TTA
1 GAGTATCACCGATTATGAAAAATCGATGGTT-TAAAAAT-AAAACAGGGATTA
* * * *
585798 GAGTATCATCGATTGTGAAAAATCGGTGGTTTAAAAATAAAACTGGGATTA
1 GAGTATCACCGATTATGAAAAATCGATGGTTTAAAAATAAAACAGGGATTA
585849 GAGTATC
1 GAGTATC
585856 CCATCAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 8 0.16
51 39 0.78
52 3 0.06
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (51 bp):
GAGTATCACCGATTATGAAAAATCGATGGTTTAAAAATAAAACAGGGATTA
Found at i:585929 original size:133 final size:129
Alignment explanation
Indices: 585662--586054 Score: 328
Period size: 133 Copynumber: 3.0 Consensus size: 129
585652 AGAAATAACG
* ** * * * ** *
585662 GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAAAT-AAGCTGGGGTTGGAGTATT
1 GGGTTAGAGTATCCCTAATTATAAAAAATCGATGGTTTA-AAAATAAAACCAGGGTTAGAGTA-T
* * * * * *
585726 CTC-TCAGAAATAACGGAGTTGGAGTATCCCCGATTATGAAAAATCGATGTTCTAGAAATAAAAA
64 CCCATCAAAAATAATGGGGTTGGAGTAT-CCCGATTGTGAAAAATCAATGTTCTAGAAATAAAAA
585790 CA
128 CA
* * * * * *
585792 GGGTTAGAGTAT-CATCGATTGTGAAAAATCGGTGGTTTAAAAATAAAA-CTGGGATTAGAGTAT
1 GGGTTAGAGTATCCCT-AATTATAAAAAATCGATGGTTTAAAAATAAAACCAGGG-TTAGAGTAT
* *
585855 CCCATCAAAAATATTCATGGGGTTGGAGTATCAACGATTGTGAAAAATCAATGTT-TTGAAAATA
64 CCCATCAAAAATA---ATGGGGTTGGAGTATC-CCGATTGTGAAAAATCAATGTTCTAG-AAATA
* *
585919 AAATCG
124 AAAACA
* * * *
585925 GGGTTGGAGTATCCCTAATTATAAAAAATCTATGGTTTGAAAATAAAACCAGGGTTAGGGTATCC
1 GGGTTAGAGTATCCCTAATTATAAAAAATCGATGGTTTAAAAATAAAACCAGGGTTAGAGTATCC
* * * ** * *
585990 CCTCGAAAATAATGGGGTTGGAGTATTCCCGATGGTGAAAAATCGGTATTTTAGAAATAAAAACA
66 CATCAAAAATAATGGGGTTGGAGTA-TCCCGATTGTGAAAAATCAATGTTCTAGAAATAAAAACA
586055 TGAATAAAAT
Statistics
Matches: 210, Mismatches: 40, Indels: 26
0.76 0.14 0.09
Matches are distributed among these distances:
129 12 0.06
130 88 0.42
131 4 0.02
132 3 0.01
133 97 0.46
134 6 0.03
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (129 bp):
GGGTTAGAGTATCCCTAATTATAAAAAATCGATGGTTTAAAAATAAAACCAGGGTTAGAGTATCC
CATCAAAAATAATGGGGTTGGAGTATCCCGATTGTGAAAAATCAATGTTCTAGAAATAAAAACA
Found at i:588338 original size:20 final size:20
Alignment explanation
Indices: 588313--588369 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
588303 GGTAAAACCC
*
588313 AGAATGTATCGATACAACGA
1 AGAATGTATCGATACAACAA
*
588333 AGAATGTATCGATACAATAA
1 AGAATGTATCGATACAACAA
* *
588353 AGGATGTATCAATACAA
1 AGAATGTATCGATACAA
588370 ATTGTAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (20 bp):
AGAATGTATCGATACAACAA
Found at i:588795 original size:3 final size:3
Alignment explanation
Indices: 588789--588819 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
588779 CTACTACTAC
588789 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
588820 GCTTTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Done.