Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014281.1 Kokia drynarioides strain JFW-HI SEQ_129314, whole genome shotgun sequence
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: 206545
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 241 characters in sequence are not A, C, G, or T
Found at i:19493 original size:23 final size:24
Alignment explanation
Indices: 19467--19511 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
19457 TTTTCTATTT
* *
19467 TTAATATATTA-AAATATTAATGA
1 TTAATATAATATAAATAATAATGA
19490 TTAATATAATATAAATAATAAT
1 TTAATATAATATAAATAATAAT
19512 AATTTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TTAATATAATATAAATAATAATGA
Found at i:19686 original size:21 final size:22
Alignment explanation
Indices: 19653--19693 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19643 ATTTTGTTAA
19653 TTTTATAAGTATATTAATGTAT
1 TTTTATAAGTATATTAATGTAT
* *
19675 TTTTTTAA-TATATTGATGT
1 TTTTATAAGTATATTAATGT
19694 GATTACATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (22 bp):
TTTTATAAGTATATTAATGTAT
Found at i:19908 original size:22 final size:21
Alignment explanation
Indices: 19849--19913 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 21
19839 ATTATTTCAA
19849 GTTTTTTTATTTTTAATTAAT
1 GTTTTTTTATTTTTAATTAAT
*
19870 GTTTTGATGATATTTTTAATTAAT
1 GTTTT--T-TTATTTTTAATTAAT
19894 GTATTTTTTATTTTTAATTA
1 GT-TTTTTTATTTTTAATTA
19914 TTTTTATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.13
22 12 0.32
23 2 0.05
24 16 0.42
25 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (21 bp):
GTTTTTTTATTTTTAATTAAT
Found at i:20032 original size:21 final size:22
Alignment explanation
Indices: 19990--20032 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19980 AATAAAAGAG
*
19990 TTAAAAATAAAAATTATATTAA
1 TTAAAAATAAAAATAATATTAA
*
20012 TTAAAAGTAAAAATAAT-TTAA
1 TTAAAAATAAAAATAATATTAA
20033 AATATCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAAAATAAAAATAATATTAA
Found at i:20035 original size:38 final size:36
Alignment explanation
Indices: 19979--20066 Score: 88
Period size: 38 Copynumber: 2.4 Consensus size: 36
19969 TTGATTTTAT
* * *
19979 AAATAAAAGAGTTAAAAATA-AAAATTATATTAATTAA
1 AAATAAAAAAATTTAAAATACAAAA--ATATTAATTAA
* *
20016 AAGTAAAAATAATTTAAAATATCATAAATATTAATTAA
1 AAATAAAAA-AATTTAAAATA-CAAAAATATTAATTAA
20054 AAATAAAAAAATT
1 AAATAAAAAAATT
20067 GAAAGAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
37 11 0.26
38 28 0.67
40 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (36 bp):
AAATAAAAAAATTTAAAATACAAAAATATTAATTAA
Found at i:20065 original size:21 final size:21
Alignment explanation
Indices: 19990--20065 Score: 54
Period size: 22 Copynumber: 3.8 Consensus size: 21
19980 AATAAAAGAG
*
19990 TTAAAAATAAAAATTATATTAA
1 TTAAAAATAAAAA-AATATTAA
*
20012 TTAAAAGT---AAAA-A-TAA
1 TTAAAAATAAAAAAATATTAA
* * *
20028 TTTAAAATATCATAAATATTAA
1 TTAAAAATA-AAAAAATATTAA
20050 TTAAAAATAAAAAAAT
1 TTAAAAATAAAAAAAT
20066 TGAAAGAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 13
0.66 0.13 0.21
Matches are distributed among these distances:
16 9 0.22
17 1 0.03
18 1 0.03
19 2 0.05
20 3 0.08
21 6 0.15
22 18 0.45
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
TTAAAAATAAAAAAATATTAA
Found at i:22886 original size:16 final size:16
Alignment explanation
Indices: 22852--22897 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
22842 AATATTATTT
22852 ATTAATTTAA-TTT-TA
1 ATTAA-TTAATTTTCTA
22867 ATTAATTAATTTTCTA
1 ATTAATTAATTTTCTA
* *
22883 ATTAAATATTTTTCT
1 ATTAATTAATTTTCT
22898 CAACTAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 15 0.56
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTAATTAATTTTCTA
Found at i:25408 original size:23 final size:23
Alignment explanation
Indices: 25382--25433 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
25372 TATTCGGTTT
*
25382 ATTCGAGTT-ATTCGAATTTGAAA
1 ATTCGAGTTGATTCGAATTCG-AA
* *
25405 ATTCAATTTGATTCGAATTCGAA
1 ATTCGAGTTGATTCGAATTCGAA
25428 ATTCGA
1 ATTCGA
25434 AAAAAATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (23 bp):
ATTCGAGTTGATTCGAATTCGAA
Found at i:27468 original size:24 final size:24
Alignment explanation
Indices: 27436--27487 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
27426 TCACGTATCA
27436 ATACTTTAATTTTCCCAATTATTG
1 ATACTTTAATTTTCCCAATTATTG
*
27460 ATACTTTAATTTTCTCAATTATTG
1 ATACTTTAATTTTCCCAATTATTG
27484 ATAC
1 ATAC
27488 ATATACCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (24 bp):
ATACTTTAATTTTCCCAATTATTG
Found at i:31710 original size:312 final size:312
Alignment explanation
Indices: 31130--31776 Score: 859
Period size: 312 Copynumber: 2.1 Consensus size: 312
31120 CTCGAATGTC
* * *
31130 TTTT-CTAAGGCTAGCTGATTTAAGATAACAACCTCCGATTATTTGGGTTAGTTGATTTAAACTC
1 TTTTACTAAGGCTAGTTGATTTAAGATAACAACCTCCGATTATTTGAGTTAGCTGATTTAAACTC
* * *
31194 GCAACTCCTAATAGCTCGTTGACCTACGTTCATAGTTGATTTTACAAAGGCTCGCTGATTTAAGA
66 GCAACTCCTAACAGCTCGCTGACCTACGTTCATAGTTGATTTTACAAAGGCTCGCTGATATAAGA
* * * *
31259 TCGTAGCCTCCGATTATTTGAGATAGCTAATTTAAGATCGCAAATCTTAACAACTCGCTGACCTA
131 TCGCAACCTCCGATTATTTGAGATAGCTAATTTAAGATCGCAAATCCTAACAACTCACTGACCTA
* * * * ** **
31324 CTTTCACAACTGATTTTACTTAGGCTCGTTGATTTAAGATCGCAGCCTTTGATTATTTGAGTTGG
196 CTTTCACAACTGATTTTACTAAGGCTCGCTAATTTAAGATCGCAACCTTCAATTATTTGAGTTAA
* * *
31389 TTAATTTAAGATCGCAACTCCTAACAGCTCATTGACTTACTTTCACAGTTGA
261 CTAATTTAAGATCGCAACTCCTAACAGCTCATTGACCTACGTTCACAGTTGA
* ***
31441 TTTTACTAAGGCTCGTTGATTTAAGATCGTAACCTCCGATTATTTGAGTTAGCTGATTTAAGA-T
1 TTTTACTAAGGCTAGTTGATTTAAGATAACAACCTCCGATTATTTGAGTTAGCTGATTTAA-ACT
* * * * * * *
31505 TGCAACTTCTAACATCTCGCTGACTTATGTTCATAGTTGATTTTACTAAGGCTCGTTGATATAAG
65 CGCAACTCCTAACAGCTCGCTGACCTACGTTCATAGTTGATTTTACAAAGGCTCGCTGATATAAG
* * * * * *
31570 ATCGCAACCTCCGATTATTTGAGTTAGTTGATTTAAGATCGTAACTCCTAACAGCTCACTGACCT
130 ATCGCAACCTCCGATTATTTGAGATAGCTAATTTAAGATCGCAAATCCTAACAACTCACTGACCT
*
31635 A-TGTTTACAACTGATTTTACTAAGGCTCGCTAATTTAAGATCGCAACCTTCAATTATTTGAGTT
195 ACT-TTCACAACTGATTTTACTAAGGCTCGCTAATTTAAGATCGCAACCTTCAATTATTTGAGTT
* * *
31699 AACTGATTTAAGATCGCAACTCCTAATAGCTCGTTGACCTACGTTCACAGTTGA
259 AACTAATTTAAGATCGCAACTCCTAACAGCTCATTGACCTACGTTCACAGTTGA
* *
31753 TATTACTAAGGTTAGTTGATTTAA
1 TTTTACTAAGGCTAGTTGATTTAA
31777 AATAGCAGCC
Statistics
Matches: 288, Mismatches: 45, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
311 5 0.02
312 282 0.98
313 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (312 bp):
TTTTACTAAGGCTAGTTGATTTAAGATAACAACCTCCGATTATTTGAGTTAGCTGATTTAAACTC
GCAACTCCTAACAGCTCGCTGACCTACGTTCATAGTTGATTTTACAAAGGCTCGCTGATATAAGA
TCGCAACCTCCGATTATTTGAGATAGCTAATTTAAGATCGCAAATCCTAACAACTCACTGACCTA
CTTTCACAACTGATTTTACTAAGGCTCGCTAATTTAAGATCGCAACCTTCAATTATTTGAGTTAA
CTAATTTAAGATCGCAACTCCTAACAGCTCATTGACCTACGTTCACAGTTGA
Found at i:31775 original size:104 final size:104
Alignment explanation
Indices: 31130--31776 Score: 758
Period size: 104 Copynumber: 6.2 Consensus size: 104
31120 CTCGAATGTC
* * ** * *
31130 TTTT-CTAAGGCTAGCTGATTTAAGATAACAACCTCCGATTATTTGGGTTAGTTGATTTAA-ACT
1 TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGA-T
* * *
31193 CGCAACTCCTAATAGCTCGTTGACCTACGTTCATAGTTGA
65 CGCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
* * * * * *
31233 TTTTACAAAGGCTCGCTGATTTAAGATCGTAGCCTCCGATTATTTGAGATAGCTAATTTAAGATC
1 TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGATC
* * * * **
31298 GCAAATCTTAACAACTCGCTGACCTACTTTCACAACTGA
66 GCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
* * ** * * *
31337 TTTTACTTAGGCTCGTTGATTTAAGATCGCAGCCTTTGATTATTTGAGTTGGTTAATTTAAGATC
1 TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGATC
** * *
31402 GCAACTCCTAACAGCTCATTGACTTACTTTCACAGTTGA
66 GCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
* *
31441 TTTTACTAAGGCTCGTTGATTTAAGATCGTAACCTCCGATTATTTGAGTTAGCTGATTTAAGATT
1 TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGATC
* * * * *
31506 GCAACTTCTAACATCTCGCTGACTTATGTTCATAGTTGA
66 GCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
* *
31545 TTTTACTAAGGCTCGTTGATATAAGATCGCAACCTCCGATTATTTGAGTTAGTTGATTTAAGATC
1 TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGATC
* * * * **
31610 GTAACTCCTAACAGCTCACTGACCTATGTTTACAACTGA
66 GCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
* * * * *
31649 TTTTACTAAGGCTCGCTAATTTAAGATCGCAACCTTCAATTATTTGAGTTAACTGATTTAAGATC
1 TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGATC
* *
31714 GCAACTCCTAATAGCTCGTTGACCTACGTTCACAGTTGA
66 GCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
* * *
31753 TATTACTAAGGTTAGTTGATTTAA
1 TTTTACTAAGGCTCGTTGATTTAA
31777 AATAGCAGCC
Statistics
Matches: 457, Mismatches: 85, Indels: 3
0.84 0.16 0.01
Matches are distributed among these distances:
103 4 0.01
104 452 0.99
105 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (104 bp):
TTTTACTAAGGCTCGTTGATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATTTAAGATC
GCAACTCCTAACAGCTCGCTGACCTACGTTCACAGTTGA
Found at i:32633 original size:20 final size:19
Alignment explanation
Indices: 32599--32638 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
32589 ATTGGAATTC
**
32599 TGAAAATTTTTTAATCTTTT
1 TGAAAATTTAATAAT-TTTT
32619 TGAAAATTTAATAATTTTT
1 TGAAAATTTAATAATTTTT
32638 T
1 T
32639 AATTGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
TGAAAATTTAATAATTTTT
Found at i:41845 original size:13 final size:12
Alignment explanation
Indices: 41823--41857 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
41813 TACATATCTC
41823 ATTTTTTTATTT
1 ATTTTTTTATTT
41835 ATTTATTTTATTT
1 ATTT-TTTTATTT
41848 ATTTTTTTAT
1 ATTTTTTTAT
41858 GATGTGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:43371 original size:6 final size:6
Alignment explanation
Indices: 43360--43393 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
43350 AAGATACCAA
43360 AGAGCG AGAGCG AGAGCG AGAGCG AGAGCG AGAG
1 AGAGCG AGAGCG AGAGCG AGAGCG AGAGCG AGAG
43394 AGAAGGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGCG
Found at i:44077 original size:18 final size:18
Alignment explanation
Indices: 44054--44096 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44044 AGAATATGTT
44054 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
44072 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
44090 TTAATTA
1 TTAATTA
44097 CACCTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:62173 original size:2 final size:2
Alignment explanation
Indices: 62166--62203 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
62156 TCTATCTATC
62166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62204 ATGATAATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62300 original size:12 final size:13
Alignment explanation
Indices: 62282--62312 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
62272 AAGTAAACAG
62282 ATTTTTTTGTTTT
1 ATTTTTTTGTTTT
62295 -TTTTTTTGTTTT
1 ATTTTTTTGTTTT
62307 ATTTTT
1 ATTTTT
62313 GGCAGAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.87
Consensus pattern (13 bp):
ATTTTTTTGTTTT
Found at i:66020 original size:18 final size:16
Alignment explanation
Indices: 65988--66031 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
65978 ATGTGATGAG
65988 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
66004 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
66018 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
66032 ACTTTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:69613 original size:33 final size:33
Alignment explanation
Indices: 69570--69632 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
69560 TCTTAATTTG
*
69570 AAATTCAAATTAATCCTTTTAAAATCCTAACTA
1 AAATTCAAATTAATCATTTTAAAATCCTAACTA
* * *
69603 AAATTTAAATTATTCATTTTCAAATCCTAA
1 AAATTCAAATTAATCATTTTAAAATCCTAA
69633 TTGAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (33 bp):
AAATTCAAATTAATCATTTTAAAATCCTAACTA
Found at i:69719 original size:2 final size:2
Alignment explanation
Indices: 69712--69745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
69702 CCTAAACTCC
69712 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
69746 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:70095 original size:29 final size:28
Alignment explanation
Indices: 70062--70214 Score: 130
Period size: 28 Copynumber: 5.4 Consensus size: 28
70052 GTGTACCCGC
* *
70062 ATTTTACAAATTTTATAGTTTTGTCACT
1 ATTTTTCAAATTTTATAGTTTTGCCACT
*
70090 ATTTTTCAAATTTTATAATTTTGCCACT
1 ATTTTTCAAATTTTATAGTTTTGCCACT
* *
70118 AATTTTTCAAATTTTACAGTTCTGCCACT
1 -ATTTTTCAAATTTTATAGTTTTGCCACT
* * * *
70147 ATTTTTTTTAGATTTTACA-ATTTGCCACT
1 A--TTTTTCAAATTTTATAGTTTTGCCACT
* * *
70176 AGTTTTCCAAATTTT-TCAGTTCTGTCACT
1 A-TTTTTCAAATTTTAT-AGTTTTGCCACT
*
70205 ATTCTTCAAA
1 ATTTTTCAAA
70215 AAAAATTATA
Statistics
Matches: 100, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
28 44 0.44
29 42 0.42
30 14 0.14
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (28 bp):
ATTTTTCAAATTTTATAGTTTTGCCACT
Found at i:70187 original size:58 final size:59
Alignment explanation
Indices: 70062--70207 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 59
70052 GTGTACCCGC
* * *
70062 ATTTTACAAATTTTATAGTTTTGTCACTA--TTTTTCAAATTTTATAATTTTGCCACTA
1 ATTTTACAAATTTTACAGTTCTGTCACTATTTTTTTCAAATTTTACAATTTTGCCACTA
* * * *
70119 ATTTTTCAAATTTTACAGTTCTGCCACTATTTTTTTTAGATTTTACAA-TTTGCCACTA
1 ATTTTACAAATTTTACAGTTCTGTCACTATTTTTTTCAAATTTTACAATTTTGCCACTA
* * *
70177 GTTTTCCAAATTTTTCAGTTCTGTCACTATT
1 ATTTTACAAATTTTACAGTTCTGTCACTATT
70208 CTTCAAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
57 25 0.33
58 37 0.49
59 14 0.18
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (59 bp):
ATTTTACAAATTTTACAGTTCTGTCACTATTTTTTTCAAATTTTACAATTTTGCCACTA
Found at i:71236 original size:6 final size:6
Alignment explanation
Indices: 71227--71252 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
71217 TTATTTTTAT
71227 TATTAC TATTAC TATTAC TATTAC TA
1 TATTAC TATTAC TATTAC TATTAC TA
71253 CTATCGTTTA
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:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAC
Found at i:71859 original size:34 final size:35
Alignment explanation
Indices: 71816--71883 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
71806 TTTTGCTTAC
**
71816 TTGATTGTTTATGAT-TATGAATGAATTGAAATTA
1 TTGATTGTTTAAAATATATGAATGAATTGAAATTA
*
71850 TTGATTGTTTAAAATATGTGAATGAATTGAAATT
1 TTGATTGTTTAAAATATATGAATGAATTGAAATT
71884 TATAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.46
Consensus pattern (35 bp):
TTGATTGTTTAAAATATATGAATGAATTGAAATTA
Found at i:72465 original size:33 final size:32
Alignment explanation
Indices: 72422--72490 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
72412 TTAAATTTGA
*
72422 AATTAAAATTAATCCTTTTAAAATCCTAACTAG
1 AATTAAAATTAATCATTTTAAAATCCTAA-TAG
* * * *
72455 AATTCAAATTACTTATTTTCAAATCCTAATAG
1 AATTAAAATTAATCATTTTAAAATCCTAATAG
72487 AATT
1 AATT
72491 TATCTTTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.39
Consensus pattern (32 bp):
AATTAAAATTAATCATTTTAAAATCCTAATAG
Found at i:72971 original size:28 final size:28
Alignment explanation
Indices: 72888--73020 Score: 135
Period size: 28 Copynumber: 4.7 Consensus size: 28
72878 CAAATTGTAT
* * *
72888 AGTTTTGCCATTGTTTTTCCAAATTTTAC
1 AGTTTTGCCACTATTTTT-CAGATTTTAC
* * *
72917 AGTTTTGCCA-TAGGTTTTCCTGATTTTTC
1 AGTTTTGCCACTA--TTTTTCAGATTTTAC
*
72946 AGTTCTGCCACTATTTTTCAGATTTTAC
1 AGTTTTGCCACTATTTTTCAGATTTTAC
*
72974 AGTTTTGCCACTA-TTATCAGATTTTAC
1 AGTTTTGCCACTATTTTTCAGATTTTAC
* *
73001 AATTTTGCCACTATTCTTCA
1 AGTTTTGCCACTATTTTTCA
73021 AAAAAATTAC
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
27 25 0.29
28 29 0.34
29 26 0.30
30 6 0.07
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (28 bp):
AGTTTTGCCACTATTTTTCAGATTTTAC
Found at i:72993 original size:27 final size:28
Alignment explanation
Indices: 72888--73013 Score: 123
Period size: 29 Copynumber: 4.5 Consensus size: 28
72878 CAAATTGTAT
* *
72888 AGTTTTGCCA-TTGTTTTTCCAAATTTTAC
1 AGTTTTGCCACTAG-TTTT-CAGATTTTAC
* *
72917 AGTTTTGCCA-TAGGTTTTCCTGATTTTTC
1 AGTTTTGCCACTA-GTTTT-CAGATTTTAC
* *
72946 AGTTCTGCCACTATTTTTCAGATTTTAC
1 AGTTTTGCCACTAGTTTTCAGATTTTAC
*
72974 AGTTTTGCCACTA-TTATCAGATTTTAC
1 AGTTTTGCCACTAGTTTTCAGATTTTAC
*
73001 AATTTTGCCACTA
1 AGTTTTGCCACTA
73014 TTCTTCAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.30
28 20 0.24
29 36 0.43
30 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (28 bp):
AGTTTTGCCACTAGTTTTCAGATTTTAC
Found at i:73014 original size:27 final size:27
Alignment explanation
Indices: 72951--73015 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
72941 TTTTCAGTTC
* *
72951 TGCCACTATTTTTCAGATTTTACAGTTT
1 TGCCACTA-TTATCAGATTTTACAATTT
72979 TGCCACTATTATCAGATTTTACAATTT
1 TGCCACTATTATCAGATTTTACAATTT
73006 TGCCACTATT
1 TGCCACTATT
73016 CTTCAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 27 0.77
28 8 0.23
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (27 bp):
TGCCACTATTATCAGATTTTACAATTT
Found at i:86946 original size:20 final size:20
Alignment explanation
Indices: 86895--86969 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
86885 AGCAATTCTA
*
86895 ACTTGTTTGAAAATTATTTTG
1 ACTTGTTT-AAAATCATTTTG
*
86916 A--TGTGTTAAAATGATTTTG
1 ACTTGT-TTAAAATCATTTTG
*
86935 ACTTGTTTAAAATCATTTTA
1 ACTTGTTTAAAATCATTTTG
86955 ACTTGGTTTTAAAAT
1 ACTT-G-TTTAAAAT
86970 TGTTTCAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 15 0.33
20 18 0.39
21 5 0.11
22 8 0.17
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.49
Consensus pattern (20 bp):
ACTTGTTTAAAATCATTTTG
Found at i:91598 original size:23 final size:23
Alignment explanation
Indices: 91568--91615 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
91558 GCGATAGGAA
* *
91568 CTAAATCTGAATCTGTTATGCAT
1 CTAAATCTGAATCCGTTAAGCAT
91591 CTAAATCTGAATCCGTTAAGCAT
1 CTAAATCTGAATCCGTTAAGCAT
91614 CT
1 CT
91616 GACTTTGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (23 bp):
CTAAATCTGAATCCGTTAAGCAT
Found at i:91662 original size:23 final size:23
Alignment explanation
Indices: 91611--91655 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
91601 ATCCGTTAAG
*
91611 CATCTGACTTTGTATTTGTTATA
1 CATCTGAATTTGTATTTGTTATA
91634 CATCTGAATTTGT-TTCTGTTAT
1 CATCTGAATTTGTATT-TGTTAT
91656 GTATCTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (23 bp):
CATCTGAATTTGTATTTGTTATA
Found at i:93156 original size:45 final size:45
Alignment explanation
Indices: 93087--93174 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
93077 ACAAAAAATA
*
93087 ATCATCTTATCATTCATATCATATATCATAGTT-AACCAATTAACG
1 ATCATCTTATCATTCATATCATATAACATA-TTCAACCAATTAACG
* *
93132 ATCATCTTATCATTTGAT-TTATATAACATATTCAACCAATTAA
1 ATCATCTTATCA-TTCATATCATATAACATATTCAACCAATTAA
93175 TAATTATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.05
45 32 0.84
46 4 0.11
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (45 bp):
ATCATCTTATCATTCATATCATATAACATATTCAACCAATTAACG
Found at i:94187 original size:3 final size:3
Alignment explanation
Indices: 94179--94208 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
94169 TATGTGAAAA
94179 AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
94209 ATATAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:94214 original size:9 final size:10
Alignment explanation
Indices: 94178--94216 Score: 64
Period size: 9 Copynumber: 4.1 Consensus size: 10
94168 GTATGTGAAA
94178 AAATAATAAT
1 AAATAATAAT
94188 AAATAATAAT
1 AAATAATAAT
94198 -AATAATAAT
1 AAATAATAAT
94207 AAAT-ATAAT
1 AAATAATAAT
94216 A
1 A
94217 GGCTTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATAATAAT
Found at i:97170 original size:6 final size:6
Alignment explanation
Indices: 97159--97215 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
97149 TGATCAAAAT
** * *
97159 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGTGAT TGAAAT
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
97207 TGAAAG TGA
1 TGAAAG TGA
97216 TATGAATTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:100096 original size:25 final size:23
Alignment explanation
Indices: 100068--100113 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
100058 GTTGAATCCA
100068 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
100093 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
100114 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:104526 original size:104 final size:104
Alignment explanation
Indices: 104346--104548 Score: 370
Period size: 104 Copynumber: 2.0 Consensus size: 104
104336 GATAAAATAT
* *
104346 TCTAATAATAAATTTTGTGATATTCCAGTGATAGGGACTGGAAAAACCCAGATAATGTTGAGAAC
1 TCTAATAATAAATTTTGTGATATTCCAATGATAGGAACTGGAAAAACCCAGATAATGTTGAGAAC
104411 CTAAACCAAATAAAATTTATGGAAGATCATCTCATTGCG
66 CTAAACCAAATAAAATTTATGGAAGATCATCTCATTGCG
104450 TCTAATAATAAATTTTGTGATATTCCAATGATAGGAACTGGAAAAACCCAGATAATGTTGAGAAC
1 TCTAATAATAAATTTTGTGATATTCCAATGATAGGAACTGGAAAAACCCAGATAATGTTGAGAAC
* *
104515 CTAAATCAAATAAAATTTATGGAGGATCATCTCA
66 CTAAACCAAATAAAATTTATGGAAGATCATCTCA
104549 CTGCATCTCT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (104 bp):
TCTAATAATAAATTTTGTGATATTCCAATGATAGGAACTGGAAAAACCCAGATAATGTTGAGAAC
CTAAACCAAATAAAATTTATGGAAGATCATCTCATTGCG
Found at i:105731 original size:21 final size:21
Alignment explanation
Indices: 105694--105734 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
105684 GTTCTTTTAC
*
105694 TGTTTTGGTGTCTTTTTTTGA
1 TGTTTTGGTATCTTTTTTTGA
*
105715 TGTTTTGGTATTGTTTTTTT
1 TGTTTTGGTA-TCTTTTTTT
105735 TACTATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.05, C:0.02, G:0.22, T:0.71
Consensus pattern (21 bp):
TGTTTTGGTATCTTTTTTTGA
Found at i:105773 original size:15 final size:15
Alignment explanation
Indices: 105753--105818 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
105743 TGATGTCGTT
105753 TTGCTGTTATTTTTG
1 TTGCTGTTATTTTTG
*
105768 TTGCTG---TTTTTA
1 TTGCTGTTATTTTTG
* * *
105780 TTGCTATTTTTTTATT
1 TTGCTGTTATTTT-TG
105796 TTGCTGTTATTTTTG
1 TTGCTGTTATTTTTG
105811 TTGCTGTT
1 TTGCTGTT
105819 TTAGTTGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
12 10 0.24
15 19 0.46
16 12 0.29
ACGTcount: A:0.08, C:0.08, G:0.17, T:0.68
Consensus pattern (15 bp):
TTGCTGTTATTTTTG
Found at i:105798 original size:43 final size:44
Alignment explanation
Indices: 105751--105866 Score: 150
Period size: 43 Copynumber: 2.7 Consensus size: 44
105741 TTTGATGTCG
105751 TTTTGCTGTTATTTTTGTTGCTGTTTTTATTGCTATTTTT-TTA
1 TTTTGCTGTTATTTTTGTTGCTGTTTTTATTGCTATTTTTGTTA
* *
105794 TTTTGCTGTTATTTTTGTTGCTG-TTTTAGTTGTTATTTTTGTTG
1 TTTTGCTGTTATTTTTGTTGCTGTTTTTA-TTGCTATTTTTGTTA
* * *
105838 TTTGGATGTTATTTTT-ATGC-GTTTTTATT
1 TTTTGCTGTTATTTTTGTTGCTGTTTTTATT
105867 ATTATTTCGT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
42 8 0.12
43 41 0.63
44 16 0.25
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.68
Consensus pattern (44 bp):
TTTTGCTGTTATTTTTGTTGCTGTTTTTATTGCTATTTTTGTTA
Found at i:105809 original size:12 final size:12
Alignment explanation
Indices: 105751--105839 Score: 62
Period size: 12 Copynumber: 7.8 Consensus size: 12
105741 TTTGATGTCG
*
105751 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* *
105763 TTTTGTTGCTGT
1 TTTTGTTGTTAT
* *
105775 TTTTATTGCTA-
1 TTTTGTTGTTAT
105786 -TTT-TT-TTA-
1 TTTTGTTGTTAT
*
105794 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* *
105806 TTTTGTTGCTGT
1 TTTTGTTGTTAT
*
105818 TTTAGTTGTTAT
1 TTTTGTTGTTAT
105830 TTTTGTTGTT
1 TTTTGTTGTT
105840 TGGATGTTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
8 2 0.03
9 5 0.08
10 4 0.07
11 3 0.05
12 45 0.76
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:109224 original size:7 final size:7
Alignment explanation
Indices: 109212--109242 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
109202 ATTAAATTTG
109212 AAAATTA
1 AAAATTA
109219 AAAATTA
1 AAAATTA
109226 AAAATTA
1 AAAATTA
109233 AAAATTA
1 AAAATTA
109240 AAA
1 AAA
109243 TGAATTTGGG
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:116370 original size:13 final size:13
Alignment explanation
Indices: 116352--116376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116342 ATAAACTGTT
116352 ATATACATACATG
1 ATATACATACATG
116365 ATATACATACAT
1 ATATACATACAT
116377 ATTTTAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
ATATACATACATG
Found at i:117444 original size:41 final size:40
Alignment explanation
Indices: 117399--117477 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
117389 CTTTTAGTAG
117399 CGTTTGGACAGAAAACGCCGCAAAAGGTAAAGCAATAGCAA
1 CGTTTGGACA-AAAACGCCGCAAAAGGTAAAGCAATAGCAA
** * * *
117440 CGTTTTTATATAAACTCCGCAAAAGGTAAAGCAATAGC
1 CGTTTGGACAAAAACGCCGCAAAAGGTAAAGCAATAGC
117478 GGTGTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 26 0.79
41 7 0.21
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (40 bp):
CGTTTGGACAAAAACGCCGCAAAAGGTAAAGCAATAGCAA
Found at i:117516 original size:40 final size:41
Alignment explanation
Indices: 117411--117509 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 41
117401 TTTGGACAGA
117411 AAAC-GCCGCAAAAGGTAAAGCAATAGCAACGTTTTTATAT
1 AAACTGCCGCAAAAGGTAAAGCAATAGCAACGTTTTTATAT
*** *
117451 AAACT-CCGCAAAAGGTAAAGCAATAGCGGTGTTTTTTTAT
1 AAACTGCCGCAAAAGGTAAAGCAATAGCAACGTTTTTATAT
117491 AAA-TGCCGCAAAAGGTAAA
1 AAACTGCCGCAAAAGGTAAA
117510 AAAATAGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 52 0.98
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (41 bp):
AAACTGCCGCAAAAGGTAAAGCAATAGCAACGTTTTTATAT
Found at i:117580 original size:41 final size:41
Alignment explanation
Indices: 117531--117734 Score: 214
Period size: 41 Copynumber: 5.0 Consensus size: 41
117521 GTTTATAGAA
* *
117531 AAAACGCCGCTAAAGATCATAGCATTAGCGGCGCTTATGGG
1 AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTTATGAG
* * ** * *
117572 AAAGCGCCGCTAAAGTTCAGAGCATTAGCGATGCTTTTGGG
1 AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTTATGAG
* * * * *
117613 AAAACACCACTAAAGGTCGGAGCATTAGCAGCGCTTATGAG
1 AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTTATGAG
* * * *
117654 AAAACGTCGCTAAAGATCAGAGCATTAGCGGCTCTTCCA-CAC
1 AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTT--ATGAG
*
117696 AAAA-GCTGCTAAAGATCAGAGCATTAGCGGCGCTTATGA
1 AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTTATGA
117735 TAAAGCTCCA
Statistics
Matches: 131, Mismatches: 29, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 123 0.94
42 5 0.04
43 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAGATCAGAGCATTAGCGGCGCTTATGAG
Found at i:119628 original size:47 final size:48
Alignment explanation
Indices: 119560--119710 Score: 227
Period size: 47 Copynumber: 3.2 Consensus size: 48
119550 ATTTGTCCCC
*
119560 AAACCCC-AAATTTCTCTAATCCCTGATTTTTAATTTCTCCTCTCT-A
1 AAACCCCAAAATTTCTCTAATCCCTAATTTTTAATTTCTCCTCTCTCA
* * *
119606 AAACCCCAAAATTTCGCCAATCCTTAATTTTTAATTTCTCCTCTCTCA
1 AAACCCCAAAATTTCTCTAATCCCTAATTTTTAATTTCTCCTCTCTCA
* *
119654 AACCCCCAAAATTT-TCTAATCCCTAATTCTTAATTTCTCCTCTCTCA
1 AAACCCCAAAATTTCTCTAATCCCTAATTTTTAATTTCTCCTCTCTCA
119701 AAACCCCAAA
1 AAACCCCAAA
119711 TCCCAAATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
46 7 0.08
47 72 0.77
48 14 0.15
ACGTcount: A:0.30, C:0.32, G:0.01, T:0.36
Consensus pattern (48 bp):
AAACCCCAAAATTTCTCTAATCCCTAATTTTTAATTTCTCCTCTCTCA
Found at i:122577 original size:59 final size:59
Alignment explanation
Indices: 122485--122607 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
122475 GATTATCACA
122485 TCTTGATGTAAGATTTACTGCCAGTTGCTTTGCAGTGTTGTATGTCAAAAAAGGTGACG
1 TCTTGATGTAAGATTTACTGCCAGTTGCTTTGCAGTGTTGTATGTCAAAAAAGGTGACG
*
122544 TCTTGATGTAAGATTTATTGCCAGTTGCTTTGCAGTGTTGTATGTCAAAAAAGGTGACG
1 TCTTGATGTAAGATTTACTGCCAGTTGCTTTGCAGTGTTGTATGTCAAAAAAGGTGACG
122603 TCTTG
1 TCTTG
122608 TATAATTGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (59 bp):
TCTTGATGTAAGATTTACTGCCAGTTGCTTTGCAGTGTTGTATGTCAAAAAAGGTGACG
Found at i:125456 original size:18 final size:17
Alignment explanation
Indices: 125433--125483 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
125423 CAAACTCCCT
125433 TTAAATTTATGTTAAAAA
1 TTAAATTTAT-TTAAAAA
* *
125451 TTAAATTTGTTTCAAAAT
1 TTAAATTTATTT-AAAAA
125469 TTAAATTTATTTAAA
1 TTAAATTTATTTAAA
125484 TTTATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
TTAAATTTATTTAAAAA
Found at i:125476 original size:6 final size:6
Alignment explanation
Indices: 125465--125552 Score: 71
Period size: 6 Copynumber: 15.5 Consensus size: 6
125455 ATTTGTTTCA
* **
125465 AAATTT AAATTT --ATTT AAATTT -ATTTT AAATTT AAATTT -GTTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
125509 GAATTT AAATTT -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
125553 ATTATTATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
4 4 0.06
5 16 0.25
6 40 0.62
7 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (6 bp):
AAATTT
Found at i:125485 original size:28 final size:27
Alignment explanation
Indices: 125451--125567 Score: 91
Period size: 27 Copynumber: 4.3 Consensus size: 27
125441 ATGTTAAAAA
*
125451 TTAAATTTGTTTCAAAATTTAAATTTAT
1 TTAAATTTATTT-AAAATTTAAATTTAT
* *
125479 TTAAATTTATTTTAAATTTAAATTTGT
1 TTAAATTTATTTAAAATTTAAATTTAT
**
125506 TT---TGAATTT-AAATTT-AATTTAAGT
1 TTAAATTTATTTAAAATTTAAATTT-A-T
* *
125530 TTAAATTTATTTTCAAATTTAAAATTAT
1 TTAAATTTA-TTTAAAATTTAAATTTAT
125558 TATAAATTTA
1 T-TAAATTTA
125568 AGTAAAGCTC
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
22 5 0.07
23 6 0.08
24 8 0.11
27 17 0.24
28 16 0.23
29 15 0.21
30 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (27 bp):
TTAAATTTATTTAAAATTTAAATTTAT
Found at i:125494 original size:11 final size:10
Alignment explanation
Indices: 125467--125498 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
125457 TTGTTTCAAA
125467 ATTTAAATTT
1 ATTTAAATTT
125477 ATTTAAATTT
1 ATTTAAATTT
125487 ATTTTAAATTT
1 A-TTTAAATTT
125498 A
1 A
125499 AATTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:125499 original size:17 final size:17
Alignment explanation
Indices: 125477--125568 Score: 121
Period size: 17 Copynumber: 5.4 Consensus size: 17
125467 ATTTAAATTT
125477 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
125494 ATTTAAATTTGTTTTGA
1 ATTTAAATTTATTTTAA
*
125511 ATTTAAATTTAATTTAA
1 ATTTAAATTTATTTTAA
*
125528 GTTTAAATTTATTTTCAA
1 ATTTAAATTTATTTT-AA
* *
125546 ATTTAAAATTATTATAA
1 ATTTAAATTTATTTTAA
125563 ATTTAA
1 ATTTAA
125569 GTAAAGCTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 50 0.78
18 14 0.22
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:125524 original size:11 final size:11
Alignment explanation
Indices: 125466--125568 Score: 70
Period size: 11 Copynumber: 9.2 Consensus size: 11
125456 TTTGTTTCAA
125466 AATTTAAATTT
1 AATTTAAATTT
125477 -ATTTAAATTT
1 AATTTAAATTT
*
125487 ATTTTAAATTT
1 AATTTAAATTT
**
125498 AAATTT-GTTTT
1 -AATTTAAATTT
125509 GAATTTAAATTT
1 -AATTTAAATTT
*
125521 AATTTAAGTTT
1 AATTTAAATTT
*
125532 AAATTT-ATTTT
1 -AATTTAAATTT
*
125543 CAAATTTAAAATT
1 --AATTTAAATTT
125556 -ATTATAAATTT
1 AATT-TAAATTT
125567 AA
1 AA
125569 GTAAAGCTCA
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
10 13 0.18
11 37 0.51
12 19 0.26
13 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:127367 original size:30 final size:29
Alignment explanation
Indices: 127330--127537 Score: 211
Period size: 29 Copynumber: 7.4 Consensus size: 29
127320 CGAAAATTCT
**
127330 ATTTTTACCCTTGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCC
* *
127359 ATTTTTTA-CCCCGAAACTTCCTAAAATTCC
1 A-TTTTTACCCCCG-AACTTCCAAAAATCCC
127389 ATTTTTACCCCCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCC
** *
127418 ATTTTTAACCCCAAAACTTCCAAAAATTCC
1 ATTTTT-ACCCCCGAACTTCCAAAAATCCC
127448 ATTTTTACCCCCGAACTTCC-AAAA----
1 ATTTTTACCCCCGAACTTCCAAAAATCCC
**
127472 A----TACCCCGAAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCC
* *
127497 ATTTTTACCCTCGAACTTCCAAAAATCCT
1 ATTTTTACCCCCGAACTTCCAAAAATCCC
127526 ATTTTTGACCCC
1 ATTTTT-ACCCC
127538 AAAATTACCG
Statistics
Matches: 147, Mismatches: 18, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
20 13 0.09
21 4 0.03
24 1 0.01
25 1 0.01
28 4 0.03
29 68 0.46
30 56 0.38
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (29 bp):
ATTTTTACCCCCGAACTTCCAAAAATCCC
Found at i:127414 original size:59 final size:59
Alignment explanation
Indices: 127322--127537 Score: 272
Period size: 59 Copynumber: 3.8 Consensus size: 59
127312 TTTGACCCCG
* ** *
127322 AAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTTACCCCGAAACTTCCT
1 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAAACTTCCA
* *
127381 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAAACTTCCA
127440 AAAATTCCATTTTTACCCCCGAACTTCC-AAAA----A-----TACCCCGAAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAAACTTCCA
* * * *
127489 AAAATCCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTGACCCC
1 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCC
127538 AAAATTACCG
Statistics
Matches: 136, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
49 40 0.29
50 4 0.03
54 2 0.01
58 4 0.03
59 86 0.63
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.31
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAAACTTCCA
Found at i:127480 original size:19 final size:20
Alignment explanation
Indices: 127456--127493 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
127446 CCATTTTTAC
127456 CCCCG-AACTTCCAAAAATA
1 CCCCGAAACTTCCAAAAATA
127475 CCCCGAAACTTCCAAAAAT
1 CCCCGAAACTTCCAAAAAT
127494 CCCATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.37, G:0.05, T:0.16
Consensus pattern (20 bp):
CCCCGAAACTTCCAAAAATA
Found at i:127484 original size:49 final size:49
Alignment explanation
Indices: 127425--127522 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
127415 CCCATTTTTA
*
127425 ACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAAT
1 ACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAAT
* *
127474 ACCCCGAAACTTCCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAAT
1 ACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAAT
127523 CCTATTTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.38, C:0.35, G:0.03, T:0.24
Consensus pattern (49 bp):
ACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAAT
Found at i:128933 original size:21 final size:20
Alignment explanation
Indices: 128909--128958 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
128899 CTACAACTTA
128909 AAGCTGAGGCAGCAGCAAGGG
1 AAGC-GAGGCAGCAGCAAGGG
*
128930 AAGCAGAGGCAGCAGCGAGGG
1 AAGC-GAGGCAGCAGCAAGGG
128951 AAGCGAGG
1 AAGCGAGG
128959 GAAGCAGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.34, C:0.18, G:0.46, T:0.02
Consensus pattern (20 bp):
AAGCGAGGCAGCAGCAAGGG
Found at i:128964 original size:21 final size:21
Alignment explanation
Indices: 128909--128965 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
128899 CTACAACTTA
* *
128909 AAGCTGAGGCAGCAGCAAGGG
1 AAGCAGAGGAAGCAGCAAGGG
* *
128930 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGAAGCAGCAAGGG
128951 AAGC-GAGGGAAGCAG
1 AAGCAGA-GGAAGCAG
128966 AGGTAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.35, C:0.18, G:0.46, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGAAGCAGCAAGGG
Found at i:129193 original size:15 final size:15
Alignment explanation
Indices: 129173--129205 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
129163 ATTTGAAGTT
129173 ATTGGTTGGATTTAA
1 ATTGGTTGGATTTAA
*
129188 ATTGGTTGGATTTGA
1 ATTGGTTGGATTTAA
129203 ATT
1 ATT
129206 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTAA
Found at i:129337 original size:42 final size:42
Alignment explanation
Indices: 129272--129539 Score: 220
Period size: 43 Copynumber: 6.1 Consensus size: 42
129262 ATCTGTTAAT
* * *
129272 TTTAGCGGGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTC
1 TTTAGCGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
* * * * *
129314 TTTAGCGCGTTTATAGTAGAAGCG-TGCTAAAGACCATTTTC
1 TTTAGCGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
* *
129355 TTTAGCAGCTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
1 TTT---AGC---GC-G--TTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
* *
129406 TTTAGTGGCGTTTGTAGGAAAAGCGCAGCTAAAGACCATGTT-
1 TTTAG-CGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
* * *
129448 TTATAGCGGCGTTTAT-GGGAAAGCACCGCTAAAGACCATGTTC
1 TT-TAGC-GCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
* *
129491 TTTAGTGGCGTTTGT-GAGAAAAGCGCCGCTAAAAACCATGTTC
1 TTTAG-CGCGTTTGTAG-GAAAAGCGCCGCTAAAGACCATGTTC
*
129534 TATAGC
1 TTTAGC
129540 AGCAGTTTTC
Statistics
Matches: 180, Mismatches: 30, Indels: 32
0.74 0.12 0.13
Matches are distributed among these distances:
41 18 0.10
42 55 0.31
43 68 0.38
44 3 0.02
45 1 0.01
46 2 0.01
47 2 0.01
48 3 0.02
50 10 0.06
51 18 0.10
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (42 bp):
TTTAGCGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:129522 original size:85 final size:86
Alignment explanation
Indices: 129365--129539 Score: 273
Period size: 85 Copynumber: 2.0 Consensus size: 86
129355 TTTAGCAGCT
* *
129365 TAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTAGGAAAAGC
1 TAGCGGCATTTATGGGGAAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTAGGAAAAGC
* *
129430 GCAGCTAAAGACCATGTTTTA
66 GCAGCTAAAAACCATGTTCTA
*
129451 TAGCGGCGTTTAT-GGGAAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTGT-GAGAAAAG
1 TAGCGGCATTTATGGGGAAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTAG-GAAAAG
*
129514 CGCCGCTAAAAACCATGTTCTA
65 CGCAGCTAAAAACCATGTTCTA
129536 TAGC
1 TAGC
129540 AGCAGTTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
84 1 0.01
85 70 0.85
86 11 0.13
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (86 bp):
TAGCGGCATTTATGGGGAAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTAGGAAAAGC
GCAGCTAAAAACCATGTTCTA
Found at i:130195 original size:34 final size:34
Alignment explanation
Indices: 130146--130222 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
130136 GATGTTCAAC
* *
130146 CTTTAACCTCTCTTGACTTTTAACCTTTCT-TCTT
1 CTTTAACCTCCCTTGACCTTTAACCTTT-TATCTT
*
130180 CTTTAACGTCCCTTGACCTTTAACCTTTTATCTT
1 CTTTAACCTCCCTTGACCTTTAACCTTTTATCTT
*
130214 CCTTAACCT
1 CTTTAACCT
130223 TTCATATTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.17, C:0.31, G:0.04, T:0.48
Consensus pattern (34 bp):
CTTTAACCTCCCTTGACCTTTAACCTTTTATCTT
Found at i:135136 original size:17 final size:17
Alignment explanation
Indices: 135114--135175 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
135104 TGGATGTTCA
135114 ACTTTTAACCTCCCTTG
1 ACTTTTAACCTCCCTTG
* *
135131 ACTTTTAACCTTCCAT-
1 ACTTTTAACCTCCCTTG
135147 -CTTCCTTAACCTCCCTTG
1 ACTT--TTAACCTCCCTTG
*
135165 ACCTTTAACCT
1 ACTTTTAACCT
135176 TCTATCTTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 3 0.08
17 31 0.86
19 2 0.06
ACGTcount: A:0.19, C:0.37, G:0.03, T:0.40
Consensus pattern (17 bp):
ACTTTTAACCTCCCTTG
Found at i:135161 original size:34 final size:34
Alignment explanation
Indices: 135118--135192 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
135108 TGTTCAACTT
*
135118 TTAACCTCCCTTGACTTTTAACCTTCCATCTTCC
1 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
*
135152 TTAACCTCCCTTGACCTTTAACCTTCTATCTTCC
1 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
135186 TTAACCT
1 TTAACCT
135193 TTCTTATTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.19, C:0.37, G:0.03, T:0.41
Consensus pattern (34 bp):
TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
Found at i:135189 original size:17 final size:16
Alignment explanation
Indices: 135135--135193 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
135125 CCCTTGACTT
135135 TTAACCTTCCATCTTCC
1 TTAACCTT-CATCTTCC
*
135152 TTAACC-TC-CCTTGACC
1 TTAACCTTCATCTT--CC
135168 TTTAACCTTCTATCTTCC
1 -TTAACCTTC-ATCTTCC
135186 TTAACCTT
1 TTAACCTT
135194 TCTTATTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 3 0.09
17 20 0.59
18 4 0.12
20 3 0.09
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAACCTTCATCTTCC
Found at i:145017 original size:30 final size:30
Alignment explanation
Indices: 144977--145038 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
144967 AATTTATATC
*
144977 TTTATAATTTTTAA-AAGATTAAATTA-AATT
1 TTTATAA-TTTTAATAA-ATTAAAATATAATT
*
145007 TTTATTATTTTAATAAATTAAAATATAATT
1 TTTATAATTTTAATAAATTAAAATATAATT
145037 TT
1 TT
145039 ATGCTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTATAATTTTAATAAATTAAAATATAATT
Found at i:147276 original size:7 final size:7
Alignment explanation
Indices: 147264--147289 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
147254 CCTTCCTCTC
147264 TTTTTCT
1 TTTTTCT
147271 TTTTTCT
1 TTTTTCT
147278 TTTTTCT
1 TTTTTCT
147285 TTTTT
1 TTTTT
147290 TTCTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:147381 original size:30 final size:29
Alignment explanation
Indices: 147347--147412 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
147337 AATTTGTCTA
*
147347 TAGTCCTTGTACTTTTC-TTAATTAAAAATT
1 TAGTCCTTGTA-TTTACATT-ATTAAAAATT
* * *
147377 TAGTCTTTGTATTTACATTTTTATAAATT
1 TAGTCCTTGTATTTACATTATTAAAAATT
147406 TAGTCCT
1 TAGTCCT
147413 ATTTTTCGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (29 bp):
TAGTCCTTGTATTTACATTATTAAAAATT
Found at i:147827 original size:17 final size:18
Alignment explanation
Indices: 147807--147840 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
147797 ATTTTATTTG
147807 TATTTAAAA-AATAAAAT
1 TATTTAAAATAATAAAAT
147824 TATTTAAAATAATAAAA
1 TATTTAAAATAATAAAA
147841 CACATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATTTAAAATAATAAAAT
Found at i:149602 original size:10 final size:10
Alignment explanation
Indices: 149587--149624 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
149577 AAAGATTTGA
*
149587 ATATTTTTAT
1 ATATTTTAAT
149597 ATATTTTAAT
1 ATATTTTAAT
149607 ATATTTTAAT
1 ATATTTTAAT
149617 ATATTTTA
1 ATATTTTA
149625 TACTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTTAAT
Found at i:149618 original size:18 final size:18
Alignment explanation
Indices: 149566--149618 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
149556 TTTATTAAAA
* * *
149566 TTAAAATATTTAAAGATT
1 TTAATATATTTTAATATT
*
149584 TGAATAT-TTTTATATATT
1 TTAATATATTTTA-ATATT
149602 TTAATATATTTTAATAT
1 TTAATATATTTTAATAT
149619 ATTTTATACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TTAATATATTTTAATATT
Found at i:149633 original size:29 final size:28
Alignment explanation
Indices: 149581--149635 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
149571 ATATTTAAAG
149581 ATTTGAATATTTTTATATATTTTAATAT
1 ATTTGAATATTTTTATATATTTTAATAT
*
149609 ATTTTAATATATTTTATACT-TTTTAAT
1 ATTTGAATAT-TTTTATA-TATTTTAAT
149636 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 14 0.58
30 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTTGAATATTTTTATATATTTTAATAT
Found at i:150922 original size:63 final size:62
Alignment explanation
Indices: 150813--150941 Score: 143
Period size: 63 Copynumber: 2.1 Consensus size: 62
150803 ATTTTTAAAA
* ** * * * **
150813 TTTTTAGAGTTAGGTCTAAATTGATAGATTTTGTAAATGTTGAGGGCCAAATTT-ATTGACTTT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGGCCAAATTTGA-TGA-TTT
* *
150876 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTTAGGGCTAAATTTGATGATTT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGGCCAAATTTGATGATTT
150938 TTTT
1 TTTT
150942 ATATTTAGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
62 7 0.13
63 47 0.85
64 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (62 bp):
TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGGCCAAATTTGATGATTT
Found at i:154620 original size:21 final size:21
Alignment explanation
Indices: 154596--154639 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
154586 AATTCAGGTA
154596 TTAAATTA-AATAAAAAAAAAT
1 TTAAA-TACAATAAAAAAAAAT
*
154617 TTAAATACCAATAAGAAAAAAT
1 TTAAATA-CAATAAAAAAAAAT
154639 T
1 T
154640 CCAAATTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 5 0.25
22 13 0.65
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TTAAATACAATAAAAAAAAAT
Found at i:156547 original size:96 final size:96
Alignment explanation
Indices: 156370--156550 Score: 258
Period size: 96 Copynumber: 1.9 Consensus size: 96
156360 GAAAAGGATG
**
156370 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAACGCGCAAATTTTCAAAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAACGCGCAAATTTTCAAAATCGA
*
156435 AGATAAGGAAACATTGCCTCAATTAAGGGTA
66 AGATAAAGAAACATTGCCTCAATTAAGGGTA
* * * *
156466 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTCGAAACTCG
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAACGCGCAAATTTTC-AAAATCG
*
156531 AA-ATAAA-AGAATATTGCCTC
65 AAGATAAAGA-AACATTGCCTC
156551 GATTTTAAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
95 1 0.01
96 66 0.88
97 8 0.11
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAACGCGCAAATTTTCAAAATCGA
AGATAAAGAAACATTGCCTCAATTAAGGGTA
Found at i:156982 original size:30 final size:29
Alignment explanation
Indices: 156950--157199 Score: 200
Period size: 29 Copynumber: 8.5 Consensus size: 29
156940 AATCAAGATA
156950 AAAAATGGAATTTTTGGACA-TTCGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGT
* * ***
156979 -AAAATGGTAATTTTTTGAAAATTTTAGGGT
1 AAAAATGG-AA-TTTTTGGAAGTTCGGGGGT
* * *
157009 CAAAAATGAAATTTTTGGAGGTTCGGGAGT
1 -AAAAATGGAATTTTTGGAAGTTCGGGGGT
* * **
157039 AAAAATGTAATTTTTGAAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
** *
157068 AAAAATGGAATTTTTGGAAGTTTTGAGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
157097 CAAAAATGGAATTTTTGGAAGTTCGGCGGT
1 -AAAAATGGAATTTTTGGAAGTTCGGGGGT
* * **
157127 AAAAATGGAATTTTTTGAAGTTTCGAGATT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT
* *
157157 AAAAATAGAATTTTTGGAAATTTC-GGGGT
1 AAAAATGGAATTTTTGG-AAGTTCGGGGGT
* *
157186 AAAAGTGTAATTTT
1 AAAAATGGAATTTT
157200 CGAACAGTTT
Statistics
Matches: 174, Mismatches: 39, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
28 7 0.04
29 83 0.48
30 74 0.43
31 4 0.02
32 6 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:157024 original size:60 final size:58
Alignment explanation
Indices: 156897--157085 Score: 186
Period size: 59 Copynumber: 3.2 Consensus size: 58
156887 GATCAAGAAC
* * * * * * *
156897 GAAATTTGTGGATATCCGGGGGTAAAATGGTAATTTTTAGGAAAA-TCAAGATAAAAAAT
1 GAAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTT-TGAAAATTTAGGGT-AAAAAT
*
156956 GGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTTGAAAATTTTAGGGTCAAAAAT
1 GAAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTTGAAAA-TTTAGGGT-AAAAAT
** * *
157016 GAAATTTTTGGAGGTTCGGGAGTAAAAAT-GTAA-TTTTTGAAAGTTTAGGGGTAAAAAT
1 GAAATTTTTGGACATTCGGGGGT-AAAATGGTAATTTTTTGAAAATTTA-GGGTAAAAAT
*
157074 GGAATTTTTGGA
1 GAAATTTTTGGA
157086 AGTTTTGAGG
Statistics
Matches: 111, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
58 26 0.23
59 47 0.42
60 33 0.30
61 5 0.05
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
GAAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTTGAAAATTTAGGGTAAAAAT
Found at i:157110 original size:59 final size:58
Alignment explanation
Indices: 156950--157199 Score: 217
Period size: 59 Copynumber: 4.2 Consensus size: 58
156940 AATCAAGATA
* *
156950 AAAAATGGAATTTTTGGACA--TTCGGGGGT-AAAATGGTAATTTTTTGAAAATTTTA-GGGT
1 AAAAATGGAATTTTTGGA-AGTTTC-GAGGTAAAAATGG-AA-TTTTTG-AAAGTTTAGGGGT
* * * *
157009 CAAAAATGAAATTTTTGG-AGGTTCGGGAGTAAAAATGTAATTTTTGAAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGAG-GTAAAAATGGAATTTTTGAAAGTTTAGGGGT
* * *
157068 AAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAG-TTCGGCGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGAAAGTTTAGG-GGT
* * * *
157127 AAAAATGGAATTTTTTGAAGTTTCGAGATTAAAAATAGAATTTTTGGAAA-TTTCGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAG-GTAAAAATGGAATTTTT-GAAAGTTTAGGGGT
* *
157186 AAAAGTGTAATTTT
1 AAAAATGGAATTTT
157200 CGAACAGTTT
Statistics
Matches: 162, Mismatches: 17, Indels: 23
0.80 0.08 0.11
Matches are distributed among these distances:
58 30 0.19
59 94 0.58
60 32 0.20
61 6 0.04
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGAAAGTTTAGGGGT
Found at i:158967 original size:6 final size:6
Alignment explanation
Indices: 158956--159005 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
158946 ATTTTGAAAA
* * * *
158956 TAAATT TAAATT CAAATT TAAA-A TAAATC TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
159002 TAAA
1 TAAA
159006 ATGGGCCTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATT
Found at i:158989 original size:17 final size:17
Alignment explanation
Indices: 158969--159005 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
158959 ATTTAAATTC
158969 AAATTTAAAATAAATCT
1 AAATTTAAAATAAATCT
*
158986 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATCT
159003 AAA
1 AAA
159006 ATGGGCCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAAATAAATCT
Found at i:158999 original size:11 final size:11
Alignment explanation
Indices: 158952--159007 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
158942 TTAAATTTTG
158952 AAAATAAATTT
1 AAAATAAATTT
*
158963 AAATTCAAATTT
1 AAAAT-AAATTT
158975 AAAATAAA--T
1 AAAATAAATTT
*
158984 ---CTAAATTT
1 AAAATAAATTT
158992 AAAATAAATTT
1 AAAATAAATTT
159003 AAAAT
1 AAAAT
159008 GGGCCTGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
6 4 0.11
8 1 0.03
9 1 0.03
11 19 0.54
12 10 0.29
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:159673 original size:193 final size:199
Alignment explanation
Indices: 159337--159919 Score: 716
Period size: 193 Copynumber: 2.9 Consensus size: 199
159327 CTTTGGCCTT
* * * ** ** * * *
159337 CTTCTCAGTATCTCA-TCAGAGAGACGACCGCATCACTTGTTTTGATCCATTTCTCTGTGTTTTA
1 CTTCTCTGTATCTCATTAAGA-AGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCA
* * *
159401 TCAGGAAGACGGATTTGGTTCACTTCCCCGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTTG
65 TCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTTG
* * *
159466 CTCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTCGGAGATTTGTTCGCATTGA-GTTGG-T-
130 CCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGGTCGAAGATTTGTTCGCATTGACGTGGGTTG
159527 A-T-A
195 ATTGA
* *
159530 CTTCTCTGTATCTCATTAAGAAGATGACCCCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATTAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
*
159595 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTG-TTTCG
66 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTT-G
*
159659 CCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTCGCATTGAGCGTGGGTT
130 CCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGGTCGAAGATTTGTTCGCATTGA-CGTGGG-T
*
159724 TGATTTGGT
193 TGA-TT-GA
* * * *** * * *
159733 CTTCTTCTCAGTATCTCATCAAGAAGGTGACTGCATTGTTTATCTCAATCTGCTTCTCTGTATCT
1 CTTC-TCT--GTATCTCATTAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCT
159798 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAA-CTTTTTATTGCTT
63 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTT
** * *
159862 TGCCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGGTTTAAGATTTGCTCGCTTTGA
128 TGCCCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGGTCGAAGATTTGTTCGCATTGA
159920 GCCTTTTTTC
Statistics
Matches: 336, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
192 3 0.01
193 133 0.40
194 27 0.08
196 4 0.01
198 1 0.00
199 1 0.00
201 1 0.00
203 4 0.01
204 3 0.01
205 62 0.18
206 97 0.29
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (199 bp):
CTTCTCTGTATCTCATTAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTTGC
CCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGGTCGAAGATTTGTTCGCATTGACGTGGGTTGA
TTGA
Found at i:171322 original size:96 final size:96
Alignment explanation
Indices: 171145--171329 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
171135 TGGAATGATG
** * * *
171145 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTTGTAAGTTAAGGCGTAATTTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGAAAGTTAAGGCGTAATTTTTCAGAATCGA
*
171210 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
* * *
171241 TTCGATTATTTTGATTTGAAGAAAAATTACACCTAGAAAGTTAAGGCGTAAATTTTTGA-AACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGAAAGTTAAGGCGT-AATTTTTCAGAA-TC
*
171305 GAA-ATAAA-AGAATATTGCCTCGATT
64 GAAGATAAAGA-AACATTGCCTCGATT
171330 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 62 0.82
97 13 0.17
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGAAAGTTAAGGCGTAATTTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:171669 original size:60 final size:58
Alignment explanation
Indices: 171595--171909 Score: 298
Period size: 60 Copynumber: 5.3 Consensus size: 58
171585 AAAAAGGATC
* * * * *
171595 AAAAATAGAATTTTTAGACATTCGGAGGT-AAAATGGTAATTTTTTGAAAGTTTCGGGGTT
1 AAAAATGGAATTTTTGGAGATTCGGAGGTAAAAATGG-AA-TTTTTGGAAGTTTAGGGG-T
* * * *
171655 AAAAATGTAATTTTTAGAGGTTC-GAGGGTAAAAATGTAATTTTTGGAAGTTT-GTGGGT
1 AAAAATGGAATTTTTGGAGATTCGGA-GGTAAAAATGGAATTTTTGGAAGTTTAG-GGGT
* *
171713 AAAAATGAAATTTTTGGAGGTTCGG-GAGTAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAGATTCGGAG-GTAAAAATGGAATTTTTGGAAGTTTAGGGGT
* ** * *
171771 AAAAATGTAATTTTTGGA-AGTTTTGAGGGTTAAAAATGGAATTTTTGGAATTTTAAGGGT
1 AAAAATGGAATTTTTGGAGA-TTCGGA-GG-TAAAAATGGAATTTTTGGAAGTTTAGGGGT
* * * * *
171831 AAAAATGGAATTTTTGGATGTTTTGGGGGGTAAAAATGGAATTTTTTGAAGTTTCGGGGTT
1 AAAAATGGAATTTTTGGA-G-ATTCGGAGGTAAAAATGGAATTTTTGGAAGTTTAGGGG-T
171892 AAAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
171910 AATTTAAGGG
Statistics
Matches: 217, Mismatches: 24, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.00
58 71 0.33
59 20 0.09
60 95 0.44
61 27 0.12
62 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAGATTCGGAGGTAAAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:171897 original size:30 final size:29
Alignment explanation
Indices: 171615--171934 Score: 324
Period size: 29 Copynumber: 10.8 Consensus size: 29
171605 TTTTTAGACA
*
171615 TTCGGAGGT-AAAATGGTAATTTTTTGAAAGT
1 TTCGG-GGTAAAAATGG-AA-TTTTTGGAAGT
* * *
171646 TTCGGGGTTAAAAATGTAATTTTTAG-AGG
1 TTCGGGG-TAAAAATGGAATTTTTGGAAGT
*
171675 TTCGAGGGTAAAAATGTAATTTTTGGAAGT
1 TTCG-GGGTAAAAATGGAATTTTTGGAAGT
* *
171705 TT-GTGGGTAAAAATGAAATTTTTGG-AGG
1 TTCG-GGGTAAAAATGGAATTTTTGGAAGT
171733 TTCGGGAGTAAAAATGGAATTTTTGGAAGT
1 TTCGGG-GTAAAAATGGAATTTTTGGAAGT
* *
171763 TTAGGGGTAAAAATGTAATTTTTGGAAGT
1 TTCGGGGTAAAAATGGAATTTTTGGAAGT
* *
171792 TTTGAGGGTTAAAAATGGAATTTTTGGAATT
1 TTCG-GGG-TAAAAATGGAATTTTTGGAAGT
** *
171823 TTAAGGGTAAAAATGGAATTTTTGGATGTT
1 TTCGGGGTAAAAATGGAATTTTTGGAAG-T
* *
171853 TTGGGGGGTAAAAATGGAATTTTTTGAAGT
1 TT-CGGGGTAAAAATGGAATTTTTGGAAGT
*
171883 TTCGGGGTTAAAAATGGAATTTTTGGAAAT
1 TTCGGGG-TAAAAATGGAATTTTTGGAAGT
** *
171913 TTAAGGGTAAAAATGTAATTTT
1 TTCGGGGTAAAAATGGAATTTT
171935 CGAATAGTTT
Statistics
Matches: 247, Mismatches: 30, Indels: 26
0.82 0.10 0.09
Matches are distributed among these distances:
28 6 0.02
29 125 0.51
30 58 0.23
31 52 0.21
32 6 0.02
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
TTCGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:173721 original size:6 final size:6
Alignment explanation
Indices: 173710--173793 Score: 88
Period size: 6 Copynumber: 14.7 Consensus size: 6
173700 ATTTTGAAAA
173710 TAAATT TAAATT TAAA-T TAAATT TAAATT TAAGA-T T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT
* * * *
173756 CAAATT TAAA-A TAAATC TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
173794 AGGGGCCCGG
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
4 1 0.02
5 16 0.25
6 47 0.72
7 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:173732 original size:17 final size:17
Alignment explanation
Indices: 173695--173793 Score: 87
Period size: 17 Copynumber: 5.7 Consensus size: 17
173685 TAATAATTCT
*
173695 TTTAAATTTTGAAAATAAA
1 TTTAAA-TTT-AAATTAAA
173714 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
173731 TTTAAATTTAAGATT-AA
1 TTTAAATTTAA-ATTAAA
*
173748 TTTAAATTCAAATTTAAA
1 TTTAAATTTAAA-TTAAA
* *
173766 -ATAAATCTAAATTTAAA
1 TTTAAATTTAAA-TTAAA
*
173783 -ATAAATTTAAA
1 TTTAAATTTAAA
173794 AGGGGCCCGG
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
16 1 0.01
17 56 0.79
18 8 0.11
19 6 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:173736 original size:23 final size:22
Alignment explanation
Indices: 173711--173782 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 22
173701 TTTTGAAAAT
173711 AAATTTAAATTTAAATTAAATTT
1 AAATTTAAA-TTAAATTAAATTT
* *
173734 AAATTTAAGATTAATTTAAATTC
1 AAATTTAA-ATTAAATTAAATTT
*
173757 AAATTTAAAATAAATCTAAATTT
1 AAATTTAAATTAAAT-TAAATTT
173780 AAA
1 AAA
173783 ATAAATTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 5 0.12
23 36 0.86
24 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (22 bp):
AAATTTAAATTAAATTAAATTT
Found at i:173794 original size:11 final size:11
Alignment explanation
Indices: 173706--173794 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
173696 TTAAATTTTG
173706 AAAATAAATTT
1 AAAATAAATTT
*
173717 AAATTTAAA-TT
1 AAA-ATAAATTT
*
173728 AAATTTAAATTT
1 AAA-ATAAATTT
* *
173740 AAGATTAATTT
1 AAAATAAATTT
*
173751 AAATTCAAATTT
1 AAAAT-AAATTT
173763 AAAATAAA--T
1 AAAATAAATTT
*
173772 ---CTAAATTT
1 AAAATAAATTT
173780 AAAATAAATTT
1 AAAATAAATTT
173791 AAAA
1 AAAA
173795 GGGGCCCGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
6 4 0.07
8 1 0.02
9 1 0.02
11 37 0.62
12 17 0.28
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:177053 original size:19 final size:19
Alignment explanation
Indices: 177011--177053 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
177001 AGAACTAAAA
* *
177011 CTAAATTGAAACTAAATTT
1 CTAAACTGAAACTAAACTT
* *
177030 TTAAACTGAAATTAAACTT
1 CTAAACTGAAACTAAACTT
177049 CTAAA
1 CTAAA
177054 ATCTACTCTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (19 bp):
CTAAACTGAAACTAAACTT
Found at i:180604 original size:12 final size:12
Alignment explanation
Indices: 180579--180611 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
180569 CTTATCAAGA
180579 TAAATATTAAAT
1 TAAATATTAAAT
180591 TAAAT-TTAATAT
1 TAAATATTAA-AT
180603 TAAATATTA
1 TAAATATTA
180612 TTAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:180626 original size:19 final size:21
Alignment explanation
Indices: 180578--180629 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
180568 ACTTATCAAG
180578 ATAAATATTAAATTAAATTTAAT
1 ATAAATATT--ATTAAATTTAAT
180601 ATTAAATATTATTAAA-TTAAT
1 A-TAAATATTATTAAATTTAAT
180622 A-AAATATT
1 ATAAATATT
180630 TATCTACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
21 6 0.21
22 6 0.21
23 1 0.04
24 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAATATTATTAAATTTAAT
Found at i:181577 original size:26 final size:27
Alignment explanation
Indices: 181530--181581 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
181520 CAAATGATTT
181530 TAAAATTATTAAAATTAGTTTAAAATA
1 TAAAATTATTAAAATTAGTTTAAAATA
*
181557 TAAAATTATT-AAATTATTTTAAAAT
1 TAAAATTATTAAAATTAGTTTAAAAT
181582 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAAATTATTAAAATTAGTTTAAAATA
Found at i:181587 original size:11 final size:10
Alignment explanation
Indices: 181528--181586 Score: 58
Period size: 11 Copynumber: 6.3 Consensus size: 10
181518 AACAAATGAT
181528 TTTAAAATTA
1 TTTAAAATTA
181538 -TTAAAATTA
1 TTTAAAATTA
181547 GTTTAAAA-TA
1 -TTTAAAATTA
181557 --TAAAATTA
1 TTTAAAATTA
181565 -TT-AAATTA
1 TTTAAAATTA
181573 TTTTAAAATTA
1 -TTTAAAATTA
181584 TTT
1 TTT
181587 TTAAAATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
7 5 0.12
8 8 0.19
9 10 0.24
10 7 0.17
11 12 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:181590 original size:12 final size:11
Alignment explanation
Indices: 181521--181593 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
181511 TCATGTCAAC
*
181521 AAATGATTTTA
1 AAATTATTTTA
181532 AAATTA--TTA
1 AAATTATTTTA
*
181541 AAATTAGTTTA
1 AAATTATTTTA
181552 AAA-TA---TA
1 AAATTATTTTA
181559 AAATTA--TT-
1 AAATTATTTTA
181567 AAATTATTTTA
1 AAATTATTTTA
181578 AAATTATTTTTA
1 AAATTA-TTTTA
181590 AAAT
1 AAAT
181594 ATAAAACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
7 5 0.09
8 8 0.15
9 10 0.19
10 4 0.08
11 17 0.32
12 9 0.17
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:181594 original size:38 final size:38
Alignment explanation
Indices: 181529--181612 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
181519 ACAAATGATT
*
181529 TTAAAATTA--TTAAAATTAGTTTAAAATATAAAATTA
1 TTAAAATTATTTTAAAATTAGTTTAAAATATAAAACTA
*
181565 TT-AAATTATTTTAAAATTATTTTTAAAATATAAAACTA
1 TTAAAATTATTTTAAAATTA-GTTTAAAATATAAAACTA
181603 TTAAAATTAT
1 TTAAAATTAT
181613 AATCATTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 6 0.14
36 2 0.05
37 9 0.21
38 18 0.43
39 7 0.17
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (38 bp):
TTAAAATTATTTTAAAATTAGTTTAAAATATAAAACTA
Found at i:181598 original size:19 final size:19
Alignment explanation
Indices: 181521--181614 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
181511 TCATGTCAAC
*
181521 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTA-TA
*
181541 AAATTAGTTTAAAA-TATA
1 AAATTATTTTAAAATTATA
*
181559 AAATTA--TTAAATTATTTTA
1 AAATTATTTTAAA--ATTATA
181578 AAATTATTTTTAAAA-TATA
1 AAATTA-TTTTAAAATTATA
*
181597 AAACTA--TTAAAATTATA
1 AAATTATTTTAAAATTATA
181614 A
1 A
181615 TCATTATCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
16 11 0.18
17 5 0.08
18 9 0.15
19 19 0.31
20 13 0.21
22 5 0.08
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATTATTTTAAAATTATA
Found at i:182474 original size:37 final size:35
Alignment explanation
Indices: 182413--182493 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 35
182403 GTGATTTTGA
*
182413 TGAGAAGAAGAAATAGTGTTGGATG-GAAAAATGG
1 TGAGAAGAAGAAATAGTGTTGGATGAAAAAAATGG
* *
182447 TGAGAAGAAGAAGTGGTGTTAGAGGATGAAAAAAATGG
1 TGAGAAGAAGAAATAGTGTT---GGATGAAAAAAATGG
182485 -GA-AAGAAGA
1 TGAGAAGAAGA
182494 TGAAATTGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 18 0.45
36 7 0.17
37 7 0.17
38 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.17
Consensus pattern (35 bp):
TGAGAAGAAGAAATAGTGTTGGATGAAAAAAATGG
Found at i:182585 original size:28 final size:29
Alignment explanation
Indices: 182549--182623 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 29
182539 AAAATTATTT
182549 AATAATTTTTATAATTTTATATTT-AAAA
1 AATAATTTTTATAATTTTATATTTAAAAA
* **
182577 AAT-ATTTTTAAAAAATTATATTTAAAAA
1 AATAATTTTTATAATTTTATATTTAAAAA
*
182605 AATAATTTTAATAATTTTA
1 AATAATTTTTATAATTTTA
182624 AAATTATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 17 0.45
28 10 0.26
29 11 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATAATTTTTATAATTTTATATTTAAAAA
Found at i:182588 original size:13 final size:13
Alignment explanation
Indices: 182570--182615 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
182560 TAATTTTATA
182570 TTTAAAAAATATT
1 TTTAAAAAATATT
182583 TTTAAAAAATTATAT
1 TTTAAAAAA-TAT-T
* *
182598 TTAAAAAAATAAT
1 TTTAAAAAATATT
182611 TTTAA
1 TTTAA
182616 TAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 14 0.50
14 5 0.18
15 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:182590 original size:14 final size:14
Alignment explanation
Indices: 182573--182615 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
182563 TTTTATATTT
182573 AAAAAATATTTTTA
1 AAAAAATATTTTTA
* *
182587 AAAAATTATATTTA
1 AAAAAATATTTTTA
*
182601 AAAAAATAATTTTA
1 AAAAAATATTTTTA
182615 A
1 A
182616 TAATTTTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATATTTTTA
Found at i:182620 original size:27 final size:26
Alignment explanation
Indices: 182549--182620 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
182539 AAAATTATTT
*
182549 AATAATTTTTATAATTTTATATTTAAAA
1 AATAATTTTAATAA--TTATATTTAAAA
* *
182577 AATATTTTTAAAAAATTATATTTAAAAA
1 AATAATTTT-AATAATTATATTT-AAAA
182605 AATAATTTTAATAATT
1 AATAATTTTAATAATT
182621 TTAAAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 14 0.38
28 20 0.54
29 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATAATTTTAATAATTATATTTAAAA
Found at i:198383 original size:43 final size:43
Alignment explanation
Indices: 198322--198410 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
198312 CATGTGTGTG
198322 TAAGCATTGATGAATGAATCAGTGTCCTATTTGATTATGATGT
1 TAAGCATTGATGAATGAATCAGTGTCCTATTTGATTATGATGT
* * *
198365 TAAGCGTTGATGAATGAATCGGTGTCCTGTTTGATTATGATGT
1 TAAGCATTGATGAATGAATCAGTGTCCTATTTGATTATGATGT
198408 TAA
1 TAA
198411 CGATATGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (43 bp):
TAAGCATTGATGAATGAATCAGTGTCCTATTTGATTATGATGT
Found at i:205484 original size:141 final size:137
Alignment explanation
Indices: 205323--205577 Score: 327
Period size: 141 Copynumber: 1.8 Consensus size: 137
205313 TTATTATTTG
* * * *
205323 TAATATGATGCATTTTTGTGTTTAAAATTCATTTCACTTATAATTTAATTTATTCTTTTTTATTT
1 TAATATGATACATTTATGTGTTTAAAATTCATTTCACTTACAATTT-A--T-TT-TTTTTCATTT
* *
205388 TAATGT-CATACGTATTTCGT-TGA-TATTATTAATTAATTTCAAACCATAAGTTTTTTTATTGT
61 TAAT-TCCATACATATTTCATAT-ACTATTATTAATTAATTTCAAACCATAAGTTTTTTTATTGT
205450 ATGTTATTTATTCT
124 ATGTTATTTATTCT
* * *
205464 TAATATGATATATTTATGTGTTTAAAATTCATTTCACTTGCAATTTATTTTTTTTCATTTTAGTT
1 TAATATGATACATTTATGTGTTTAAAATTCATTTCACTTACAATTTATTTTTTTTCATTTTAATT
* *
205529 CCATACATATTTCATATACTATTATTAATTAGTTTCAAACCATACGTTT
66 CCATACATATTTCATATACTATTATTAATTAATTTCAAACCATAAGTTT
205578 AAAATTCATT
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
135 1 0.01
136 25 0.25
137 31 0.31
138 1 0.01
140 1 0.01
141 41 0.41
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.53
Consensus pattern (137 bp):
TAATATGATACATTTATGTGTTTAAAATTCATTTCACTTACAATTTATTTTTTTTCATTTTAATT
CCATACATATTTCATATACTATTATTAATTAATTTCAAACCATAAGTTTTTTTATTGTATGTTAT
TTATTCT
Found at i:205583 original size:91 final size:87
Alignment explanation
Indices: 205483--205665 Score: 260
Period size: 87 Copynumber: 2.1 Consensus size: 87
205473 ATATTTATGT
**
205483 GTTTAAAATTCATTTCACTTGCAATTTATTTTTTTTCATTTTAGTTCCATA-CATATTTCATATA
1 GTTTAAAATTCATTTCACTCACAATTTATTTTTTTTCATTTTA-----ATACCATATTTCATATA
205547 CTATTATTAATTAGTTTCAAACCATAC
61 CTATTATTAATTAGTTTCAAACCATAC
* **
205574 GTTTAAAATTCATTTCACTCACAATTTATTTTTTTTCATTTTAATACCATATTTCATGTGTTATT
1 GTTTAAAATTCATTTCACTCACAATTTATTTTTTTTCATTTTAATACCATATTTCATATACTATT
205639 ATTAATTAGTTTCAAACCATAC
66 ATTAATTAGTTTCAAACCATAC
*
205661 ATTTA
1 GTTTA
205666 TTTATTTATT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
86 3 0.04
87 41 0.48
91 41 0.48
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (87 bp):
GTTTAAAATTCATTTCACTCACAATTTATTTTTTTTCATTTTAATACCATATTTCATATACTATT
ATTAATTAGTTTCAAACCATAC
Done.