Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 105 of 193
Found at i:33783812 original size:16 final size:16
Alignment explanation
Indices: 33783788--33783833 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
33783778 ACTGTTATTA
*
33783788 TTATTAATATTATCTT
1 TTATAAATATTATCTT
33783804 TTATAAATATTATCTT
1 TTATAAATATTATCTT
33783820 TTATAAATATTATC
1 TTATAAATATTATC
33783834 ATATATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATAAATATTATCTT
Found at i:33784496 original size:15 final size:14
Alignment explanation
Indices: 33784467--33784505 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
33784457 ATTGGGTTTA
33784467 ACATTTGTATTTGG
1 ACATTTGTATTTGG
*
33784481 ACATTATGTGTTTGG
1 ACATT-TGTATTTGG
33784496 ACATTT-TATT
1 ACATTTGTATT
33784506 AAATTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 6 0.27
15 13 0.59
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (14 bp):
ACATTTGTATTTGG
Found at i:33784526 original size:17 final size:16
Alignment explanation
Indices: 33784504--33784643 Score: 147
Period size: 17 Copynumber: 8.3 Consensus size: 16
33784494 GGACATTTTA
*
33784504 TTAAATTTATAATAATT
1 TTAAATTTA-AATAAAT
33784521 TTAAATTTAAATTAAAT
1 TTAAATTTAAA-TAAAT
*
33784538 TCAAATTTAAATTAAAT
1 TTAAATTTAAA-TAAAT
33784555 TTAAATTT-AATAAAT
1 TTAAATTTAAATAAAT
* *
33784570 CTAAATTTAAAAATAATT
1 TTAAATTT--AAATAAAT
*
33784588 TTAAATTTAAAAATAATT
1 TTAAATTT--AAATAAAT
33784606 TTAAATTTAAATAAAT
1 TTAAATTTAAATAAAT
*
33784622 TTAATTTTAAAATAAAT
1 TTAAATTT-AAATAAAT
33784639 TTAAA
1 TTAAA
33784644 ATGGTTTGGT
Statistics
Matches: 109, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
15 12 0.11
16 18 0.17
17 48 0.44
18 31 0.28
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:33784531 original size:6 final size:6
Alignment explanation
Indices: 33784520--33784643 Score: 102
Period size: 6 Copynumber: 22.0 Consensus size: 6
33784510 TTATAATAAT
*
33784520 TTTAAA TTTAAA -TTAAA TTCAAA TTTAAA -TTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * ** *
33784565 --TAAA TCTAAA TTTAAA AATAAT TTTAAA TTTAAA AATAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
33784611 TTTAAA --TAAA TTTAAT TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33784644 ATGGTTTGGT
Statistics
Matches: 91, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
3 1 0.01
4 6 0.07
5 16 0.18
6 68 0.75
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:33784590 original size:67 final size:66
Alignment explanation
Indices: 33784505--33784645 Score: 184
Period size: 67 Copynumber: 2.2 Consensus size: 66
33784495 GACATTTTAT
* *
33784505 TAAATTTATAATAATTTTAAATTT-AAATTAAATTCAAATTTAAATTAAATTTAAATTTAATAAA
1 TAAATTTAAAATAATTTTAAATTTAAAAATAAATTCAAATTTAAA-TAAATTTAAATTTAATAAA
33784569 TC
65 TC
* *
33784571 TAAATTTAAAAATAATTTTAAATTTAAAAATAATTTTAAATTTAAATAAATTT-AATTT--TAAA
1 TAAATTT-AAAATAATTTTAAATTTAAAAATAAATTCAAATTTAAATAAATTTAAATTTAATAAA
*
33784633 -A
65 TC
33784634 TAAATTTAAAAT
1 TAAATTTAAAAT
33784646 GGTTTGGTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
62 5 0.07
63 7 0.10
64 4 0.06
66 12 0.18
67 23 0.34
68 17 0.25
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (66 bp):
TAAATTTAAAATAATTTTAAATTTAAAAATAAATTCAAATTTAAATAAATTTAAATTTAATAAAT
C
Found at i:33787435 original size:16 final size:16
Alignment explanation
Indices: 33787414--33787444 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33787404 GTTATTAATG
33787414 TTTAACAATTCAATAT
1 TTTAACAATTCAATAT
33787430 TTTAACAATTCAATA
1 TTTAACAATTCAATA
33787445 ACCAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAACAATTCAATAT
Found at i:33788508 original size:37 final size:37
Alignment explanation
Indices: 33788457--33788538 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
33788447 ATTCTTGGTT
* *
33788457 CACCGACACAAAGCCTACTAGGCACGAAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
*
33788494 CACCGGCACGAAGCCTACTAGGCACAAAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
33788531 CACCGGCA
1 CACCGGCA
33788539 AAATTTGTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.38, C:0.34, G:0.21, T:0.07
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
Found at i:33799188 original size:47 final size:47
Alignment explanation
Indices: 33799119--33799258 Score: 280
Period size: 47 Copynumber: 3.0 Consensus size: 47
33799109 ATATTAAGCC
33799119 TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGACT
1 TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGACT
33799166 TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGACT
1 TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGACT
33799213 TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGAC
1 TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGAC
33799259 ATTGGTAAGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (47 bp):
TACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGACT
Found at i:33799925 original size:53 final size:53
Alignment explanation
Indices: 33799842--33799942 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
33799832 AGTCGCAACA
*
33799842 TGGTACTTATGTGAGGTCGCGACGAACTCAAGTCAG-TCAGTGAGGTCGTGATG
1 TGGTACCTATGTGAGGTCGCGACGAACTCAAGTCAGAT-AGTGAGGTCGTGATG
* * * *
33799895 TGGTACCTATGTGCGGTTGCGATGAGCTCAAGTCAGATAGTGAGGTCG
1 TGGTACCTATGTGAGGTCGCGACGAACTCAAGTCAGATAGTGAGGTCG
33799943 CAATATGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 41 0.98
54 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.27
Consensus pattern (53 bp):
TGGTACCTATGTGAGGTCGCGACGAACTCAAGTCAGATAGTGAGGTCGTGATG
Found at i:33813124 original size:31 final size:31
Alignment explanation
Indices: 33813081--33813139 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
33813071 CACAAGTACG
33813081 TAACATTCTCAAGAGTGCCATTTGTTCAACA
1 TAACATTCTCAAGAGTGCCATTTGTTCAACA
* *
33813112 TAACTTTCTCAAGAGTGCCATTTTTTCA
1 TAACATTCTCAAGAGTGCCATTTGTTCA
33813140 TGGGAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (31 bp):
TAACATTCTCAAGAGTGCCATTTGTTCAACA
Found at i:33816864 original size:2 final size:2
Alignment explanation
Indices: 33816857--33816886 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33816847 GTTATGATAA
33816857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33816887 TTAAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33819217 original size:30 final size:30
Alignment explanation
Indices: 33819182--33819326 Score: 157
Period size: 30 Copynumber: 4.8 Consensus size: 30
33819172 ACATTAAAAC
*
33819182 CGGGTCAAATTTGAATTTTT-GAAAACTTCA
1 CGGGTCAAATTGGAATTTTTAGAAAA-TTCA
*** *
33819212 CGGGTCAAATCAAAATTTTTAGAAAATTGA
1 CGGGTCAAATTGGAATTTTTAGAAAATTCA
* * * *
33819242 GGGGTCGAATTGGAATTTTTGGAAAATTTA
1 CGGGTCAAATTGGAATTTTTAGAAAATTCA
* *
33819272 AGGGTCAAATTGGAATTTTTGGAAAATTCA
1 CGGGTCAAATTGGAATTTTTAGAAAATTCA
* *
33819302 GGGGTCAAATTTGAATTTTTAGAAA
1 CGGGTCAAATTGGAATTTTTAGAAA
33819327 GTTTAGGGTA
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
30 92 0.95
31 5 0.05
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (30 bp):
CGGGTCAAATTGGAATTTTTAGAAAATTCA
Found at i:33819258 original size:60 final size:60
Alignment explanation
Indices: 33819183--33819326 Score: 182
Period size: 60 Copynumber: 2.4 Consensus size: 60
33819173 CATTAAAACC
* *
33819183 GGGTCAAATTTGAATTTTT-GAAAACTTCACGGGTCAAATCAAAATTTTTAGAAAATTGAG
1 GGGTCAAATTTGAATTTTTAGAAAA-TTCAAGGGTCAAATCAAAATTTTTAGAAAATTCAG
* * * * *** *
33819243 GGGTCGAATTGGAATTTTTGGAAAATTTAAGGGTCAAATTGGAATTTTTGGAAAATTCAG
1 GGGTCAAATTTGAATTTTTAGAAAATTCAAGGGTCAAATCAAAATTTTTAGAAAATTCAG
33819303 GGGTCAAATTTGAATTTTTAGAAA
1 GGGTCAAATTTGAATTTTTAGAAA
33819327 GTTTAGGGTA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 66 0.93
61 5 0.07
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (60 bp):
GGGTCAAATTTGAATTTTTAGAAAATTCAAGGGTCAAATCAAAATTTTTAGAAAATTCAG
Found at i:33821080 original size:40 final size:40
Alignment explanation
Indices: 33821036--33821159 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
33821026 TCGGGATAAG
*
33821036 AGATCTGATGGTCTTCAATCTGCCCTCTTGTTAGGGTAAA
1 AGATCTGATGATCTTCAATCTGCCCTCTTGTTAGGGTAAA
* * *
33821076 AGATCTAATAATCTTCAATCTGCCCTCTGGTTAGGG-AAA
1 AGATCTGATGATCTTCAATCTGCCCTCTTGTTAGGGTAAA
* * *
33821115 GAGATCAGATGATCTTTAATTTGCCCTC-TGATTAGGGTAAA
1 -AGATCTGATGATCTTCAATCTGCCCTCTTG-TTAGGGTAAA
33821156 AGAT
1 AGAT
33821160 TGGATTGCTT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 4 0.06
40 64 0.90
41 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (40 bp):
AGATCTGATGATCTTCAATCTGCCCTCTTGTTAGGGTAAA
Found at i:33821357 original size:50 final size:50
Alignment explanation
Indices: 33821240--33821363 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
33821230 CAGGAGTATA
* * * *
33821240 AGATTCATCC-TTACGACTTTAATATGCCCCTCTGCAGCTTTAGGTAAATG
1 AGATTCA-CCATTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGTAAATG
*
33821290 AGATTCACCATTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATG
1 AGATTCACCATTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGTAAATG
*** *
33821340 AGATTTGTCATTCCGGCTTCAATC
1 AGATTCACCATTACGGCTTCAATC
33821364 CGTTCCTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 2 0.03
50 62 0.97
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (50 bp):
AGATTCACCATTACGGCTTCAATCTGCCCCTCTACAGCTTTAGGTAAATG
Found at i:33831913 original size:59 final size:60
Alignment explanation
Indices: 33831838--33831995 Score: 194
Period size: 59 Copynumber: 2.6 Consensus size: 60
33831828 CATTAAAATC
*
33831838 GGGTCAAATTTGAATTTTTGGAAACTTCAGGAGTCAAATCAAAATTTTTGG-AAAA-TTGG
1 GGGTCAAATTTGAATTTTTGGAAACTTCAGG-GTCAAATCAAAATTTTTGGAAAAATTTAG
* * * * **
33831897 GGGTCGAATTGGAATTTTTGGAAAATTTGAGGGTCAAATTTAAATTTTTGGAAAAATTTAG
1 GGGTCAAATTTGAATTTTTGG-AAACTTCAGGGTCAAATCAAAATTTTTGGAAAAATTTAG
* *
33831958 GGGTCAAATTTGAATTTTTGGAAAGTTTAGGGGTCAAA
1 GGGTCAAATTTGAATTTTTGGAAACTTCA-GGGTCAAA
33831996 AACAATTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 36 0.43
60 18 0.21
61 30 0.36
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (60 bp):
GGGTCAAATTTGAATTTTTGGAAACTTCAGGGTCAAATCAAAATTTTTGGAAAAATTTAG
Found at i:33831962 original size:31 final size:30
Alignment explanation
Indices: 33831838--33831995 Score: 185
Period size: 30 Copynumber: 5.3 Consensus size: 30
33831828 CATTAAAATC
* *
33831838 GGGTCAAATTTGAATTTTTGGAAACTTCAG
1 GGGTCAAATTTGAATTTTTGGAAAATTTAG
* *** *
33831868 GAGTCAAATCAAAATTTTTGGAAAA-TTGG
1 GGGTCAAATTTGAATTTTTGGAAAATTTAG
* *
33831897 GGGTCGAATTGGAATTTTTGGAAAATTT-G
1 GGGTCAAATTTGAATTTTTGGAAAATTTAG
*
33831926 AGGGTCAAATTTAAATTTTTGGAAAAATTTAG
1 -GGGTCAAATTTGAATTTTTGG-AAAATTTAG
*
33831958 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAATTTAG
33831988 GGGTCAAA
1 GGGTCAAA
33831996 AACAATTTTA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
29 23 0.21
30 56 0.52
31 27 0.25
32 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTAG
Found at i:33833511 original size:30 final size:32
Alignment explanation
Indices: 33833454--33833512 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
33833444 TGTTGCTATT
33833454 ATATTGCTAATAATTTTATTCTTATTGTTTGA
1 ATATTGCTAATAATTTTATTCTTATTGTTTGA
33833486 ATATTG-T-ATAACTTTTATT-TTATTGTT
1 ATATTGCTAATAA-TTTTATTCTTATTGTT
33833513 AATTTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 12 0.46
31 8 0.31
32 6 0.23
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.59
Consensus pattern (32 bp):
ATATTGCTAATAATTTTATTCTTATTGTTTGA
Found at i:33833614 original size:34 final size:33
Alignment explanation
Indices: 33833576--33833643 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 33
33833566 ATTATATAAC
33833576 TAAAAAGACTTT-TTTTAATGTATTTTT-AATTTAT
1 TAAAAAGA-TTTATTTTAA--TATTTTTAAATTTAT
*
33833610 TAAAAATATTTATTTTAATATTTTTAAATTTAT
1 TAAAAAGATTTATTTTAATATTTTTAAATTTAT
33833643 T
1 T
33833644 TGATGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 7 0.23
33 11 0.35
34 13 0.42
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (33 bp):
TAAAAAGATTTATTTTAATATTTTTAAATTTAT
Found at i:33834170 original size:6 final size:6
Alignment explanation
Indices: 33834156--33834189 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
33834146 TGCATTCTCA
33834156 TTCCTTT TTCCTT TTCCTT TTCCTT TTCCTT TTC
1 TTCC-TT TTCCTT TTCCTT TTCCTT TTCCTT TTC
33834190 TCCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCCTT
Found at i:33835312 original size:64 final size:66
Alignment explanation
Indices: 33835181--33835322 Score: 150
Period size: 64 Copynumber: 2.2 Consensus size: 66
33835171 AAGTAGTGTC
* ** * * *
33835181 TAAAAATTATTTTGATAAAAGAAAATAAGGTTAAATAACTATAGTATCTAAGTATAAAGTAATAT
1 TAAATATTATTTTGATAAAAGAAAATAAAATTAAATAACTACAATATCTAAGTATAAAGTAACAT
33835246 T
66 T
* * * *
33835247 TAAATATTATTTTGAT-AAA-AAAATAAAATTAGATAATTACAATATCTGAG-ATAAATTGAACA
1 TAAATATTATTTTGATAAAAGAAAATAAAATTAAATAACTACAATATCTAAGTATAAAGT-AACA
33835309 TT
65 TT
33835311 T-AAT-TTATTTTG
1 TAAATATTATTTTG
33835323 TTTTTCATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
62 8 0.12
63 9 0.14
64 30 0.46
65 3 0.05
66 15 0.23
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (66 bp):
TAAATATTATTTTGATAAAAGAAAATAAAATTAAATAACTACAATATCTAAGTATAAAGTAACAT
T
Found at i:33837760 original size:96 final size:95
Alignment explanation
Indices: 33837614--33837787 Score: 330
Period size: 96 Copynumber: 1.8 Consensus size: 95
33837604 GAGGCTGAAT
33837614 ATTAATTAATTAATACAATTGAGTGCATTCCTTTCAAAAGCCCTTAGATTTAGACTTTCTTTAAA
1 ATTAATTAATTAATACAATTGAGTGCATTCCTTTCAAAAGCCCTTAGATTTAGACTTTCTTTAAA
33837679 TTTAATTAAATTATGGAGGCTTTGAATATTA
66 TTTAATT-AATTATGGAGGCTTTGAATATTA
*
33837710 ATTAATTAATTAATACGATTGAGTGCATTCCTTTCAAAAGCCCTTAGATTTAGACTTTCTTTAAA
1 ATTAATTAATTAATACAATTGAGTGCATTCCTTTCAAAAGCCCTTAGATTTAGACTTTCTTTAAA
33837775 TTTAATTAATTAT
66 TTTAATTAATTAT
33837788 ACAAAACCCA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
95 6 0.08
96 71 0.92
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (95 bp):
ATTAATTAATTAATACAATTGAGTGCATTCCTTTCAAAAGCCCTTAGATTTAGACTTTCTTTAAA
TTTAATTAATTATGGAGGCTTTGAATATTA
Found at i:33838848 original size:3 final size:3
Alignment explanation
Indices: 33838834--33838867 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
33838824 ATTTTATTAA
*
33838834 ATT ATAT ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
33838868 TAATAACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:33842153 original size:13 final size:13
Alignment explanation
Indices: 33842137--33842197 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
33842127 ATAAATCAAG
33842137 TTTTT-AAAAGTA
1 TTTTTCAAAAGTA
*
33842149 TTTTTCAAAATTA
1 TTTTTCAAAAGTA
*
33842162 TTTTTTC-GAAGTA
1 -TTTTTCAAAAGTA
33842175 TTTTTCAAAAGTA
1 TTTTTCAAAAGTA
*
33842188 TTTCTCAAAA
1 TTTTTCAAAA
33842198 TAATGTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.27
13 24 0.59
14 6 0.15
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (13 bp):
TTTTTCAAAAGTA
Found at i:33842167 original size:26 final size:26
Alignment explanation
Indices: 33842137--33842190 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
33842127 ATAAATCAAG
*
33842137 TTTTTAAAAGTATTTTTCAAAATTAT
1 TTTTTAAAAGTATTTTTCAAAAGTAT
**
33842163 TTTTTCGAAGTATTTTTCAAAAGTAT
1 TTTTTAAAAGTATTTTTCAAAAGTAT
33842189 TT
1 TT
33842191 CTCAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTTTAAAAGTATTTTTCAAAAGTAT
Found at i:33847740 original size:109 final size:111
Alignment explanation
Indices: 33847618--33847839 Score: 421
Period size: 109 Copynumber: 2.0 Consensus size: 111
33847608 GAGGGAGAAA
33847618 CAGAAGAGAATGAAAAATAAAGAAAAAAAAGAAAGTTAAAAATCAT-AAATAAAAAGTTAATTTG
1 CAGAAGAGAATGAAAAATAAAGAAAAAAAAGAAAGTTAAAAATCATAAAATAAAAAGTTAATTTG
33847682 CTC-AAAAAAAATAGGGACCAATTATATAATTTAACCTAAAATTTT
66 CTCAAAAAAAAATAGGGACCAATTATATAATTTAACCTAAAATTTT
*
33847727 CAGAAGAGAATGAAAAATAAAGAAAAGAAAGAAAGTTAAAAATCATAAAATAAAAAGTTAATTTG
1 CAGAAGAGAATGAAAAATAAAGAAAAAAAAGAAAGTTAAAAATCATAAAATAAAAAGTTAATTTG
33847792 CTCAAAAAAAAATAGGGACCAATTATATAATTTAACCTAAAATTTT
66 CTCAAAAAAAAATAGGGACCAATTATATAATTTAACCTAAAATTTT
33847838 CA
1 CA
33847840 TTTAAAATGA
Statistics
Matches: 110, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
109 45 0.41
110 21 0.19
111 44 0.40
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (111 bp):
CAGAAGAGAATGAAAAATAAAGAAAAAAAAGAAAGTTAAAAATCATAAAATAAAAAGTTAATTTG
CTCAAAAAAAAATAGGGACCAATTATATAATTTAACCTAAAATTTT
Found at i:33848270 original size:19 final size:20
Alignment explanation
Indices: 33848246--33848284 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
33848236 GTAAATTATT
33848246 AAAAAAAT-AAATATTTTTA
1 AAAAAAATAAAATATTTTTA
33848265 AAAAAAATACAAATATTTTT
1 AAAAAAATA-AAATATTTTT
33848285 TAAGACGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAAATAAAATATTTTTA
Found at i:33848452 original size:141 final size:141
Alignment explanation
Indices: 33848296--33848577 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 141
33848286 AAGACGGCTT
33848296 GTACAATAAATAAAATACACAGTCAATGTAGCAAATATTGACCCAATTTATCTATAATATATATA
1 GTACAATAAATAAAATACACAGTCAATGTAGCAAATATTGACCCAATTTATCTATAATATATATA
33848361 AAAGTATAACAACTGGCACTGAGACTAAACTTTATCAAGCTGGAAATAGGGAACTCCTTTTTGGA
66 AAAGTATAACAACTGGCACTGAGACTAAACTTTATCAAGCTGGAAATAGGGAACTCCTTTTTGGA
33848426 ACTGCCTTTGA
131 ACTGCCTTTGA
33848437 GTACAATAAATAAAATACACAGTCAATGTAGCAAATATTGACCCAATTTATCTATAATATATATA
1 GTACAATAAATAAAATACACAGTCAATGTAGCAAATATTGACCCAATTTATCTATAATATATATA
33848502 AAAGTATAACAACTGGCACTGAGACTAAACTTTATCAAGCTGGAAATAGGGAACTCCTTTTTGGA
66 AAAGTATAACAACTGGCACTGAGACTAAACTTTATCAAGCTGGAAATAGGGAACTCCTTTTTGGA
33848567 ACTGCCTTTGA
131 ACTGCCTTTGA
33848578 TCTTAGGCTC
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (141 bp):
GTACAATAAATAAAATACACAGTCAATGTAGCAAATATTGACCCAATTTATCTATAATATATATA
AAAGTATAACAACTGGCACTGAGACTAAACTTTATCAAGCTGGAAATAGGGAACTCCTTTTTGGA
ACTGCCTTTGA
Found at i:33849360 original size:18 final size:19
Alignment explanation
Indices: 33849337--33849372 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
33849327 GTATATCCGA
33849337 TTGTTTTTAATTT-TTTTG
1 TTGTTTTTAATTTATTTTG
33849355 TTGTTTTTAATTTATTTT
1 TTGTTTTTAATTTATTTT
33849373 AAAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (19 bp):
TTGTTTTTAATTTATTTTG
Found at i:33849684 original size:187 final size:186
Alignment explanation
Indices: 33849279--33849770 Score: 696
Period size: 187 Copynumber: 2.6 Consensus size: 186
33849269 CCTTTATCAA
* * *
33849279 TTAAGAGGCGGCA-TCACTGTTCACATACTGGTAAAATACGAGTTTAGGGTATA-TCCGATTGTT
1 TTAAGAGGCGACACT-ACTATTCACATATTGGTAAAATACGAGTTTAGGGTATACT-CGATTGTT
* *
33849342 TTTAATTTTTTTG-TTGTTTTTAATTTATTTTAAAATTATTTTTGCACTAATCCTTGTAACAAAT
64 TTTAATTTTTTTGTTTTTTTTTAATTTATTTTAAAATTA-TTTTGCACTAATCCTTCTAACAAAT
33849406 TTTTTTATATTTTTAAATTATAAAATAAAAAATAATAATATTTTATTGGTGGTGCCCAG
128 TTTTTTATATTTTTAAATTATAAAATAAAAAATAATAATATTTTATTGGTGGTGCCCAG
*
33849465 TTAAGAGGCGACACTACTATTCACATATTGGTAAAATACGAGTTTAGGGTATACTCGACTGTTTT
1 TTAAGAGGCGACACTACTATTCACATATTGGTAAAATACGAGTTTAGGGTATACTCGATTGTTTT
*
33849530 TAATTTTTTTGTTTTTTTTTAATTTGTTTTAAAATTA-TTTGCACTAATCCTTCTGACACAAATT
66 TAATTTTTTTGTTTTTTTTTAATTTATTTTAAAATTATTTTGCACTAATCCTTCT-A-ACAAATT
* * * *
33849594 TTTTTATTATATTTTTAATTATAAAATAAATAATAATAATA-TTTATTTGTGGTGTCCAG
129 TTTTTA-TAT-TTTTAAATTATAAAATAAAAAATAATAATATTTTATTGGTGGTGCCCAG
* *
33849653 TTTAGAGGCGACACTAC-ATTCACATATTGGTAAAATACGAGTTTAGGATATAC-CTGATTGTTT
1 TTAAGAGGCGACACTACTATTCACATATTGGTAAAATACGAGTTTAGGGTATACTC-GATTGTTT
*
33849716 TT-ATTTTATTT-TTTTGTTTTTAACTTATTTTAAAATTATTTTTGCACTAATCCTT
65 TTAATTTT-TTTGTTTT-TTTTTAATTTATTTTAAAATTA-TTTTGCACTAATCCTT
33849771 GCCTTCATAT
Statistics
Matches: 278, Mismatches: 16, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
185 16 0.06
186 79 0.28
187 105 0.38
188 35 0.13
189 43 0.15
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (186 bp):
TTAAGAGGCGACACTACTATTCACATATTGGTAAAATACGAGTTTAGGGTATACTCGATTGTTTT
TAATTTTTTTGTTTTTTTTTAATTTATTTTAAAATTATTTTGCACTAATCCTTCTAACAAATTTT
TTTATATTTTTAAATTATAAAATAAAAAATAATAATATTTTATTGGTGGTGCCCAG
Found at i:33849743 original size:19 final size:19
Alignment explanation
Indices: 33849710--33849746 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33849700 ATATACCTGA
**
33849710 TTGTTTTTATTTTATTTTT
1 TTGTTTTTAACTTATTTTT
33849729 TTGTTTTTAACTTATTTT
1 TTGTTTTTAACTTATTTT
33849747 AAAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (19 bp):
TTGTTTTTAACTTATTTTT
Found at i:33850136 original size:3 final size:3
Alignment explanation
Indices: 33850128--33850158 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
33850118 ACACCAATAA
33850128 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
33850159 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:33854034 original size:17 final size:17
Alignment explanation
Indices: 33854008--33854084 Score: 109
Period size: 17 Copynumber: 4.5 Consensus size: 17
33853998 AATCATTTTA
*
33854008 AAATTCATTTTAAAATT
1 AAATTTATTTTAAAATT
33854025 AAATTTATTTTAAAATT
1 AAATTTATTTTAAAATT
* *
33854042 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAAATT
*
33854059 AAATTTATTTTAAATTT
1 AAATTTATTTTAAAATT
*
33854076 AGATTTATT
1 AAATTTATT
33854085 AAATTTAGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTATTTTAAAATT
Found at i:33854041 original size:12 final size:12
Alignment explanation
Indices: 33854000--33854024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33853990 GCCAGCCAAA
33854000 TCATTTTAAAAT
1 TCATTTTAAAAT
33854012 TCATTTTAAAAT
1 TCATTTTAAAAT
33854024 T
1 T
33854025 AAATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:33854076 original size:6 final size:6
Alignment explanation
Indices: 33854016--33854113 Score: 59
Period size: 6 Copynumber: 17.3 Consensus size: 6
33854006 TAAAATTCAT
* * * *
33854016 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
33854062 TTT-AT TTTAAA TTTAGA TTT--A -TTAAA TTTAGA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33854105 TTTAGAA TT
1 TTTA-AA TT
33854114 AATGTAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 15 0.22
6 44 0.64
7 5 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:33854091 original size:26 final size:26
Alignment explanation
Indices: 33854057--33854108 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
33854047 TATGTTAAAG
* *
33854057 TTAAATTTA-TTTTAAATTTAGATTTA
1 TTAAATTTAGATTT-AATTTAAATTTA
33854083 TTAAATTTAGATTTAATTTAAATTTA
1 TTAAATTTAGATTTAATTTAAATTTA
33854109 GAATTAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TTAAATTTAGATTTAATTTAAATTTA
Found at i:33854102 original size:11 final size:11
Alignment explanation
Indices: 33854023--33854108 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
33854013 CATTTTAAAA
*
33854023 TTAAATTTATT
1 TTAAATTTAAT
*
33854034 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
33854046 TTATGTTAAAG
1 TTAAATTTAAT
*
33854057 TTAAATTTATT
1 TTAAATTTAAT
33854068 TTAAATTTAGAT
1 TTAAATTTA-AT
*
33854080 TT--ATTAAAT
1 TTAAATTTAAT
*
33854089 TTAGATTTAAT
1 TTAAATTTAAT
33854100 TTAAATTTA
1 TTAAATTTA
33854109 GAATTAATGT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 37 0.65
12 12 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:33854103 original size:17 final size:17
Alignment explanation
Indices: 33854016--33854144 Score: 106
Period size: 17 Copynumber: 7.6 Consensus size: 17
33854006 TAAAATTCAT
* *
33854016 TTTAAAATTAAATTTAT
1 TTTAAATTTAAATTTAA
*
33854033 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
* *
33854049 TGTTAAAGTTAAATTTAT
1 T-TTAAATTTAAATTTAA
*
33854067 TTTAAATTTAGATTT-A
1 TTTAAATTTAAATTTAA
*
33854083 -TTAAATTTAGATTTAA
1 TTTAAATTTAAATTTAA
33854099 TTTAAATTTAGAA-TTAA
1 TTTAAATTTA-AATTTAA
* *
33854116 TGTAAATTTTAAAATT-A
1 TTTAAA-TTTAAATTTAA
33854133 TTATAAATTTAA
1 TT-TAAATTTAA
33854145 TAGAGTGTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
15 14 0.15
16 2 0.02
17 67 0.71
18 12 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:33854131 original size:18 final size:18
Alignment explanation
Indices: 33854095--33854142 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
33854085 AAATTTAGAT
* *
33854095 TTAATTTAAA-TTTAGAA
1 TTAATATAAATTTTAAAA
*
33854112 TTAATGTAAATTTTAAAA
1 TTAATATAAATTTTAAAA
*
33854130 TTATTATAAATTT
1 TTAATATAAATTT
33854143 AATAGAGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTAATATAAATTTTAAAA
Found at i:33854794 original size:9 final size:9
Alignment explanation
Indices: 33854780--33854815 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
33854770 AGAGTATTTA
33854780 AATATTAAT
1 AATATTAAT
**
33854789 AATATTGTT
1 AATATTAAT
33854798 AATATTAAT
1 AATATTAAT
33854807 AATATTAAT
1 AATATTAAT
33854816 GGCAGTAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
AATATTAAT
Found at i:33855934 original size:30 final size:30
Alignment explanation
Indices: 33855903--33856097 Score: 245
Period size: 30 Copynumber: 6.6 Consensus size: 30
33855893 AAACTGTCCA
*
33855903 AAAATTACATTTTAACCCTAAAA-TTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
33855932 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
33855962 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
33855992 AAAATTACATTTTGACCTTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
33856022 AAAATTACATTTTGACCCTAAAAGTTCT-A
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * * * *
33856051 AAAATTGCATTTTAACCCCAAAAATTTT-A
1 AAAATTACATTTTGACCCTAAAACTTTTCC
33856080 AAAATTACCATTTT-ACCC
1 AAAATTA-CATTTTGACCC
33856098 CCGAATCTTC
Statistics
Matches: 150, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
29 55 0.37
30 95 0.63
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:33855935 original size:29 final size:29
Alignment explanation
Indices: 33855903--33856127 Score: 240
Period size: 30 Copynumber: 7.7 Consensus size: 29
33855893 AAACTGTCCA
* *
33855903 AAAATTACATTTTAACCCTAAAATTTTCC
1 AAAATTACATTTTGACCCCAAAATTTTCC
33855932 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAA-TTTTCC
33855962 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAA-TTTTCC
**
33855992 AAAATTACATTTTGACCTTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAA-TTTTCC
* * *
33856022 AAAATTACATTTTGACCCTAAAA-GTTCTA
1 AAAATTACATTTTGACCCCAAAATTTTC-C
* * *
33856051 AAAATTGCATTTTAACCCCAAAAATTTT-A
1 AAAATTACATTTTGACCCC-AAAATTTTCC
** *
33856080 AAAATTACCATTTT-ACCCCCGAATCTTCC
1 AAAATTA-CATTTTGACCCCAAAATTTTCC
* *
33856109 AAAATTCCATTTTTACCCC
1 AAAATTACATTTTGACCCC
33856128 GATTTCACCA
Statistics
Matches: 172, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
28 14 0.08
29 60 0.35
30 96 0.56
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAAATTTTCC
Found at i:33855954 original size:19 final size:19
Alignment explanation
Indices: 33855930--33855984 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 19
33855920 CTAAAATTTT
33855930 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
33855949 CC-AAA--AC-TTTT----
1 CCAAAATTACATTTTGACC
33855960 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
33855979 CCAAAA
1 CCAAAA
33855985 CTTTTCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.29
16 2 0.07
18 3 0.11
19 8 0.29
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:33856147 original size:29 final size:30
Alignment explanation
Indices: 33856080--33856209 Score: 100
Period size: 29 Copynumber: 4.5 Consensus size: 30
33856070 AAAAATTTTA
33856080 AAAATTACCA-TTTTACCCCCGAATCTTCC
1 AAAATTACCATTTTTACCCCCGAATCTTCC
33856109 AAAATT-CCATTTTTA-CCCCG-AT-TTCACC
1 AAAATTACCATTTTTACCCCCGAATCTT--CC
* *
33856137 AAAATTACCA-TTTTACCACCCTAAACTTTCC
1 AAAATTACCATTTTTACC-CCCGAATC-TTCC
* *
33856168 -AAATT-CCATTTTTAACCTC-AAT-TTCAC
1 AAAATTACCATTTTTACCCCCGAATCTTC-C
33856195 AAAAATTACCATTTT
1 -AAAATTACCATTTT
33856210 GCCTCAAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 27
0.72 0.04 0.24
Matches are distributed among these distances:
26 5 0.06
27 3 0.04
28 23 0.28
29 25 0.30
30 21 0.26
31 3 0.04
33 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCCCGAATCTTCC
Found at i:33856200 original size:59 final size:57
Alignment explanation
Indices: 33856079--33856209 Score: 183
Period size: 59 Copynumber: 2.3 Consensus size: 57
33856069 CAAAAATTTT
* *
33856079 AAAAATTACCATTTTACCCCCGAATCTTCCAAAATTCCATTTTTACCCCGATTTCAC
1 AAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTACCCCAATTTCAC
* * *
33856136 CAAAATTACCATTTTACCACCCTAAACTTTCC-AAATTCCATTTTTAACCTCAATTTCAC
1 AAAAATTACCATTTTACC-CCCGAAAC-TTCCAAAATTCCATTTTT-ACCCCAATTTCAC
33856195 AAAAATTACCATTTT
1 AAAAATTACCATTTT
33856210 GCCTCAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 17 0.26
58 19 0.29
59 29 0.45
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCCGAAACTTCCAAAATTCCATTTTTACCCCAATTTCAC
Found at i:33863045 original size:12 final size:12
Alignment explanation
Indices: 33863028--33863060 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33863018 AGCCAGATGT
33863028 GAAAGAAAGGAA
1 GAAAGAAAGGAA
*
33863040 GAAAGAAATGAA
1 GAAAGAAAGGAA
33863052 GAAAGAAAG
1 GAAAGAAAG
33863061 AGAGAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (12 bp):
GAAAGAAAGGAA
Found at i:33868056 original size:46 final size:46
Alignment explanation
Indices: 33868006--33868240 Score: 108
Period size: 46 Copynumber: 5.1 Consensus size: 46
33867996 CCCTTTGAAA
33868006 TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
1 TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
* * * * * * * * * ****
33868052 TTGAAAT-TGAAGTAAAGCTGGA-TAACAA-G-CCTTCGTCCCTCTGAAA
1 TTGAAGTAAG-AGT-AAGATGAAGCACCAACGTCATT--TTCCTATCCTC
33868098 TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
1 TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
* * * * * * * * * ****
33868144 TTGAAAT-TGAAGTAAAGCTGGA-TAACAA-G-CCTTCGTCCCTCTGAAA
1 TTGAAGTAAG-AGT-AAGATGAAGCACCAACGTCATT--TTCCTATCCTC
33868190 TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
1 TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
33868236 TTGAA
1 TTGAA
33868241 ATTGAAGTAA
Statistics
Matches: 121, Mismatches: 52, Indels: 32
0.59 0.25 0.16
Matches are distributed among these distances:
44 6 0.05
45 16 0.13
46 77 0.64
47 16 0.13
48 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (46 bp):
TTGAAGTAAGAGTAAGATGAAGCACCAACGTCATTTTCCTATCCTC
Found at i:33868104 original size:92 final size:92
Alignment explanation
Indices: 33867844--33868286 Score: 814
Period size: 92 Copynumber: 4.8 Consensus size: 92
33867834 GATCAGATCA
* *
33867844 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGCCTTCGTCCCTCT
1 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
* *
33867909 GAAATTGAAGTAAGAGTAAGAAGAAGG
66 GAAATTGAAGTAAGAGTAAGATGAAGC
** *
33867936 ACCAATATCATTTTCCTATCCTCTTGAAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTT
1 ACCAACGTCATTTTCCTATCCTCTTG-AAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTC
33868001 TGAAATTGAAGTAAGAGTAAGATGAAGC
65 TGAAATTGAAGTAAGAGTAAGATGAAGC
33868029 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
1 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
33868094 GAAATTGAAGTAAGAGTAAGATGAAGC
66 GAAATTGAAGTAAGAGTAAGATGAAGC
33868121 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
1 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
33868186 GAAATTGAAGTAAGAGTAAGATGAAGC
66 GAAATTGAAGTAAGAGTAAGATGAAGC
33868213 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
1 ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
33868278 GAAATTGAA
66 GAAATTGAA
33868287 ATAAAACCTC
Statistics
Matches: 342, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 256 0.75
93 86 0.25
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (92 bp):
ACCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
GAAATTGAAGTAAGAGTAAGATGAAGC
Found at i:33868579 original size:17 final size:17
Alignment explanation
Indices: 33868553--33868649 Score: 117
Period size: 17 Copynumber: 5.8 Consensus size: 17
33868543 AATCATTTTA
*
33868553 AAATTCATTTTAAAATT
1 AAATTTATTTTAAAATT
33868570 AAATTTATTTTAAAATT
1 AAATTTATTTTAAAATT
* *
33868587 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAAATT
*
33868604 AAATTTATTTTAAATTT
1 AAATTTATTTTAAAATT
* *
33868621 AGATTTA--TTAAATTT
1 AAATTTATTTTAAAATT
*
33868636 AAATTTAATTTAAA
1 AAATTTATTTTAAA
33868650 TTTAGAATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
15 14 0.20
17 57 0.80
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAAATT
Found at i:33868586 original size:12 final size:12
Alignment explanation
Indices: 33868545--33868569 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33868535 GCCAGCCAAA
33868545 TCATTTTAAAAT
1 TCATTTTAAAAT
33868557 TCATTTTAAAAT
1 TCATTTTAAAAT
33868569 T
1 T
33868570 AAATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:33868616 original size:11 final size:11
Alignment explanation
Indices: 33868568--33868653 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
33868558 CATTTTAAAA
*
33868568 TTAAATTTATT
1 TTAAATTTAAT
*
33868579 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
33868591 TTATGTTAAAG
1 TTAAATTTAAT
*
33868602 TTAAATTTATT
1 TTAAATTTAAT
33868613 TTAAATTTAGAT
1 TTAAATTTA-AT
*
33868625 TT--ATTAAAT
1 TTAAATTTAAT
33868634 TTAAATTTAAT
1 TTAAATTTAAT
33868645 TTAAATTTA
1 TTAAATTTA
33868654 GAATTAATGT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 38 0.66
12 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:33868621 original size:6 final size:6
Alignment explanation
Indices: 33868561--33868658 Score: 68
Period size: 6 Copynumber: 17.3 Consensus size: 6
33868551 TAAAATTCAT
* * * *
33868561 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
33868607 TTT-AT TTTAAA TTTAGA TTT--A -TTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33868650 TTTAGAA TT
1 TTTA-AA TT
33868659 AATGTAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 16 0.23
6 45 0.63
7 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:33868650 original size:17 final size:17
Alignment explanation
Indices: 33868561--33868689 Score: 115
Period size: 17 Copynumber: 7.6 Consensus size: 17
33868551 TAAAATTCAT
* *
33868561 TTTAAAATTAAATTTAT
1 TTTAAATTTAAATTTAA
*
33868578 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
* *
33868594 TGTTAAAGTTAAATTTAT
1 T-TTAAATTTAAATTTAA
*
33868612 TTTAAATTTAGATTT-A
1 TTTAAATTTAAATTTAA
33868628 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
33868644 TTTAAATTTAGAA-TTAA
1 TTTAAATTTA-AATTTAA
* *
33868661 TGTAAATTTTAAAATT-A
1 TTTAAA-TTTAAATTTAA
33868678 TTATAAATTTAA
1 TT-TAAATTTAA
33868690 TAGAGTGTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.14
16 2 0.02
17 67 0.71
18 13 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:33869342 original size:9 final size:9
Alignment explanation
Indices: 33869328--33869363 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
33869318 AGAGTATTTA
33869328 AATATTAAT
1 AATATTAAT
**
33869337 AATATTGTT
1 AATATTAAT
33869346 AATATTAAT
1 AATATTAAT
33869355 AATATTAAT
1 AATATTAAT
33869364 GGCAGTAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
AATATTAAT
Found at i:33870539 original size:19 final size:19
Alignment explanation
Indices: 33870515--33870569 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 19
33870505 CAAAACTTTT
33870515 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
33870534 CC-AAA--AC-TTTT----
1 CCAAAATTACATTTTGACC
33870545 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
33870564 CCAAAA
1 CCAAAA
33870570 CTTTTCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.29
16 2 0.07
18 3 0.11
19 8 0.29
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:33870682 original size:29 final size:30
Alignment explanation
Indices: 33870455--33870683 Score: 256
Period size: 30 Copynumber: 7.7 Consensus size: 30
33870445 CTAAACTGTC
* *
33870455 CAAAAATTATATTTTGACCTCAAAAC-TTT
1 CAAAAATTACATTTTGACCCCAAAACTTTT
*
33870484 CTAAAAATTACTTTTTGACCCCAAAACTTTT
1 C-AAAAATTACATTTTGACCCCAAAACTTTT
*
33870515 CCAAAATTACATTTTGACCCCAAAACTTTT
1 CAAAAATTACATTTTGACCCCAAAACTTTT
*
33870545 CCAAAATTACATTTTGACCCCAAAACTTTT
1 CAAAAATTACATTTTGACCCCAAAACTTTT
*
33870575 CCAAAATTACATTTT-AGCCCTC-AAACTTTT
1 CAAAAATTACATTTTGA-CCC-CAAAACTTTT
* * **
33870605 CTAAAATTACATTTT-AACCTTAAA-TTTT
1 CAAAAATTACATTTTGACCCCAAAACTTTT
* *
33870633 CTAAAAATTACATTTTAACCCTAAAACTTTT
1 C-AAAAATTACATTTTGACCCCAAAACTTTT
33870664 -AAAAATTACCATTTT-ACCCC
1 CAAAAATTA-CATTTTGACCCC
33870684 CGAATCTTTC
Statistics
Matches: 179, Mismatches: 12, Indels: 18
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.03
29 32 0.18
30 133 0.74
31 9 0.05
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAAAATTACATTTTGACCCCAAAACTTTT
Found at i:33870697 original size:29 final size:28
Alignment explanation
Indices: 33870665--33870822 Score: 94
Period size: 29 Copynumber: 5.5 Consensus size: 28
33870655 AAAACTTTTA
*
33870665 AAAATTACCATTTTACCCCCGAATCTT-TC
1 AAAATTACCATTTTACCCCCG-AT-TTCCC
*
33870694 AAAATT-CCATTTTTTA-CCTCGATTTCACC
1 AAAATTACCA--TTTTACCCCCGATTTC-CC
* *
33870723 AAAACTACCATTTTACCCCCCAAACTTT-CC
1 AAAATTACCATTTTA-CCCCC-GA-TTTCCC
*
33870753 -AAATT-CCATTTTTAACCCCGATTTCCC
1 AAAATTACCA-TTTTACCCCCGATTTCCC
** ***
33870780 AAAAATTACCATTTTACCCCAAAAAACCC
1 -AAAATTACCATTTTACCCCCGATTTCCC
33870809 AAAATTACCATTTT
1 AAAATTACCATTTT
33870823 GTCCCCGAGT
Statistics
Matches: 101, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
26 3 0.03
27 5 0.05
28 31 0.31
29 42 0.42
30 16 0.16
31 1 0.01
32 3 0.03
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGATTTCCC
Found at i:33870732 original size:58 final size:58
Alignment explanation
Indices: 33870664--33870799 Score: 202
Period size: 58 Copynumber: 2.3 Consensus size: 58
33870654 TAAAACTTTT
* * * *
33870664 AAAAATTACCATTTTACCCCCGAATCTTTCAAAATTCCATTTTTTACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCCAAACTTTCAAAATTCCATTTTTAACCCCGATTTC-CC
* *
33870723 -AAAACTACCATTTTACCCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCCC
1 AAAAATTACCATTTTACCCCCCAAACTTTCAAAATTCCATTTTTAACCCCGATTTCCC
33870780 AAAAATTACCATTTTACCCC
1 AAAAATTACCATTTTACCCC
33870800 AAAAAACCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 67 0.97
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCCAAACTTTCAAAATTCCATTTTTAACCCCGATTTCCC
Found at i:33870820 original size:58 final size:57
Alignment explanation
Indices: 33870665--33870822 Score: 151
Period size: 58 Copynumber: 2.7 Consensus size: 57
33870655 AAAACTTTTA
* ** * * * *
33870665 AAAATTACCATTTTACCCCCGAATCTTTCAAAATTCCATTTTTTACCTCGATTTCACC
1 AAAACTACCATTTTACCCCAAAAAC-TCCAAAATTCCATTTTTAACCCCGATTTCACC
**
33870723 AAAACTACCATTTTACCCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTC-CC
1 AAAACTACCATTTTACCCCAAAAAC--TCCAAAATTCCATTTTTAACCCCGATTTCACC
*
33870780 AAAAATTACCATTTTACCCCAAAAAAC-CCAAAATTACCATTTT
1 -AAAACTACCATTTTACCCC-AAAAACTCCAAAATT-CCATTTT
33870823 GTCCCCGAGT
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
56 2 0.02
57 7 0.08
58 70 0.81
59 7 0.08
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (57 bp):
AAAACTACCATTTTACCCCAAAAACTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:33875637 original size:53 final size:53
Alignment explanation
Indices: 33875558--33875806 Score: 322
Period size: 53 Copynumber: 4.7 Consensus size: 53
33875548 TTGTGCCAAA
* * * *
33875558 GATTAAAAGCCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTGTCACA
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * *
33875611 GATTAAAAGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* *
33875664 GATTAAAGGTCCGATGATTATGTGTCATCGTGAGTTATATGAATCCTAAT-ACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCT-ATCACG
* * * * * *
33875717 GATTAAGGGTCCGATGACTTTGTGTCATCGTGAGATACACGAATCC-ATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* *
33875769 GATTAAAGGTCTGATGACTCTGTGTCATCGCGAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
33875807 CAAATGCGAA
Statistics
Matches: 171, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
51 2 0.01
52 34 0.20
53 133 0.78
54 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
Found at i:33877871 original size:23 final size:25
Alignment explanation
Indices: 33877845--33877891 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
33877835 TCCAATTAGG
33877845 AAATTAT-TGTTTAG-ATTTAATTC
1 AAATTATCTGTTTAGAATTTAATTC
*
33877868 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTGTTTAGAATTTAATT
33877892 TGGATCCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (25 bp):
AAATTATCTGTTTAGAATTTAATTC
Found at i:33878306 original size:15 final size:15
Alignment explanation
Indices: 33878269--33878307 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
33878259 TTATGTGTGC
*
33878269 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
33878284 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
33878298 TTAATTCTTG
1 TTAATTCTTG
33878308 TTTGATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:33885035 original size:16 final size:16
Alignment explanation
Indices: 33885010--33885042 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33885000 TTTATTTTAT
33885010 TTTTAACTTAGATTAA
1 TTTTAACTTAGATTAA
*
33885026 TTTTAGCTTAGATTAA
1 TTTTAACTTAGATTAA
33885042 T
1 T
33885043 ACTCTTCACA
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:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (16 bp):
TTTTAACTTAGATTAA
Found at i:33891996 original size:22 final size:22
Alignment explanation
Indices: 33891958--33892002 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
33891948 CACTGTTGTT
* *
33891958 GCCCTTGCCATGCGTTGTTGCC
1 GCCCTTGCCATACGTTGCTGCC
*
33891980 GCCCTTGCCATATGTTGCTGCC
1 GCCCTTGCCATACGTTGCTGCC
33892002 G
1 G
33892003 AACACCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.36, G:0.27, T:0.31
Consensus pattern (22 bp):
GCCCTTGCCATACGTTGCTGCC
Found at i:33893063 original size:3 final size:3
Alignment explanation
Indices: 33893055--33893080 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33893045 ACAGCAAGTT
33893055 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
33893081 TCTTGAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33893106 original size:3 final size:3
Alignment explanation
Indices: 33893098--33893143 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
33893088 GAAGATCTTA
33893098 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
33893144 TATTTCAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33894287 original size:31 final size:32
Alignment explanation
Indices: 33894215--33894291 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 32
33894205 CTTTATATAA
33894215 TTATTTTTATATTAAACTATATTAAAATATTTT
1 TTATTTTTATATTAAACTATATTAAAATA-TTT
* *
33894248 TTAGTTTTATATTAAACTATATTCAAATA-TT
1 TTATTTTTATATTAAACTATATTAAAATATTT
33894279 TTATTTTTATATT
1 TTATTTTTATATT
33894292 TTCTGAGTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 14 0.34
33 27 0.66
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (32 bp):
TTATTTTTATATTAAACTATATTAAAATATTT
Found at i:33895078 original size:6 final size:6
Alignment explanation
Indices: 33895058--33895088 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
33895048 ATGATGCTTT
33895058 GAAAAA GAGAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GA-AAAA GAAAAA GAAAAA GAAAAA
33895089 ATAGAGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:33897828 original size:18 final size:18
Alignment explanation
Indices: 33897787--33897830 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
33897777 CCAAACTCAT
*
33897787 TTTAAATTTGTTTTAAGA
1 TTTAAATTTGTTTTAAAA
33897805 -TTAAATTTGTTTTAAAA
1 TTTAAATTTGTTTTAAAA
33897822 TTTAAATTT
1 TTTAAATTT
33897831 AATTTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTAAATTTGTTTTAAAA
Found at i:33897844 original size:35 final size:35
Alignment explanation
Indices: 33897787--33897862 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
33897777 CCAAACTCAT
** * *
33897787 TTTAAATTTGTTTTAAGATTAAATTTGTTTTAAAA
1 TTTAAATTTAATTTAAGATTAAATTTATCTTAAAA
* * *
33897822 TTTAAATTTAATTTGAGTTTAAATTTATCTTCAAA
1 TTTAAATTTAATTTAAGATTAAATTTATCTTAAAA
33897857 TTTAAA
1 TTTAAA
33897863 ATTATTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (35 bp):
TTTAAATTTAATTTAAGATTAAATTTATCTTAAAA
Found at i:33899833 original size:30 final size:30
Alignment explanation
Indices: 33899739--33899833 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 30
33899729 TAAACTATCC
*
33899739 AAAAATTATATTTTGACCCCCAAACTT-TT
1 AAAAATTATATTTTTACCCCCAAACTTCTT
* **
33899768 CCAAAATTATATTTTTTAACCCAAAAACTTC-T
1 -AAAAATTATA-TTTTT-ACCCCCAAACTTCTT
* *
33899800 AAAAATTACATTTTTACCCCCGAACTTCTT
1 AAAAATTATATTTTTACCCCCAAACTTCTT
33899830 AAAA
1 AAAA
33899834 TCCCGATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
29 10 0.19
30 19 0.37
31 12 0.23
32 11 0.21
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAAATTATATTTTTACCCCCAAACTTCTT
Found at i:33903901 original size:18 final size:18
Alignment explanation
Indices: 33903878--33903912 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
33903868 CGCTATAGTA
33903878 GGTTTTATAATTAAATAG
1 GGTTTTATAATTAAATAG
33903896 GGTTTTATAATTAAATA
1 GGTTTTATAATTAAATA
33903913 ATATATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (18 bp):
GGTTTTATAATTAAATAG
Found at i:33907369 original size:29 final size:30
Alignment explanation
Indices: 33907327--33907406 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
33907317 GAATTGAATC
* *
33907327 AAATCAAAATTTCATGTATATAATTACACA-
1 AAATC-AAAGTTCATGTATACAATTACACAT
*
33907357 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATACAATTACACA-T
* *
33907388 AAACCATAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
33907407 GTTTTGATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.49
30 5 0.12
31 17 0.40
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATACAATTACACAT
Found at i:33917770 original size:19 final size:21
Alignment explanation
Indices: 33917746--33917789 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33917736 TTTTTCATTC
33917746 TTTTC-TA-CTTCTCCATCTG
1 TTTTCTTACCTTCTCCATCTG
*
33917765 TTTTCTTACCTTCTCCATTTG
1 TTTTCTTACCTTCTCCATCTG
33917786 TTTT
1 TTTT
33917790 AACATATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 2 0.09
21 15 0.68
ACGTcount: A:0.09, C:0.27, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTCTTACCTTCTCCATCTG
Found at i:33920018 original size:13 final size:12
Alignment explanation
Indices: 33920000--33920073 Score: 55
Period size: 13 Copynumber: 6.1 Consensus size: 12
33919990 AAGTACTCAA
33920000 AATTTAAGTATTG
1 AATTTAAGT-TTG
* *
33920013 AATTTAAATTATA
1 AATTTAAGTT-TG
33920026 AATTTAA-TTTG
1 AATTTAAGTTTG
33920037 -ATTTAAGTATTG
1 AATTTAAGT-TTG
* *
33920049 AATTTAAATTATA
1 AATTTAAGTT-TG
33920062 AATTTAA-TTTG
1 AATTTAAGTTTG
33920073 A
1 A
33920074 TATATTACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 9 0.18
13 31 0.62
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
AATTTAAGTTTG
Found at i:33920042 original size:36 final size:36
Alignment explanation
Indices: 33920001--33920074 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
33919991 AGTACTCAAA
33920001 ATTTAAGTATTGAATTTAAATTATAAATTTAATTTG
1 ATTTAAGTATTGAATTTAAATTATAAATTTAATTTG
33920037 ATTTAAGTATTGAATTTAAATTATAAATTTAATTTG
1 ATTTAAGTATTGAATTTAAATTATAAATTTAATTTG
33920073 AT
1 AT
33920075 ATATTACTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (36 bp):
ATTTAAGTATTGAATTTAAATTATAAATTTAATTTG
Found at i:33920052 original size:18 final size:19
Alignment explanation
Indices: 33919999--33920058 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
33919989 TAAGTACTCA
33919999 AAATTTAAGTATTGAATTT
1 AAATTTAAGTATTGAATTT
*
33920018 AAATTATAA--ATTTAATTT
1 AAATT-TAAGTATTGAATTT
*
33920036 -GATTTAAGTATTGAATTT
1 AAATTTAAGTATTGAATTT
33920054 AAATT
1 AAATT
33920059 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 16 0.48
19 8 0.24
20 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.48
Consensus pattern (19 bp):
AAATTTAAGTATTGAATTT
Found at i:33920070 original size:18 final size:18
Alignment explanation
Indices: 33920013--33920071 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
33920003 TTAAGTATTG
33920013 AATTTAAATTATAAATTT
1 AATTTAAATTATAAATTT
* *
33920031 AATTT-GATT-TAAGTATTG
1 AATTTAAATTATAA--ATTT
33920049 AATTTAAATTATAAATTT
1 AATTTAAATTATAAATTT
33920067 AATTT
1 AATTT
33920072 GATATATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 21 0.64
19 3 0.09
20 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
AATTTAAATTATAAATTT
Found at i:33920260 original size:20 final size:21
Alignment explanation
Indices: 33920230--33920278 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
33920220 GTAATTTTTT
*
33920230 ATAATATAATACAATATTAAA
1 ATAATATAATACAAAATTAAA
*
33920251 ATAA-ATAATATAAAATT-AA
1 ATAATATAATACAAAATTAAA
*
33920270 ATTATATAA
1 ATAATATAA
33920279 AAAATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATATAATACAAAATTAAA
Found at i:33920270 original size:15 final size:14
Alignment explanation
Indices: 33920242--33920280 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
33920232 AATATAATAC
33920242 AATATTAAAATAAAT
1 AATA-TAAAATAAAT
33920257 AATATAAAATTAAAT
1 AATATAAAA-TAAAT
*
33920272 TATATAAAA
1 AATATAAAA
33920281 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATAAAATAAAT
Found at i:33920344 original size:16 final size:17
Alignment explanation
Indices: 33920320--33920352 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33920310 TGTTTTTATT
33920320 TTGGATTCG-ATTTTGA
1 TTGGATTCGAATTTTGA
*
33920336 TTGGTTTCGAATTTTGA
1 TTGGATTCGAATTTTGA
33920353 AAAACCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.52
Consensus pattern (17 bp):
TTGGATTCGAATTTTGA
Found at i:33921993 original size:13 final size:15
Alignment explanation
Indices: 33921962--33921996 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
33921952 AGGTGAAAAA
33921962 AAATAAATATTTGAT
1 AAATAAATATTTGAT
33921977 AAATAAATA-TT-AT
1 AAATAAATATTTGAT
33921990 AAATAAA
1 AAATAAA
33921997 AAAGATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 2 0.10
15 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAATAAATATTTGAT
Found at i:33922727 original size:35 final size:35
Alignment explanation
Indices: 33922673--33922743 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
33922663 ATATCTGCTT
* * *
33922673 TTTTTTACATAATATTTAGATCTATCCATAACCCC
1 TTTTTTACACAATACTTAGATCTACCCATAACCCC
*
33922708 TTTTTTACACAATACTTAGATCTACCCATAATCCC
1 TTTTTTACACAATACTTAGATCTACCCATAACCCC
33922743 T
1 T
33922744 CTTAACCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (35 bp):
TTTTTTACACAATACTTAGATCTACCCATAACCCC
Found at i:33923757 original size:21 final size:20
Alignment explanation
Indices: 33923731--33923788 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
33923721 TACATGTTCA
33923731 TAAGGTATCAATACCTA-CT
1 TAAGGTATCAATACCTACCT
* * * *
33923750 CTAGAGGTAACTATACATGCCT
1 -TA-AGGTATCAATACCTACCT
33923772 TAAGGTATCAATACCTA
1 TAAGGTATCAATACCTA
33923789 GGTCTTCATA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
20 13 0.46
21 13 0.46
22 2 0.07
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (20 bp):
TAAGGTATCAATACCTACCT
Found at i:33923868 original size:21 final size:21
Alignment explanation
Indices: 33923827--33923871 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
33923817 TTTTTATAGA
*
33923827 AAGTATCGATACCCTCTTTGT
1 AAGTATCGATACCCTATTTGT
33923848 AAGTATCGATA-CCTATGTTGT
1 AAGTATCGATACCCTAT-TTGT
33923869 AAG
1 AAG
33923872 GTCACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (21 bp):
AAGTATCGATACCCTATTTGT
Found at i:33924572 original size:13 final size:13
Alignment explanation
Indices: 33924554--33924591 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
33924544 CCGACCCAAT
33924554 AAAAAAACAAAAA
1 AAAAAAACAAAAA
33924567 AAAAAAACAAAAA
1 AAAAAAACAAAAA
*
33924580 ATAAAAACAAAA
1 AAAAAAACAAAA
33924592 CCAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:33924585 original size:18 final size:17
Alignment explanation
Indices: 33924564--33924605 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
33924554 AAAAAAACAA
33924564 AAAAAAAAAACAAAAAAT
1 AAAAAAAAAAC-AAAAAT
* *
33924582 AAAAACAAAACCAAAAT
1 AAAAAAAAAACAAAAAT
33924599 AAAAAAA
1 AAAAAAA
33924606 TATACGTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAT
Found at i:33924604 original size:7 final size:7
Alignment explanation
Indices: 33924555--33924591 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
33924545 CGACCCAATA
33924555 AAAAAAC
1 AAAAAAC
33924562 AAAAAA-
1 AAAAAAC
33924568 AAAAAAC
1 AAAAAAC
33924575 AAAAAA-
1 AAAAAAC
*
33924581 TAAAAAC
1 AAAAAAC
33924588 AAAA
1 AAAA
33924592 CCAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
6 11 0.42
7 15 0.58
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAAAAC
Found at i:33933058 original size:32 final size:31
Alignment explanation
Indices: 33932997--33933066 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
33932987 AATACAGCCC
* *
33932997 TTTA-TTTTTATCTTATTTGTTTATTTTTAT
1 TTTATTTTTTATCTTATCTATTTATTTTTAT
33933027 TTTATTTTTTATGCTTATCTATTT-TTGTTTAT
1 TTTATTTTTTAT-CTTATCTATTTATT-TTTAT
33933059 TTTATTTT
1 TTTATTTT
33933067 ATTTGTATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 4 0.11
31 9 0.26
32 22 0.63
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (31 bp):
TTTATTTTTTATCTTATCTATTTATTTTTAT
Found at i:33934678 original size:70 final size:67
Alignment explanation
Indices: 33934595--33934727 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
33934585 TTTGAATAAG
* * * *
33934595 AAAAGACAAAACTACGTCGTTTTGATAAATGTTTACCTTTGCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGACAAAACTACGTCATTTTAATAAATGTTTACC--CG-TAAAGTTAAAAGACAAAACCATT
33934660 AAGTT
63 AAGTT
* * *
33934665 AAAAGGCAAAACTATGTCATTTTAATAAATGTTTACCCGTTAAGTTAAAAGACAAAACCATTA
1 AAAAGACAAAACTACGTCATTTTAATAAATGTTTACCCGTAAAGTTAAAAGACAAAACCATTA
33934728 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 22 0.39
68 1 0.02
70 33 0.59
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (67 bp):
AAAAGACAAAACTACGTCATTTTAATAAATGTTTACCCGTAAAGTTAAAAGACAAAACCATTAAG
TT
Found at i:33936575 original size:14 final size:14
Alignment explanation
Indices: 33936556--33936585 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
33936546 AATAATAATA
33936556 AAATCAAATGACAT
1 AAATCAAATGACAT
33936570 AAATCAAATGACAT
1 AAATCAAATGACAT
33936584 AA
1 AA
33936586 TTCTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (14 bp):
AAATCAAATGACAT
Found at i:33945524 original size:21 final size:21
Alignment explanation
Indices: 33945496--33945572 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
33945486 AATAGTGCAA
33945496 ACTTCTACCGATACAAATGAC
1 ACTTCTACCGATACAAATGAC
* *
33945517 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAATGAC
* * * ***
33945538 TCTTTTACCTATACAAATCTT
1 ACTTCTACCGATACAAATGAC
33945559 ACTTCTACCGATAC
1 ACTTCTACCGATAC
33945573 TAAAAACTCT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGATACAAATGAC
Found at i:33945752 original size:21 final size:21
Alignment explanation
Indices: 33945726--33945765 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33945716 TACCTTGTAC
* *
33945726 TTCTACCGATACATGCATGGG
1 TTCTACCGAAACAAGCATGGG
33945747 TTCTACCGAAACAAGCATG
1 TTCTACCGAAACAAGCATG
33945766 CAGAATCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TTCTACCGAAACAAGCATGGG
Found at i:33953606 original size:41 final size:41
Alignment explanation
Indices: 33953548--33953747 Score: 265
Period size: 41 Copynumber: 4.8 Consensus size: 41
33953538 TTAACCATAT
*
33953548 TCTCATTCTCATCTCGAGACATGAGTCTTCCCTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
* * * *
33953589 TCTCATTCACATTTCGAGACATGAGTCTTCCTTATTCATAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
33953630 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTT-AATCAAAA
* * **
33953672 TCTCATTCTCATTTCGAGACATGAGTCTTCCATTTATACAATT
1 TCTCATTCTCATCTCGAGACATGAGTCTTCC-TTAAT-CAAAA
* * *
33953715 TCTCATGCTCAACCCGAGACATGAGTCTTCCTT
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTT
33953748 TTTATACACC
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
41 67 0.48
42 40 0.29
43 32 0.23
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.35
Consensus pattern (41 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
Found at i:33953679 original size:83 final size:83
Alignment explanation
Indices: 33953517--33953747 Score: 306
Period size: 83 Copynumber: 2.8 Consensus size: 83
33953507 TCTTATGCTC
* * ** *
33953517 TTTCGAGTCATAAGTCTTCTTTTA-ACCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCCT
1 TTTCGAGACATGAGTCTTCCATTATA-CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTT
33953581 AATCAAAATCTCATTCACA
65 AATCAAAATCTCATTCACA
* *
33953600 TTTCGAGACATGAGTCTTCC-TTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
1 TTTCGAGACATGAGTCTTCCATTATACATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTT-
*
33953664 AATCAAAATCTCATTCTCA
65 AATCAAAATCTCATTCACA
* * *
33953683 TTTCGAGACATGAGTCTTCCATTTATACA-ATTTCTCATGCTCAACCCGAGACATGAGTCTTCCT
1 TTTCGAGACATGAGTCTTCCA-TTATACATA-TTCTCATTCTCATCTCGAGACATGAGTCTTCCT
33953747 T
64 T
33953748 TTTATACACC
Statistics
Matches: 131, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
82 39 0.30
83 55 0.42
84 1 0.01
85 36 0.27
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (83 bp):
TTTCGAGACATGAGTCTTCCATTATACATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
ATCAAAATCTCATTCACA
Found at i:33958096 original size:28 final size:25
Alignment explanation
Indices: 33958056--33958112 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 25
33958046 AATTCCACAT
* *
33958056 AAATTTGAAACCATATACATTTGAAAAA
1 AAATTTAAAACCAAATA-A-TT-AAAAA
33958084 AAATTTAAAACCAAATAATTAAAAA
1 AAATTTAAAACCAAATAATTAAAAA
33958109 AAAT
1 AAAT
33958113 AAGATACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 1 0.04
28 15 0.56
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (25 bp):
AAATTTAAAACCAAATAATTAAAAA
Found at i:33958264 original size:19 final size:20
Alignment explanation
Indices: 33958216--33958284 Score: 79
Period size: 19 Copynumber: 3.4 Consensus size: 20
33958206 GAATTTTTAT
33958216 AATTTTTAAAAATATAAATTTTG
1 AATTTTTAAAAAT-T--ATTTTG
*
33958239 TAATTTTTATAAA-TATTTTG
1 -AATTTTTAAAAATTATTTTG
33958259 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
33958278 AATTTTT
1 AATTTTT
33958285 TTTTGTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 8 0.20
19 11 0.27
20 10 0.24
22 1 0.02
24 11 0.27
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:33959422 original size:437 final size:429
Alignment explanation
Indices: 33958581--33959863 Score: 1341
Period size: 437 Copynumber: 3.0 Consensus size: 429
33958571 TAAAACTCGA
* * ** *
33958581 AATT-TTGCATTAACTAAAGAATATT-TGAATTTTTGTTTTTAAATAAAATGTGATTTACTCTAA
1 AATTATTGCATTAATTGAAGAATATTCAAAATTTTTGTTTTTAAATAAAATGTAATTTACTCTAA
* * * *
33958644 AAATATATAAATTTATGAAGTTTTATTTTACGAGGTCACATTTAAATACTAAAGTTGAACTTGTA
66 AAATATATAAATATATGAAGTTTAATTTTAC-AGGTCACAATTAAATACTAAAATTGAACTTGTA
* * *
33958709 TTTTTTTTTTAAATTAAGATAACATGCGTTTAACAAGGTATTGATTTTGAACGTTGCAAGAGTGC
130 ---TTTTTTTAAATTAAGACAACATGCGTTTAACAAGGTATCGATTTTGAGCGTTGCAAGAGTGC
* * * * *
33958774 TAAAAT-TTTATCGTGTGTAATTGACTT-TCGAACTCAAATTTTTCTTTGGATTTTAACGTAGGC
192 TAAAATCTTTAT-GCGCGTAATTGA-TTCTCGAACTCAAATTATT-TTTGGA--TTAAAGCAGGC
* * * *
33958837 CCAAAATTATATTTTTTAAAGGAGTTTTAAAATTTTA-TTTTAAACGATGATTTT-TAGATGTTC
252 CCAAAATTATATTTTTTAAAGGAATTTTAAAATTTTATTTTTAAAAGATGGTTTTGTAGGTGTTC
* * ** *
33958900 GGTCACACCCAAT-AAAAAAAGATAGATGGCAACTCTTCGTTTTTAAAT-AAATAATCTCGTATT
317 GGTCACA-CCAATAAAAAAAAGAT-GATGACAA-TCCTCACTTTTAAATAAAAT-AT-T-GTGTT
*
33958963 TTTCTTAAAATAAAA-C-CATGTTTTCAAATATCCGTCAAGCTTATTGTTTTTTTT
376 TTTCTTAAAATAAAACCTCATGTTTTCAAATAT-TGTCAAGCTTATT-TTTTTTTT
33959017 AATTATTGCATTAATTGAAGAATATTCAAAACTTTTTGTTTTTAAATAAAATGTAATTTACTCTA
1 AATTATTGCATTAATTGAAGAATATTCAAAA-TTTTTGTTTTTAAATAAAATGTAATTTACTCTA
* * * *
33959082 AAAATATATAAATATATGAAGTTTCATTTTACAGATCACACTTAAATACTAAAATTGAATTTGTA
65 AAAATATATAAATATATGAAGTTTAATTTTACAGGTCACAATTAAATACTAAAATTGAACTTGTA
* * * *
33959147 TAATTTTCTAAATTAAGACAATATGCGTTTAATAAGGTATCGATTTTGAGCGTTACAAGAGTGCT
130 T--TTTTTTAAATTAAGACAACATGCGTTTAACAAGGTATCGATTTTGAGCGTTGCAAGAGTGCT
* * *
33959212 AAAATCTTTAATGCACGTAATTGATTCTCGAATTCAAATTGTTTTTGGA-TAAAGCAGGCCCAAA
193 AAAATCTTT-ATGCGCGTAATTGATTCTCGAACTCAAATTATTTTTGGATTAAAGCAGGCCCAAA
* *
33959276 ATTTTCTTTTTTAAAGGAATTTTAAAATTTTATTTTTAAAAGATGGTTTTGTAGGTGTTCGGTCA
257 ATTATATTTTTTAAAGGAATTTTAAAATTTTATTTTTAAAAGATGGTTTTGTAGGTGTTCGGTCA
33959341 CACCAATAAAAAAAAGATCGATGACAATTCCTCACTTTTAAATAAAATATTGTGTTTTTCTTAAA
322 CACCAATAAAAAAAAGAT-GATGACAA-TCCTCACTTTTAAATAAAATATTGTGTTTTTCTTAAA
* * *
33959406 ATAAAACCTTCATGTTTTCAAATATTGTGAAGCTTATTATTATTTT
385 ATAAAACC-TCATGTTTTCAAATATTGTCAAGCTTATTTTTTTTTT
**
33959452 --TTA---CATTAATTGAAGAATATTCAAAAAATTTGTTTTTAAAT---A---AA---A-TCT--
1 AATTATTGCATTAATTGAAGAATATTCAAAATTTTTGTTTTTAAATAAAATGTAATTTACTCTAA
* * * *
33959500 -AGT-T-T--TTATATGAAGTTTAATTTTATGAGGTCACAATTAAATACTAAAATTGAACTCGTA
66 AAATATATAAATATATGAAGTTTAATTTTA-CAGGTCACAATTAAATACTAAAATTGAACTTGTA
** * *
33959560 TTTTTTTAAATTAAGACAACATGTATTTAACAAGCTACCGATTTTGAGCGTTGCAA-AGATGCTA
130 TTTTTTTAAATTAAGACAACATGCGTTTAACAAGGTATCGATTTTGAGCGTTGCAAGAG-TGCTA
* * * * * *
33959624 AAA-CTTTTATTCTGCATAATTGACTCTTGAACTCAAATATATCTTTGGATTTTAATGCAGGCCC
194 AAATC-TTTATGC-GCGTAATTGATTCTCGAACTCAAAT-TATTTTTGGA--TTAAAGCAGGCCC
*
33959688 AAAATTATATTTTTTAAAGGAATTTT-AAATTTTCATTTTTAAAAGATGGTTTTGTAGGTGTACG
254 AAAATTATATTTTTTAAAGGAATTTTAAAATTTT-ATTTTTAAAAGATGGTTTTGTAGGTGTTCG
* * * * ** ***
33959752 ATTACACCCA-AAAAAAAAGGTGATGAC--TCCT-TGTTTTAAATAAAATCCCGTGTTTTTCTTA
318 GTCACACCAATAAAAAAAAGATGATGACAATCCTCACTTTTAAATAAAATATTGTGTTTTTCTTA
33959813 AAATAAAACCTCTATGTTTTCAAATATATGTCAAGCTTATTATTATTTTTT
383 AAATAAAACCTC-ATGTTTTCAAATAT-TGTCAAGCTTATT-TT-TTTTTT
33959864 CAACTGAAAA
Statistics
Matches: 735, Mismatches: 84, Indels: 80
0.82 0.09 0.09
Matches are distributed among these distances:
408 2 0.00
409 49 0.07
410 22 0.03
411 79 0.11
412 31 0.04
413 36 0.05
414 18 0.02
415 72 0.10
416 2 0.00
419 3 0.00
420 1 0.00
423 2 0.00
426 1 0.00
429 13 0.02
430 23 0.03
433 3 0.00
434 61 0.08
435 29 0.04
436 61 0.08
437 106 0.14
438 57 0.08
439 64 0.09
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (429 bp):
AATTATTGCATTAATTGAAGAATATTCAAAATTTTTGTTTTTAAATAAAATGTAATTTACTCTAA
AAATATATAAATATATGAAGTTTAATTTTACAGGTCACAATTAAATACTAAAATTGAACTTGTAT
TTTTTTAAATTAAGACAACATGCGTTTAACAAGGTATCGATTTTGAGCGTTGCAAGAGTGCTAAA
ATCTTTATGCGCGTAATTGATTCTCGAACTCAAATTATTTTTGGATTAAAGCAGGCCCAAAATTA
TATTTTTTAAAGGAATTTTAAAATTTTATTTTTAAAAGATGGTTTTGTAGGTGTTCGGTCACACC
AATAAAAAAAAGATGATGACAATCCTCACTTTTAAATAAAATATTGTGTTTTTCTTAAAATAAAA
CCTCATGTTTTCAAATATTGTCAAGCTTATTTTTTTTTT
Found at i:33962458 original size:31 final size:31
Alignment explanation
Indices: 33962389--33962458 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
33962379 TTTAACAGTC
*
33962389 CAGTAACTTAAATAAAATCTTTCGAATAATT
1 CAGTGACTTAAATAAAATCTTTCGAATAATT
* * * **
33962420 TAGTGACTTAAATGAAATTTTTTTAATAATT
1 CAGTGACTTAAATAAAATCTTTCGAATAATT
*
33962451 CATTGACT
1 CAGTGACT
33962459 ACTTTGTAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (31 bp):
CAGTGACTTAAATAAAATCTTTCGAATAATT
Found at i:33962735 original size:73 final size:73
Alignment explanation
Indices: 33962608--33962755 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
33962598 ATTAATTAGA
* *
33962608 AATAAGTAAACAAATTATTTACAAAATCTTTCAAAGTTGACAACAAATTTTTCTCCCTTAGATTG
1 AATAAGTAAACAAATTATTTACAAAATCTGTCAAAGTTGACAACAAATTATTCTCCCTTAGATTG
33962673 CTCATGCC
66 CTCATGCC
* * *
33962681 AATAAGTAAACAAATTATTTACACAATCTGTCAAATTTGACAACAGATTATTCTCCCTTAGATTG
1 AATAAGTAAACAAATTATTTACAAAATCTGTCAAAGTTGACAACAAATTATTCTCCCTTAGATTG
33962746 CTCATGCC
66 CTCATGCC
33962754 AA
1 AA
33962756 CACTCCCCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (73 bp):
AATAAGTAAACAAATTATTTACAAAATCTGTCAAAGTTGACAACAAATTATTCTCCCTTAGATTG
CTCATGCC
Found at i:33966265 original size:43 final size:43
Alignment explanation
Indices: 33966210--33966292 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
33966200 TACCTCAGAG
* *
33966210 AAGGAAGTGTTAGCAGTGGTTTTTGCTTGCCAAAACTCTCAGT
1 AAGGAAGTGTTAGCAATGGTTTTTGCTTGCAAAAACTCTCAGT
*
33966253 AAGGAAGTGTTAGTAATGGTTTTTGCTTGCAAAAACTCTC
1 AAGGAAGTGTTAGCAATGGTTTTTGCTTGCAAAAACTCTC
33966293 GATTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (43 bp):
AAGGAAGTGTTAGCAATGGTTTTTGCTTGCAAAAACTCTCAGT
Found at i:33976221 original size:19 final size:19
Alignment explanation
Indices: 33976193--33976236 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
33976183 TTAGATTTTA
* *
33976193 AAATTTAATTGCATTTAGT
1 AAATTAAATTGCATTGAGT
**
33976212 AAATTAAATTTTATTGAGT
1 AAATTAAATTGCATTGAGT
33976231 AAATTA
1 AAATTA
33976237 CACTCATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (19 bp):
AAATTAAATTGCATTGAGT
Found at i:33977181 original size:15 final size:15
Alignment explanation
Indices: 33977145--33977175 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33977135 TAGGCTTTGT
33977145 GCCG-GTGTTATCAA
1 GCCGTGTGTTATCAA
33977159 GCCGTGTGTTATCAA
1 GCCGTGTGTTATCAA
33977174 GC
1 GC
33977176 TTTGTGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (15 bp):
GCCGTGTGTTATCAA
Found at i:33983623 original size:16 final size:16
Alignment explanation
Indices: 33983594--33983640 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
33983584 ATCTTTTTCG
33983594 AATCCCTAAAATATTAA
1 AATCCCT-AAATATTAA
*
33983611 AATCCCTAAATATCAA
1 AATCCCTAAATATTAA
*
33983627 AATCCCCAAATATT
1 AATCCCTAAATATT
33983641 TGAATCCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (16 bp):
AATCCCTAAATATTAA
Found at i:33984546 original size:33 final size:33
Alignment explanation
Indices: 33984508--33984634 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
33984498 TGTTGATTGT
* ***
33984508 TAGGGAGGGTGATAATGAAGTTATAGAAGTTGA
1 TAGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
33984541 TAGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
1 TAGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
*
33984574 TGGGGAGGGTGATG-TAGAAGGGGTAGAAGTTGA
1 TAGGGAGGGTGATGAT-GAAGGGGTAGAAGTTGA
33984607 T-GGAGAGGGTGATGATGAAGGGGTAGAA
1 TAGG-GAGGGTGATGATGAAGGGGTAGAA
33984635 TCTGATGTTG
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
32 3 0.03
33 82 0.95
34 1 0.01
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.22
Consensus pattern (33 bp):
TAGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
Found at i:33984601 original size:66 final size:65
Alignment explanation
Indices: 33984531--33984727 Score: 211
Period size: 66 Copynumber: 3.0 Consensus size: 65
33984521 AATGAAGTTA
*
33984531 TAGAAGTTGATAGGGAGGGTGATGATGAAGGGGTAGAAGTTGATGGGGAGGGTGATGTAGAAGGG
1 TAGAAGTTGAT-GGGAGGGTGATGATGAAGGGGTAGAAGTTGATGTGGAGGGTGATGTAGAAGGG
33984596 G
65 G
* ** * *
33984597 TAGAAGTTGATGGAGAGGGTGATGATGAAGGGGTAGAA-TCTGATGTTGAATGTGATCT-GAAAA
1 TAGAAGTTGATGG-GAGGGTGATGATGAAGGGGTAGAAGT-TGATGTGGAGGGTGATGTAG-AAG
33984660 GGG
63 GGG
* * * * * *
33984663 TAAAAGCTGTTGAGGAAGGTGATG-TAGGAGGGGTAGAAGCTGATGTGGAGGGTGATGTAGAAGG
1 TAGAAGTTGATG-GGAGGGTGATGAT-GAAGGGGTAGAAGTTGATGTGGAGGGTGATGTAGAAGG
33984727 G
64 G
33984728 TCTACTGTTG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
65 5 0.05
66 100 0.93
67 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.45, T:0.23
Consensus pattern (65 bp):
TAGAAGTTGATGGGAGGGTGATGATGAAGGGGTAGAAGTTGATGTGGAGGGTGATGTAGAAGGGG
Found at i:33984697 original size:33 final size:33
Alignment explanation
Indices: 33984548--33984727 Score: 125
Period size: 33 Copynumber: 5.5 Consensus size: 33
33984538 TGATAGGGAG
* * * *
33984548 GGTGATG-ATGAAGGGGTAGAAGTTGATGGGGAG
1 GGTGATGTA-GAAGGGGTAAAAGCTGATGAGGAA
* * *
33984581 GGTGATGTAGAAGGGGTAGAAGTTGATG-GAGAG
1 GGTGATGTAGAAGGGGTAAAAGCTGATGAG-GAA
* * **
33984614 GGTGATG-ATGAAGGGGTAGAATCTGATGTTGAA
1 GGTGATGTA-GAAGGGGTAAAAGCTGATGAGGAA
* * * *
33984647 TGTGATCT-GAAAAGGGTAAAAGCTGTTGAGGAA
1 GGTGATGTAG-AAGGGGTAAAAGCTGATGAGGAA
* * * *
33984680 GGTGATGTAGGAGGGGTAGAAGCTGATGTGGAG
1 GGTGATGTAGAAGGGGTAAAAGCTGATGAGGAA
33984713 GGTGATGTAGAAGGG
1 GGTGATGTAGAAGGG
33984728 TCTACTGTTG
Statistics
Matches: 119, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
32 3 0.03
33 114 0.96
34 2 0.02
ACGTcount: A:0.29, C:0.02, G:0.46, T:0.23
Consensus pattern (33 bp):
GGTGATGTAGAAGGGGTAAAAGCTGATGAGGAA
Found at i:33984839 original size:51 final size:51
Alignment explanation
Indices: 33984763--33984874 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
33984753 GTAAAGTTGC
* * * *
33984763 TACTGATGAATATGCTGCTGATTTTGCAACATTAGATGGAGAGGATAATTT
1 TACTGATGAATATGATGCTAATTTTGCAACATCAGATGGAGAGGATAATGT
*
33984814 TACTGATGAATATGATGCTAATTTTGCAACATCAGATGGAGTGGATAATGT
1 TACTGATGAATATGATGCTAATTTTGCAACATCAGATGGAGAGGATAATGT
*
33984865 TGCTGATGAA
1 TACTGATGAA
33984875 GTTACTGATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (51 bp):
TACTGATGAATATGATGCTAATTTTGCAACATCAGATGGAGAGGATAATGT
Found at i:33991613 original size:17 final size:17
Alignment explanation
Indices: 33991593--33991627 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33991583 TTCCACTTTA
33991593 CTTTATTCA-TTTATTTT
1 CTTTATT-ATTTTATTTT
33991610 CTTTATTATTTTATTTT
1 CTTTATTATTTTATTTT
33991627 C
1 C
33991628 ATAAAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
CTTTATTATTTTATTTT
Found at i:34004822 original size:38 final size:38
Alignment explanation
Indices: 34004720--34004833 Score: 165
Period size: 38 Copynumber: 3.0 Consensus size: 38
34004710 CTTTCTCAAC
* *
34004720 ATTCACCATTTCTGGTTCTGGTGAAACCGGTTCTGGTT
1 ATTCACCACTTCTGGTTCTGGTGAAATCGGTTCTGGTT
* *
34004758 ATTCACCACTTCTAGTTCTAGTGAAATCGGTTCTGGTT
1 ATTCACCACTTCTGGTTCTGGTGAAATCGGTTCTGGTT
* * *
34004796 ATTCACCACTTCTGGTTTTGGTGAAATTGATTCTGGTT
1 ATTCACCACTTCTGGTTCTGGTGAAATCGGTTCTGGTT
34004834 CAAGCAAAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (38 bp):
ATTCACCACTTCTGGTTCTGGTGAAATCGGTTCTGGTT
Found at i:34013924 original size:19 final size:19
Alignment explanation
Indices: 34013868--34013928 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
34013858 AATTTCAAAT
34013868 TATATATTTTAT-TATAT-
1 TATATATTTTATATATATA
*
34013885 TTTATATTTTTAGTATATATA
1 TATATA-TTTTA-TATATATA
*
34013906 TATATATTTTATATGTATA
1 TATATATTTTATATATATA
34013925 TATA
1 TATA
34013929 ATTGATTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.14
18 5 0.14
19 12 0.32
20 10 0.27
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TATATATTTTATATATATA
Found at i:34014705 original size:16 final size:15
Alignment explanation
Indices: 34014686--34014719 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
34014676 AAAATTTTTT
34014686 AAAAAGAAAAGAAAAA
1 AAAAAGAAAA-AAAAA
*
34014702 AAAAATAAAAAAAAA
1 AAAAAGAAAAAAAAA
34014717 AAA
1 AAA
34014720 GATTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:34018024 original size:25 final size:24
Alignment explanation
Indices: 34017969--34018024 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
34017959 GCTTGTCTAC
*
34017969 TTGTT-TGATTTTTTTGTTACATT
1 TTGTTGTGATTTTTTTGTTAAATT
**
34017992 AGGATTGTGATTTTTTTGATTAAATT
1 TTG-TTGTGATTTTTTTG-TTAAATT
34018018 TTGTTGT
1 TTGTTGT
34018025 TACTTAACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 1 0.04
24 2 0.08
25 15 0.60
26 7 0.28
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.62
Consensus pattern (24 bp):
TTGTTGTGATTTTTTTGTTAAATT
Found at i:34035034 original size:3 final size:3
Alignment explanation
Indices: 34035016--34035060 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
34035006 ATTTTCGTTA
*
34035016 TAT T-T TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
34035061 TAGGCTATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:34042974 original size:20 final size:20
Alignment explanation
Indices: 34042937--34042974 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34042927 CACTATAACC
*
34042937 AATTAATTATTTTGAATTTT
1 AATTAATTATTATGAATTTT
34042957 AATTAATTAATTAT-AATT
1 AATTAATT-ATTATGAATT
34042975 AAAAAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTAATTATTATGAATTTT
Found at i:34046635 original size:31 final size:32
Alignment explanation
Indices: 34046600--34046664 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
34046590 TATTTTATTG
* *
34046600 TTAATTTTATTATTATTTTAGAGGCATTT-TT
1 TTAATTTTATTACTATTTTAAAGGCATTTGTT
* *
34046631 TTAATTTTGTTACTATTTTAAATGCATTTGTT
1 TTAATTTTATTACTATTTTAAAGGCATTTGTT
34046663 TT
1 TT
34046665 TTAAGTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.62
Consensus pattern (32 bp):
TTAATTTTATTACTATTTTAAAGGCATTTGTT
Found at i:34047058 original size:17 final size:17
Alignment explanation
Indices: 34047036--34047069 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34047026 AAGAGGATCA
34047036 ACAAAAAGTCAAATTTT
1 ACAAAAAGTCAAATTTT
34047053 ACAAAAAGTCAAATTTT
1 ACAAAAAGTCAAATTTT
34047070 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
ACAAAAAGTCAAATTTT
Found at i:34049247 original size:23 final size:24
Alignment explanation
Indices: 34049216--34049265 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
34049206 TTTTTATATT
* *
34049216 TTAATACTTTTTAATTTAAAAAAA
1 TTAATACTTTTAAAATTAAAAAAA
34049240 TTAA-ACTTTTAAAATTAAAAAAA
1 TTAATACTTTTAAAATTAAAAAAA
34049263 TTA
1 TTA
34049266 GTAATTACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAATACTTTTAAAATTAAAAAAA
Found at i:34051326 original size:19 final size:19
Alignment explanation
Indices: 34051299--34051335 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34051289 TTATAGTCTA
*
34051299 ATTTGCATGCTAAAATCAG
1 ATTTACATGCTAAAATCAG
*
34051318 ATTTACATGCTAGAATCA
1 ATTTACATGCTAAAATCA
34051336 AATTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
ATTTACATGCTAAAATCAG
Found at i:34064425 original size:76 final size:76
Alignment explanation
Indices: 34064334--34064525 Score: 226
Period size: 78 Copynumber: 2.5 Consensus size: 76
34064324 CTTTTGCACT
* * * *
34064334 CAACGCTAGTTGGATAACCGACGAATATATAGGGTGTGCCCA-ATACTAGAGAGATAAATTGACA
1 CAACACTAGTCGGATAACCGACGAATATATAGCGTGTGCCCAGA-ACTAGACAGATAAATTGACA
*
34064398 AGGATTTGCA-C
65 AGGATTTACAGC
* * * *
34064409 CTAGCACTAGTCGGATAACCAACGAATATATATAACGTGTGCCCAGAACTAGCCAGATAAATTGA
1 C-AACACTAGTCGGATAACCGACG-A-ATATATAGCGTGTGCCCAGAACTAGACAGATAAATTGA
*
34064474 CAATGATTTACAGC
63 CAAGGATTTACAGC
* *
34064488 CAACACTAGTCGGATAATCGACGAATATATAGTGTGTG
1 CAACACTAGTCGGATAACCGACGAATATATAGCGTGTG
34064526 TAACAGTCTG
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
75 1 0.01
76 30 0.31
77 2 0.02
78 61 0.63
79 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (76 bp):
CAACACTAGTCGGATAACCGACGAATATATAGCGTGTGCCCAGAACTAGACAGATAAATTGACAA
GGATTTACAGC
Done.