Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 126 of 207
Found at i:38472727 original size:13 final size:13
Alignment explanation
Indices: 38472709--38472752 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
38472699 TAGCTTGACA
38472709 AACTGATTCTATT
1 AACTGATTCTATT
**
38472722 AACTGATT-TGACC
1 AACTGATTCT-ATT
38472735 AACTGATTCTATT
1 AACTGATTCTATT
38472748 AACTG
1 AACTG
38472753 TTTATTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (13 bp):
AACTGATTCTATT
Found at i:38472733 original size:26 final size:26
Alignment explanation
Indices: 38472703--38472752 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
38472693 GCAGGCTAGC
38472703 TTGACAAACTGATTCTATTAACTGAT
1 TTGACAAACTGATTCTATTAACTGAT
*
38472729 TTGACCAACTGATTCTATTAACTG
1 TTGACAAACTGATTCTATTAACTG
38472753 TTTATTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (26 bp):
TTGACAAACTGATTCTATTAACTGAT
Found at i:38473489 original size:18 final size:18
Alignment explanation
Indices: 38473438--38473496 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
38473428 TAGGGTTTTG
*
38473438 TTTTATTTTTGTTTATATT
1 TTTTATTTTT-TATATATT
*
38473457 TTTTAAGTTTATTATATATT
1 TTTT-A-TTTTTTATATATT
38473477 TTTTATTTTTTATA-ATT
1 TTTTATTTTTTATATATT
38473494 TTT
1 TTT
38473497 GAGATGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 6 0.17
18 8 0.23
19 5 0.14
20 12 0.34
21 4 0.11
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTATATATT
Found at i:38473560 original size:24 final size:24
Alignment explanation
Indices: 38473528--38473576 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
38473518 TTAATTTGGA
* *
38473528 ATTTAAAAGCATTGTGTTTACACC
1 ATTTAAAAGCATCGTATTTACACC
38473552 ATTTAAAAGCATCGTATTTACACC
1 ATTTAAAAGCATCGTATTTACACC
38473576 A
1 A
38473577 ATTGTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (24 bp):
ATTTAAAAGCATCGTATTTACACC
Found at i:38476225 original size:21 final size:20
Alignment explanation
Indices: 38476178--38476225 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
38476168 CAATGACTAC
38476178 AATTTTTTTATATTTTTATGA
1 AATTTTTTTATATTTTTA-GA
*
38476199 AATTTTTTTATGTTTTTA-A
1 AATTTTTTTATATTTTTAGA
38476218 ATATTTTT
1 A-ATTTTT
38476226 ATAACTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 17 0.68
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
AATTTTTTTATATTTTTAGA
Found at i:38485142 original size:39 final size:39
Alignment explanation
Indices: 38485058--38485168 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
38485048 AGATACTAAT
** *
38485058 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
38485098 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
38485138 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
38485169 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:38492931 original size:40 final size:42
Alignment explanation
Indices: 38492897--38492981 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 42
38492887 CCGAAGGTAT
*
38492897 TTGTGCGAG-ATATT-AATTCCGGGTTAAGTCCCGAAGGCCA
1 TTGTGCGAGTATATTAAAATCCGGGTTAAGTCCCGAAGGCCA
*
38492937 TTGTGCGAGTTATTTTAAAATCCGGGTTAAGTCCCGAAGG-CA
1 TTGTGCGAG-TATATTAAAATCCGGGTTAAGTCCCGAAGGCCA
38492979 TTG
1 TTG
38492982 AATGAGTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 9 0.22
42 9 0.22
43 22 0.55
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
TTGTGCGAGTATATTAAAATCCGGGTTAAGTCCCGAAGGCCA
Found at i:38501569 original size:27 final size:27
Alignment explanation
Indices: 38501539--38501716 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38501529 ATATTGAGTC
* * * *
38501539 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38501566 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38501593 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38501621 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38501648 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38501675 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38501702 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38501717 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38501678 original size:82 final size:81
Alignment explanation
Indices: 38501560--38501715 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38501550 TGCTATATAA
* *
38501560 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38501625 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38501642 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38501706 CACTTAGTGC
65 CACTTAGTGC
38501716 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38505485 original size:40 final size:40
Alignment explanation
Indices: 38505430--38505509 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
38505420 GGAGGTTCAT
*
38505430 CAGTCTCTTCTTAGCTTAAGGGTTAAACTCTGATGGGGCC
1 CAGTCTCTTCTTAGCTTAAGGGTTAAACTCCGATGGGGCC
38505470 CAGTCTCTTCTTAGCTTAAGGGTTAAACTCCGATGGGGCC
1 CAGTCTCTTCTTAGCTTAAGGGTTAAACTCCGATGGGGCC
38505510 TTGTTCATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (40 bp):
CAGTCTCTTCTTAGCTTAAGGGTTAAACTCCGATGGGGCC
Found at i:38513097 original size:70 final size:70
Alignment explanation
Indices: 38512980--38513970 Score: 736
Period size: 70 Copynumber: 14.2 Consensus size: 70
38512970 ATGATCCCTC
* * * * *
38512980 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAAACTTTAGGCTTACAAGTCCAATACCGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
**
38513045 AATAT
66 AACCT
** * ** * *
38513050 CCAAAACAGTTAGCATGAGCTCAAGCTCCCAATTGTAATCTTAAGGCTCACAAGTTTAATACTGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
38513115 AACCT
66 AACCT
* * * * * * ** ** * **
38513120 CTAAAATAGTTAGAGTGAGCTCAAGCTTCGAGTTGAAAA-CTTAAGGCTCGTAGGTTCAATATTG
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACT-AAAATCTTAAGGCTCACAAGTTCAATACCG
*
38513184 CAGCCT
65 CAACCT
* * * ** * * *
38513190 CCAAAATAGTTAGTGTGAGCTCAAGCTCCCAACTGCAATCTTAAGGCTCATAGGTTCAATATCGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
38513255 AACCT
66 AACCT
* * * * * * *
38513260 CTAAAAAAGTTAGCGAGAACTCAAGCTCCCAGCTAAAATCTTAAAGCTCGCAAGTTCAATACCGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
*
38513325 AGCCT
66 AACCT
* * * * * * *
38513330 CTAAAATAGTTAGTGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGA-AGGTTCAATACCG
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGC-TCACAAGTTCAATACCG
38513394 CAACCT
65 CAACCT
* * * * **
38513400 CCAAAACAGTTAGTGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGA-AGGTTCAATAATG
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTC-ACAAGTTCAATACCG
*
38513464 CAGCCT
65 CAACCT
* * * * * *
38513470 CCAAAATAGTTAGCGTGAGCTCAAGCT-CCAAGCTGAAAA-CTTAAGGCTTGA-AGGTTCAACAT
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAA-CT-AAAATCTTAAGGC-TCACAAGTTCAATAC
*** *
38513532 TATAGCCT
63 CGCAACCT
* * * * * * * *
38513540 CCAAAAGAGTTAGCGTGAGGTCAAGCTCCCAGCTATAATCTTAAGGCTCGCATGTTCAATACTGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
*
38513605 AGCCT
66 AACCT
* * * * *** * * * * * * *
38513610 TCAAAATAGTTAGCGAGAACTCAAGCTTTTAGCTAAAATCTTAAAGCTCATAGGTTTAATAACGT
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
*
38513675 AGCCT
66 AACCT
* * * * * * * *
38513680 CTAAAATAGTTAGCGCGAGCTCAAGCTACCAGCTAAAATCTTAAGGCTCGCAGGTTAAATACCAC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
38513745 AACCT
66 AACCT
* * * * * ** *
38513750 CCAAAATAGTTAGCACGAGCCCAAGCTCTCAACTAAAATATTAAGGCTTGCAAGTTCAATACC-A
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
38513814 AACCT
66 AACCT
* * * ** **
38513819 CTAAAACAGTCAGCGCGGGCTCAAGCTCCCAACTGTAATCTTAAGGCTTGCAAGTTCAATACCGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
38513884 AACCT
66 AACCT
* * * ** * * * *
38513889 CCAAAATAGTTAGCGCGAGCTTAAACTCCCAGTTGAAATCTTAAGGCCCACAACTTCAATACCAC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
**
38513954 TGCCT
66 AACCT
*
38513959 CCAAAATAGTTA
1 CCAAAACAGTTA
38513971 ACGTGAGGTA
Statistics
Matches: 743, Mismatches: 167, Indels: 22
0.80 0.18 0.02
Matches are distributed among these distances:
69 68 0.09
70 665 0.90
71 10 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (70 bp):
CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTAAAATCTTAAGGCTCACAAGTTCAATACCGC
AACCT
Found at i:38513239 original size:140 final size:139
Alignment explanation
Indices: 38512982--38513950 Score: 854
Period size: 140 Copynumber: 6.9 Consensus size: 139
38512972 GATCCCTCCC
* ** * * *
38512982 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAAACTTTAGGCTTACAAGTCCAATACCGCAA
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCT-AAAACTTAAGGCTCGCAGGTTCAATACCGCAG
** * ** * * * *
38513047 TATCCAAAACAGTTAGCATGAGCTCAAGCTCCCAATTGTAATCTTAAGGCTCACAAGTTTAATAC
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGCTCACAGGTTCAATAC
38513112 TGCAACCTCT
130 TGCAACCTCT
* * * * * * * **
38513122 AAAATAGTTAGAGTGAGCTCAAGCTTCGAGTTGAAAACTTAAGGCTCGTAGGTTCAATATTGCAG
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCT-AAAACTTAAGGCTCGCAGGTTCAATACCGCAG
* * * *
38513187 CCTCCAAAATAGTTAGTGTGAGCTCAAGCTCCCAACTGCAATCTTAAGGCTCATAGGTTCAATA-
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGCTCACAGGTTCAATAC
38513251 TCGCAACCTCT
130 T-GCAACCTCT
* * * * *
38513262 AAAAAAGTTAGCGAGAACTCAAGCTCCCAGCTAAAATCTTAAAGCTCGCAAGTTCAATACCGCAG
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAA-CTTAAGGCTCGCAGGTTCAATACCGCAG
* * * * * *
38513327 CCTCTAAAATAGTTAGTGCGAGCTCAAGCTCCCAAGTAAAATTTTAAGGCTTGA-AGGTTCAATA
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGC-TCACAGGTTCAATA
* *
38513391 CCGCAACCTCC
129 CTGCAACCTCT
* * * **
38513402 AAAACAGTTAGTGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAATGCAG
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTA-AAACTTAAGGCTCGCAGGTTCAATACCGCAG
* * * *
38513467 CCTCCAAAATAGTTAGCGTGAGCTCAAGCT-CCAAGCTGAAAACTTAAGGCTTGA-AGGTTCAAC
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAA-CTGAAATCTTAAGGC-TCACAGGTTCAAT
* ** * *
38513530 ATTATAGCCTCC
128 ACTGCAACCTCT
* * * * * *
38513542 AAAAGAGTTAGCGTGAGGTCAAGCTCCCAGCTATAATCTTAAGGCTCGCATGTTCAATACTGCAG
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTA-AAACTTAAGGCTCGCAGGTTCAATACCGCAG
* * * *** * * * * *
38513607 CCTTCAAAATAGTTAGCGAGAACTCAAGCTTTTAGCTAAAATCTTAAAGCTCATAGGTTTAATAA
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGCTCACAGGTTCAAT-A
* *
38513672 C-GTAGCCTCT
129 CTGCAACCTCT
* * * * *
38513682 AAAATAGTTAGCGCGAGCTCAAGCTACCAGCTAAAATCTTAAGGCTCGCAGGTTAAATACCACAA
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAA-CTTAAGGCTCGCAGGTTCAATACCGCAG
* * * * * ** *
38513747 CCTCCAAAATAGTTAGCACGAGCCCAAGCTCTCAACTAAAATATTAAGGCTTGCAAGTTCAATAC
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGCTCACAGGTTCAATAC
38513812 --CAAACCTCT
130 TGC-AACCTCT
* * * * * * * *
38513821 AAAACAGTCAGCGCGGGCTCAAGCTCCCAACTGTAATCTTAAGGCTTGCAAGTTCAATACCGCAA
1 AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCT-AAAACTTAAGGCTCGCAGGTTCAATACCGCAG
* * ** * **
38513886 CCTCCAAAATAGTTAGCGCGAGCTTAAACTCCCAGTTGAAATCTTAAGGCCCACAACTTCAATAC
65 CCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGCTCACAGGTTCAATAC
38513951 CACTGCCTCC
Statistics
Matches: 673, Mismatches: 144, Indels: 25
0.80 0.17 0.03
Matches are distributed among these distances:
139 124 0.18
140 543 0.81
141 6 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (139 bp):
AAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAACTTAAGGCTCGCAGGTTCAATACCGCAGC
CTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGAAATCTTAAGGCTCACAGGTTCAATACT
GCAACCTCT
Found at i:38513376 original size:210 final size:210
Alignment explanation
Indices: 38512980--38513970 Score: 890
Period size: 210 Copynumber: 4.7 Consensus size: 210
38512970 ATGATCCCTC
* * * * * *
38512980 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAAACTTTAGGCTTACAA-GTCCAATACCG
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTACAATCTTAAGGC-T-CAAGGTTCAATATCG
** * ** ** ** * *
38513044 CAATATCCAAAACAGTTAGCATGAGCTCAAGCTCCCAATTGTAATCTTAAGGCTCACAAGTTTAA
64 CAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCGCAAGTTCAA
** * * * * * * * *
38513109 TACTGCAACCTCTAAAATAGTTAGAGTGAGCTCAAGCT-TCGAGTTGAAAA-CTTAAGGCTCGTA
129 TACCACAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAAGCT-AAAATCTTAAGGCTCGCA
* *
38513172 GGTTCAATATTGCAGCCT
193 GGTTCAATACTGCAACCT
* * * *
38513190 CCAAAATAGTTAGTGTGAGCTCAAGCTCCCAACTGCAATCTTAAGGCTCATAGGTTCAATATCGC
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTACAATCTTAAGGCTCA-AGGTTCAATATCGC
* * * * *
38513255 AACCTCTAAAAAAGTTAGCGAGAACTCAAGCTCCCAGCTAAAATCTTAAAGCTCGCAAGTTCAAT
65 AACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCGCAAGTTCAAT
* * * * * *
38513320 ACCGCAGCCTCTAAAATAGTTAGTGCGAGCTCAAGCTCCCAAG-TAAAATTTTAAGGCTTGAAGG
130 ACCACAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAAGCTAAAATCTTAAGGCTCGCAGG
*
38513384 TTCAATACCGCAACCT
195 TTCAATACTGCAACCT
* *
38513400 CCAAAACAGTTAGTGCGAGCTCAAGCTCCCAGCTACAATCTTAAGGCTCGAAGGTTCAATAAT-G
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTACAATCTTAAGGCTC-AAGGTTCAAT-ATCG
* * * *
38513464 CAGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTCCAAGCTGAAAA-CTTAAGGCTTG-AAGGTTC
64 CAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCT-AAAATCTTAAGGCTCGCAA-GTTC
* ** * * * * *
38513527 AACATTATAGCCTCCAAAAGAGTTAGCGTGAGGTCAAGCTCCC-AGCTATAATCTTAAGGCTCGC
127 AATACCACAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAAGCTAAAATCTTAAGGCTCGC
* *
38513591 ATGTTCAATACTGCAGCCT
192 AGGTTCAATACTGCAACCT
* * * * *** * * * * * *
38513610 TCAAAATAGTTAGCGAGAACTCAAGCTTTTAGCTAAAATCTTAAAGCTCATAGGTTTAATAACGT
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTACAATCTTAAGGCTCA-AGGTTCAATATCGC
* * * * *
38513675 AGCCTCTAAAATAGTTAGCGCGAGCTCAAGCTACCAGCTAAAATCTTAAGGCTCGCAGGTTAAAT
65 AACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCGCAAGTTCAAT
* * * * * * *
38513740 ACCACAACCTCCAAAATAGTTAGCACGAGCCCAAGCTCTCAA-CTAAAATATTAAGGCTTGCAAG
130 ACCACAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAAGCTAAAATCTTAAGGCTCGCAGG
38513804 TTCAATAC--CAAACCT
195 TTCAATACTGC-AACCT
* * * ** *
38513819 CTAAAACAGTCAGCGCGGGCTCAAGCTCCCAACTGTAATCTTAAGGCTTGCAA-GTTCAATACCG
1 CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTACAATCTTAAGGC-T-CAAGGTTCAATATCG
* * * * * * *
38513883 CAACCTCCAAAATAGTTAGCGCGAGCTTAAACTCCCAGTTGAAATCTTAAGGCCCACAACTTCAA
64 CAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCGCAAGTTCAA
*
38513948 TACCACTGCCTCCAAAATAGTTA
129 TACCACAGCCTCCAAAATAGTTA
38513971 ACGTGAGGTA
Statistics
Matches: 632, Mismatches: 132, Indels: 35
0.79 0.17 0.04
Matches are distributed among these distances:
208 3 0.00
209 135 0.21
210 480 0.76
211 14 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (210 bp):
CCAAAACAGTTAGCGCGAGCTCAAGCTCCCAACTACAATCTTAAGGCTCAAGGTTCAATATCGCA
ACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAGCTAAAATCTTAAGGCTCGCAAGTTCAATA
CCACAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAAGCTAAAATCTTAAGGCTCGCAGGT
TCAATACTGCAACCT
Found at i:38514172 original size:18 final size:18
Alignment explanation
Indices: 38514124--38514194 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
38514114 GTTTAAATTC
* *
38514124 AAAATTTAGTGTAAGCTTG
1 AAAATTTACT-TAAGTTTG
* *
38514143 AAATTTTGCTTAAGTTTG
1 AAAATTTACTTAAGTTTG
** *
38514161 AAGGTTTACTTAGGTTTG
1 AAAATTTACTTAAGTTTG
*
38514179 AAAATTTTCTTAAGTT
1 AAAATTTACTTAAGTT
38514195 CATAAAGAGA
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
18 33 0.82
19 7 0.17
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (18 bp):
AAAATTTACTTAAGTTTG
Found at i:38518128 original size:25 final size:25
Alignment explanation
Indices: 38518100--38518161 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
38518090 TTCAGCTCTT
*
38518100 ATTACTCATCT-AGCATGAGCTTCCC
1 ATTACTCAGCTCA-CATGAGCTTCCC
* *
38518125 ATTATTCAGCTCACATGAGCTTCAC
1 ATTACTCAGCTCACATGAGCTTCCC
* *
38518150 GTTATTCAGCTC
1 ATTACTCAGCTC
38518162 GGAGGAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (25 bp):
ATTACTCAGCTCACATGAGCTTCCC
Found at i:38518169 original size:25 final size:25
Alignment explanation
Indices: 38518116--38518171 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
38518106 CATCTAGCAT
* *
38518116 GAGCTTCCCATTATTCAGCTCACAT
1 GAGCTTCACATTATTCAGCTCACAG
* **
38518141 GAGCTTCACGTTATTCAGCTCGGAG
1 GAGCTTCACATTATTCAGCTCACAG
38518166 GAGCTT
1 GAGCTT
38518172 ACCGTTTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (25 bp):
GAGCTTCACATTATTCAGCTCACAG
Found at i:38519250 original size:12 final size:12
Alignment explanation
Indices: 38519233--38519262 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38519223 TCAGGGAGTT
38519233 ACACGGGCAAAG
1 ACACGGGCAAAG
*
38519245 ACACGGGCATAG
1 ACACGGGCAAAG
38519257 ACACGG
1 ACACGG
38519263 CCATGTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.33, T:0.03
Consensus pattern (12 bp):
ACACGGGCAAAG
Found at i:38522544 original size:122 final size:123
Alignment explanation
Indices: 38522320--38522564 Score: 404
Period size: 122 Copynumber: 2.0 Consensus size: 123
38522310 TTAGTTGGTT
* *
38522320 ATTACTGGAGATTTCTAAAAGGTTTTTCGATGATAGCTACACCAATGACACGACTATAATAGAAA
1 ATTACTGGAGATTTCAAAAAGGTTTTTCAATGATAGCTACACCAATGACACGACTATAATAGAAA
38522385 GATGTGAAATTTGAATGGTCTGGTAAATGTCAACAAAGTTTTAACCAGTTAAAAGCTC
66 GATGTGAAATTTGAATGGTCTGGTAAATGTCAACAAAGTTTTAACCAGTTAAAAGCTC
* * * *
38522443 ATTATTGGAGATTTGAAAAACGG-TTTTCAATGATAGCTACACGAATGA-ACGACTCTAATAGAA
1 ATTACTGGAGATTTCAAAAA-GGTTTTTCAATGATAGCTACACCAATGACACGACTATAATAGAA
*
38522506 AGATGTGAAATTTGAATGGTCTGGTAAATGTCAGCAAAGTTTTAACCAGTTAAAAGCTC
65 AGATGTGAAATTTGAATGGTCTGGTAAATGTCAACAAAGTTTTAACCAGTTAAAAGCTC
38522565 TGTTGACCGA
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
122 72 0.63
123 40 0.35
124 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (123 bp):
ATTACTGGAGATTTCAAAAAGGTTTTTCAATGATAGCTACACCAATGACACGACTATAATAGAAA
GATGTGAAATTTGAATGGTCTGGTAAATGTCAACAAAGTTTTAACCAGTTAAAAGCTC
Found at i:38532530 original size:18 final size:18
Alignment explanation
Indices: 38532504--38532539 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38532494 CGCTTCTGAC
*
38532504 TGTCGATCTCATTTTCCT
1 TGTCAATCTCATTTTCCT
*
38532522 TGTCAATCTCCTTTTCCT
1 TGTCAATCTCATTTTCCT
38532540 CTAACACTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.08, T:0.50
Consensus pattern (18 bp):
TGTCAATCTCATTTTCCT
Found at i:38532636 original size:3 final size:3
Alignment explanation
Indices: 38532628--38532698 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
38532618 GTTTGACCCT
* *
38532628 TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG TTG TTA TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
38532676 TTC TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TT
38532699 TTTACTATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.03, C:0.01, G:0.28, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:38534356 original size:11 final size:10
Alignment explanation
Indices: 38534335--38534364 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
38534325 TCCGTTGTAC
38534335 TTTTATTTTT
1 TTTTATTTTT
38534345 TTTTATTTTT
1 TTTTATTTTT
*
38534355 TTTTGTTTTT
1 TTTTATTTTT
38534365 GTGTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:38545611 original size:21 final size:21
Alignment explanation
Indices: 38545563--38545612 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
38545553 TGTGTACTCC
* *
38545563 ATTTTTTTTTTAATTCTTTTG
1 ATTTTTTTTATAATTATTTTG
** *
38545584 AAATTTTTTATAATTATTTTT
1 ATTTTTTTTATAATTATTTTG
38545605 ATTTTTTT
1 ATTTTTTT
38545613 CCATTAAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTTTTTTTATAATTATTTTG
Found at i:38552101 original size:23 final size:23
Alignment explanation
Indices: 38552048--38552103 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
38552038 ATGTTTAAAC
*
38552048 TTATTATTATCTTAAATTTATCA
1 TTATTATTATCTTAAATCTATCA
* * *
38552071 TTAATATTATC-TAAGTCTATTA
1 TTATTATTATCTTAAATCTATCA
38552093 TATATTATTAT
1 T-TATTATTAT
38552104 TTCAGATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTATTATCTTAAATCTATCA
Found at i:38556216 original size:18 final size:18
Alignment explanation
Indices: 38556150--38556217 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
38556140 ATTTTTTTAA
* *
38556150 ATATAAATTA-TAAAATT
1 ATATAAATAATTATAATT
* *
38556167 CATAAAAAT-ATTAGAATT
1 -ATATAAATAATTATAATT
*
38556185 TTATAAATAATTATAATT
1 ATATAAATAATTATAATT
*
38556203 ATATATATAATTATA
1 ATATAAATAATTATA
38556218 TGAAAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 7 0.17
18 34 0.83
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAAATAATTATAATT
Found at i:38557316 original size:13 final size:14
Alignment explanation
Indices: 38557293--38557321 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38557283 AATTTATTTT
38557293 TATATAAAAATTAA
1 TATATAAAAATTAA
38557307 TATA-AAAAATTAA
1 TATATAAAAATTAA
38557320 TA
1 TA
38557322 CGGGTCGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TATATAAAAATTAA
Found at i:38558293 original size:14 final size:15
Alignment explanation
Indices: 38558276--38558331 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 15
38558266 AAAATATTTT
38558276 TTAATTATTTAATT-
1 TTAATTATTTAATTA
* *
38558290 TTAAGTAGTTAATTA
1 TTAATTATTTAATTA
*
38558305 TTATATTGTTTAAATTA
1 TTA-ATTATTT-AATTA
38558322 TTAATT-TTTA
1 TTAATTATTTA
38558332 TGTTTATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 13 0.38
15 6 0.18
16 7 0.21
17 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (15 bp):
TTAATTATTTAATTA
Found at i:38560823 original size:30 final size:30
Alignment explanation
Indices: 38560787--38560846 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
38560777 TTAAAACAAA
38560787 AAAAATAAAGATCTAAAAATCCTTTTTATT
1 AAAAATAAAGATCTAAAAATCCTTTTTATT
38560817 AAAAATAAAGATCTAAAAATCCTTTTTATT
1 AAAAATAAAGATCTAAAAATCCTTTTTATT
38560847 TTCCTTGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATAAAGATCTAAAAATCCTTTTTATT
Found at i:38563231 original size:24 final size:24
Alignment explanation
Indices: 38563204--38563249 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
38563194 GAATTAAACC
38563204 TCAAATT-TTAGCATAATATAAATA
1 TCAAATTGTTA-CATAATATAAATA
*
38563228 TCAAATTGTTACATAATCTAAA
1 TCAAATTGTTACATAATATAAA
38563250 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (24 bp):
TCAAATTGTTACATAATATAAATA
Found at i:38565663 original size:30 final size:30
Alignment explanation
Indices: 38565629--38565754 Score: 157
Period size: 30 Copynumber: 4.2 Consensus size: 30
38565619 GGCAATATAT
38565629 ATGTATACCTATATACAAATCAATTCGGCA
1 ATGTATACCTATATACAAATCAATTCGGCA
* * *
38565659 ATGTATATCC-ATATACAAATTAATTCGACG
1 ATGTATA-CCTATATACAAATCAATTCGGCA
* * *
38565689 ACGTATATCTATATACAAATAAATTCGGCA
1 ATGTATACCTATATACAAATCAATTCGGCA
*
38565719 ATGTATACCCATATAC-AATCAATTCGGCA
1 ATGTATACCTATATACAAATCAATTCGGCA
*
38565748 ATATATA
1 ATGTATA
38565755 AAACATATAC
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
29 19 0.23
30 60 0.74
31 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (30 bp):
ATGTATACCTATATACAAATCAATTCGGCA
Found at i:38565705 original size:60 final size:59
Alignment explanation
Indices: 38565631--38565744 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 59
38565621 CAATATATAT
* * *
38565631 GTATACCTATATACAAATCAATTCGGCAATGTATATCCATATACAAATTAATTCGACGAC
1 GTATACCTATATACAAATAAATTCGGCAATGTATACCCATATAC-AATCAATTCGACGAC
*
38565691 GTATATCTATATACAAATAAATTCGGCAATGTATACCCATATACAATCAATTCG
1 GTATACCTATATACAAATAAATTCGGCAATGTATACCCATATACAATCAATTCG
38565745 GCAATATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 9 0.18
60 41 0.82
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (59 bp):
GTATACCTATATACAAATAAATTCGGCAATGTATACCCATATACAATCAATTCGACGAC
Found at i:38565762 original size:30 final size:29
Alignment explanation
Indices: 38565699--38565765 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
38565689 ACGTATATCT
* **
38565699 ATATACAAATAAATTCGGCAATGTATACCC
1 ATATAC-AATAAATTCGGCAATATATAAAC
*
38565729 ATATACAATCAATTCGGCAATATATAAAAC
1 ATATACAATAAATTCGGCAATATAT-AAAC
38565759 ATATACA
1 ATATACA
38565766 TTTGAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (29 bp):
ATATACAATAAATTCGGCAATATATAAAC
Found at i:38585235 original size:19 final size:19
Alignment explanation
Indices: 38585211--38585256 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
38585201 TGTTACACTA
*
38585211 TTTCTCAAATTTTCATT-TT
1 TTTCTCAAAATTTC-TTATT
38585230 TTTCTCAAAATTTCTTATT
1 TTTCTCAAAATTTCTTATT
*
38585249 TGTCTCAA
1 TTTCTCAA
38585257 TTGGATCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTCTCAAAATTTCTTATT
Found at i:38586389 original size:37 final size:37
Alignment explanation
Indices: 38586348--38586445 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 37
38586338 CATCAATCCA
38586348 TATAATAGTAAGATTTGCTC-AGTTAAGCTCCATTCAG
1 TATAATAGTAAGATTTGCTCGA-TTAAGCTCCATTCAG
* * * *
38586385 TATAATGGTATGATTTGCTCGATTAAGCTTCATTTAG
1 TATAATAGTAAGATTTGCTCGATTAAGCTCCATTCAG
* * *
38586422 TAGAACATTAAGATTTGGCTCGAT
1 TATAATAGTAAGATTT-GCTCGAT
38586446 AGAGCATACT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
37 42 0.84
38 8 0.16
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (37 bp):
TATAATAGTAAGATTTGCTCGATTAAGCTCCATTCAG
Found at i:38589934 original size:28 final size:26
Alignment explanation
Indices: 38589890--38589941 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
38589880 ATATTATTAA
38589890 TATAATATATAAATGTTATAATAAGG
1 TATAATATATAAATGTTATAATAAGG
*
38589916 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-AATGTTATAATAA
38589942 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TATAATATATAAATGTTATAATAAGG
Found at i:38590658 original size:85 final size:85
Alignment explanation
Indices: 38590510--38590677 Score: 327
Period size: 85 Copynumber: 2.0 Consensus size: 85
38590500 AAGGGTTAAA
38590510 TTTTAATATGTTTAGATCGAGAACCGAAGAAAACAAAATTAGATTGGGGGAAGTCAAACGTGGTT
1 TTTTAATATGTTTAGATCGAGAACCGAAGAAAACAAAATTAGATTGGGGGAAGTCAAACGTGGTT
38590575 GATTAGTCGATTTCGTCCCT
66 GATTAGTCGATTTCGTCCCT
*
38590595 TTTTGATATGTTTAGATCGAGAACCGAAGAAAACAAAATTAGATTGGGGGAAGTCAAACGTGGTT
1 TTTTAATATGTTTAGATCGAGAACCGAAGAAAACAAAATTAGATTGGGGGAAGTCAAACGTGGTT
38590660 GATTAGTCGATTTCGTCC
66 GATTAGTCGATTTCGTCC
38590678 GTCAATATTC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (85 bp):
TTTTAATATGTTTAGATCGAGAACCGAAGAAAACAAAATTAGATTGGGGGAAGTCAAACGTGGTT
GATTAGTCGATTTCGTCCCT
Found at i:38590980 original size:41 final size:41
Alignment explanation
Indices: 38590926--38591087 Score: 189
Period size: 41 Copynumber: 3.9 Consensus size: 41
38590916 TATATCAGTG
* * * *
38590926 ATATTCAGGCTTTATGCCTAGCAGACTTTATGCTGATGAATT
1 ATATT-AGGCTTTATGCCTAGCAGGCTTTATGCCGATGTATC
*
38590968 ATATTAGGCTTTATGCCTAGCAGGCTTTATGCCGATGTACC
1 ATATTAGGCTTTATGCCTAGCAGGCTTTATGCCGATGTATC
* * * *
38591009 ATATCAGGCTTTATACATAGCAGGCTTTGTGCCGATGTATC
1 ATATTAGGCTTTATGCCTAGCAGGCTTTATGCCGATGTATC
* * * * *
38591050 ATATTTGGATTTGTGTCTAGTAGGCTTTATGCCGATGT
1 ATATTAGGCTTTATGCCTAGCAGGCTTTATGCCGATGT
38591088 GGTATCTAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 96 0.95
42 5 0.05
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
ATATTAGGCTTTATGCCTAGCAGGCTTTATGCCGATGTATC
Found at i:38591075 original size:82 final size:82
Alignment explanation
Indices: 38590930--38591087 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 82
38590920 TCAGTGATAT
* * * * *
38590930 TCAGGCTTTATGCCTAGCAGACTTTATGCTGATGAATTATATTAGGCTTTATGCCTAGCAGGCTT
1 TCAGGCTTTATACATAGCAGACTTTATGCCGATGAATCATATTAGGATTTATGCCTAGCAGGCTT
38590995 TATGCCGATGTACCATA
66 TATGCCGATGTACCATA
* * * * * * *
38591012 TCAGGCTTTATACATAGCAGGCTTTGTGCCGATGTATCATATTTGGATTTGTGTCTAGTAGGCTT
1 TCAGGCTTTATACATAGCAGACTTTATGCCGATGAATCATATTAGGATTTATGCCTAGCAGGCTT
38591077 TATGCCGATGT
66 TATGCCGATGT
38591088 GGTATCTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (82 bp):
TCAGGCTTTATACATAGCAGACTTTATGCCGATGAATCATATTAGGATTTATGCCTAGCAGGCTT
TATGCCGATGTACCATA
Found at i:38597970 original size:28 final size:26
Alignment explanation
Indices: 38597926--38597977 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
38597916 ATATTATTAA
38597926 TATAATATATAAATGTTATAATAAGG
1 TATAATATATAAATGTTATAATAAGG
*
38597952 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-AATGTTATAATAA
38597978 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TATAATATATAAATGTTATAATAAGG
Found at i:38598931 original size:41 final size:41
Alignment explanation
Indices: 38598886--38599038 Score: 171
Period size: 41 Copynumber: 3.7 Consensus size: 41
38598876 GTGATTTCAT
* **
38598886 GCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATATCAG
1 GCTTTATGCCTAGCAGGCTTTGTGCCGATGAACCATATCAG
* * *
38598927 GCTTTATGCCTAGCAGGCTTTATGTCGATGTACCATATCAG
1 GCTTTATGCCTAGCAGGCTTTGTGCCGATGAACCATATCAG
* * **
38598968 GCTTTATGCCTAGCAGGCTTTGTGCCGATGTATCATATTTG
1 GCTTTATGCCTAGCAGGCTTTGTGCCGATGAACCATATCAG
* * * * *
38599009 GATTTGTGTCTAGTAGGCTTTATGCCGATG
1 GCTTTATGCCTAGCAGGCTTTGTGCCGATG
38599039 TGGTATCGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
GCTTTATGCCTAGCAGGCTTTGTGCCGATGAACCATATCAG
Found at i:38599027 original size:82 final size:82
Alignment explanation
Indices: 38598886--38599039 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 82
38598876 GTGATTTCAT
* * *
38598886 GCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATATCAGGCTTTATGCCTAGCAGGCTTTATG
1 GCTTTATGCCTAGCAGGCTTTGTGCCGATGAATCATATCAGGATTTATGCCTAGCAGGCTTTATG
*
38598951 TCGATGTACCATATCAG
66 CCGATGTACCATATCAG
* ** * * *
38598968 GCTTTATGCCTAGCAGGCTTTGTGCCGATGTATCATATTTGGATTTGTGTCTAGTAGGCTTTATG
1 GCTTTATGCCTAGCAGGCTTTGTGCCGATGAATCATATCAGGATTTATGCCTAGCAGGCTTTATG
38599033 CCGATGT
66 CCGATGT
38599040 GGTATCGAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 62 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (82 bp):
GCTTTATGCCTAGCAGGCTTTGTGCCGATGAATCATATCAGGATTTATGCCTAGCAGGCTTTATG
CCGATGTACCATATCAG
Found at i:38613389 original size:19 final size:18
Alignment explanation
Indices: 38613361--38613403 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
38613351 TTTAGAATGT
*
38613361 AAAAATTAAATTAAAAAC
1 AAAAATTAAAATAAAAAC
*
38613379 AAAATATTAAAATAAAAAT
1 AAAA-ATTAAAATAAAAAC
38613398 AAAAAT
1 AAAAAT
38613404 GGCTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAAAATAAAAAC
Found at i:38616510 original size:25 final size:25
Alignment explanation
Indices: 38616479--38616543 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
38616469 TATTTAAAAA
* *
38616479 ATTAAATATAATA-ATTTATTTTTAT
1 ATTAAATA-AATATAATTATTTATAT
38616504 ATTAAATAAATATAATTATTTATAT
1 ATTAAATAAATATAATTATTTATAT
38616529 ATGT-AAT-AATATAAT
1 AT-TAAATAAATATAAT
38616544 GTAAAATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 12 0.33
25 23 0.64
26 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTAAATAAATATAATTATTTATAT
Found at i:38616805 original size:23 final size:22
Alignment explanation
Indices: 38616746--38616806 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
38616736 TTTATAATTT
*
38616746 TCAT-AATTTTTATTTGAAAAC
1 TCATAAATTTTTTTTTGAAAAC
* *
38616767 -CTTAACTTTGTTTTTTTGAAAAC
1 TCATAA-ATT-TTTTTTTGAAAAC
38616790 TCATAAATTTTATTTTT
1 TCATAAATTTT-TTTTT
38616807 AAATTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
20 2 0.07
21 1 0.03
22 4 0.13
23 19 0.63
24 4 0.13
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (22 bp):
TCATAAATTTTTTTTTGAAAAC
Found at i:38622944 original size:30 final size:29
Alignment explanation
Indices: 38622899--38622977 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
38622889 TTCAAAGGTG
* *
38622899 GCAACATAGCAGCAACATGCAAGAAACCA
1 GCAACACAGCTGCAACATGCAAGAAACCA
* *
38622928 TGCAACACAGCTGCAACATGCAAGTAATCA
1 -GCAACACAGCTGCAACATGCAAGAAACCA
*
38622958 GGAACACAGCTG-AAGCATGC
1 GCAACACAGCTGCAA-CATGC
38622978 TAATGTCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.05
29 16 0.37
30 25 0.58
ACGTcount: A:0.42, C:0.27, G:0.20, T:0.11
Consensus pattern (29 bp):
GCAACACAGCTGCAACATGCAAGAAACCA
Found at i:38623915 original size:44 final size:44
Alignment explanation
Indices: 38623862--38623951 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
38623852 TTTGCCAAAA
38623862 CTTTTGACCAAGTTTAGTTTGAGGTATTCAAAGACCGAAACTAT
1 CTTTTGACCAAGTTTAGTTTGAGGTATTCAAAGACCGAAACTAT
*
38623906 CTTTTGACCAAGTTTAGTTTGAGGTATTCAAAGGCCGAAACTAT
1 CTTTTGACCAAGTTTAGTTTGAGGTATTCAAAGACCGAAACTAT
38623950 CT
1 CT
38623952 GCCTAAACCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (44 bp):
CTTTTGACCAAGTTTAGTTTGAGGTATTCAAAGACCGAAACTAT
Found at i:38626635 original size:15 final size:15
Alignment explanation
Indices: 38626617--38626676 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 15
38626607 ATAAAAGGAA
38626617 AATAAAATTAATAAT
1 AATAAAATTAATAAT
*
38626632 AATAATGAAAATAATAAT
1 AAT-A--AAATTAATAAT
38626650 AA-AATAATTAACTAAAT
1 AATAA-AATTAA-T-AAT
38626667 AATAAAATTA
1 AATAAAATTA
38626677 CTAAAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 1 0.03
15 8 0.22
16 3 0.08
17 10 0.28
18 14 0.39
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAAAATTAATAAT
Found at i:38627784 original size:32 final size:30
Alignment explanation
Indices: 38627739--38627799 Score: 95
Period size: 32 Copynumber: 2.0 Consensus size: 30
38627729 TGGGTTATTG
*
38627739 GGCTTGTTTGGGTTGAGGGTTAATTGGGCT
1 GGCTTGTTTGGGTTGAGAGTTAATTGGGCT
38627769 GGCTTGTAATTGGGTTGAGAGTTAATTGGGC
1 GGCTTGT--TTGGGTTGAGAGTTAATTGGGC
38627800 CCAAGCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 7 0.25
32 21 0.75
ACGTcount: A:0.15, C:0.07, G:0.41, T:0.38
Consensus pattern (30 bp):
GGCTTGTTTGGGTTGAGAGTTAATTGGGCT
Found at i:38627794 original size:16 final size:16
Alignment explanation
Indices: 38627746--38627798 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
38627736 TTGGGCTTGT
*
38627746 TTGGGTTGAGGGTTAA
1 TTGGGTTGAGAGTTAA
* **
38627762 TTGGGCTG-GCTTGTAA
1 TTGGGTTGAGAGT-TAA
38627778 TTGGGTTGAGAGTTAA
1 TTGGGTTGAGAGTTAA
38627794 TTGGG
1 TTGGG
38627799 CCCAAGCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.17, C:0.04, G:0.42, T:0.38
Consensus pattern (16 bp):
TTGGGTTGAGAGTTAA
Found at i:38628220 original size:44 final size:43
Alignment explanation
Indices: 38628152--38628354 Score: 225
Period size: 44 Copynumber: 4.7 Consensus size: 43
38628142 GATGTGATCT
38628152 ACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 ACTCTACTGCAACTTCAGAGAGATAAGAT-TGTGGTTTTAATCC
* * * *
38628196 ACTCCACTGCAACTTCAGAGAGATAGGATTAGT-TTCTTTAATCT
1 ACTCTACTGCAACTTCAGAGAGATAAGATT-GTGGT-TTTAATCC
* *** *
38628240 ACTCTACTGCAACTTCAGGGAGATAAGATTG-GG-TACGATCT
1 ACTCTACTGCAACTTCAGAGAGATAAGATTGTGGTTTTAATCC
*
38628281 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 ACTCTACTGCAACTTCAGAGAGATAAGAT-TGTGGTTTTAATCC
* *
38628325 ACTCCACTGCAACTTCATG-GAGATAGGATT
1 ACTCTACTGCAACTTCA-GAGAGATAAGATT
38628355 TGCTATCTTC
Statistics
Matches: 132, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
41 32 0.24
42 2 0.02
43 6 0.05
44 91 0.69
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
ACTCTACTGCAACTTCAGAGAGATAAGATTGTGGTTTTAATCC
Found at i:38628503 original size:45 final size:45
Alignment explanation
Indices: 38628454--38628853 Score: 649
Period size: 45 Copynumber: 8.9 Consensus size: 45
38628444 TTTGATTTGT
* * * *
38628454 TTCGCTGCTAGTACAGGAAGACAAGATCTACTATCTTTGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
*
38628499 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
38628544 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
* *
38628589 TTCGCTGCCAATGCAGGAAGACAAGATCTACTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
* * *
38628634 -TCACTGTCATTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
**
38628678 TTTACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
*
38628723 TTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
*
38628768 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
* *
38628813 TTCGCTGCCAATACAAGAAGACAAGATCTGCTACCTTCGAT
1 TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGAT
38628854 GATCTGTTCT
Statistics
Matches: 334, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
44 39 0.12
45 295 0.88
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (45 bp):
TTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
Found at i:38628700 original size:179 final size:180
Alignment explanation
Indices: 38628465--38628853 Score: 645
Period size: 179 Copynumber: 2.2 Consensus size: 180
38628455 TCGCTGCTAG
* * * *
38628465 TACAGGAAGACAAGATCTACTATCTTTGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGC
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGC
*
38628530 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCT
66 TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCT
* * *
38628595 GCCAATGCAGGAAGACAAGATCTACTATCTTCGATCTAC-TCACTGTCAT
131 GCCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACTGCCAA
*
38628644 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTTTACTGCCAATACAGGAAGACAAGATCTGC
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGC
38628709 TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCT
66 TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCT
* * *
38628774 GCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAA
131 GCCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACTGCCAA
* *
38628824 TACAAGAAGACAAGATCTGCTACCTTCGAT
1 TACAGGAAGACAAGATCTGCTATCTTCGAT
38628854 GATCTGTTCT
Statistics
Matches: 195, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
179 160 0.82
180 35 0.18
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (180 bp):
TACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGC
TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCT
GCCAATACAGGAAGACAAGATCTACTATCTTCGATCTACTTCACTGCCAA
Found at i:38641156 original size:8 final size:9
Alignment explanation
Indices: 38641128--38641157 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38641118 ATAAATAAAT
38641128 AAATTAACA
1 AAATTAACA
38641137 AAATTAACA
1 AAATTAACA
38641146 AAATT-ACA
1 AAATTAACA
38641154 AAAT
1 AAAT
38641158 CTAAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATTAACA
Found at i:38641609 original size:3 final size:3
Alignment explanation
Indices: 38641601--38641663 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
38641591 AAAATAAAAT
* * *
38641601 TAA TAA TAA CTAA TAA AAA TGA TAA TAA TAA AAA TAA TAA TAA -AA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38641646 TAA TTAA CTAAA TAA TAA
1 TAA -TAA -T-AA TAA TAA
38641664 AATTGCTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 2 0.04
3 37 0.76
4 8 0.16
5 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:38641631 original size:15 final size:15
Alignment explanation
Indices: 38641602--38641665 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
38641592 AAATAAAATT
38641602 AATAATAACTAATAAA
1 AATAATAA-TAATAAA
*
38641618 AATGATAATAATAAA
1 AATAATAATAATAAA
38641633 AATAATAATAA-AATA
1 AATAATAATAATAA-A
*
38641648 ATTAACTAAATAATAAA
1 AATAA-T-AATAATAAA
38641665 A
1 A
38641666 TTGCTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.05
15 22 0.54
16 8 0.20
17 7 0.17
18 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:38641637 original size:12 final size:12
Alignment explanation
Indices: 38641593--38641663 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 12
38641583 ATAAAAGGAA
*
38641593 AATAAAATTAAT
1 AATAAAAATAAT
*
38641605 AAT--AACTAAT
1 AATAAAAATAAT
*
38641615 AA-AAATGATAAT
1 AATAAA-AATAAT
38641627 AATAAAAATAAT
1 AATAAAAATAAT
38641639 AAT-AAAATAATT
1 AATAAAAATAA-T
38641651 AACTAAATAATAA
1 AA-TAAA-AATAA
38641664 AATTGCTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 8 0.17
11 8 0.17
12 20 0.43
13 4 0.09
14 2 0.04
15 5 0.11
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:38644267 original size:7 final size:7
Alignment explanation
Indices: 38644204--38644292 Score: 54
Period size: 7 Copynumber: 11.4 Consensus size: 7
38644194 TTCATATTTT
38644204 AAATTAA
1 AAATTAA
*
38644211 AAATAAA
1 AAATTAA
38644218 AAATTTTAAA
1 AAA--TT-AA
38644228 AAATT-A
1 AAATTAA
*
38644234 TAATCTAAA
1 AAAT-T-AA
38644243 AAATTCAA
1 AAATT-AA
38644251 AAATTATAA
1 AAA-T-TAA
38644260 AAATTAAA
1 AAATT-AA
*
38644268 AATATTTA
1 AA-ATTAA
38644276 AAATTAA
1 AAATTAA
38644283 AAATTAA
1 AAATTAA
38644290 AAA
1 AAA
38644293 AAATTTTAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
6 4 0.06
7 25 0.38
8 16 0.25
9 14 0.22
10 6 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATTAA
Found at i:38644283 original size:23 final size:23
Alignment explanation
Indices: 38644197--38644292 Score: 81
Period size: 23 Copynumber: 4.0 Consensus size: 23
38644187 ATTACTTTTC
* *
38644197 ATATTTTAAATTAAAAATAAAAA
1 ATATTTAAAATTAAAAATTAAAA
*
38644220 AT-TTTAAAAAATT-ATAATCTAAAA
1 ATATTT--AAAATTAAAAAT-TAAAA
*
38644244 A-ATTCAAAAATTATAAAAATTAAAA
1 ATATT-TAAAA-T-TAAAAATTAAAA
38644269 ATATTTAAAATTAAAAATTAAAA
1 ATATTTAAAATTAAAAATTAAAA
38644292 A
1 A
38644293 AAATTTTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
22 3 0.05
23 23 0.40
24 14 0.24
25 11 0.19
26 7 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATTTAAAATTAAAAATTAAAA
Found at i:38644294 original size:16 final size:16
Alignment explanation
Indices: 38644209--38644294 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 16
38644199 ATTTTAAATT
* *
38644209 AAAAATAAAAAATTTTA
1 AAAAATTAAAAA-TTAA
*
38644226 AAAAATT-ATAATCT-A
1 AAAAATTAAAAAT-TAA
*
38644241 AAAAATTCAAAAATTAT
1 AAAAATT-AAAAATTAA
*
38644258 AAAAATTAAAAA-TATT
1 AAAAATTAAAAATTA-A
*
38644274 TAAAATTAAAAATTAA
1 AAAAATTAAAAATTAA
38644290 AAAAA
1 AAAAA
38644295 ATTTTAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
15 11 0.20
16 26 0.46
17 19 0.34
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAAATTAA
Found at i:38644353 original size:28 final size:28
Alignment explanation
Indices: 38644291--38644354 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
38644281 AAAAATTAAA
38644291 AAAAATTTTAAAAATCATTTAAAAAGTT
1 AAAAATTTTAAAAATCATTTAAAAAGTT
* * *
38644319 TACAATTATT-AAAATTATTTAAAAA-TT
1 AAAAATT-TTAAAAATCATTTAAAAAGTT
38644346 CAAAAATTT
1 -AAAAATTT
38644355 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
27 3 0.10
28 24 0.83
29 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAAATTTTAAAAATCATTTAAAAAGTT
Found at i:38644563 original size:19 final size:20
Alignment explanation
Indices: 38644510--38644566 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
38644500 TATTCGTTAA
* *
38644510 AATAATAAAAATATAT-ATT
1 AATATTAAATATATATAATT
* *
38644529 AATATT-AATTTTTATAATT
1 AATATTAAATATATATAATT
38644548 AA-ATTAAATATATATAATT
1 AATATTAAATATATATAATT
38644567 TGTTATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTAAATATATATAATT
Found at i:38646022 original size:124 final size:124
Alignment explanation
Indices: 38645813--38646176 Score: 550
Period size: 124 Copynumber: 2.9 Consensus size: 124
38645803 GGTCCGGAAA
** * * *
38645813 GAAATAATTTTGAGTTGACATTTCTGATCAAATAGAATAAAATCGCTTCTAGCAAGATGCTATTT
1 GAAATAATTTT-TTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTT
* **
38645878 GAGAAGAATTTGTGAAATCGCGCCCTCGTGGATACGCTTTTGCTACAGTAGGTCATGGAT
65 GAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAT
38645938 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
1 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
* *
38646003 AGAAGAATTTGTAAAATCGCGCCCTTGTGGACGCGCTTTTGCTAAAGTAGGTCATGGAT
66 AGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAT
* * * * *
38646062 AAAAT-ATGTTTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTA
1 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
* *
38646126 AGAAGAATTTGTGAAAATCGCGCCCTCGTGGGCGCGTTTTTGCTACAGTAG
66 AGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
38646177 CATGTTTGGG
Statistics
Matches: 219, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
123 67 0.31
124 141 0.64
125 11 0.05
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
AGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAT
Found at i:38652044 original size:20 final size:20
Alignment explanation
Indices: 38651997--38652045 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
38651987 TTTTCCTTTT
38651997 AATTTTCTTTTATTGCACCAC
1 AATTTTC-TTTATTGCACCAC
* * * *
38652018 AAATTTCTTTCTTGTACTAC
1 AATTTTCTTTATTGCACCAC
38652038 AATTTTCT
1 AATTTTCT
38652046 AACAGAGGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (20 bp):
AATTTTCTTTATTGCACCAC
Found at i:38654914 original size:29 final size:30
Alignment explanation
Indices: 38654859--38654915 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
38654849 TTTTGTTCTT
*
38654859 TCTTTTGTTTTTCTCTGTTTCCCTTTGCTC
1 TCTTTTCTTTTTCTCTGTTTCCCTTTGCTC
*
38654889 TCTTTTCTTCTTTCT-T-TTTCCTTTTGC
1 TCTTTTCTT-TTTCTCTGTTTCCCTTTGC
38654916 GATTGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 9 0.38
31 5 0.21
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (30 bp):
TCTTTTCTTTTTCTCTGTTTCCCTTTGCTC
Found at i:38660830 original size:65 final size:65
Alignment explanation
Indices: 38660718--38660858 Score: 158
Period size: 65 Copynumber: 2.2 Consensus size: 65
38660708 GTCGTACCAT
** * * ** *
38660718 AGCTCTTTGTGAACGTCTTATTATATGATCGGTTGTGATCTTGCATATATTGGGGACACAAATAC
1 AGCTCTTTGTGAACGTCTTATTATATGATCAATTGTGATCTTACATATATCGCAGACACAAACAC
* * * *
38660783 AGCTCTTTGTGAGCGTCTTGTTTTATGATCAATTGTGATGC-TACATATGTCGCAGACACAAACA
1 AGCTCTTTGTGAACGTCTTATTATATGATCAATTGTGAT-CTTACATATATCGCAGACACAAACA
38660847 C
65 C
*
38660848 AACTCTTTGTG
1 AGCTCTTTGTG
38660859 TGTGTCCTGA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
65 62 0.98
66 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (65 bp):
AGCTCTTTGTGAACGTCTTATTATATGATCAATTGTGATCTTACATATATCGCAGACACAAACAC
Found at i:38660944 original size:26 final size:26
Alignment explanation
Indices: 38660915--38660970 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
38660905 GAAGCTCTTA
* *
38660915 ATTAAAGGCTCTTCGTGAGCTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTG
* *
38660941 ATTAAAAGTTCTTTGTGAACTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTG
38660967 ATTA
1 ATTA
38660971 TGCCTCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (26 bp):
ATTAAAAGCTCTTCGTGAACTTCCTG
Found at i:38673100 original size:17 final size:17
Alignment explanation
Indices: 38673068--38673117 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
38673058 CATGTGATCT
38673068 GCCCGTGTGCGCCCACAC
1 GCCCGTGTG-GCCCACAC
38673086 GCCCGTGTGGCCCACAC
1 GCCCGTGTGGCCCACAC
38673103 GCCCGTGTGGCCCAC
1 GCCCGTGTGGCCCAC
38673118 TTGGCCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.10, C:0.48, G:0.30, T:0.12
Consensus pattern (17 bp):
GCCCGTGTGGCCCACAC
Found at i:38675984 original size:26 final size:26
Alignment explanation
Indices: 38675954--38676011 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
38675944 TTGGAGCTCT
*
38675954 TGATTAAAAGCTCTTCATGAGCTTCC
1 TGATTAAAAGCTCTTCATGAACTTCC
* **
38675980 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAAGCTCTTCATGAACTTCC
38676006 TGATTA
1 TGATTA
38676012 TGCCTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (26 bp):
TGATTAAAAGCTCTTCATGAACTTCC
Found at i:38676096 original size:26 final size:26
Alignment explanation
Indices: 38676060--38676116 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
38676050 TTTCCCGATA
*
38676060 GGCTCTTTGTGAGCTTCATGATTA-AT
1 GGCTCATTGTGAGCTTCATG-TTATAT
* *
38676086 GGCTCATTGTGAGTTTCCTGTTATAT
1 GGCTCATTGTGAGCTTCATGTTATAT
38676112 GGCTC
1 GGCTC
38676117 GAGAGAGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.42
Consensus pattern (26 bp):
GGCTCATTGTGAGCTTCATGTTATAT
Found at i:38681098 original size:44 final size:44
Alignment explanation
Indices: 38680949--38681098 Score: 117
Period size: 44 Copynumber: 3.4 Consensus size: 44
38680939 TAGGGGTAAG
* * * * **
38680949 ATATGCTATGCTATGATATGTGATAAGAAAAGTTTCGATATG-C
1 ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
* * * * * *
38680992 AATATGATATGCTATGACATGTTACTTAG-TAT-ACTCCAATATGAA
1 -ATATGATATGCTATGATATG-TAATAAGATATGTC-CCGATATGAC
* * *
38681037 ATTTGATATGATGTGATATGTAATAAGATATGTCCCGATATGAC
1 ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
38681081 ATATGATATGCTATGATA
1 ATATGATATGCTATGATA
38681099 CATTCCGTTA
Statistics
Matches: 77, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
43 5 0.06
44 67 0.87
45 5 0.06
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (44 bp):
ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
Found at i:38687582 original size:13 final size:13
Alignment explanation
Indices: 38687566--38687603 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
38687556 TTATCAGAAG
*
38687566 CACTTTTTCACAA
1 CACTTTTTCAAAA
*
38687579 CACTTTTTAAAAA
1 CACTTTTTCAAAA
38687592 CA-TTTTTCAAAA
1 CACTTTTTCAAAA
38687604 GTAATGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
CACTTTTTCAAAA
Found at i:38690782 original size:47 final size:46
Alignment explanation
Indices: 38690713--38690804 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 46
38690703 CTGCCAATTA
*
38690713 ATAATATTATGGACAAGCCACCACTTTTGTAGATAAACTACCACTTT
1 ATAATATTATAGACAAGCCACCAC-TTTGTAGATAAACTACCACTTT
* * *
38690760 ATAATATTGTAGACAAGCCACCACTTTGTATATAAACTGCCACTT
1 ATAATATTATAGACAAGCCACCACTTTGTAGATAAACTACCACTT
38690805 CTTGCTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 19 0.46
47 22 0.54
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (46 bp):
ATAATATTATAGACAAGCCACCACTTTGTAGATAAACTACCACTTT
Found at i:38690883 original size:20 final size:21
Alignment explanation
Indices: 38690850--38690890 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
38690840 ATATGGCCAC
*
38690850 AAAAATTTACTTTTTCACTTT
1 AAAAATTTAATTTTTCACTTT
38690871 AAAAA-TTAATTTTTCACTTT
1 AAAAATTTAATTTTTCACTTT
38690891 GTCATGGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAATTTAATTTTTCACTTT
Found at i:38699609 original size:10 final size:10
Alignment explanation
Indices: 38699575--38699642 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
38699565 CCCTTTTTTT
38699575 TAATTTTT-A
1 TAATTTTTAA
* *
38699584 CAATTTTACAA
1 TAATTTT-TAA
38699595 T-ATTTTTAA
1 TAATTTTTAA
*
38699604 TAATTTCTTTA
1 TAATTT-TTAA
*
38699615 TAATTTTTTA
1 TAATTTTTAA
38699625 TAATGTTTTAGA
1 TAAT-TTTTA-A
38699637 TAATTT
1 TAATTT
38699643 AATTTTCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 9 0.19
10 17 0.36
11 16 0.34
12 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:38699617 original size:11 final size:10
Alignment explanation
Indices: 38699596--38699634 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
38699586 ATTTTACAAT
*
38699596 ATTTTTAATA
1 ATTTTTTATA
38699606 ATTTCTTTATA
1 ATTT-TTTATA
38699617 ATTTTTTATA
1 ATTTTTTATA
*
38699627 ATGTTTTA
1 ATTTTTTA
38699635 GATAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:38706782 original size:19 final size:19
Alignment explanation
Indices: 38706758--38706796 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38706748 CAGTTGAGGG
* *
38706758 TAATTAGTGATTTAATTGA
1 TAATTAGGGATTTAAATGA
38706777 TAATTAGGGATTTAAATGA
1 TAATTAGGGATTTAAATGA
38706796 T
1 T
38706797 CATAGGCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (19 bp):
TAATTAGGGATTTAAATGA
Found at i:38706863 original size:18 final size:18
Alignment explanation
Indices: 38706837--38706875 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
38706827 AGGAATAAGA
38706837 AATTCAATTAGGTTAATT
1 AATTCAATTAGGTTAATT
* *
38706855 AATTTAATTAGTTTAATT
1 AATTCAATTAGGTTAATT
38706873 AAT
1 AAT
38706876 ACTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (18 bp):
AATTCAATTAGGTTAATT
Found at i:38708471 original size:16 final size:16
Alignment explanation
Indices: 38708450--38708495 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38708440 AAGGGCTTAT
38708450 ATTTTAATTTGTTTTA
1 ATTTTAATTTGTTTTA
38708466 ATTTTAATTT-TCTTTA
1 ATTTTAATTTGT-TTTA
* *
38708482 TTTTTCATTTGTTT
1 ATTTTAATTTGTTT
38708496 GTTTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (16 bp):
ATTTTAATTTGTTTTA
Found at i:38713864 original size:24 final size:24
Alignment explanation
Indices: 38713832--38713879 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
38713822 GTGACAAAAT
38713832 TTTTGATTTATTTGAGAAATTAAA
1 TTTTGATTTATTTGAGAAATTAAA
38713856 TTTTGATTTATTTGAGAAATTAAA
1 TTTTGATTTATTTGAGAAATTAAA
38713880 CTTTAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TTTTGATTTATTTGAGAAATTAAA
Found at i:38713892 original size:24 final size:24
Alignment explanation
Indices: 38713841--38713892 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
38713831 TTTTTGATTT
* * ***
38713841 ATTTGAGAAATTAAATTTTGATTT
1 ATTTGAGAAATTAAACTTTAAAAC
38713865 ATTTGAGAAATTAAACTTTAAAAC
1 ATTTGAGAAATTAAACTTTAAAAC
38713889 ATTT
1 ATTT
38713893 TTATAAAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (24 bp):
ATTTGAGAAATTAAACTTTAAAAC
Found at i:38720392 original size:19 final size:19
Alignment explanation
Indices: 38720333--38720392 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
38720323 GAAAAATTTA
**
38720333 TTTATATTAATTTAGCCATT
1 TTTATATTAATTTA-AAATT
**
38720353 TTTATATTAATTTAATGTT
1 TTTATATTAATTTAAAATT
*
38720372 TTTATTTTAATTTAAAATT
1 TTTATATTAATTTAAAATT
38720391 TT
1 TT
38720393 ACATTCTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATATTAATTTAAAATT
Found at i:38723242 original size:14 final size:15
Alignment explanation
Indices: 38723218--38723262 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
38723208 TTATTTTAAA
38723218 AAATATTTGAAAAAG
1 AAATATTTGAAAAAG
38723233 AAAT-TTTGAAAAA-
1 AAATATTTGAAAAAG
* *
38723246 AAA-AATTGAAAATG
1 AAATATTTGAAAAAG
38723260 AAA
1 AAA
38723263 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 10 0.38
14 12 0.46
15 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.24
Consensus pattern (15 bp):
AAATATTTGAAAAAG
Found at i:38723312 original size:21 final size:22
Alignment explanation
Indices: 38723288--38723329 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38723278 GATTTTTTTT
38723288 GAAAAA-AATTGGAAAAAAAAG
1 GAAAAATAATTGGAAAAAAAAG
* *
38723309 GAAAAATATTTTGAAAAAAAA
1 GAAAAATAATTGGAAAAAAAA
38723330 ATTCAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (22 bp):
GAAAAATAATTGGAAAAAAAAG
Found at i:38723764 original size:6 final size:6
Alignment explanation
Indices: 38723753--38723792 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
38723743 TTGTCTTTTA
*
38723753 TTTATT TTTATT TTTATT TTTATT CTTATT ATTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT TTT
38723793 TCTTCCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:38724385 original size:19 final size:20
Alignment explanation
Indices: 38724343--38724387 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
38724333 AGTTCAATAT
*
38724343 TATTATATTATTTTATTTTA
1 TATTATATTATTATATTTTA
38724363 TATT-TATTATTAT-TTTTA
1 TATTATATTATTATATTTTA
38724381 CTATTAT
1 -TATTAT
38724388 GTATTTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATATTATTATATTTTA
Found at i:38724962 original size:16 final size:16
Alignment explanation
Indices: 38724941--38724973 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38724931 TGTACTTTTA
38724941 TTTTTATTTTTAGTTG
1 TTTTTATTTTTAGTTG
*
38724957 TTTTTATTTTTATTTG
1 TTTTTATTTTTAGTTG
38724973 T
1 T
38724974 GAGAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTTAGTTG
Found at i:38724964 original size:22 final size:23
Alignment explanation
Indices: 38724914--38724971 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
38724904 TTTGCTTTAG
* *
38724914 TTATTTTTACTTTTGGTTGTACTT
1 TTATTTTTATTTTTAGTTGTA-TT
38724938 TTATTTTTATTTTTAGTTGT-TT
1 TTATTTTTATTTTTAGTTGTATT
38724960 TTATTTTTATTT
1 TTATTTTTATTT
38724972 GTGAGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 14 0.44
24 18 0.56
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (23 bp):
TTATTTTTATTTTTAGTTGTATT
Found at i:38727328 original size:6 final size:7
Alignment explanation
Indices: 38727310--38727334 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38727300 TGAAAAGCTC
38727310 ATTTTTA
1 ATTTTTA
38727317 ATTTTTA
1 ATTTTTA
38727324 ATTTTTA
1 ATTTTTA
38727331 ATTT
1 ATTT
38727335 CTTGTTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:38730496 original size:47 final size:48
Alignment explanation
Indices: 38730431--38730524 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 48
38730421 TCGCATATCA
* * * *
38730431 CACACCGTAGCCATATCCCGGCTATGGTTTTACACGGAAA-CACATAT
1 CACACCGTAGCCATATCCCAGATATGGTCTTACAAGGAAATCACATAT
38730478 CACACCG-ATGCCATATCCCAGATATGGTCTTACAAGGAAATCACATA
1 CACACCGTA-GCCATATCCCAGATATGGTCTTACAAGGAAATCACATA
38730525 ATCATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
46 1 0.02
47 34 0.83
48 6 0.15
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (48 bp):
CACACCGTAGCCATATCCCAGATATGGTCTTACAAGGAAATCACATAT
Found at i:38751806 original size:20 final size:20
Alignment explanation
Indices: 38751781--38751819 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
38751771 AACATTCAAA
38751781 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
38751801 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
38751820 ACCATATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:38754547 original size:24 final size:24
Alignment explanation
Indices: 38754502--38754548 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
38754492 CATTAAAGTC
* **
38754502 CATAATTCAACCATTTTGTATACT
1 CATAATTCAACCAGTTCATATACT
38754526 CATAATTCAACCAGTTCATATAC
1 CATAATTCAACCAGTTCATATAC
38754549 GTTTGCATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (24 bp):
CATAATTCAACCAGTTCATATACT
Found at i:38754940 original size:26 final size:26
Alignment explanation
Indices: 38754904--38754957 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
38754894 TGTTGAATTG
38754904 ATAGTTAATTAAGGTACATAGACCAA
1 ATAGTTAATTAAGGTACATAGACCAA
38754930 ATAGTTAATTAAGGTACATAGACCAA
1 ATAGTTAATTAAGGTACATAGACCAA
38754956 AT
1 AT
38754958 TGTAAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (26 bp):
ATAGTTAATTAAGGTACATAGACCAA
Found at i:38756264 original size:17 final size:19
Alignment explanation
Indices: 38756232--38756269 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
38756222 ACTGATAACC
38756232 TAACACAAATATATATATT
1 TAACACAAATATATATATT
38756251 TAACACAAATATATATATT
1 TAACACAAATATATATATT
38756270 CAACTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
TAACACAAATATATATATT
Found at i:38758389 original size:16 final size:16
Alignment explanation
Indices: 38758368--38758400 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38758358 TTTGCTGTAT
38758368 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
38758384 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
38758400 T
1 T
38758401 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:38758651 original size:16 final size:16
Alignment explanation
Indices: 38758614--38758655 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38758604 TTAATCATAT
*
38758614 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
38758630 TT-AAATATATTATAA
1 TTAAAATATATTATAA
38758645 TTAAAATATAT
1 TTAAAATATAT
38758656 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:38758662 original size:14 final size:15
Alignment explanation
Indices: 38758623--38758664 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38758613 TTTAAACATA
*
38758623 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38758638 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38758652 A-TATAATTTAATA
1 ATTATAATTAAATA
38758665 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38758756 original size:120 final size:120
Alignment explanation
Indices: 38758612--38759148 Score: 916
Period size: 120 Copynumber: 4.5 Consensus size: 120
38758602 ATTTAATCAT
*
38758612 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
38758677 GTCAATATTGTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * * *
38758733 AATTAACATAATCATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
38758798 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
38758853 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
38758918 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
38758973 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
38759037 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
38759092 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
38759149 TAAAATAATT
Statistics
Matches: 399, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
119 110 0.28
120 286 0.72
121 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:38758895 original size:18 final size:17
Alignment explanation
Indices: 38758874--38758908 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38758864 TTATTATTAA
*
38758874 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38758892 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38758909 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38759015 original size:18 final size:17
Alignment explanation
Indices: 38758994--38759028 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38758984 TTATTATTAA
*
38758994 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38759012 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38759029 TCTAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38761513 original size:38 final size:38
Alignment explanation
Indices: 38761390--38761523 Score: 171
Period size: 46 Copynumber: 3.3 Consensus size: 38
38761380 GACAGAAACT
* *
38761390 GAGCAAATCGGCAGAAAAGAAAGGAAAAG-AATAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
38761427 GAGCAAATCGGCAGAAAAGAAAAGAAAATAAATAGAGGAACAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAG-----AAA-AGA--AACAGAGG
38761473 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
38761511 GAGCAAATCGGCA
1 GAGCAAATCGGCA
38761524 AAAGCTAGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 17
0.82 0.02 0.16
Matches are distributed among these distances:
37 23 0.27
38 21 0.24
40 3 0.03
41 3 0.03
42 3 0.03
43 2 0.02
46 31 0.36
ACGTcount: A:0.54, C:0.10, G:0.30, T:0.05
Consensus pattern (38 bp):
GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
Found at i:38773694 original size:25 final size:25
Alignment explanation
Indices: 38773659--38773725 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
38773649 TCTCGAGCCA
* **
38773659 TATAACAGGAAGCTCATGTAAGCTG
1 TATAACGGGAAGCTCATCCAAGCTG
* * *
38773684 TATAACGGGAAGCTTATCCAGGTTG
1 TATAACGGGAAGCTCATCCAAGCTG
38773709 TATAACGGGAAGCTCAT
1 TATAACGGGAAGCTCAT
38773726 AAGAGTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (25 bp):
TATAACGGGAAGCTCATCCAAGCTG
Found at i:38773851 original size:22 final size:23
Alignment explanation
Indices: 38773808--38773854 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
38773798 GAATAGCCAT
* *
38773808 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
*
38773831 ATATC-GGAAGCTCTAGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
38773853 AT
1 AT
38773855 TAATTAGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCC
Found at i:38773883 original size:26 final size:26
Alignment explanation
Indices: 38773847--38773906 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
38773837 GAAGCTCTAG
* *
38773847 AGAGCCATTAATTAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAACTCACAA
* * *
38773873 AGAGCCTTTAATCAGGAAACTCGCGA
1 AGAGCCATTAATCAGGAAACTCACAA
38773899 AGAGCCAT
1 AGAGCCAT
38773907 ATATCGGGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAACTCACAA
Found at i:38774383 original size:16 final size:15
Alignment explanation
Indices: 38774362--38774395 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
38774352 AAATTTAACA
*
38774362 TCAATTCATGTTCATT
1 TCAATTCA-GTTCAGT
38774378 TCAATTCAGTTCAGT
1 TCAATTCAGTTCAGT
38774393 TCA
1 TCA
38774396 CCTCTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TCAATTCAGTTCAGT
Found at i:38788195 original size:41 final size:43
Alignment explanation
Indices: 38788085--38788332 Score: 153
Period size: 44 Copynumber: 5.7 Consensus size: 43
38788075 ACCCCAATCC
*
38788085 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACTACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAAC-ACAGATCT
* * * * **
38788129 TTTCTCTCTGAAGTTACAGTAGAGCAGATCGCAAC-CAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACACAGATCT
* * * *
38788170 TATCTCCCTAAAGTTGTAGTGGAGCAGA-CACAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCA-AA-ACA-CAGATCT
* * * * * * *
38788214 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAGAACCGCAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCA-AAACACAGATCT
* * * * * **
38788258 TATCTCCCTAAAGTTGCAGTGAAACGGATCAAAATGATGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAA-CACAGATCT
* * * *
38788302 CATCTCTCTGAAGTTGCAGTAGAGTAGATCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCA
38788333 CATCAGACTT
Statistics
Matches: 150, Mismatches: 46, Indels: 16
0.71 0.22 0.08
Matches are distributed among these distances:
40 1 0.01
41 26 0.17
42 4 0.03
43 4 0.03
44 112 0.75
45 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACACAGATCT
Found at i:38800333 original size:25 final size:25
Alignment explanation
Indices: 38800257--38800384 Score: 166
Period size: 25 Copynumber: 5.0 Consensus size: 25
38800247 ATTTTTCTTG
* *
38800257 AAATTTTACCAGGGGCAAAATTGTCA
1 AAATTTTA-CAAGGGTAAAATTGTCA
* **
38800283 AAATTTTACCAGAGACAAAATTGTCA
1 AAATTTTACAAG-GGTAAAATTGTCA
*
38800309 AAATTTTATAAGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
*
38800334 AAATTTTATAAGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
*
38800359 AAATTTTACAGGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
38800384 A
1 A
38800385 TTTTGTTGAG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
25 62 0.67
26 30 0.33
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (25 bp):
AAATTTTACAAGGGTAAAATTGTCA
Found at i:38800396 original size:25 final size:24
Alignment explanation
Indices: 38800299--38800403 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 24
38800289 TACCAGAGAC
* *
38800299 AAAATTGTCAAAATTTTATAAGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
* *
38800324 AAAATTGTCAAAATTTTATAAGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
**
38800349 AAAATTGTCAAAATTTTACAGGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
38800374 AAAATTGTC-AATTTTGTTGAGGGGT
1 AAAATTGTCAAATTTT-TT-AGGGGT
38800399 AAAAT
1 AAAAT
38800404 AAGGATGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
23 6 0.08
25 68 0.92
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (24 bp):
AAAATTGTCAAATTTTTTAGGGGT
Found at i:38806998 original size:13 final size:13
Alignment explanation
Indices: 38806958--38806999 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
38806948 TTACTGAAAA
38806958 TAATTAATAATAT
1 TAATTAATAATAT
* *
38806971 TAA-TAATTTAGAT
1 TAATTAA-TAATAT
38806984 TAATTAATAATAT
1 TAATTAATAATAT
38806997 TAA
1 TAA
38807000 AAAATAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
TAATTAATAATAT
Found at i:38813573 original size:30 final size:30
Alignment explanation
Indices: 38813537--38813606 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
38813527 CGATCGAAAA
** *
38813537 AAAATCAAGATTCACTTTTTTGTTTTCAAG
1 AAAATCAAGATTCACTTTCGTATTTTCAAG
38813567 AAAATCAAGATTCACTTTCGTATTTTCAAG
1 AAAATCAAGATTCACTTTCGTATTTTCAAG
38813597 AAAATCAAGA
1 AAAATCAAGA
38813607 AATTGAATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
AAAATCAAGATTCACTTTCGTATTTTCAAG
Found at i:38819340 original size:16 final size:17
Alignment explanation
Indices: 38819313--38819360 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
38819303 GTCCAAAATT
*
38819313 ATATGTATTAATTTATA
1 ATATATATTAATTTATA
38819330 ATATA-ATTAATTT-TA
1 ATATATATTAATTTATA
*
38819345 ATTTATATCTAATTTA
1 ATATATAT-TAATTTA
38819361 ATTTGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
ATATATATTAATTTATA
Found at i:38819346 original size:22 final size:22
Alignment explanation
Indices: 38819320--38819364 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
38819310 ATTATATGTA
38819320 TTAATTTATAATATAA-TTAATT
1 TTAATTTAT-ATATAATTTAATT
*
38819342 TTAATTTATATCTAATTTAATT
1 TTAATTTATATATAATTTAATT
38819364 T
1 T
38819365 GGGTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTTATATATAATTTAATT
Found at i:38820872 original size:29 final size:29
Alignment explanation
Indices: 38820830--38820888 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
38820820 TCACAGTCCC
38820830 TATGGGTATGATAACTCGACATTTACTAG
1 TATGGGTATGATAACTCGACATTTACTAG
38820859 TATGGGTATGATAACTCGACATTTACTAG
1 TATGGGTATGATAACTCGACATTTACTAG
38820888 T
1 T
38820889 CACTTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (29 bp):
TATGGGTATGATAACTCGACATTTACTAG
Found at i:38831145 original size:27 final size:29
Alignment explanation
Indices: 38831100--38831169 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
38831090 CACAAATTTG
38831100 AAATTTAGTCCATGCAC-TTT-AATTTTA
1 AAATTTAGTCCATGCACTTTTAAATTTTA
* * **
38831127 GAATTTAGTCCCTTTACTTTTTAAATTTTA
1 AAATTTAGTCCATGCAC-TTTTAAATTTTA
38831157 AAATTTAGGTCCA
1 AAATTTA-GTCCA
38831170 ACTATTAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.39
29 3 0.09
30 13 0.39
31 4 0.12
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (29 bp):
AAATTTAGTCCATGCACTTTTAAATTTTA
Found at i:38844453 original size:28 final size:28
Alignment explanation
Indices: 38844422--38844475 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
38844412 TTAAAATTTG
38844422 ATATATAAT-T-TTTAAAAATTAAAATAAA
1 ATATATAATATATTT-AAAA-TAAAATAAA
*
38844450 ATATTTAATATATTTAAAATAAAATA
1 ATATATAATATATTTAAAATAAAATA
38844476 CTTACCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 15 0.65
29 5 0.22
30 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATATAATATATTTAAAATAAAATAAA
Found at i:38844456 original size:21 final size:21
Alignment explanation
Indices: 38844409--38844475 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
38844399 AAAGCTTTTT
* * *
38844409 TATTTAAAATTTGATATATAA
1 TATTTAAAATTTAAAATAAAA
* *
38844430 TTTTTAAAAATTAAAATAAAA
1 TATTTAAAATTTAAAATAAAA
38844451 TATTTAATATATTTAAAATAAAA
1 TATTTAA-A-ATTTAAAATAAAA
38844474 TA
1 TA
38844476 CTTACCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 22 0.59
22 1 0.03
23 14 0.38
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
TATTTAAAATTTAAAATAAAA
Found at i:38874353 original size:75 final size:75
Alignment explanation
Indices: 38874230--38874441 Score: 291
Period size: 76 Copynumber: 2.8 Consensus size: 75
38874220 TGATTCCGCC
* * * *
38874230 AAGGGCTTGCTAACTGCTGATTCCACGATTCATTCGTGGTTGCTAAGTGCTGATTCCACCGTAT-
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTC-TTTGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
38874294 TTTAAATGTGA
65 ATTAAATGTGA
*
38874305 AAGGGGTTACTAAGTGCTGATTCCCCGATTCTTTGATGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCTTTG-TGGTTGCTAAGTGCTGATTCCACCGTATC
*
38874370 ATTGAATGTGA
65 ATTAAATGTGA
* * * *
38874381 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTC-TTTGTGGTTGCTAAGTGCTGATTCCACCG
38874442 ATAACGGATA
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
74 3 0.02
75 55 0.45
76 62 0.51
77 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCTTTGTGGTTGCTAAGTGCTGATTCCACCGTATCA
TTAAATGTGA
Found at i:38881731 original size:33 final size:33
Alignment explanation
Indices: 38881659--38881990 Score: 193
Period size: 33 Copynumber: 9.6 Consensus size: 33
38881649 TGAATATAAA
*
38881659 GGTGGTTGCTAAGTGCTGATTCCCC----CA-A
1 GGTGGTTGCTAAGTGCTGATTCCCCGATTCATT
* *
38881687 GG-GGTTGCTAAGTGCTGATTCCGCGGTTCATT
1 GGTGGTTGCTAAGTGCTGATTCCCCGATTCATT
*
38881719 GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGT
1 GGTGGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T
* * *
38881758 GAAGGGGGTTGCTAAGTGTTGATT-CCC---TCA-A
1 ---GGTGGTTGCTAAGTGCTGATTCCCCGATTCATT
38881789 GG-GGTTGCTAAGTGCTGATTCCCCGATTCATT
1 GGTGGTTGCTAAGTGCTGATTCCCCGATTCATT
* *
38881821 GGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGT
1 GGTGGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T
* *
38881860 GAAAGGGGTTTCTAAGTGCTGATTCCCCGATTCATT
1 G---GTGGTTGCTAAGTGCTGATTCCCCGATTCATT
* *
38881896 GGTGGTTGCTAAGTGCTGATTCCACGGTATCATT
1 GGTGGTTGCTAAGTGCTGATTCCCCGAT-TCATT
* *
38881930 GAATGTGAAAGGAGTTGCTAAGTGCTGATTCCCCGAATCACT
1 G---GT-----G-GTTGCTAAGTGCTGATTCCCCGATTCATT
38881972 GGTGGTTGCTAAGTGCTGA
1 GGTGGTTGCTAAGTGCTGA
38881991 ATCCACTGAT
Statistics
Matches: 239, Mismatches: 25, Indels: 75
0.71 0.07 0.22
Matches are distributed among these distances:
27 38 0.16
28 7 0.03
31 5 0.02
32 4 0.02
33 78 0.33
34 13 0.05
35 1 0.00
36 2 0.01
37 8 0.03
38 6 0.03
39 5 0.02
40 3 0.01
41 4 0.02
42 44 0.18
43 21 0.09
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (33 bp):
GGTGGTTGCTAAGTGCTGATTCCCCGATTCATT
Found at i:38881838 original size:102 final size:102
Alignment explanation
Indices: 38881657--38881918 Score: 380
Period size: 102 Copynumber: 2.5 Consensus size: 102
38881647 ATTGAATATA
* * * *
38881657 AAGGTGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCGCGGTTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
38881722 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
38881759 AAGGGGGTTGCTAAGTGTTGATTCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
38881824 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
* * *
38881861 AAAGGGGTTTCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCC
1 AAGGGGGTTGCTAAGTGCTGATT-CCC---TCA-AGG-GGTTGCTAAGTGCTGATTCC
38881919 ACGGTATCAT
Statistics
Matches: 143, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
102 115 0.80
103 3 0.02
106 3 0.02
107 2 0.01
108 20 0.14
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
Found at i:38881910 original size:75 final size:76
Alignment explanation
Indices: 38881787--38881990 Score: 338
Period size: 75 Copynumber: 2.7 Consensus size: 76
38881777 TGATTCCCTC
38881787 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
38881852 -TTAAATGTGA
66 ATTAAATGTGA
* * *
38881862 AAGGGGTTTCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACGGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
*
38881927 ATTGAATGTGA
66 ATTAAATGTGA
* * *
38881938 AAGGAGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGA
38881991 ATCCACTGAT
Statistics
Matches: 120, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 62 0.52
76 58 0.48
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.32
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
ATTAAATGTGA
Found at i:38881981 original size:76 final size:75
Alignment explanation
Indices: 38881787--38881996 Score: 339
Period size: 76 Copynumber: 2.8 Consensus size: 75
38881777 TGATTCCCTC
*
38881787 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
38881852 TTAAATGTGA
66 TTAAATGTGA
* *
38881862 AAGGGGTTTCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACGGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
38881927 ATTGAATGTGA
66 -TTAAATGTGA
* * * *
38881938 AAGGAGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCAC
38881997 TGATAACGGA
Statistics
Matches: 125, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
75 62 0.50
76 63 0.50
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:38892975 original size:17 final size:17
Alignment explanation
Indices: 38892953--38892991 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38892943 TTTGTTAGTT
38892953 TTGATTAAAGGATTA-AA
1 TTGATTAAAGG-TTAGAA
*
38892970 TTGATTAAATGTTAGAA
1 TTGATTAAAGGTTAGAA
38892987 TTGAT
1 TTGAT
38892992 AGGGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TTGATTAAAGGTTAGAA
Done.