Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 78 of 109
Found at i:25031318 original size:7 final size:7
Alignment explanation
Indices: 25031306--25031344 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
25031296 CGTCTCTCCC
25031306 TCTTTTT
1 TCTTTTT
25031313 TCTTTTT
1 TCTTTTT
25031320 TCTTTTTT
1 TC-TTTTT
*
25031328 TTTTTTT
1 TCTTTTT
25031335 TGCTTTTT
1 T-CTTTTT
25031343 TC
1 TC
25031345 CCCTATTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 16 0.57
8 12 0.43
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (7 bp):
TCTTTTT
Found at i:25031329 original size:16 final size:16
Alignment explanation
Indices: 25031308--25031343 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
25031298 TCTCTCCCTC
*
25031308 TTTTTTCTTTTTT-CT
1 TTTTTTTTTTTTTGCT
25031323 TTTTTTTTTTTTTGCT
1 TTTTTTTTTTTTTGCT
25031339 TTTTT
1 TTTTT
25031344 CCCCTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTTTTTGCT
Found at i:25031684 original size:16 final size:17
Alignment explanation
Indices: 25031642--25031678 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25031632 TCCTTACTTA
*
25031642 TTTTCC-TTTTTTTTGT
1 TTTTCCATTTTTTTTCT
25031658 TTTTCCATTTTTTTTCT
1 TTTTCCATTTTTTTTCT
25031675 TTTT
1 TTTT
25031679 GATTTTCGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTCCATTTTTTTTCT
Found at i:25053106 original size:23 final size:23
Alignment explanation
Indices: 25053045--25053126 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 23
25053035 ATGGAATAGG
* * **
25053045 ACGAGACAACGCCGAAGCGTATA
1 ACGAGACAACACCAAAGCGCGTA
* * *
25053068 ACAAGACAATACCAAAGTGCGTA
1 ACGAGACAACACCAAAGCGCGTA
* *
25053091 ACGAGACAACATCAAAGCGTGTA
1 ACGAGACAACACCAAAGCGCGTA
*
25053114 ACGGGACAACACC
1 ACGAGACAACACC
25053127 GAAGTACGTA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.43, C:0.26, G:0.22, T:0.10
Consensus pattern (23 bp):
ACGAGACAACACCAAAGCGCGTA
Found at i:25053122 original size:46 final size:46
Alignment explanation
Indices: 25053045--25053137 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 46
25053035 ATGGAATAGG
* * * *
25053045 ACGAGACAACGCCGAAGCGTATAACAAGACAATACCAAAGTGCGTA
1 ACGAGACAACACCAAAGCGTATAACAAGACAACACCAAAGTACGTA
* * ** *
25053091 ACGAGACAACATCAAAGCGTGTAACGGGACAACACCGAAGTACGTA
1 ACGAGACAACACCAAAGCGTATAACAAGACAACACCAAAGTACGTA
25053137 A
1 A
25053138 ACAAAGAGCA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.43, C:0.24, G:0.23, T:0.11
Consensus pattern (46 bp):
ACGAGACAACACCAAAGCGTATAACAAGACAACACCAAAGTACGTA
Found at i:25053811 original size:3 final size:3
Alignment explanation
Indices: 25053803--25053829 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25053793 GAATCAAGCT
25053803 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
25053830 ATTTGGCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:25068841 original size:131 final size:131
Alignment explanation
Indices: 25068604--25069132 Score: 630
Period size: 131 Copynumber: 4.0 Consensus size: 131
25068594 TAGTGATTAG
* * * * *
25068604 TAAATCAGCTAACACAAATGAGATTGTTCATGATATTAAATCGAATTAACTTAGATTGTGATATT
1 TAAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATT
* * * * * * * * *
25068669 AAATCAACAAACCTTAACGATATTAGCTGTGATTTTTAATCAGCGAGTTGTTTTGAGATGCGATC
66 AAATCAACGAACCTTAACGATATCAACTGCGATATTAAATCAACGAGTTGTTTGGAGTTGCGATC
25068734 T
131 T
* * * * *
25068735 TGAATCAGCTAATTCAAATAGGATTGTTCATGAAATTAAATCGAATGAACTTACGTTGCGATATT
1 TAAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATT
* * * * *
25068800 AAATCAATGAACCTTAATGATATCAACTGCGATATTAAATCAGCTAGTTGTTTGGAGTTGCGATA
66 AAATCAACGAACCTTAACGATATCAACTGCGATATTAAATCAACGAGTTGTTTGGAGTTGCGATC
25068865 T
131 T
* * * * *
25068866 TAAATCAGGTAACTCAAACAAGATTGTTCATGGTATTAAATCAAATGAACTTAGGTTGTGATATT
1 TAAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATT
* * * * * *
25068931 AAATCAACGAACCTCAATGATATCAACTACGATATTAAATCAATGAGCTATTTGGAGTTGCGATC
66 AAATCAACGAACCTTAACGATATCAACTGCGATATTAAATCAACGAGTTGTTTGGAGTTGCGATC
25068996 T
131 T
** * *
25068997 TAAATCATTTAAGTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACGATATT
1 TAAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATT
* * * * *
25069062 AAATCAGA-GAACCTTAACAATATC-AGTCGTGATATTAAATCAACGAGTTGTTTGGACTTGTGA
66 AAATCA-ACGAACCTTAACGATATCAACT-GCGATATTAAATCAACGAGTTGTTTGGAGTTGCGA
25069125 TCT
129 TCT
25069128 TAAAT
1 TAAAT
25069133 TAGCAAACCT
Statistics
Matches: 336, Mismatches: 60, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
130 2 0.01
131 333 0.99
132 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (131 bp):
TAAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATT
AAATCAACGAACCTTAACGATATCAACTGCGATATTAAATCAACGAGTTGTTTGGAGTTGCGATC
T
Found at i:25069143 original size:67 final size:67
Alignment explanation
Indices: 25069056--25069203 Score: 165
Period size: 67 Copynumber: 2.2 Consensus size: 67
25069046 CTTAGGTTAC
* * **
25069056 GATATTAAATCAG-AGAACCTTAACA-ATATCAGTCGTGATATTAAATCAACGAGTTGTTTGGAC
1 GATATTAAATTAGCA-AACCTTAA-ATATATCAGTCGCGATATTAAATCAACGAACTGTTTGGAC
25069119 TTGT
64 TTGT
* * * * ** *
25069123 GATCTTAAATTAGCAAACCTTAAATATATTAGTTGCGATCTTAAATCAGTGAACTGTTTGGAGTT
1 GATATTAAATTAGCAAACCTTAAATATATCAGTCGCGATATTAAATCAACGAACTGTTTGGACTT
25069188 GT
66 GT
25069190 GATATTAAATTAGC
1 GATATTAAATTAGC
25069204 TGACTCAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 1 0.01
67 65 0.97
68 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (67 bp):
GATATTAAATTAGCAAACCTTAAATATATCAGTCGCGATATTAAATCAACGAACTGTTTGGACTT
GT
Found at i:25080133 original size:20 final size:20
Alignment explanation
Indices: 25080108--25080154 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
25080098 AATAAGAAGG
25080108 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
25080128 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
25080148 ATATAAA
1 ATATAAA
25080155 GACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:25083568 original size:2 final size:2
Alignment explanation
Indices: 25083561--25083586 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25083551 ATTGACAATG
25083561 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
25083587 TAGTTTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25088308 original size:20 final size:21
Alignment explanation
Indices: 25088273--25088318 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
25088263 TTGCTCTTAT
*
25088273 TAAAAGTTAGAAAAAAAATTA
1 TAAAAGATAGAAAAAAAATTA
*
25088294 TAAAAGATA-AAAAAATATTA
1 TAAAAGATAGAAAAAAAATTA
25088314 TAAAA
1 TAAAA
25088319 ATGATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
TAAAAGATAGAAAAAAAATTA
Found at i:25088654 original size:28 final size:26
Alignment explanation
Indices: 25088613--25088752 Score: 95
Period size: 28 Copynumber: 5.1 Consensus size: 26
25088603 TTTATAAAAG
* *
25088613 TTTATATTTCTATATATTTTAAAATTT
1 TTTATATTTTTATAAATTTT-AAATTT
*
25088640 TTTATGATTTTTATAAAATTTTATATTT
1 TTTAT-ATTTTTAT-AAATTTTAAATTT
* *
25088668 TTTCATATTTTTAATAAATTTTTAATAT
1 TTT-ATATTTTT-ATAAATTTTAAATTT
* *
25088696 TTGA-ATTTTTATTAAAATTTTATAA-TA
1 TTTATATTTTTA-T-AAATTTTA-AATTT
* * *
25088723 TTTATAGCTTTTATTAATTTTAATTTT
1 TTTATA-TTTTTATAAATTTTAAATTT
25088750 TTT
1 TTT
25088753 TATAAAAGTA
Statistics
Matches: 88, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
25 1 0.01
26 8 0.09
27 27 0.31
28 37 0.42
29 15 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATATTTTTATAAATTTTAAATTT
Found at i:25088676 original size:46 final size:52
Alignment explanation
Indices: 25088601--25088719 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 52
25088591 CTTTATAAAT
*
25088601 TTTTTATAAAAGTTTATATTTCTATATA-TTTT-A-AAATTTTT-TA-TG-A
1 TTTTTATAAAATTTTATATTTCTATATATTTTTAATAAATTTTTATATTGAA
*
25088647 TTTTTATAAAATTTTATATTT-TTTCATATTTTTAATAAATTTTTAATATTTGAA
1 TTTTTATAAAATTTTATATTTCTAT-ATATTTTTAATAAATTTTT-ATA-TTGAA
25088701 TTTTTATTAAAATTTTATA
1 TTTTTA-TAAAATTTTATA
25088720 ATATTTATAG
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
45 2 0.03
46 23 0.38
47 4 0.07
48 1 0.02
49 8 0.13
51 2 0.03
53 2 0.03
54 7 0.11
55 12 0.20
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (52 bp):
TTTTTATAAAATTTTATATTTCTATATATTTTTAATAAATTTTTATATTGAA
Found at i:25088735 original size:29 final size:29
Alignment explanation
Indices: 25088628--25088739 Score: 99
Period size: 29 Copynumber: 4.0 Consensus size: 29
25088618 ATTTCTATAT
* * *
25088628 ATTTTAAAATTTTTTATGATTTTTA-TAAA
1 ATTTTATAATATTTCAT-ATTTTTATTAAA
* * *
25088657 ATTTTATATTTTTTCATATTTTTAAT-AA
1 ATTTTATAATATTTCATATTTTTATTAAA
*
25088685 ATTTT-TAATATTTGA-ATTTTTATTAAA
1 ATTTTATAATATTTCATATTTTTATTAAA
*
25088712 ATTTTATAATATTT-ATAGCTTTTATTAA
1 ATTTTATAATATTTCATA-TTTTTATTAA
25088740 TTTTAATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.11
27 15 0.21
28 23 0.33
29 24 0.34
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTTTATAATATTTCATATTTTTATTAAA
Found at i:25091637 original size:3 final size:3
Alignment explanation
Indices: 25091625--25091712 Score: 115
Period size: 3 Copynumber: 29.3 Consensus size: 3
25091615 CATTATTTAT
* *
25091625 TTA TTA -TA TTA TTG TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
25091672 TTA TTA TTA TTA TTA TCA TTC TTG TTA TTA TTTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T
25091713 CATTTCTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:25092342 original size:16 final size:16
Alignment explanation
Indices: 25092299--25092342 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
25092289 TTTTTCCTTA
25092299 TTTA-TTTA-TTTATT
1 TTTATTTTATTTTATT
*
25092313 TGTTATCTTATTTTATT
1 T-TTATTTTATTTTATT
25092330 TTTATTTTATTTT
1 TTTATTTTATTTT
25092343 TCCTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 14 0.56
17 7 0.28
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:25097082 original size:5 final size:5
Alignment explanation
Indices: 25097072--25097096 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25097062 TTCATGCATC
25097072 TACAT TACAT TACAT TACAT TACAT
1 TACAT TACAT TACAT TACAT TACAT
25097097 GCATTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TACAT
Found at i:25105522 original size:127 final size:127
Alignment explanation
Indices: 25105368--25105640 Score: 431
Period size: 127 Copynumber: 2.1 Consensus size: 127
25105358 AGAACTACAT
**
25105368 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTGATCTCCCTAAGCAGTAGTGG
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTGATCTCCCTAAGCAGTAGTGG
* *
25105433 AGCAGACAA-AGGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCACGG
66 AGCAGACAAGA-GAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAG
* * *
25105495 GTCTTATCTCCGTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTTATCTCCCTAGGCAGTAGTGG
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTGATCTCCCTAAGCAGTAGTGG
* ** *
25105560 AGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAT
66 AGCAGACAAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAG
25105622 GTCTTATCTCCCTAAGCAG
1 GTCTTATCTCCCTAAGCAG
25105641 AAGCAGTAGT
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
127 132 0.99
128 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (127 bp):
GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTGATCTCCCTAAGCAGTAGTGG
AGCAGACAAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAG
Found at i:25105526 original size:43 final size:40
Alignment explanation
Indices: 25105368--25105913 Score: 244
Period size: 40 Copynumber: 12.8 Consensus size: 40
25105358 AGAACTACAT
****
25105368 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAA
*
25105408 GTCTGATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAGGAAACCAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC--A--AAA-CAA
* ** * *
25105452 -TCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCACGG
1 GTCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAA-CA--A
* **
25105495 GTCTTATCTCCGTAAGCAGTAGTGGAGCAGATCGCAACAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAA
*
25105535 GTCTTATCTCCCTAGGCAGTAGTGGAGCAGA-CGAGAGAAACCAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-AAA-CAA
* ** * ** *
25105579 -TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACA
1 GTCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAA-CA-A
25105621 TGTCTTATCTCCCTAAGCAGAAGCAGTAGTGGAGCAGA-CGAGAGAAACCAA
1 -GTCTTATCTCCCT------AAGCAGTAGTGGAGCAGATC---A-AAA-CAA
* * ** * ** *
25105672 -TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCACA
1 GTCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAA-CA-A
* *** *
25105714 TGTCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGCATCAA
1 -GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAA
*
25105755 GTCTTATCTCCCTAAGAAGTAGTGGAGCAGA-CAAAGGAAACTAA
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC--A--AAAC-AA
* ** * * * *
25105799 -TCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACTACA
1 GTCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAAC-A-A
* ** *
25105841 GATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAA
1 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAA
25105882 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
25105914 GGAAAAAAAT
Statistics
Matches: 383, Mismatches: 80, Indels: 86
0.70 0.15 0.16
Matches are distributed among these distances:
39 2 0.01
40 118 0.31
41 27 0.07
42 10 0.03
43 89 0.23
44 105 0.27
49 24 0.06
51 2 0.01
52 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (40 bp):
GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAACAA
Found at i:25105601 original size:87 final size:86
Alignment explanation
Indices: 25105535--25105741 Score: 324
Period size: 93 Copynumber: 2.3 Consensus size: 86
25105525 ATCGCAACAA
25105535 GTCTTATCTCCCTAGGCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCA
1 GTCTTATCTCCCTAGGCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCA
25105600 GTGGAGTGGATTAAAACCACAT
66 GT-GAGTGGATTAAAACCACAT
*
25105622 GTCTTATCTCCCTAAGCAGAAGCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTTCCTGAA
1 GTCTTATCTCCCT----AG--GCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAA
25105687 GTTGCAGTGGAGTGGATTAAAACCACAT
60 GTTGCAGT-GAGTGGATTAAAACCACAT
*
25105715 GTCTTATCTCCCTAAGCAGTAGTGGAG
1 GTCTTATCTCCCTAGGCAGTAGTGGAG
25105742 TAGATTGCAT
Statistics
Matches: 112, Mismatches: 2, Indels: 12
0.89 0.02 0.10
Matches are distributed among these distances:
87 25 0.22
89 1 0.01
91 2 0.02
93 84 0.75
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (86 bp):
GTCTTATCTCCCTAGGCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCA
GTGAGTGGATTAAAACCACAT
Found at i:25105630 original size:44 final size:44
Alignment explanation
Indices: 25105582--25105727 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
25105572 AAACCAATCC
25105582 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACATGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACATGTCT
** * * * *
25105626 TATCTCCCTAAGCAGAAGCAGTAGTGGAGCAGACGA-GAGAAACCA-A--TCC
1 TATCTCCCT-----GAAGTTGCAGTGGAG-TG--GATTA-AAACCACATGTCT
*
25105675 TATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCACATGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACATGTCT
25105719 TATCTCCCT
1 TATCTCCCT
25105728 AAGCAGTAGT
Statistics
Matches: 75, Mismatches: 14, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
41 8 0.11
42 2 0.03
43 1 0.01
44 31 0.41
49 22 0.29
50 1 0.01
51 2 0.03
52 8 0.11
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACATGTCT
Found at i:25105661 original size:93 final size:93
Alignment explanation
Indices: 25105550--25105733 Score: 359
Period size: 93 Copynumber: 2.0 Consensus size: 93
25105540 ATCTCCCTAG
25105550 GCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 GCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
25105615 ACCACATGTCTTATCTCCCTAAGCAGAA
66 ACCACATGTCTTATCTCCCTAAGCAGAA
*
25105643 GCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAA
1 GCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
25105708 ACCACATGTCTTATCTCCCTAAGCAG
66 ACCACATGTCTTATCTCCCTAAGCAG
25105734 TAGTGGAGTA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (93 bp):
GCAGTAGTGGAGCAGACGAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
ACCACATGTCTTATCTCCCTAAGCAGAA
Found at i:25105677 original size:220 final size:220
Alignment explanation
Indices: 25105421--25105860 Score: 670
Period size: 220 Copynumber: 2.0 Consensus size: 220
25105411 TGATCTCCCT
*
25105421 AAGCAGTAGTGGAGCAGACAAAGGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTA
1 AAGCAGTAGTGGAGCAGACAAAGGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* * *
25105486 AAACCACGGGTCTTATCTCCGTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTTATCTCCCTAGG
66 AAACCACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTTATCTCCCTAAG
* * **
25105551 CAGTAGTGGAGCAGAC-GAGAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
131 AAGTAGTGGAGCAGACAAAG-GAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAA
25105615 ACCACATG-TCTTATCTCCCTAAGCAG
195 ACCACA-GATCTTATCTCCCTAAGCAG
* * **
25105641 AAGCAGTAGTGGAGCAGAC-GAGAGAAACCAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATT
1 AAGCAGTAGTGGAGCAGACAAAG-GAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATT
* * * *
25105705 AAAACCACATGTCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGCATCAAGTCTTATCTCCCTAA
65 AAAACCACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTTATCTCCCTAA
*
25105770 GAAGTAGTGGAGCAGACAAAGGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAA
130 GAAGTAGTGGAGCAGACAAAGGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAA
*
25105835 ACTACAGATCTTATCTCCCTAAGCAG
195 ACCACAGATCTTATCTCCCTAAGCAG
25105861 TAGTGGAGCA
Statistics
Matches: 199, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
219 3 0.02
220 194 0.97
221 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (220 bp):
AAGCAGTAGTGGAGCAGACAAAGGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
AAACCACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAACAAGTCTTATCTCCCTAAG
AAGTAGTGGAGCAGACAAAGGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAA
CCACAGATCTTATCTCCCTAAGCAG
Found at i:25105831 original size:127 final size:127
Alignment explanation
Indices: 25105645--25105965 Score: 452
Period size: 127 Copynumber: 2.5 Consensus size: 127
25105635 AAGCAGAAGC
* * * *
25105645 AGTAGTGGAGCAGAC-GAGAGAAACCAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAA
1 AGTAGTGGAGCAGACAAAG-GAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
* * *
25105709 CCACATG-TCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGCATCAAGTCTTATCTCCCTAAGA
65 CCACA-GATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGA
*
25105772 AGTAGTGGAGCAGACAAAGGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAAC
1 AGTAGTGGAGCAGACAAAGGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC
* *
25105837 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGC
66 CACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGA
* * * *
25105899 AGTAGTGGAGCAGATGGAAA--AAAATAATACTATCTCCCTGAATTTGCAGTGGAGCGGATTAAA
1 AGTAGTGGAGCAGA--CAAAGGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
25105962 ACCA
64 ACCA
25105966 AATCTCATCC
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
126 1 0.01
127 168 0.97
128 2 0.01
129 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (127 bp):
AGTAGTGGAGCAGACAAAGGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC
CACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGA
Found at i:25119513 original size:3 final size:3
Alignment explanation
Indices: 25119505--25119530 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25119495 CCTTCCCCTT
25119505 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
25119531 TATGTTCTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:25130684 original size:49 final size:49
Alignment explanation
Indices: 25130402--25130671 Score: 531
Period size: 49 Copynumber: 5.5 Consensus size: 49
25130392 GGGTAAAGAG
25130402 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
25130451 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
25130500 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
25130549 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
25130598 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
*
25130647 ATCCCATGTAAGACCATGTCTGGGA
1 ATCCCATGTAAGACCATATCTGGGA
25130672 CATGGCTTTG
Statistics
Matches: 220, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 220 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (49 bp):
ATCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAAC
Found at i:25134587 original size:40 final size:40
Alignment explanation
Indices: 25134458--25134593 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
25134448 CGTTTGGATA
* * *
25134458 AAAAACGCCACTAAAAATCGAGCAATAGCGGCGTTTTACG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTCG
* * * * * * *
25134498 TAAAACGCCTCTAAAGATCGAGCGTTAGCGGTGTTTCTAG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTCG
* * *
25134538 GAAAGCGCCGCTAAAAAT-TAGCATTAGCGGCGTTTTTCG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTCG
25134577 AAAAAACGCCGC-AAAAA
1 -AAAAACGCCGCTAAAAA
25134594 GTCTAAGTCC
Statistics
Matches: 75, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
39 21 0.28
40 54 0.72
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTCG
Found at i:25134747 original size:41 final size:41
Alignment explanation
Indices: 25134625--25134814 Score: 281
Period size: 41 Copynumber: 4.6 Consensus size: 41
25134615 TTTGTACCTT
* *
25134625 TCAGATCTTTAGCGGCGTTTTTAAAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTT-GAAAAAGCGCCACTAATGC
* * *
25134667 TCAGATCTTTTGCGGCATTTTTTGAGAAAGCGCCACTAATGC
1 TCAGATCTTTAGCGGC-GTTTTTGAAAAAGCGCCACTAATGC
* *
25134709 TCAGATCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGC
* *
25134750 TTAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGC
25134791 TCAGATCTTTAGCGGCGTTTTTGA
1 TCAGATCTTTAGCGGCGTTTTTGA
25134815 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
41 81 0.61
42 46 0.35
43 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGC
Found at i:25141055 original size:43 final size:43
Alignment explanation
Indices: 25140977--25141082 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 43
25140967 CGTTTTTGCA
* * * * *
25140977 AAAAGCGTCGCTAAAGGT-TTGTTCTTTAGTGGCGTTTGTGAC
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATCAC
*
25141019 AGAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATCAC
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATCAC
*
25141062 AAAAGCGCCGCTAAGGGTCAT
1 AAAAGCGCCGCTAAAGGTCAT
25141083 AGCCTTTAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 16 0.29
43 39 0.71
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATCAC
Found at i:25149873 original size:19 final size:20
Alignment explanation
Indices: 25149831--25149873 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
25149821 TCATGCTTTC
*
25149831 TATTCACATTTCCATATTCA
1 TATTCACATTTCCAAATTCA
*
25149851 -ATTCACATTTTCAAATT-A
1 TATTCACATTTCCAAATTCA
25149869 TATTC
1 TATTC
25149874 CACAATTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATTTCCAAATTCA
Found at i:25150279 original size:18 final size:17
Alignment explanation
Indices: 25150227--25150280 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
25150217 TTTCCAATTC
25150227 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
25150244 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
*
25150262 TCAATATCAAACTCACTT
1 TCAAT-TCAAATTCACTT
25150280 T
1 T
25150281 TTCATTCACT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 6 0.20
18 22 0.73
19 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:25151069 original size:16 final size:17
Alignment explanation
Indices: 25151050--25151093 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
25151040 CTTTTTCTCC
25151050 CTGTTTCGTTTCTA-TT
1 CTGTTTCGTTTCTATTT
25151066 CTGTTTC-TTTCTATTT
1 CTGTTTCGTTTCTATTT
*
25151082 CT-TTTTGTTTCT
1 CTGTTTCGTTTCT
25151094 TTTTATGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.05, C:0.18, G:0.09, T:0.68
Consensus pattern (17 bp):
CTGTTTCGTTTCTATTT
Found at i:25161854 original size:34 final size:34
Alignment explanation
Indices: 25161800--25161873 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
25161790 TCCATGCAAG
25161800 TGTT-TAATATTTATATTTTAAAGGCTAAAAAGT
1 TGTTATAATATTTATATTTTAAAGGCTAAAAAGT
* *
25161833 TGTTATAATA-TTATATGTTTAAAGGTTAAAATGT
1 TGTTATAATATTTATAT-TTTAAAGGCTAAAAAGT
*
25161867 TATTATA
1 TGTTATA
25161874 CTGTTCTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 10 0.28
34 26 0.72
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (34 bp):
TGTTATAATATTTATATTTTAAAGGCTAAAAAGT
Found at i:25165666 original size:18 final size:18
Alignment explanation
Indices: 25165645--25165681 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25165635 TGAGTTTTCG
*
25165645 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
25165663 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
25165681 A
1 A
25165682 CCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:25167723 original size:2 final size:2
Alignment explanation
Indices: 25167718--25167755 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
25167708 ATATATATGC
*
25167718 GT GT GT GAT -T GT CT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT G-T GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
25167756 CTCAATATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.03, C:0.03, G:0.45, T:0.50
Consensus pattern (2 bp):
GT
Found at i:25172709 original size:20 final size:20
Alignment explanation
Indices: 25172657--25172710 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
25172647 AGACTAAAAT
25172657 AAAATATTTT-TTTAATATA
1 AAAATATTTTATTTAATATA
*
25172676 AAAAT-TTTACATTTAGATA-A
1 AAAATATTT-TATTTA-ATATA
25172696 AAAATATTTTATTTA
1 AAAATATTTTATTTA
25172711 TATTATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 15 0.52
21 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATATTTTATTTAATATA
Found at i:25189473 original size:22 final size:22
Alignment explanation
Indices: 25189425--25189483 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
25189415 CAGCTTGTAT
* *
25189425 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTTT-AGCTCGACA
*
25189448 GAGCTTACCGTTTAGCTCGATA
1 GAGCTTACCGTTTAGCTCGACA
25189470 GAGCTTACCGTTTA
1 GAGCTTACCGTTTA
25189484 TCGGCTCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
GAGCTTACCGTTTAGCTCGACA
Found at i:25189499 original size:26 final size:23
Alignment explanation
Indices: 25189425--25189505 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 23
25189415 CAGCTTGTAT
* *
25189425 GAGCTTACCGTTTCAGCTCTA-CG
1 GAGCTTACCGTTT-AGCTCAAGAG
* *
25189448 GAGCTTACCGTTTAGCTCGATA-
1 GAGCTTACCGTTTAGCTCAAGAG
25189470 GAGCTTACCGTTTATCGGCTCAAGAG
1 GAGCTTACCGTTTA---GCTCAAGAG
25189496 GAGCTTACCG
1 GAGCTTACCG
25189506 ATCATGGCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
22 20 0.41
23 13 0.27
25 6 0.12
26 10 0.20
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
GAGCTTACCGTTTAGCTCAAGAG
Found at i:25189790 original size:34 final size:34
Alignment explanation
Indices: 25189659--25189778 Score: 204
Period size: 34 Copynumber: 3.5 Consensus size: 34
25189649 TAAAAGTTAT
25189659 ATGATTTACATGGTTTATAAGTTACATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
25189693 ATGATTTACATGGCTTATAAGTTACATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
* *
25189727 ATGATTTACATGGTTTATAAGCTAAATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
25189761 ATGATTTACATGGATTAT
1 ATGATTTACATGGTTTAT
25189779 TTGTTATATG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 81 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (34 bp):
ATGATTTACATGGTTTATAAGTTACATGAAATAC
Found at i:25195325 original size:315 final size:315
Alignment explanation
Indices: 25194753--25195386 Score: 1106
Period size: 315 Copynumber: 2.0 Consensus size: 315
25194743 TCAGTCCGAA
25194753 AGAGTTATACAGATACTTGAGGATATGTTGCGTCGTTGCATACTTAAATTTGAAGGTAGCTGGGA
1 AGAGTTATACAGATACTTGAGGATATGTTGCGTCGTTGCATACTTAAATTTGAAGGTAGCTGGGA
25194818 GAAACACTTACCTCTGATTAAATTTGCATATAACAACAACTTCCAGACGAGTTTGAAAATGGCTC
66 GAAACACTTACCTCTGATTAAATTTGCATATAACAACAACTTCCAGACGAGTTTGAAAATGGCTC
* *
25194883 CGTACGAAGCTTTATGTCAGACACCGTTATGCTGGACAGAATTGAGTTAGAAAAAGATTCACAGG
131 CGTACGAAGCTTTATGTCAGACACCGTTATACTGGACAGAATTGAGTGAGAAAAAGATTCACAGG
* *
25194948 GTTGAATTGATCATAGAAACCGAAGAAAAAATGAAAGTGATTTGAGACAATTTAAAAGCAGCTTC
196 GTTGAATTGATCAGAGAAACCAAAGAAAAAATGAAAGTGATTTGAGACAATTTAAAAGCAGCTTC
*
25195013 AAATAGACAGAAATCATATGCGGATTTGAAACGTAAAGAAATAAAGTTTCAAGTC
261 AAATAGACAGAAATCATACGCGGATTTGAAACGTAAAGAAATAAAGTTTCAAGTC
* * *
25195068 AGAGTTATACAGATATTTGAGGATATGTTGCGTTGTTGCATACTTGAATTTGAAGGTAGCTGGGA
1 AGAGTTATACAGATACTTGAGGATATGTTGCGTCGTTGCATACTTAAATTTGAAGGTAGCTGGGA
* *
25195133 GAAACACTTACCTCTGATTAAATTTGCATATAACAACAGCTTCTAGACGAGTTTGAAAATGGCTC
66 GAAACACTTACCTCTGATTAAATTTGCATATAACAACAACTTCCAGACGAGTTTGAAAATGGCTC
* * *
25195198 CGTATGAAGCTTTATGTCGGACACCGTTATACTGGACAGAATTGAGTGAGAAAAAGATTCACGGG
131 CGTACGAAGCTTTATGTCAGACACCGTTATACTGGACAGAATTGAGTGAGAAAAAGATTCACAGG
* *
25195263 GTTGAATTGATCAGAGAAACTAAAGAAAAAGTGAAAGTGATTTGAGACAATTTAAAAGCAGCTTC
196 GTTGAATTGATCAGAGAAACCAAAGAAAAAATGAAAGTGATTTGAGACAATTTAAAAGCAGCTTC
* * *
25195328 AGATAGACAGAAATCATACGCGGATTTGAAACGTAAAGAAATAGAGTTTCAGGTC
261 AAATAGACAGAAATCATACGCGGATTTGAAACGTAAAGAAATAAAGTTTCAAGTC
25195383 AGAG
1 AGAG
25195387 ATCGAGTATT
Statistics
Matches: 301, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
315 301 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (315 bp):
AGAGTTATACAGATACTTGAGGATATGTTGCGTCGTTGCATACTTAAATTTGAAGGTAGCTGGGA
GAAACACTTACCTCTGATTAAATTTGCATATAACAACAACTTCCAGACGAGTTTGAAAATGGCTC
CGTACGAAGCTTTATGTCAGACACCGTTATACTGGACAGAATTGAGTGAGAAAAAGATTCACAGG
GTTGAATTGATCAGAGAAACCAAAGAAAAAATGAAAGTGATTTGAGACAATTTAAAAGCAGCTTC
AAATAGACAGAAATCATACGCGGATTTGAAACGTAAAGAAATAAAGTTTCAAGTC
Found at i:25197584 original size:9 final size:9
Alignment explanation
Indices: 25197562--25197654 Score: 50
Period size: 9 Copynumber: 10.8 Consensus size: 9
25197552 GGTTTATAAG
*
25197562 TTACATGAA
1 TTACATGAT
*
25197571 ATACATGAT
1 TTACATGAT
*
25197580 TTACATGGT
1 TTACATGAT
* *
25197589 TT--ATAAG
1 TTACATGAT
*
25197596 TTACATGAA
1 TTACATGAT
*
25197605 ATACATGAT
1 TTACATGAT
*
25197614 TTACATGGT
1 TTACATGAT
* *
25197623 TT--ATAAG
1 TTACATGAT
*
25197630 TTACATGAA
1 TTACATGAT
*
25197639 ATACATGAT
1 TTACATGAT
25197648 TTACATG
1 TTACATG
25197655 GATTATTTGT
Statistics
Matches: 59, Mismatches: 21, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
7 8 0.14
9 51 0.86
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (9 bp):
TTACATGAT
Found at i:25197672 original size:34 final size:34
Alignment explanation
Indices: 25197544--25197660 Score: 225
Period size: 34 Copynumber: 3.4 Consensus size: 34
25197534 AAGTTATATA
25197544 ATTTACATGGTTTATAAGTTACATGAAATACATG
1 ATTTACATGGTTTATAAGTTACATGAAATACATG
25197578 ATTTACATGGTTTATAAGTTACATGAAATACATG
1 ATTTACATGGTTTATAAGTTACATGAAATACATG
25197612 ATTTACATGGTTTATAAGTTACATGAAATACATG
1 ATTTACATGGTTTATAAGTTACATGAAATACATG
*
25197646 ATTTACATGGATTAT
1 ATTTACATGGTTTAT
25197661 TTGTTATATG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 82 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (34 bp):
ATTTACATGGTTTATAAGTTACATGAAATACATG
Found at i:25202184 original size:54 final size:55
Alignment explanation
Indices: 25202092--25202198 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 55
25202082 CGGTCACAGG
* * *
25202092 CTGTTACACGGCCATGTGACCCTATTTCGAATCACACACAGTTTGGC-ACACGAT
1 CTGTGACACGGCCATGTGACCATATTTCGAATCACACACAGTCTGGCGACACGAT
* * * ** *
25202146 CTGTGACATGGCCATGTGATCATGTTTCGAATTGCACACGGTCTGGCGACACG
1 CTGTGACACGGCCATGTGACCATATTTCGAATCACACACAGTCTGGCGACACG
25202199 GCCGTGTAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
54 38 0.88
55 5 0.12
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (55 bp):
CTGTGACACGGCCATGTGACCATATTTCGAATCACACACAGTCTGGCGACACGAT
Found at i:25209734 original size:60 final size:60
Alignment explanation
Indices: 25209616--25209744 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
25209606 TTTTTTTAAC
* * * *
25209616 TTTTAGAATTATAATTAAATTGATAAATTTTATAAATGTTCAAGACTAAATTTATTGAAT
1 TTTTAGAATTAAAATTAAATTAACAAATTTTATAAATATTCAAGACTAAATTTATTGAAT
* ** *
25209676 GTTTTAGAATTAAAATTAAA-TAACAAATTTTGA-AAATATTGAAGGTTAAATTTGTTGAAT
1 -TTTTAGAATTAAAATTAAATTAACAAATTTT-ATAAATATTCAAGACTAAATTTATTGAAT
25209736 TTTTA-AATT
1 TTTTAGAATT
25209745 TAAGACCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.07
59 5 0.08
60 31 0.53
61 19 0.32
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (60 bp):
TTTTAGAATTAAAATTAAATTAACAAATTTTATAAATATTCAAGACTAAATTTATTGAAT
Found at i:25212189 original size:5 final size:6
Alignment explanation
Indices: 25212174--25212198 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25212164 CATGCTTTCT
25212174 TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG T
25212199 CAAATACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:25213301 original size:9 final size:9
Alignment explanation
Indices: 25213287--25213379 Score: 132
Period size: 9 Copynumber: 10.3 Consensus size: 9
25213277 TGGTTAAAAA
25213287 TTAACCGAT
1 TTAACCGAT
*
25213296 TTAACCGAC
1 TTAACCGAT
25213305 TTAACCGAT
1 TTAACCGAT
*
25213314 TTAACTGAT
1 TTAACCGAT
*
25213323 TTAACCGAC
1 TTAACCGAT
*
25213332 TTAACCAAT
1 TTAACCGAT
25213341 TTAACCGAT
1 TTAACCGAT
*
25213350 TTAACCGAC
1 TTAACCGAT
*
25213359 TTAACCGAC
1 TTAACCGAT
25213368 TTAACCGAT
1 TTAACCGAT
25213377 TTA
1 TTA
25213380 GTTCAACTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (9 bp):
TTAACCGAT
Found at i:25213317 original size:27 final size:27
Alignment explanation
Indices: 25213287--25213379 Score: 159
Period size: 27 Copynumber: 3.4 Consensus size: 27
25213277 TGGTTAAAAA
25213287 TTAACCGATTTAACCGACTTAACCGAT
1 TTAACCGATTTAACCGACTTAACCGAT
* *
25213314 TTAACTGATTTAACCGACTTAACCAAT
1 TTAACCGATTTAACCGACTTAACCGAT
*
25213341 TTAACCGATTTAACCGACTTAACCGAC
1 TTAACCGATTTAACCGACTTAACCGAT
25213368 TTAACCGATTTA
1 TTAACCGATTTA
25213380 GTTCAACTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (27 bp):
TTAACCGATTTAACCGACTTAACCGAT
Found at i:25214545 original size:15 final size:14
Alignment explanation
Indices: 25214516--25214549 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
25214506 AGAAAGAAAA
25214516 AAGAAAAACTAAAG
1 AAGAAAAACTAAAG
*
25214530 AAGAAAGAACTGAAG
1 AAGAAA-AACTAAAG
25214545 AAGAA
1 AAGAA
25214550 CTGAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.68, C:0.06, G:0.21, T:0.06
Consensus pattern (14 bp):
AAGAAAAACTAAAG
Found at i:25216753 original size:99 final size:99
Alignment explanation
Indices: 25216597--25216795 Score: 299
Period size: 99 Copynumber: 2.0 Consensus size: 99
25216587 ACCCCTAAAG
* ** *
25216597 GCGCGTCTTCAACCCAGAACTGGTCCTTTCTGCTTTTCAAACCCTCTGCCGCCATTGCATGTGCA
1 GCGCGACTTCAACCCAGAACCAGTCCTTTCTGCTTTTCAAACCCTCTGCCACCATTGCATGTGCA
* * *
25216662 GTAGTGTTTCCTCCTTTGACGATGAAGTTAAAAC
66 ATAATGTTTCCTCCTCTGACGATGAAGTTAAAAC
* * *
25216696 GCGCGACTTCAACCCAGAACCAGTCCTTTGTGTTTTTCAGACCCTCTGCCACCATTGCATGTGCA
1 GCGCGACTTCAACCCAGAACCAGTCCTTTCTGCTTTTCAAACCCTCTGCCACCATTGCATGTGCA
*
25216761 ATAATGTTTCCTCCTCTGGCGATGAAGTTAAAAC
66 ATAATGTTTCCTCCTCTGACGATGAAGTTAAAAC
25216795 G
1 G
25216796 ACATGCTGAG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (99 bp):
GCGCGACTTCAACCCAGAACCAGTCCTTTCTGCTTTTCAAACCCTCTGCCACCATTGCATGTGCA
ATAATGTTTCCTCCTCTGACGATGAAGTTAAAAC
Found at i:25219859 original size:17 final size:18
Alignment explanation
Indices: 25219822--25219859 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25219812 CTGCTATTTT
*
25219822 AAATGAAAACAAAATGAA
1 AAATGAAAACAAAATAAA
*
25219840 AAAT-AAAAGAAAATAAA
1 AAATGAAAACAAAATAAA
25219857 AAA
1 AAA
25219860 ATATAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (18 bp):
AAATGAAAACAAAATAAA
Found at i:25226977 original size:56 final size:56
Alignment explanation
Indices: 25226915--25227026 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
25226905 ATAAGGAGGT
25226915 TCGATTATTTCAGTTCAAAGAATAAATCATACCCTGTAAGTTAGGGGCACAACTTC
1 TCGATTATTTCAGTTCAAAGAATAAATCATACCCTGTAAGTTAGGGGCACAACTTC
* *
25226971 TCGATTATTTTAGTTTAAAGAATAAATCATACCCTGTAAGTTAGGGGCACAACTTC
1 TCGATTATTTCAGTTCAAAGAATAAATCATACCCTGTAAGTTAGGGGCACAACTTC
25227027 CCAAATCCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (56 bp):
TCGATTATTTCAGTTCAAAGAATAAATCATACCCTGTAAGTTAGGGGCACAACTTC
Found at i:25227663 original size:23 final size:22
Alignment explanation
Indices: 25227621--25227663 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
25227611 GAAACAAAAA
*
25227621 AAAACAAATAAAAGATTAAATT
1 AAAACAAATAAAAGAGTAAATT
25227643 AAAACAAAATAGAAA-AGTAAA
1 AAAAC-AAATA-AAAGAGTAAA
25227664 GGGACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 10 0.56
24 3 0.17
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAACAAATAAAAGAGTAAATT
Found at i:25230343 original size:39 final size:39
Alignment explanation
Indices: 25230289--25230368 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
25230279 CCATGAAGGA
*
25230289 GAACAGTGAATGACTTGCCGTGTTGCCCACTAGGGTATC
1 GAACAGTAAATGACTTGCCGTGTTGCCCACTAGGGTATC
25230328 GAACAGTAAATGACTTGCCGTGTTGCCCACTAGGGTATC
1 GAACAGTAAATGACTTGCCGTGTTGCCCACTAGGGTATC
25230367 GA
1 GA
25230369 TTTGAGGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
GAACAGTAAATGACTTGCCGTGTTGCCCACTAGGGTATC
Found at i:25238272 original size:177 final size:177
Alignment explanation
Indices: 25237935--25238272 Score: 432
Period size: 177 Copynumber: 1.9 Consensus size: 177
25237925 ACACACGGGC
25237935 GTGTCCTAGGCAGTGTGAAACCTGGAGCTAATTTTTTTCAATTTTAAATCAAGTCAGAGAGTTAC
1 GTGTCCTAGGCAGTGTGAAACCTGGAGCTAATTTTTTTCAATTTTAAATCAAGTCAGAGAGTTAC
* * * *
25238000 ACGAGCAAGGCACACAGCCGTGTGAGAGACACGGCCTGGCCACACGAGCGTATAGGATCTCACAT
66 ACGAGCAAGGCACACAGCCGTGTGAGAGACACGACCGGGCCACACGAGCGTAGAGGATCTCACAC
* * *
25238065 GGGCGTGGGAAAAGCGAAGGAAAACACACACGGCTTGGGATATGGGT
131 GGACGTAGGAAAAGCAAAGGAAAACACACACGGCTTGGGATATGGGT
* * *
25238112 GTGTCTTAGGCCGTGTGAAACC-GTGAGCTAATTTTTTTCAATTTTAAATCACGTCAGAGAGTTA
1 GTGTCCTAGGCAGTGTGAAACCTG-GAGCTAATTTTTTTCAATTTTAAATCAAGTCAGAGAGTTA
* * * * * *
25238176 CACGGGTAAGGCACACGGTCGTGTGAGAGACACGACCGGGCCATACGGGCAGGT-GA-GAGTC-C
65 CACGAGCAAGGCACACAGCCGTGTGAGAGACACGACCGGGCCACACGAGC--GTAGAGGA-TCTC
* * * *
25238238 ACACGGACGTAGGAGAAGTAAAGGAGATCACACAC
127 ACACGGACGTAGGAAAAGCAAAGGAAAACACACAC
25238273 AACCTGGACA
Statistics
Matches: 137, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
176 1 0.01
177 131 0.96
178 3 0.02
179 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (177 bp):
GTGTCCTAGGCAGTGTGAAACCTGGAGCTAATTTTTTTCAATTTTAAATCAAGTCAGAGAGTTAC
ACGAGCAAGGCACACAGCCGTGTGAGAGACACGACCGGGCCACACGAGCGTAGAGGATCTCACAC
GGACGTAGGAAAAGCAAAGGAAAACACACACGGCTTGGGATATGGGT
Found at i:25238323 original size:177 final size:177
Alignment explanation
Indices: 25237925--25238324 Score: 423
Period size: 177 Copynumber: 2.3 Consensus size: 177
25237915 GAAGGAAAAC
25237925 ACACACGGGCGTGTCCTAGGCAGTGTGAAACCTGGAGCTAATTTTTTTCAATTTTAAATCAAGTC
1 ACACACGGGCGTGTCCTAGGCAGTGTGAAACCTGG-GCTAATTTTTTTCAATTTTAAATCAAGTC
* * *
25237990 AGAGAGTTACACGAGCAAGGCACACAGCCGTGTGAGAGACACGGCCTGGCCACACGAGCGTATAG
65 AGAGAGTTACACGAGCAAGGCACACAGCCGTGTGAGAGACACGACCGGGCCACACGAGCGTAGAG
* * * * ** *
25238055 GATCTCACATGGGCGTGGGAAAAGCGAAGGAAAACACACACGGCTTGG
130 GATCTCACACGGACGTAGGAAAAGCAAAGGAAAACACACACAACCTGG
* * * * * * * *
25238103 -GATATGGGTGTGTCTTAGGCCGTGTGAAACCGTGAGCTAATTTTTTTCAATTTTAAATCACGTC
1 ACACACGGGCGTGTCCTAGGCAGTGTGAAACC-TGGGCTAATTTTTTTCAATTTTAAATCAAGTC
* * * * * *
25238167 AGAGAGTTACACGGGTAAGGCACACGGTCGTGTGAGAGACACGACCGGGCCATACGGGCAGGT-G
65 AGAGAGTTACACGAGCAAGGCACACAGCCGTGTGAGAGACACGACCGGGCCACACGAGC--GTAG
* * * *
25238231 A-GAGTC-CACACGGACGTAGGAGAAGTAAAGGAGATCACACACAACCTGG
128 AGGA-TCTCACACGGACGTAGGAAAAGCAAAGGAAAACACACACAACCTGG
* ** *
25238280 ACACACGGGCGTGTCC-ATGGCTGTGTGAAAATTGGGTTAATTTTT
1 ACACACGGGCGTGTCCTA-GGCAGTGTGAAACCTGGGCTAATTTTT
25238325 AATTGCACAT
Statistics
Matches: 178, Mismatches: 38, Indels: 13
0.78 0.17 0.06
Matches are distributed among these distances:
177 150 0.84
178 26 0.15
179 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.21
Consensus pattern (177 bp):
ACACACGGGCGTGTCCTAGGCAGTGTGAAACCTGGGCTAATTTTTTTCAATTTTAAATCAAGTCA
GAGAGTTACACGAGCAAGGCACACAGCCGTGTGAGAGACACGACCGGGCCACACGAGCGTAGAGG
ATCTCACACGGACGTAGGAAAAGCAAAGGAAAACACACACAACCTGG
Found at i:25238459 original size:19 final size:20
Alignment explanation
Indices: 25238425--25238462 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
25238415 AGCTACCTCT
*
25238425 TTTATTTTATTTATTTATTC
1 TTTATTATATTTATTTATTC
25238445 TTTATTATA-TTATTTATT
1 TTTATTATATTTATTTATT
25238463 ATTATTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTATATTTATTTATTC
Found at i:25238460 original size:12 final size:12
Alignment explanation
Indices: 25238426--25238464 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
25238416 GCTACCTCTT
*
25238426 TTATTTTATTTA
1 TTATATTATTTA
*
25238438 TT-TATTCTTTA
1 TTATATTATTTA
25238449 TTATATTATTTA
1 TTATATTATTTA
25238461 TTAT
1 TTAT
25238465 TATTTTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATATTATTTA
Found at i:25256195 original size:44 final size:44
Alignment explanation
Indices: 25256147--25256338 Score: 127
Period size: 44 Copynumber: 4.5 Consensus size: 44
25256137 TAATCCACTC
*
25256147 CACTGCAACTTCAGGGAGATAGGATTACTTTCTTCTGTCTGCTT
1 CACTGCAACTTCAGGGAGATAGGATTACTTGCTTCTGTCTGCTT
* * * * *
25256191 CACTGTAACTTCAGGGAGATA--A-GACTGGATGC-GATCTGC-T
1 CACTGCAACTTCAGGGAGATAGGATTACTTGCTTCTG-TCTGCTT
* ** * *
25256231 CTACTGCAACTTCAGAGAGATAATATCTAATT--TTAAT-TC-GCTT
1 C-ACTGCAACTTCAGGGAGATAGGAT-TACTTGCTT-CTGTCTGCTT
* *
25256274 CACTGCAACTTCAGGGAGATAGGATTA-TTGGCTT-TCATCTGCTC
1 CACTGCAACTTCAGGGAGATAGGATTACTT-GCTTCT-GTCTGCTT
*
25256318 CACTGCAACTTTAGGGAGATA
1 CACTGCAACTTCAGGGAGATA
25256339 AGACTTGCCA
Statistics
Matches: 115, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
40 5 0.04
41 31 0.27
42 24 0.21
43 10 0.09
44 43 0.37
45 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
CACTGCAACTTCAGGGAGATAGGATTACTTGCTTCTGTCTGCTT
Found at i:25256289 original size:127 final size:129
Alignment explanation
Indices: 25256089--25256343 Score: 338
Period size: 127 Copynumber: 2.0 Consensus size: 129
25256079 AGATAAATCT
* * * * * *
25256089 GATGTGATCTGCTCTACTGTAACTTTAGAGAGATGAGATTTGTGATTTTAATCCACTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATGAGATATCTAATTTTAATCCACTCCACTGCA
* * * *
25256154 ACTTCAGGGAGATAGGATTACTT-TC-TTCTGTCTGCTTCACTGTAACTTCAGGGAGATAAGACT
66 ACTTCAGGGAGATAGGATTA-TTGGCTTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
25256217 G
129 G
* * *
25256218 GATGCGATCTGCTCTACTGCAACTTCAGAGAGAT-A-ATATCTAATTTTAATTCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATGAGATATCTAATTTTAATCCACTCCACTGCA
*
25256281 ACTTCAGGGAGATAGGATTATTGGCTTTCATCTGCTCCACTGCAACTTTAGGGAGATAAGACT
66 ACTTCAGGGAGATAGGATTATTGGCTTTCATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
25256344 TGCCATCTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
126 2 0.02
127 73 0.66
128 4 0.04
129 31 0.28
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATGAGATATCTAATTTTAATCCACTCCACTGCA
ACTTCAGGGAGATAGGATTATTGGCTTTCATCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
Found at i:25256430 original size:50 final size:49
Alignment explanation
Indices: 25256376--25256617 Score: 189
Period size: 50 Copynumber: 4.8 Consensus size: 49
25256366 TGCAATGTCG
* *
25256376 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCTACTGCACCGCCA
1 GGGAAACAAGATTCGCCGTCGTGGCTTCAATCT-TTCTACTACACCGCCA
** ** * * ** *
25256426 GGGAAGTAAGATTCGCCGTTATGGCTTCAATCTTTTTAATTACAGTGTCA
1 GGGAAACAAGATTCGCCGTCGTGGCTTCAATCTTTCT-ACTACACCGCCA
* * * *
25256476 GGGAAACAAGATCCGTCGTCGTGACTTCAATCTGTTCCACTACACCGCCA
1 GGGAAACAAGATTCGCCGTCGTGGCTTCAATCT-TTCTACTACACCGCCA
* * * * ** *
25256526 -GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATGTCA
1 GGGAAA-CAAGATTCGCCGTCGTGGCTTCAATCTTTCT-ACTACACCGCCA
* * * *
25256576 GGGAAACAAGATCCACCGTCGTGACTTCAATCTGTTCCACTA
1 GGGAAACAAGATTCGCCGTCGTGGCTTCAATCT-TTCTACTA
25256618 TACCACCAAG
Statistics
Matches: 143, Mismatches: 43, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
49 10 0.07
50 124 0.87
51 9 0.06
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (49 bp):
GGGAAACAAGATTCGCCGTCGTGGCTTCAATCTTTCTACTACACCGCCA
Found at i:25256672 original size:100 final size:100
Alignment explanation
Indices: 25256368--25256664 Score: 434
Period size: 100 Copynumber: 3.0 Consensus size: 100
25256358 TGTTTAACTG
* * * * * *
25256368 CAATGTCGGGGAAACAAGATTCGCCGTCGT-AGCTTCAATCTATTCTACTGCACCGCCAGGGAAG
1 CAATGTCAGGGAAACAAGATCCGCCGTCGTGA-CTTCAATCTGTTCCACTACACCGCCAGGAAAG
*
25256432 TAAGATTCGCCGTTATGGCTTCAATCTTTTTAATTA
65 TAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTA
* *
25256468 CAGTGTCAGGGAAACAAGATCCGTCGTCGTGACTTCAATCTGTTCCACTACACCGCCAGGAAAGT
1 CAATGTCAGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCACTACACCGCCAGGAAAGT
25256533 AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTA
66 AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTA
* * * *
25256568 CAATGTCAGGGAAACAAGATCCACCGTCGTGACTTCAATCTGTTCCACTATACCACCAAGAAAGT
1 CAATGTCAGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCACTACACCGCCAGGAAAGT
** *
25256633 AAGATTCATCGTTGTGGCTTTAATCTTTTTAA
66 AAGATTCGCCGTTGTGGCTTCAATCTTTTTAA
25256665 ATGCAATGCC
Statistics
Matches: 178, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 177 0.99
101 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (100 bp):
CAATGTCAGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCACTACACCGCCAGGAAAGT
AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTA
Found at i:25257005 original size:45 final size:45
Alignment explanation
Indices: 25256941--25257074 Score: 171
Period size: 45 Copynumber: 3.0 Consensus size: 45
25256931 AGGAGACATC
* *
25256941 GATCTACCTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTT
* * *
25256986 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCCGTTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTT
* ** **
25257031 GATCTACTTTGCCACCAATATGGGAAGACAAGATCTGCTA-CTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTT
25257075 TTAACCTGCT
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
44 3 0.04
45 73 0.96
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTT
Found at i:25258551 original size:391 final size:392
Alignment explanation
Indices: 25257829--25258615 Score: 1504
Period size: 391 Copynumber: 2.0 Consensus size: 392
25257819 GTTTAGAAAT
25257829 TTCTAGAGTAATATGCAAAACTTCCCATGTGAAAGTTTTATTAGTCTCTTAATCATTATTCTAAT
1 TTCTAGAGTAATATGCAAAACTTCCCATGTGAAAGTTTTATTAGTCTCTTAATCATTATTCTAAT
*
25257894 GCAATATGCTTGCGAGAGATCATAACAATGGGTAAGAATAGAATTGATTTAAAGTATCAAGGATA
66 GCAACATGCTTGCGAGAGATCATAACAATGGGTAAGAATAGAATTGATTTAAAGTATCAAGGATA
25257959 TTAAGAATAAAAGAGGAATTGATTGGGAACACGTATCTTGAAAAAGAATGAAGTATTTCAAGAAC
131 TTAAGAATAAAAGAGGAATTGATTGGGAACACGTATCTTGAAAAAGAATGAAGTATTTCAAGAAC
*
25258024 AAAGAATTCAAAATAAATAAATAGTATGAAGACTAGTTGCCCCAGATACTACATCCTGAACTTCT
196 AAAGAATTCAAAATAAATAAATAGTATGAAGACTAGGTGCCCCAGATACTACATCCTGAACTTCT
* *
25258089 CTGTACAAACTTTCTGAAGATCATTCTGAGTTTGACATGTGTTTAGGAGATCTACAGTACACTGT
261 CTGTACAAACTGTCTGAAGATCATTCTGAGTTTGACATGTGTTTAGGAGATCTACAGTACACTGC
25258154 CAATGCCCCAAGATGTCGCCTACCCTTTCCTGTTGATTCAGGTATAGCAAGACCACTACATGCCC
326 CAATGCCCCAAGATGTCGCCTACCCTTTCCTGTTGATTCAGGTATAGCAAGACCACTACATGCCC
25258219 CA
391 CA
25258221 TTCTAGAGTAATATGCAAAACTTCCCATGTGAAAGTTTTATTAGTCTCTTAATCATTATTCTAAT
1 TTCTAGAGTAATATGCAAAACTTCCCATGTGAAAGTTTTATTAGTCTCTTAATCATTATTCTAAT
* *
25258286 GCAACATGCTTGTGAGATATCATAACAATGGGTAAGAATAGAATTGATTTAAAGTATCAA-GATA
66 GCAACATGCTTGCGAGAGATCATAACAATGGGTAAGAATAGAATTGATTTAAAGTATCAAGGATA
25258350 TTAAGAATAAAAGAGGAATTGATTGGGAACACGTATCTTGAAAAAGAATGAAGTATTTCAAGAAC
131 TTAAGAATAAAAGAGGAATTGATTGGGAACACGTATCTTGAAAAAGAATGAAGTATTTCAAGAAC
25258415 AAAGAATTCAAAATAAATAAATAGTATGAAGACTAGGTGCCCCAGATACTACATCCTGAACTTCT
196 AAAGAATTCAAAATAAATAAATAGTATGAAGACTAGGTGCCCCAGATACTACATCCTGAACTTCT
*
25258480 CTGTACAAACTGTCTGAAGATCATTCTGAGTTTGACATGTGTTTAGGAGATCTACAGTACTCTGC
261 CTGTACAAACTGTCTGAAGATCATTCTGAGTTTGACATGTGTTTAGGAGATCTACAGTACACTGC
25258545 CAATGCCCCAAGATGTCGCCTACCCTTTCCTGTTGATTCAGGTATAGCAAGACCACTACATGCCC
326 CAATGCCCCAAGATGTCGCCTACCCTTTCCTGTTGATTCAGGTATAGCAAGACCACTACATGCCC
25258610 CA
391 CA
25258612 TTCT
1 TTCT
25258616 GATCAGTATT
Statistics
Matches: 388, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
391 266 0.69
392 122 0.31
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (392 bp):
TTCTAGAGTAATATGCAAAACTTCCCATGTGAAAGTTTTATTAGTCTCTTAATCATTATTCTAAT
GCAACATGCTTGCGAGAGATCATAACAATGGGTAAGAATAGAATTGATTTAAAGTATCAAGGATA
TTAAGAATAAAAGAGGAATTGATTGGGAACACGTATCTTGAAAAAGAATGAAGTATTTCAAGAAC
AAAGAATTCAAAATAAATAAATAGTATGAAGACTAGGTGCCCCAGATACTACATCCTGAACTTCT
CTGTACAAACTGTCTGAAGATCATTCTGAGTTTGACATGTGTTTAGGAGATCTACAGTACACTGC
CAATGCCCCAAGATGTCGCCTACCCTTTCCTGTTGATTCAGGTATAGCAAGACCACTACATGCCC
CA
Found at i:25258638 original size:21 final size:21
Alignment explanation
Indices: 25258612--25258651 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25258602 ACATGCCCCA
**
25258612 TTCTGATCAGTATTTGAGTTG
1 TTCTGATCAAAATTTGAGTTG
25258633 TTCTGATCAAAATTTGAGT
1 TTCTGATCAAAATTTGAGT
25258652 CACCCTTTTC
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:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (21 bp):
TTCTGATCAAAATTTGAGTTG
Found at i:25258745 original size:7 final size:7
Alignment explanation
Indices: 25258735--25258782 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
25258725 CCATTTTACT
25258735 TTTTTCA
1 TTTTTCA
*
25258742 TTTTTTA
1 TTTTTCA
25258749 -TTTTCA
1 TTTTTCA
25258755 CTTTTTCA
1 -TTTTTCA
25258763 TTTTTCA
1 TTTTTCA
*
25258770 TTTCATCA
1 TTT-TTCA
25258778 TTTTT
1 TTTTT
25258783 TTACGACTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.15
7 17 0.50
8 12 0.35
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCA
Found at i:25258754 original size:13 final size:14
Alignment explanation
Indices: 25258735--25258782 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
25258725 CCATTTTACT
*
25258735 TTTTTCATTTTTTA
1 TTTTTCATTTTTCA
25258749 -TTTTCACTTTTTCA
1 TTTTTCA-TTTTTCA
*
25258763 TTTTTCATTTCATCA
1 TTTTTCATTT-TTCA
25258778 TTTTT
1 TTTTT
25258783 TTACGACTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 9 0.31
15 14 0.48
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTCATTTTTCA
Found at i:25258759 original size:21 final size:21
Alignment explanation
Indices: 25258726--25258772 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
25258716 TTAGCCTCTC
25258726 CATTTTACTTTTTTCATTTTT
1 CATTTTACTTTTTTCATTTTT
*
25258747 TATTTTCAC-TTTTTCATTTTT
1 CATTTT-ACTTTTTTCATTTTT
25258768 CATTT
1 CATTT
25258773 CATCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (21 bp):
CATTTTACTTTTTTCATTTTT
Found at i:25265783 original size:7 final size:7
Alignment explanation
Indices: 25265771--25265801 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
25265761 TTTTAAAAGG
25265771 AAAATAA
1 AAAATAA
25265778 AAAATAA
1 AAAATAA
25265785 AAAATAA
1 AAAATAA
25265792 AAAATAA
1 AAAATAA
25265799 AAA
1 AAA
25265802 TCGAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:25271889 original size:40 final size:40
Alignment explanation
Indices: 25271845--25271926 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
25271835 GTGCAAATAG
* *
25271845 GAGTACAAATA-TGCTATCAGGAGCACTGTAATGCTAACAT
1 GAGTACAAA-AGTACTATCAGGAGCACCGTAATGCTAACAT
*
25271885 GAGTACAAAAGTACTATCAGGAGCACCGTAGTGCTAACAT
1 GAGTACAAAAGTACTATCAGGAGCACCGTAATGCTAACAT
25271925 GA
1 GA
25271927 TGCGTATCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (40 bp):
GAGTACAAAAGTACTATCAGGAGCACCGTAATGCTAACAT
Found at i:25272478 original size:2 final size:2
Alignment explanation
Indices: 25272471--25272495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25272461 TCATGTGGCC
25272471 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25272496 GCATCTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25272777 original size:20 final size:20
Alignment explanation
Indices: 25272754--25272812 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
25272744 ATATTTTCAC
*
25272754 TATTTTCAATAATTTTTATA
1 TATTTTAAATAATTTTTATA
*
25272774 TATTTTTAAT-ATTTTTA-A
1 TATTTTAAATAATTTTTATA
* *
25272792 TTTTTTAAAATAAATTTTATA
1 TATTTT-AAATAATTTTTATA
25272813 AATATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.19
19 10 0.31
20 15 0.47
21 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTAAATAATTTTTATA
Found at i:25272780 original size:11 final size:9
Alignment explanation
Indices: 25272739--25272799 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
25272729 TTGATTAAAA
25272739 TTTTAATAT
1 TTTTAATAT
* *
25272748 TTTCACTAT
1 TTTTAATAT
*
25272757 TTTCAATAAT
1 TTTTAAT-AT
25272767 TTTTATATAT
1 TTTTA-ATAT
25272777 TTTTAATAT
1 TTTTAATAT
25272786 TTTTAAT-T
1 TTTTAATAT
25272794 TTTTAA
1 TTTTAA
25272800 AATAAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
8 7 0.15
9 24 0.52
10 13 0.28
11 2 0.04
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTAATAT
Found at i:25273758 original size:6 final size:6
Alignment explanation
Indices: 25273747--25273772 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25273737 TTGAGTGATG
25273747 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
25273773 TCTGAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:25276183 original size:117 final size:117
Alignment explanation
Indices: 25275977--25276214 Score: 440
Period size: 117 Copynumber: 2.0 Consensus size: 117
25275967 AGATTTATCT
* *
25275977 TATTAAGGTTAAGAAGTATAAATGTATCATGTTGTGGTTGTTATGATCTGTCTAGCTAGTGGAGT
1 TATTAAGGTTAAGAAGTATAAACGTATCATGTTGTGGTTGTTATGACCTGTCTAGCTAGTGGAGT
25276042 CGAGGGTTAGTCCAATGGAAATATCAACCTTATAATTAACCCTTTCTTCTTC
66 CGAGGGTTAGTCCAATGGAAATATCAACCTTATAATTAACCCTTTCTTCTTC
*
25276094 TATTAAGGTTAAGGAGTATAAACGTATCATGTTGTGGTTGTTATGACCTGTCTAGCTAGTGGAGT
1 TATTAAGGTTAAGAAGTATAAACGTATCATGTTGTGGTTGTTATGACCTGTCTAGCTAGTGGAGT
*
25276159 CGAGGGTTAGTCCAATGGAAATATCAACCTTATAATTAACCTTTTCTTCTTC
66 CGAGGGTTAGTCCAATGGAAATATCAACCTTATAATTAACCCTTTCTTCTTC
25276211 TATT
1 TATT
25276215 GGTGTCCCAA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (117 bp):
TATTAAGGTTAAGAAGTATAAACGTATCATGTTGTGGTTGTTATGACCTGTCTAGCTAGTGGAGT
CGAGGGTTAGTCCAATGGAAATATCAACCTTATAATTAACCCTTTCTTCTTC
Found at i:25279485 original size:16 final size:16
Alignment explanation
Indices: 25279464--25279495 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25279454 ACTTAGTAAT
*
25279464 TAAAAGATACAGTTAA
1 TAAAAGATACAATTAA
25279480 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
25279496 GAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:25281230 original size:22 final size:22
Alignment explanation
Indices: 25281196--25281237 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25281186 CGACGCTGTT
25281196 ATATAATACATAACTTACATTA
1 ATATAATACATAACTTACATTA
* *
25281218 ATATTATATATAACTTACAT
1 ATATAATACATAACTTACAT
25281238 AACTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAATACATAACTTACATTA
Found at i:25281241 original size:9 final size:9
Alignment explanation
Indices: 25281227--25281411 Score: 100
Period size: 9 Copynumber: 21.9 Consensus size: 9
25281217 AATATTATAT
25281227 ATAACTTAC
1 ATAACTTAC
25281236 ATAACTTA-
1 ATAACTTAC
25281244 ATTAA-TTA-
1 A-TAACTTAC
*
25281252 AT-ATTATAC
1 ATAACT-TAC
*
25281261 ATAAATTAC
1 ATAACTTAC
25281270 ATAACTTA-
1 ATAACTTAC
25281278 ATTAA-TTA-
1 A-TAACTTAC
*
25281286 AT-ATTATAC
1 ATAACT-TAC
25281295 ATAACTTAC
1 ATAACTTAC
25281304 ATAACTTAC
1 ATAACTTAC
*
25281313 --AACTTAT
1 ATAACTTAC
25281320 ATAACTTAC
1 ATAACTTAC
*
25281329 -TTA--TA-
1 ATAACTTAC
25281334 ATAACTTAC
1 ATAACTTAC
25281343 ATAA--TAC
1 ATAACTTAC
*
25281350 ATATAACTTTC
1 --ATAACTTAC
25281361 ATAACTTAC
1 ATAACTTAC
*
25281370 ATTA--TAC
1 ATAACTTAC
* *
25281377 ACAACTTAT
1 ATAACTTAC
25281386 ATAACTTAC
1 ATAACTTAC
25281395 ATAACTTAC
1 ATAACTTAC
*
25281404 ATAGCTTA
1 ATAACTTA
25281412 ATTATACTTA
Statistics
Matches: 138, Mismatches: 16, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.04
7 18 0.13
8 18 0.13
9 90 0.65
10 4 0.03
11 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.38
Consensus pattern (9 bp):
ATAACTTAC
Found at i:25281257 original size:34 final size:34
Alignment explanation
Indices: 25281214--25281311 Score: 178
Period size: 34 Copynumber: 2.9 Consensus size: 34
25281204 CATAACTTAC
*
25281214 ATTAATATTATATATAACTTACATAACTTAATTA
1 ATTAATATTATACATAACTTACATAACTTAATTA
*
25281248 ATTAATATTATACATAAATTACATAACTTAATTA
1 ATTAATATTATACATAACTTACATAACTTAATTA
25281282 ATTAATATTATACATAACTTACATAACTTA
1 ATTAATATTATACATAACTTACATAACTTA
25281312 CAACTTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (34 bp):
ATTAATATTATACATAACTTACATAACTTAATTA
Found at i:25281318 original size:16 final size:16
Alignment explanation
Indices: 25281297--25281328 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25281287 TATTATACAT
25281297 AACTTACATAACTTAC
1 AACTTACATAACTTAC
*
25281313 AACTTATATAACTTAC
1 AACTTACATAACTTAC
25281329 TTATAATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:25281332 original size:13 final size:14
Alignment explanation
Indices: 25281314--25281342 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25281304 ATAACTTACA
25281314 ACTTAT-ATAACTT
1 ACTTATAATAACTT
25281327 ACTTATAATAACTT
1 ACTTATAATAACTT
25281341 AC
1 AC
25281343 ATAATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTATAATAACTT
Found at i:25281389 original size:25 final size:26
Alignment explanation
Indices: 25281327--25281396 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
25281317 TATATAACTT
* *
25281327 ACTTATAATAACTTACATAATACATATA
1 ACTTATAATAACTTACATTATAC--ACA
*
25281355 ACTT-TCATAACTTACATTATACACA
1 ACTTATAATAACTTACATTATACACA
25281380 ACTTAT-ATAACTTACAT
1 ACTTATAATAACTTACAT
25281397 AACTTACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 17 0.45
26 1 0.03
27 16 0.42
28 4 0.11
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (26 bp):
ACTTATAATAACTTACATTATACACA
Found at i:25281484 original size:16 final size:15
Alignment explanation
Indices: 25281448--25281497 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
25281438 CCATGCGACT
*
25281448 TACATAACTTATTAA
1 TACATAACTCATTAA
*
25281463 TTCATAACTCAGTTAA
1 TACATAACTCA-TTAA
*
25281479 TACATAACTTATATAA
1 TACATAACTCAT-TAA
25281495 TAC
1 TAC
25281498 GACATAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (15 bp):
TACATAACTCATTAA
Found at i:25281504 original size:19 final size:19
Alignment explanation
Indices: 25281480--25281592 Score: 67
Period size: 19 Copynumber: 5.9 Consensus size: 19
25281470 CTCAGTTAAT
25281480 ACATAACTTATATAATACG
1 ACATAACTTATATAATACG
*
25281499 ACATAACTTAT-TAATA-T
1 ACATAACTTATATAATACG
* ** *
25281516 ATATATTTTAAGATGATACATATCTT
1 ACATAACTT---AT-ATA-ATA-C-G
25281542 ACATAACTTATATAAT---
1 ACATAACTTATATAATACG
*
25281558 ACATAACTTACATAATACG
1 ACATAACTTATATAATACG
25281577 ACATAACTTAT-TAATA
1 ACATAACTTATATAATA
25281593 TATTTATGGA
Statistics
Matches: 73, Mismatches: 9, Indels: 25
0.68 0.08 0.23
Matches are distributed among these distances:
16 15 0.21
17 6 0.08
18 10 0.14
19 21 0.29
20 2 0.03
21 2 0.03
22 5 0.07
23 5 0.07
26 7 0.10
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (19 bp):
ACATAACTTATATAATACG
Found at i:25281546 original size:9 final size:9
Alignment explanation
Indices: 25281532--25281572 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
25281522 TTTAAGATGA
*
25281532 TACATATCT
1 TACATAACT
25281541 TACATAACT
1 TACATAACT
*
25281550 TATATAA--
1 TACATAACT
25281557 TACATAACT
1 TACATAACT
25281566 TACATAA
1 TACATAA
25281573 TACGACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.22
9 21 0.78
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TACATAACT
Found at i:25281560 original size:16 final size:16
Alignment explanation
Indices: 25281541--25281575 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
25281531 ATACATATCT
*
25281541 TACATAACTTATATAA
1 TACATAACTTACATAA
25281557 TACATAACTTACATAA
1 TACATAACTTACATAA
25281573 TAC
1 TAC
25281576 GACATAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:25281594 original size:78 final size:77
Alignment explanation
Indices: 25281465--25281636 Score: 247
Period size: 78 Copynumber: 2.2 Consensus size: 77
25281455 CTTATTAATT
* * **
25281465 CATAACTCAGTTAATACATAACTTATATAATACGACATAACTTATTAATATATATAT-TTTAAGA
1 CATAACTTA-TTAATACATAACTTACATAATACGACATAACTTATTAATATATATATGGATAA-A
*
25281529 TGATACATATCTTA
64 TGATACATAACTTA
*
25281543 CATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAATATATTTATGGATAAAT
1 CATAACTTAT-TAATACATAACTTACATAATACGACATAACTTATTAATATATATATGGATAAAT
25281608 GATACATAACTTA
65 GATACATAACTTA
*
25281621 CATAATTTATTAATAC
1 CATAACTTATTAATAC
25281637 TTACATTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
77 7 0.08
78 75 0.88
79 3 0.04
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.38
Consensus pattern (77 bp):
CATAACTTATTAATACATAACTTACATAATACGACATAACTTATTAATATATATATGGATAAATG
ATACATAACTTA
Found at i:25286978 original size:21 final size:21
Alignment explanation
Indices: 25286963--25287108 Score: 75
Period size: 21 Copynumber: 6.8 Consensus size: 21
25286953 AGCAGATGTG
25286963 GCAGCGAGAGAAGCAGAGGCA
1 GCAGCGAGAGAAGCAGAGGCA
* *
25286984 GCAGCGAGAGAAGCTGAGG-T
1 GCAGCGAGAGAAGCAGAGGCA
* * * *
25287004 TCAACGAAAGTATGAGCA-ACTGCA
1 GCAGCGAGAG-A--AGCAGA-GGCA
* * *
25287028 GCAGC-AGCTTA-AAGAAGATGCG
1 GCAGCGAG---AGAAGCAGAGGCA
*
25287050 GCAGCGAGAGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCA
* * *
25287071 GCAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCA
*
25287092 GCAGCGAGGGAAGCAGA
1 GCAGCGAGAGAAGCAGA
25287109 ACAGCTTAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
20 8 0.08
21 62 0.65
22 12 0.13
23 8 0.08
24 4 0.04
26 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.39, T:0.08
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCA
Found at i:25287505 original size:43 final size:43
Alignment explanation
Indices: 25287416--25287802 Score: 591
Period size: 43 Copynumber: 9.0 Consensus size: 43
25287406 ATTAGCGGCA
*
25287416 TTTTTT-GCATAAGTGCCGCTAAAGACCATGGTCTATAGTGGC-
1 TTTTTTGGC-TAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
** *
25287458 TTTTTTTCCTAAGCGCCGCAAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
25287501 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
25287544 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* *
25287587 TTTTTCGGCTAAGCGCCGCTATA-ACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
25287629 TTTTTCGGCTAAGCGCTGCTATAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
25287672 TTTTTCGTCTAAGCGCCGCGAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* *
25287715 TTTTTAGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
25287758 TTTTTTGGATAAGCGCCGCTAAAGATCATGGTCTATAGCGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
25287801 TT
1 TT
25287803 GTAAAGAAAA
Statistics
Matches: 322, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
42 78 0.24
43 244 0.76
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
Found at i:25287644 original size:128 final size:128
Alignment explanation
Indices: 25287416--25287802 Score: 591
Period size: 128 Copynumber: 3.0 Consensus size: 128
25287406 ATTAGCGGCA
* * *
25287416 TTTTTT-GCATAAGTGCCGCTAAAGACCATGGTCTATAGTGGCTTTTTTTC-CTAAGCGCCGCAA
1 TTTTTTGGC-TAAGCGCCGCTAAAGACCATGGTCTATAGTGGC-GTTTTTCGCTAAGCGCCGCTA
25287479 AAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
64 AAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
*
25287544 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTCGGCTAAGCGCCGCTAT
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTC-GCTAAGCGCCGCTAA
* * *
25287609 A-ACCATGGTCTATAGTGGCGTTTTTCGGCTAAGCGCTGCTATAGACCATGGTCTATAGTGGCG
65 AGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * * *
25287672 TTTTTCGTCTAAGCGCCGCGAAAGACCATGGTCTATAGTGGCGTTTTTAGTCTAAGCGCCGCTAA
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTCG-CTAAGCGCCGCTAA
* * *
25287737 AGACCATGGTCTATAGTGGCGTTTTTTGGATAAGCGCCGCTAAAGATCATGGTCTATAGCGGCG
65 AGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
25287801 TT
1 TT
25287803 GTAAAGAAAA
Statistics
Matches: 236, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
127 7 0.03
128 156 0.66
129 73 0.31
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (128 bp):
TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTCGCTAAGCGCCGCTAAA
GACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
Found at i:25297548 original size:6 final size:6
Alignment explanation
Indices: 25297537--25297563 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25297527 AAGAGGAAAC
25297537 CCTAAA CCTAAA CCTAAA CCTAAA CCT
1 CCTAAA CCTAAA CCTAAA CCTAAA CCT
25297564 GGCATGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTAAA
Found at i:25299434 original size:3 final size:3
Alignment explanation
Indices: 25299426--25299464 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
25299416 GTATATATAG
* * *
25299426 TAA TAA TAA TAG TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25299465 CTTAATAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:25299439 original size:12 final size:12
Alignment explanation
Indices: 25299422--25299460 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25299412 ATGTGTATAT
25299422 ATAGTAATAATA
1 ATAGTAATAATA
*
25299434 ATAGTAATGATA
1 ATAGTAATAATA
* *
25299446 ATAATAACAATA
1 ATAGTAATAATA
25299458 ATA
1 ATA
25299461 ATAACTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (12 bp):
ATAGTAATAATA
Found at i:25299472 original size:20 final size:20
Alignment explanation
Indices: 25299447--25299506 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
25299437 GTAATGATAA
25299447 TAATAACAATAATAATAACT
1 TAATAACAATAATAATAACT
* *
25299467 TAATAACAAGAA-AATCAAATT
1 TAATAACAATAATAAT--AACT
*
25299488 TAATAAAAATAAATAATAA
1 TAATAACAAT-AATAATAA
25299507 ATAAAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 13 0.41
22 2 0.06
23 3 0.09
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
TAATAACAATAATAATAACT
Found at i:25299828 original size:19 final size:20
Alignment explanation
Indices: 25299804--25299851 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
25299794 AATCGTATCT
25299804 TCTAAGATTGC-ATATCATA
1 TCTAAGATTGCAATATCATA
25299823 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
25299844 TCTAAGAT
1 TCTAAGAT
25299852 CATATCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.41
21 16 0.59
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:25300177 original size:24 final size:24
Alignment explanation
Indices: 25300150--25300196 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
25300140 TCATTTCAAC
*
25300150 TAAAATTA-TATTTAATTTATTTTA
1 TAAAATTACTATGTAA-TTATTTTA
*
25300174 TAAATTTACTATGTAATTATTTT
1 TAAAATTACTATGTAATTATTTT
25300197 CATTTGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TAAAATTACTATGTAATTATTTTA
Found at i:25301865 original size:5 final size:5
Alignment explanation
Indices: 25301855--25301890 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
25301845 GTAAGCTAAA
25301855 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
25301891 CAATCGCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.61, G:0.19, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:25305209 original size:32 final size:32
Alignment explanation
Indices: 25305161--25305221 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
25305151 TCTCTTCTTC
*
25305161 TATTATTATTATTTTAATAATATAATATAATA
1 TATTATTATTAATTTAATAATATAATATAATA
* *
25305193 TATTATTTTTAATTTAATAATTTAATATA
1 TATTATTATTAATTTAATAATATAATATA
25305222 TTTTTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTATTATTAATTTAATAATATAATATAATA
Found at i:25309398 original size:24 final size:24
Alignment explanation
Indices: 25309369--25309417 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
25309359 TGAACAATGA
25309369 TTGTATTTCCCATTGTCACATTTG
1 TTGTATTTCCCATTGTCACATTTG
*
25309393 TTGTATTTCCTATTGTCACATTTG
1 TTGTATTTCCCATTGTCACATTTG
25309417 T
1 T
25309418 CCTTTAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.53
Consensus pattern (24 bp):
TTGTATTTCCCATTGTCACATTTG
Found at i:25324354 original size:30 final size:30
Alignment explanation
Indices: 25324313--25324374 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
25324303 GAGGAACGGC
25324313 GTCGGAAATTCTTGGATTCGATGGGATTGA
1 GTCGGAAATTCTTGGATTCGATGGGATTGA
*
25324343 GTCGTAAATTCTTGGATTCGATGGGATTGA
1 GTCGGAAATTCTTGGATTCGATGGGATTGA
25324373 GT
1 GT
25324375 TTAGATGGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (30 bp):
GTCGGAAATTCTTGGATTCGATGGGATTGA
Found at i:25331989 original size:33 final size:33
Alignment explanation
Indices: 25331947--25332013 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
25331937 GAGTTTTTGG
25331947 TGAGTTCATTCCACTTTTGCTTTTGATAAATAA
1 TGAGTTCATTCCACTTTTGCTTTTGATAAATAA
25331980 TGAGTTCATTCCACTTTTGCTTTTGATAAATAA
1 TGAGTTCATTCCACTTTTGCTTTTGATAAATAA
25332013 T
1 T
25332014 AAACTAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (33 bp):
TGAGTTCATTCCACTTTTGCTTTTGATAAATAA
Found at i:25335756 original size:16 final size:17
Alignment explanation
Indices: 25335735--25335772 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
25335725 TGGGTGCAAC
*
25335735 TAAGATGGTAACTAA-T
1 TAAGATGGAAACTAATT
25335751 TAAGATGGAAACTAATT
1 TAAGATGGAAACTAATT
25335768 TAAGA
1 TAAGA
25335773 CTCTCACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (17 bp):
TAAGATGGAAACTAATT
Found at i:25338419 original size:81 final size:81
Alignment explanation
Indices: 25338328--25338486 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 81
25338318 CCTAAACATG
* *
25338328 TCCTTAGTCTAATCGGAAATGATCAAACCGATTGGAGGACTAATATGCTATTTATCATATCCAAT
1 TCCTTAGTCTAATCGGAAATGATCAAACCGATTGGAAGACTAATATGCTATTTATCAGATCCAAT
25338393 TGGGGAGATGCCTAAT
66 TGGGGAGATGCCTAAT
** *
25338409 TCCTTAGTCTAATCGGAAATGATCAAATTGATTGGAAGACTAATATGCTATTTATCAGATCTAAT
1 TCCTTAGTCTAATCGGAAATGATCAAACCGATTGGAAGACTAATATGCTATTTATCAGATCCAAT
25338474 TGGGGAGATGCCT
66 TGGGGAGATGCCT
25338487 TATCTTGGGA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (81 bp):
TCCTTAGTCTAATCGGAAATGATCAAACCGATTGGAAGACTAATATGCTATTTATCAGATCCAAT
TGGGGAGATGCCTAAT
Found at i:25351605 original size:6 final size:6
Alignment explanation
Indices: 25351594--25351626 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
25351584 ATTGTTTTAA
25351594 TAATGT TAATGT TAATGT TAATGT TAA-GT TAAT
1 TAATGT TAATGT TAATGT TAATGT TAATGT TAAT
25351627 TATATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (6 bp):
TAATGT
Found at i:25357591 original size:3 final size:3
Alignment explanation
Indices: 25357583--25357642 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
25357573 NNNNNNNNNT
25357583 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25357631 TAA TAA TAA TAA
1 TAA TAA TAA TAA
25357643 AAAAGTGATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25360674 original size:59 final size:60
Alignment explanation
Indices: 25360572--25360762 Score: 183
Period size: 59 Copynumber: 3.2 Consensus size: 60
25360562 TTTTAAATAA
** **
25360572 AAAATTGCATTTT-GACCCTTAAACTTTTTTAAAATTATTTTTTGACCCCTTAACTTT-TT
1 AAAATTGCATTTTGGACCC-TAAACTTTCCTAAAATTACATTTTGACCCCTTAACTTTCTT
* * **
25360631 AAAATTGCATTTTGGACCCTAAACTTTCCTACATTTACATTTTGACCTTTTAACTTTCTT
1 AAAATTGCATTTTGGACCCTAAACTTTCCTAAAATTACATTTTGACCCCTTAACTTTCTT
* * * * * * * *
25360691 AAATTTTCATTTGGGCCCCTAAACTTT-CTATAAATTACATTTTGGCCCCAT-ATTTTCCT
1 AAAATTGCATTTTGGACCCTAAACTTTCCTA-AAATTACATTTTGACCCCTTAACTTTCTT
*
25360750 AAAATTACATTTT
1 AAAATTGCATTTT
25360763 TGCCCCAGAA
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
59 62 0.58
60 44 0.42
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (60 bp):
AAAATTGCATTTTGGACCCTAAACTTTCCTAAAATTACATTTTGACCCCTTAACTTTCTT
Found at i:25360738 original size:30 final size:29
Alignment explanation
Indices: 25360572--25360777 Score: 135
Period size: 30 Copynumber: 6.9 Consensus size: 29
25360562 TTTTAAATAA
* * * *
25360572 AAAATTGCATTTTGACCCTTAAACTTTTTT
1 AAAATTACATTTTGGCCCCTAAAC-TTTCT
** * * *
25360602 AAAATTATTTTTTGACCCCTTAACTTTTT
1 AAAATTACATTTTGGCCCCTAAACTTTCT
* *
25360631 AAAATTGCATTTTGGACCCTAAACTTTCCT
1 AAAATTACATTTTGGCCCCTAAACTTT-CT
* * * ** *
25360661 ACATTTACATTTTGACCTTTTAACTTTCTT
1 AAAATTACATTTTGGCCCCTAAACTTTC-T
* * *
25360691 AAATTTTCATTTGGGCCCCTAAACTTTCT
1 AAAATTACATTTTGGCCCCTAAACTTTCT
* *
25360720 ATAAATTACATTTTGGCCCC-ATATTTTCCT
1 A-AAATTACATTTTGGCCCCTAAACTTT-CT
* *
25360750 AAAATTACATTTTTGCCCCAGAAACTTT
1 AAAATTACATTTTGGCCCC-TAAACTTT
25360778 GCACCCTTTA
Statistics
Matches: 135, Mismatches: 35, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
29 51 0.38
30 79 0.59
31 5 0.04
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (29 bp):
AAAATTACATTTTGGCCCCTAAACTTTCT
Found at i:25361109 original size:26 final size:24
Alignment explanation
Indices: 25361079--25361133 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
25361069 AACACCTAGC
25361079 AAAAACAACCAAGAAGCAAAAAG-GAA
1 AAAAACAA-CAAGAA--AAAAAGTGAA
*
25361105 AAAAACAACAAGCAAAAAAGTGAA
1 AAAAACAACAAGAAAAAAAGTGAA
25361129 AAAAA
1 AAAAA
25361134 GAAAGAGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 8 0.30
25 5 0.19
26 8 0.30
ACGTcount: A:0.73, C:0.13, G:0.13, T:0.02
Consensus pattern (24 bp):
AAAAACAACAAGAAAAAAAGTGAA
Found at i:25361142 original size:24 final size:22
Alignment explanation
Indices: 25361092--25361162 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 22
25361082 AACAACCAAG
*
25361092 AAGC-AAAAAGGAAAAAAACAA
1 AAGCAAAAAAGGAAAAAAAGAA
25361113 CAAGCAAAAAAGTGAAAAAAAGAA
1 -AAGCAAAAAAG-GAAAAAAAGAA
*
25361137 AGAGCAAAGAA-GAAAAAGAAGAA
1 A-AGCAAAAAAGGAAAAA-AAGAA
25361160 AAG
1 AAG
25361163 GGGGGAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 12 0.28
23 13 0.30
24 18 0.42
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.01
Consensus pattern (22 bp):
AAGCAAAAAAGGAAAAAAAGAA
Found at i:25361153 original size:23 final size:21
Alignment explanation
Indices: 25361092--25361162 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 21
25361082 AACAACCAAG
*
25361092 AAGCAAAAAGGAAAAAAACAA
1 AAGCAAAAAGGAAAAAAAGAA
25361113 CAAGCAAAAAAGTGAAAAAAAGAA
1 -AAGC-AAAAAG-GAAAAAAAGAA
25361137 AGAGCAAAGAA-GAAAAAGAAGAA
1 A-AGCAAA-AAGGAAAAA-AAGAA
25361160 AAG
1 AAG
25361163 GGGGGAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
22 12 0.28
23 16 0.37
24 15 0.35
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.01
Consensus pattern (21 bp):
AAGCAAAAAGGAAAAAAAGAA
Found at i:25361644 original size:20 final size:22
Alignment explanation
Indices: 25361607--25361647 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25361597 GCCCAGCCGA
25361607 AAAAAAAAAGGAAGAAAGGAAG
1 AAAAAAAAAGGAAGAAAGGAAG
25361629 AAAAAAAAA-GAA-AAAGGAA
1 AAAAAAAAAGGAAGAAAGGAA
25361648 AAAGGTAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGGAAGAAAGGAAG
Found at i:25362187 original size:18 final size:18
Alignment explanation
Indices: 25362150--25362206 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
25362140 GAAAAATTAA
*
25362150 AAAAAATT-CGTG-CTTC
1 AAAAAATTCCGTGTTTTC
*
25362166 -AAAAATTCTG-GTATTTC
1 AAAAAATTCCGTGT-TTTC
*
25362183 AAAAATTTCCGTGTTTTC
1 AAAAAATTCCGTGTTTTC
25362201 AAAAAA
1 AAAAAA
25362207 AAATTTTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 8 0.26
16 1 0.03
17 3 0.10
18 17 0.55
19 2 0.06
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (18 bp):
AAAAAATTCCGTGTTTTC
Found at i:25362217 original size:21 final size:22
Alignment explanation
Indices: 25362183--25362230 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
25362173 CTGGTATTTC
25362183 AAAAATTTCCGTGTTTTCAAAA
1 AAAAATTTCCGTGTTTTCAAAA
*
25362205 AAAAATTT-TGTGTTTTCAAAA
1 AAAAATTTCCGTGTTTTCAAAA
25362226 AAAAA
1 AAAAA
25362231 GAGTTATTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (22 bp):
AAAAATTTCCGTGTTTTCAAAA
Found at i:25368524 original size:21 final size:22
Alignment explanation
Indices: 25368491--25368533 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
25368481 ATAAAAGCTT
*
25368491 CAAAAATATTAAT-TTTGTTAAA
1 CAAAAATAATAATATTT-TTAAA
25368513 CAAAAA-AATAATATTTTTAAA
1 CAAAAATAATAATATTTTTAAA
25368534 GGGATTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
CAAAAATAATAATATTTTTAAA
Found at i:25379915 original size:24 final size:24
Alignment explanation
Indices: 25379883--25379965 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
25379873 TTATCAAGAT
25379883 AAATATTAGATTAAATTTAATATA
1 AAATATTAGATTAAATTTAATATA
* *
25379907 AAATCTTAGTAAATAAATTT-ATCA-A
1 AAATATTAG--ATTAAATTTAAT-ATA
25379932 TAAATATTAGATTAAATTTAATATA
1 -AAATATTAGATTAAATTTAATATA
*
25379957 AAATCTTAG
1 AAATATTAG
25379966 TAAATTAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
24 25 0.52
25 6 0.12
26 17 0.35
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.40
Consensus pattern (24 bp):
AAATATTAGATTAAATTTAATATA
Found at i:25379943 original size:50 final size:52
Alignment explanation
Indices: 25379867--25379970 Score: 194
Period size: 50 Copynumber: 2.0 Consensus size: 52
25379857 GTAAATTAAT
25379867 ATAAATTTATCAAGATAAATATTAGATTAAATTTAATATAAAATCTTAGTAA
1 ATAAATTTATCAAGATAAATATTAGATTAAATTTAATATAAAATCTTAGTAA
25379919 ATAAATTTATC-A-ATAAATATTAGATTAAATTTAATATAAAATCTTAGTAA
1 ATAAATTTATCAAGATAAATATTAGATTAAATTTAATATAAAATCTTAGTAA
25379969 AT
1 AT
25379971 TAATAGAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 40 0.77
51 1 0.02
52 11 0.21
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (52 bp):
ATAAATTTATCAAGATAAATATTAGATTAAATTTAATATAAAATCTTAGTAA
Found at i:25380439 original size:9 final size:9
Alignment explanation
Indices: 25380421--25380456 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
25380411 TATCATATTA
25380421 AATTTAATT
1 AATTTAATT
*
25380430 AATTTGATT
1 AATTTAATT
*
25380439 ACTTTAATT
1 AATTTAATT
25380448 AATTTAATT
1 AATTTAATT
25380457 TTACTTTATC
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:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (9 bp):
AATTTAATT
Found at i:25381978 original size:18 final size:19
Alignment explanation
Indices: 25381941--25381979 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
25381931 ATCGTTTCTA
*
25381941 TTTACGAAAAACCTTAGTT
1 TTTACGAAAAACCGTAGTT
*
25381960 TTTAGGAAAAACCGT-GTT
1 TTTACGAAAAACCGTAGTT
25381978 TT
1 TT
25381980 GTGGAGTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTACGAAAAACCGTAGTT
Found at i:25393054 original size:12 final size:12
Alignment explanation
Indices: 25393037--25393077 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
25393027 AAAAAAAAGC
25393037 AAAAAGCGCAAA
1 AAAAAGCGCAAA
25393049 AAAAAGCGCAAA
1 AAAAAGCGCAAA
*
25393061 AAAAACCGCAAA
1 AAAAAGCGCAAA
25393073 AAAAA
1 AAAAA
25393078 AAGTTGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.71, C:0.17, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGCGCAAA
Found at i:25410369 original size:6 final size:6
Alignment explanation
Indices: 25410358--25410387 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
25410348 ATTGAAGATG
25410358 CTTATC CTTATC CTTATC CTTATC CTTATC
1 CTTATC CTTATC CTTATC CTTATC CTTATC
25410388 TTTTAAGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTATC
Found at i:25415699 original size:48 final size:49
Alignment explanation
Indices: 25415603--25415822 Score: 207
Period size: 48 Copynumber: 4.5 Consensus size: 49
25415593 AAAAGTTGTT
* * * * **
25415603 AATACATTGTGGATGAACCACTGGTCATTGTAGATAAAATACTGACTAA
1 AATACGTTGTGGATGAACTACTGGTCATTGCAGATAAACTGTTGACTAA
* * *
25415652 AACACGTTGCGGATGAACTACTGGTTA-TGCAGATAAACTGTTGACTAA
1 AATACGTTGTGGATGAACTACTGGTCATTGCAGATAAACTGTTGACTAA
* * * * *
25415700 AATATGTTGTGGATGAACCATTGGTCATTGGAGATAAATTGTTGACTAA
1 AATACGTTGTGGATGAACTACTGGTCATTGCAGATAAACTGTTGACTAA
** * *
25415749 AATATTTTGTGGATGAACTACTGGT--TGTGCAAATAAACT-TTCAACTAA
1 AATACGTTGTGGATGAACTACTGGTCAT-TGCAGATAAACTGTT-GACTAA
*
25415797 AATACATTGTGGATGAA-TCACTGGTC
1 AATACGTTGTGGATGAACT-ACTGGTC
25415823 GTGCAAATAA
Statistics
Matches: 140, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
47 4 0.03
48 73 0.52
49 63 0.45
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (49 bp):
AATACGTTGTGGATGAACTACTGGTCATTGCAGATAAACTGTTGACTAA
Done.