Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 3 of 345
Found at i:840841 original size:13 final size:13
Alignment explanation
Indices: 840823--840847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
840813 CATGTATGGG
840823 TTTTTTATTTTTA
1 TTTTTTATTTTTA
840836 TTTTTTATTTTT
1 TTTTTTATTTTT
840848 TTTGGTTCTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:844294 original size:5 final size:5
Alignment explanation
Indices: 844284--844322 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
844274 GCCTAAGATG
* *
844284 TGAAT TGAAT TGAAT TGAAT ATAAAT TGTAT TGAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
844323 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:844310 original size:21 final size:20
Alignment explanation
Indices: 844286--844330 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
844276 CTAAGATGTG
844286 AATTGAATTGAATTGAATATA
1 AATTGAATTGAATTGAAT-TA
* *
844307 AATTGTATTGAATTGAGTTA
1 AATTGAATTGAATTGAATTA
844327 AATT
1 AATT
844331 TACTCGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (20 bp):
AATTGAATTGAATTGAATTA
Found at i:844817 original size:26 final size:26
Alignment explanation
Indices: 844788--844851 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
844778 TGTTATATGA
844788 CTCTTCGTGAGCTTCCCGATTAAAGG
1 CTCTTCGTGAGCTTCCCGATTAAAGG
* * * *
844814 CTCTTTGTAAGCTTCCTGATTAATGG
1 CTCTTCGTGAGCTTCCCGATTAAAGG
*
844840 CTCTCCG-GAGCT
1 CTCTTCGTGAGCT
844852 ACCTGATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (26 bp):
CTCTTCGTGAGCTTCCCGATTAAAGG
Found at i:844923 original size:24 final size:24
Alignment explanation
Indices: 844896--844948 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
844886 TGGCTATCCG
*
844896 GAGCTACCTG-TTATTGGCTCGCAT
1 GAGCTACCTGATTA-TAGCTCGCAT
**
844920 GAGCTTTCTGATTATAGCTCGCAT
1 GAGCTACCTGATTATAGCTCGCAT
844944 GAGCT
1 GAGCT
844949 TCTCGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.34
Consensus pattern (24 bp):
GAGCTACCTGATTATAGCTCGCAT
Found at i:845018 original size:23 final size:23
Alignment explanation
Indices: 844971--845018 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
844961 GCCCAGATAG
844971 GCTTCCCGTTAATGGCTCTCAAGA
1 GCTTCCCGTTAATGGC-CTCAAGA
*
844995 GCTTCCTGTTATATGG-CTCAAGA
1 GCTTCCCGTTA-ATGGCCTCAAGA
845018 G
1 G
845019 AGGGCTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 10 0.45
25 4 0.18
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (23 bp):
GCTTCCCGTTAATGGCCTCAAGA
Found at i:846176 original size:2 final size:2
Alignment explanation
Indices: 846171--846198 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
846161 GTGTGTGGAA
846171 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
846199 CATACATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:849160 original size:23 final size:23
Alignment explanation
Indices: 849078--849164 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
849068 CCTGATCAGT
*
849078 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
849100 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
849120 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
849143 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
849165 TCGATAAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:849562 original size:15 final size:15
Alignment explanation
Indices: 849536--849592 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
849526 CATATATATT
849536 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
849550 ATATAATTTCAATCA
1 ATATAATTTCAATCA
* *
849565 AAATAATTTAAATCA
1 ATATAATTTCAATCA
*
849580 ATATAAATTCAAT
1 ATATAATTTCAAT
849593 AAATTCATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:852263 original size:17 final size:18
Alignment explanation
Indices: 852231--852265 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
852221 ACAATAATTA
852231 CATAAATAATTAAAAAAT
1 CATAAATAATTAAAAAAT
852249 CATAAA-AATTTAAAAAA
1 CATAAATAA-TTAAAAAA
852266 GGGAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
CATAAATAATTAAAAAAT
Found at i:856281 original size:4 final size:4
Alignment explanation
Indices: 856272--856316 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
856262 CAGCTCTAAG
856272 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
856317 GTCTCATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:856694 original size:30 final size:30
Alignment explanation
Indices: 856658--856759 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
856648 TCATTTTTTA
856658 AGGCCTGAACTTGGCAACTATTCTCACATG
1 AGGCCTGAACTTGGCAACTATTCTCACATG
* ** * * *
856688 AGGCCTGAACTT-TC-TTTTTTGTC-CAAGTT
1 AGGCCTGAACTTGGCAACTATTCTCAC-A-TG
856717 AGGCCTTGAACTTGGCAACTATTCTCACATG
1 AGGCC-TGAACTTGGCAACTATTCTCACATG
856748 AGGCCTGAACTT
1 AGGCCTGAACTT
856760 TCTTTTTTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
27 1 0.02
28 6 0.11
29 7 0.13
30 26 0.48
31 7 0.13
32 6 0.11
33 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (30 bp):
AGGCCTGAACTTGGCAACTATTCTCACATG
Found at i:856750 original size:60 final size:60
Alignment explanation
Indices: 856658--856806 Score: 273
Period size: 60 Copynumber: 2.5 Consensus size: 60
856648 TCATTTTTTA
856658 AGGCC-TGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
1 AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
856717 AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
1 AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
* *
856777 AGGCCTTGAACTTGGCAATTGTTCTCACAT
1 AGGCCTTGAACTTGGCAACTATTCTCACAT
856807 TGGAGTTAGA
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
59 5 0.06
60 82 0.94
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (60 bp):
AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
Found at i:856787 original size:30 final size:29
Alignment explanation
Indices: 856688--856789 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
856678 TTCTCACATG
856688 AGGCCTGAACTTTCTTTTTTGTCCAAGTT
1 AGGCCTGAACTTTCTTTTTTGTCCAAGTT
* *** * *
856717 AGGCCTTGAACTTGGCAACTAT-TCTCACA-TG
1 AGGCC-TGAACTT-TCTTTTTTGTC-CA-AGTT
856748 AGGCCTGAACTTTCTTTTTTGTCCAAGTT
1 AGGCCTGAACTTTCTTTTTTGTCCAAGTT
856777 AGGCCTTGAACTT
1 AGGCC-TGAACTT
856790 GGCAATTGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
28 1 0.02
29 16 0.30
30 25 0.46
31 11 0.20
32 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (29 bp):
AGGCCTGAACTTTCTTTTTTGTCCAAGTT
Found at i:856826 original size:60 final size:60
Alignment explanation
Indices: 856658--856838 Score: 262
Period size: 60 Copynumber: 3.0 Consensus size: 60
856648 TCATTTTTTA
*
856658 AGGCC-TGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
1 AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAAATTTCTTTTTTGTCCAAGTT
*
856717 AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAACTTTCTTTTTTGTCCAAGTT
1 AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAAATTTCTTTTTTGTCCAAGTT
* * *
856777 AGGCCTTGAACTTGGCAATTGTTCTCACATTG-GAG-TTAGAAATTT-TTTTTTGTCCAAGTT
1 AGGCCTTGAACTTGGCAACTATTCTCACA-TGAG-GCCT-GAAATTTCTTTTTTGTCCAAGTT
856837 AG
1 AG
856839 TTCATGATAT
Statistics
Matches: 114, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
59 5 0.04
60 100 0.88
61 9 0.08
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (60 bp):
AGGCCTTGAACTTGGCAACTATTCTCACATGAGGCCTGAAATTTCTTTTTTGTCCAAGTT
Found at i:867753 original size:32 final size:33
Alignment explanation
Indices: 867717--867781 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
867707 ACAAATATTA
* *
867717 TTGAACTTGAAAT-ATTTTA-AATATATATTTTT
1 TTGAACTCGAAATAAATTTATAATATA-ATTTTT
*
867749 TTGAACTCGAATTAAATTTATAATATAATTTTT
1 TTGAACTCGAAATAAATTTATAATATAATTTTT
867782 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 11 0.39
33 11 0.39
34 6 0.21
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (33 bp):
TTGAACTCGAAATAAATTTATAATATAATTTTT
Found at i:868079 original size:19 final size:19
Alignment explanation
Indices: 868049--868085 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
868039 ATTGAATTGA
868049 GATATAAAA-TTTAATTTC
1 GATATAAAATTTTAATTTC
868067 GATATATAAATTTTAATTT
1 GATATA-AAATTTTAATTT
868086 GGTGTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (19 bp):
GATATAAAATTTTAATTTC
Found at i:868965 original size:19 final size:19
Alignment explanation
Indices: 868934--868978 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
868924 TCTAGGTCAG
868934 TATAATT-TTTTTTATATTT
1 TATAATTATTTTTTAT-TTT
868953 T-TAATTATTTTTTATTTT
1 TATAATTATTTTTTATTTT
868971 TATAATTA
1 TATAATTA
868979 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATAATTATTTTTTATTTT
Found at i:868968 original size:17 final size:18
Alignment explanation
Indices: 868936--868972 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
868926 TAGGTCAGTA
*
868936 TAATTTTTTTTATATTTT
1 TAATTATTTTTATATTTT
868954 TAATTATTTTT-TATTTT
1 TAATTATTTTTATATTTT
868971 TA
1 TA
868973 TAATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TAATTATTTTTATATTTT
Found at i:868984 original size:19 final size:19
Alignment explanation
Indices: 868943--868985 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
868933 GTATAATTTT
**
868943 TTTTATATTTTTAATTATT
1 TTTTATATTTTTAATTAAA
868962 TTTTAT-TTTTATAATTAAA
1 TTTTATATTTT-TAATTAAA
868981 TTTTA
1 TTTTA
868986 AAAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATATTTTTAATTAAA
Found at i:882475 original size:23 final size:23
Alignment explanation
Indices: 882430--882475 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
882420 TCATTAACTT
* **
882430 TGTTTGTGAACAGGTTCGTTTAA
1 TGTTCGTGAACAGGTTCAATTAA
*
882453 TGTTCGTGAACATGTTCAATTAA
1 TGTTCGTGAACAGGTTCAATTAA
882476 GTTAAATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACAGGTTCAATTAA
Found at i:884066 original size:2 final size:2
Alignment explanation
Indices: 884059--884086 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
884049 ATTTATGATT
884059 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
884087 AAAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:884638 original size:17 final size:17
Alignment explanation
Indices: 884600--884641 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
884590 AATCCGGCAT
884600 TTAATACTTAAAATTAAA
1 TTAATA-TTAAAATTAAA
884618 TTAATATTAGAAATT-AA
1 TTAATATTA-AAATTAAA
884635 TTAATAT
1 TTAATAT
884642 AACATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAATATTAAAATTAAA
Found at i:887367 original size:29 final size:29
Alignment explanation
Indices: 887321--887378 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
887311 ATTGATTCTT
*
887321 TTTAATAATATAGAGACTAAATTAATTTA
1 TTTAATAATAGAGAGACTAAATTAATTTA
* * *
887350 TTTAATAATAGAGGGACTAATTTTATTTA
1 TTTAATAATAGAGAGACTAAATTAATTTA
887379 GTCCCTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (29 bp):
TTTAATAATAGAGAGACTAAATTAATTTA
Found at i:894633 original size:18 final size:17
Alignment explanation
Indices: 894588--894636 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
894578 TTTTGTAAAA
*
894588 TTTATTTTTTATAATTT
1 TTTATATTTTATAATTT
* * *
894605 TTTACAATTTATATGTTT
1 TTTATATTTTATA-ATTT
894623 TTTATATTTTATAA
1 TTTATATTTTATAA
894637 ATACATTTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTTTATAATTT
Found at i:895251 original size:20 final size:22
Alignment explanation
Indices: 895212--895251 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
895202 TTTAATTTTT
*
895212 TTTAGAATTATTTTATATTAGG
1 TTTAGAATTATTTTAAATTAGG
895234 TTTA-AATT-TTTTAAATTA
1 TTTAGAATTATTTTAAATTA
895252 AAGTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTAGAATTATTTTAAATTAGG
Found at i:917505 original size:26 final size:26
Alignment explanation
Indices: 917456--917505 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
917446 TCAAGTTATT
*
917456 ATGAATTCAAATTATTTTATATTTTG
1 ATGAATTCAAATTAATTTATATTTTG
*
917482 ATGATTTCAAATTTAATTTA-ATTT
1 ATGAATTCAAA-TTAATTTATATTT
917506 AATTCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (26 bp):
ATGAATTCAAATTAATTTATATTTTG
Found at i:932264 original size:30 final size:29
Alignment explanation
Indices: 932225--932299 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
932215 ATTAATAATT
**
932225 GGATCTAAATTTTAAAATTTAAAAAGTAGAG
1 GGAT-TAAATTTTAAAAGAT-AAAAGTAGAG
* * *
932256 GGATTAAATTTTTAAAGATAAAATTATAG
1 GGATTAAATTTTAAAAGATAAAAGTAGAG
932285 GGATTAAATTTTAAA
1 GGATTAAATTTTAAA
932300 TTTGTGAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 22 0.58
30 12 0.32
31 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36
Consensus pattern (29 bp):
GGATTAAATTTTAAAAGATAAAAGTAGAG
Found at i:934015 original size:19 final size:19
Alignment explanation
Indices: 933991--934027 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
933981 GAGTAATGTA
933991 GTTCGAGATTATGTTATTG
1 GTTCGAGATTATGTTATTG
* *
934010 GTTCGAGTTTTTGTTATT
1 GTTCGAGATTATGTTATT
934028 CATGCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.24, T:0.54
Consensus pattern (19 bp):
GTTCGAGATTATGTTATTG
Found at i:938792 original size:33 final size:33
Alignment explanation
Indices: 938755--938830 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
938745 TTTGATGACT
*
938755 ATGAAGATGATAGCGAATTCGTTGACGACCATG
1 ATGAAGATGATAGCGAATTCGTTGACGACCACG
* * * *
938788 ATGAAGGTGATAGCGAATTTGTTGATGACGACG
1 ATGAAGATGATAGCGAATTCGTTGACGACCACG
938821 ATGAAGATGA
1 ATGAAGATGA
938831 GGCTGACAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (33 bp):
ATGAAGATGATAGCGAATTCGTTGACGACCACG
Found at i:940317 original size:15 final size:15
Alignment explanation
Indices: 940297--940325 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
940287 AAATATTTAA
940297 GATGCATGCATGCAT
1 GATGCATGCATGCAT
940312 GATGCATGCATGCA
1 GATGCATGCATGCA
940326 ATGAAGCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (15 bp):
GATGCATGCATGCAT
Found at i:952236 original size:29 final size:29
Alignment explanation
Indices: 952177--952251 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
952167 ATTTAAATGA
* ***
952177 AAATTTTTAAAAATTTAATAATTATTTTAT
1 AAATTTTT-AAAATTAAATAATTAAAATAT
952207 AAATTTTTAAAATTAAATAATTAAAATAT
1 AAATTTTTAAAATTAAATAATTAAAATAT
952236 AAATTTATTAATAATT
1 AAATTT-TTAA-AATT
952252 TAAAGAGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 23 0.59
30 12 0.31
31 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAATTTTTAAAATTAAATAATTAAAATAT
Found at i:955147 original size:22 final size:22
Alignment explanation
Indices: 955122--955176 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
955112 AATCAAATTT
955122 AAAATTTAAAATATAAAAAATA
1 AAAATTTAAAATATAAAAAATA
* * * **
955144 AAAAGTTAAATTGTTTAAAATA
1 AAAATTTAAAATATAAAAAATA
*
955166 AAAATATAAAA
1 AAAATTTAAAA
955177 ACTATTTCTA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATTTAAAATATAAAAAATA
Found at i:957327 original size:25 final size:25
Alignment explanation
Indices: 957289--957366 Score: 75
Period size: 31 Copynumber: 2.9 Consensus size: 25
957279 AACTCTTAGG
* *
957289 TTAATATATGATTTGATTTTTAGTT
1 TTAATATTTAATTTGATTTTTAGTT
957314 TTAATATTTAATTTGTTATTTAAATTTAGTT
1 TTAATATTTAATTTG--A-TT---TTTAGTT
*
957345 TTAATATTTAATTTGATATTTA
1 TTAATATTTAATTTGATTTTTA
957367 TATTAAATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
25 17 0.39
27 1 0.02
28 3 0.07
29 1 0.02
31 22 0.50
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (25 bp):
TTAATATTTAATTTGATTTTTAGTT
Found at i:957342 original size:31 final size:31
Alignment explanation
Indices: 957307--957366 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
957297 TGATTTGATT
*
957307 TTTAGTTTTAATATTTAATTTGTTATTTAAA
1 TTTAGTTTTAATATTTAATTTGATATTTAAA
957338 TTTAGTTTTAATATTTAATTTGATATTTA
1 TTTAGTTTTAATATTTAATTTGATATTTA
957367 TATTAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.62
Consensus pattern (31 bp):
TTTAGTTTTAATATTTAATTTGATATTTAAA
Found at i:963502 original size:3 final size:3
Alignment explanation
Indices: 963496--963520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
963486 AATAACAACG
963496 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
963521 CAGAAGGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:967692 original size:26 final size:27
Alignment explanation
Indices: 967635--967693 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
967625 GATTTTTTGG
*
967635 ATTTTTATACTCTATTTTGACAAATTA
1 ATTTTTATACTCTATTTTGACAAAGTA
*
967662 ATTTTTATACAT-TA-TTTGATAAAGTA
1 ATTTTTATAC-TCTATTTTGACAAAGTA
*
967688 TTTTTT
1 ATTTTT
967694 TTCATGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 15 0.54
27 12 0.43
28 1 0.04
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (27 bp):
ATTTTTATACTCTATTTTGACAAAGTA
Found at i:970117 original size:23 final size:21
Alignment explanation
Indices: 970087--970129 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
970077 ATAGCTTAAT
970087 ATAAATAATATATATAAAAATA
1 ATAAATAATATATA-AAAAATA
*
970109 ATAATATAATATTTAAAAAAT
1 ATAA-ATAATATATAAAAAAT
970130 GTTCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAATATATAAAAAATA
Found at i:970198 original size:15 final size:14
Alignment explanation
Indices: 970141--970198 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
970131 TTCATAAAAG
*
970141 AGAAAATAAATAAA
1 AGAAAATAAACAAA
* *
970155 ATATAATAAAACAAA
1 AGAAAAT-AAACAAA
*
970170 ATGAAAATATACAAA
1 A-GAAAATAAACAAA
970185 AGAAAATACAACAA
1 AGAAAATA-AACAA
970199 GAAAAAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.35
15 18 0.53
16 4 0.12
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (14 bp):
AGAAAATAAACAAA
Found at i:970676 original size:13 final size:13
Alignment explanation
Indices: 970658--970683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
970648 TGTAATAGGG
970658 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
970671 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
970684 GAAATTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTAGTGGGGTGAT
Found at i:970723 original size:17 final size:17
Alignment explanation
Indices: 970701--970735 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
970691 GTGGCAAGTA
*
970701 GGGTGATGGAGTTAGTG
1 GGGTGATGGAATTAGTG
970718 GGGTGATGGAATTAGTG
1 GGGTGATGGAATTAGTG
970735 G
1 G
970736 TCGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.51, T:0.29
Consensus pattern (17 bp):
GGGTGATGGAATTAGTG
Found at i:971444 original size:25 final size:26
Alignment explanation
Indices: 971411--971459 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
971401 TATTAGATCA
971411 ATTTAAA-TTTA-AAATATATTATTCT
1 ATTTAAATTTTATAAATA-ATTATTCT
*
971436 ATTTGAATTTTATAAATAATTATT
1 ATTTAAATTTTATAAATAATTATT
971460 TGGATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 10 0.48
27 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTTAAATTTTATAAATAATTATTCT
Found at i:974748 original size:23 final size:23
Alignment explanation
Indices: 974713--974760 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
974703 ATAAATCATT
*
974713 ATGCTAATGATTAAATCCTAAAA
1 ATGCCAATGATTAAATCCTAAAA
* *
974736 ATGCCAATTATTAAATCTTAAAA
1 ATGCCAATGATTAAATCCTAAAA
974759 AT
1 AT
974761 CGTTCTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (23 bp):
ATGCCAATGATTAAATCCTAAAA
Found at i:976758 original size:33 final size:33
Alignment explanation
Indices: 976708--976772 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
976698 TGTTTTTATC
*
976708 CATGGGAGAGGTCATTTTGTTTTGATATTGGTA
1 CATGAGAGAGGTCATTTTGTTTTGATATTGGTA
*
976741 CATGAGAGAGTGT-ATTTTGTTTTGGTATTGGT
1 CATGAGAGAG-GTCATTTTGTTTTGATATTGGT
976773 TCTGTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.20, C:0.05, G:0.31, T:0.45
Consensus pattern (33 bp):
CATGAGAGAGGTCATTTTGTTTTGATATTGGTA
Found at i:981952 original size:205 final size:203
Alignment explanation
Indices: 981575--982253 Score: 955
Period size: 205 Copynumber: 3.3 Consensus size: 203
981565 AGAAATTAGA
* * * * *
981575 AAGTTGAGTGCCTTAATAAGGATGCATGGTATGGTGTTTCTATCTTGTAATGCTTGAAAACTGTG
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAAC--TG
*
981640 TATAAACCAGAATGGATGAAAGTATAATTGCATCTTGTG---T-T-TT-AAAATTAGTAATATTT
64 TATAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTCAAAATTAGTAATATTT
* * *
981699 CTGTCATTAACTGCTGATTTGCATGTTCTACTGCTCTGCCTTGTTTTCATTTGGATGATTTTACC
129 CTGTCATTAACTGCTGATTTTCATGTTCTACTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
981764 ATATATAATGT
194 ATATA-AATGT
981775 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
* *
981840 TAAACCAGAGTGGATTG-AAGTATTATTGCATCTTGTGTTTTGTGTATCAAAATTAGCAATATTT
66 TAAACCAGAGTGGA-TGAAAGTATAATTGCATCTTGTGTTTTGTGT-TCAAAATTAGTAATATTT
* * * *
981904 CTGTCATTAACTGCTAATTTTCATGTTCTGCTGCTCTCCCTTGTTTTCATTTAGATAATTGTACC
129 CTGTCATTAACTGCTGATTTTCATGTTCTACTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
981969 ATATAAGATGT
194 ATATAA-ATGT
* *
981980 AAGTTGAATGCCTTAGTATGGATGCATGATATAGCGTTTCCATCTTGTAATGCTTGAAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTG--
982045 TATAAACCAGAGTGGATGAAAGTATAATTGCAT-TTGTGTTTTGTGTTTCAAAAATTAGTAATAT
64 TATAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTG-TTC-AAAATTAGTAATAT
* * *
982109 TTCTGTCATTGAACTGCTGATTTT-ATTGTT-TCACTGCTCTGCCTTGATTTCTTTTGAATAATT
127 TTCTGTCATT-AACTGCTGATTTTCA-TGTTCT-ACTGCTCTGCCTTGTTTTCATTTGGATAATT
*
982172 GTACCATATAAAATGC
189 GTACCATAT-AAATGT
* *
982188 AAGTTGAATGCCTTAAGATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
982253 T
66 T
982254 GTTAACTGCT
Statistics
Matches: 430, Mismatches: 31, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
198 36 0.08
199 2 0.00
200 56 0.13
201 1 0.00
202 1 0.00
203 1 0.00
204 2 0.00
205 143 0.33
206 19 0.04
207 55 0.13
208 112 0.26
209 2 0.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (203 bp):
AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
TAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTCAAAATTAGTAATATTTCT
GTCATTAACTGCTGATTTTCATGTTCTACTGCTCTGCCTTGTTTTCATTTGGATAATTGTACCAT
ATAAATGT
Found at i:986621 original size:27 final size:28
Alignment explanation
Indices: 986567--986621 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
986557 TACGTGGTAC
* ** *
986567 TTTTATTTTTATTTTTTTATTTTGAAAA
1 TTTTAGTTTTATTTTTTTAAATTAAAAA
986595 TTTTAGTTTT-TTTTTTTAAATTAAAAA
1 TTTTAGTTTTATTTTTTTAAATTAAAAA
986622 ATGTATGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTAGTTTTATTTTTTTAAATTAAAAA
Found at i:991126 original size:30 final size:30
Alignment explanation
Indices: 991092--991152 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
991082 TCTTTATAAA
*
991092 TTTTAAATAGTT-AAATCAAAATTTTATCAT
1 TTTTAAAGAGTTAAAAT-AAAATTTTATCAT
* *
991122 TTTTAGAGAGTTAAAATATAATTTTATCAT
1 TTTTAAAGAGTTAAAATAAAATTTTATCAT
991152 T
1 T
991153 ACTAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTTAAAGAGTTAAAATAAAATTTTATCAT
Found at i:991873 original size:2 final size:2
Alignment explanation
Indices: 991868--991907 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
991858 TGAAGTCTTT
991868 TA 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 TA
991908 CCAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:994593 original size:14 final size:14
Alignment explanation
Indices: 994574--994601 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
994564 CAAAGAATGG
994574 AGAAGCAGTGTGGA
1 AGAAGCAGTGTGGA
994588 AGAAGCAGTGTGGA
1 AGAAGCAGTGTGGA
994602 CGTGGGCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.43, T:0.14
Consensus pattern (14 bp):
AGAAGCAGTGTGGA
Found at i:1020498 original size:16 final size:16
Alignment explanation
Indices: 1020477--1020509 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1020467 TTCGTTTCCG
1020477 TTATTTTGTTCTGATA
1 TTATTTTGTTCTGATA
1020493 TTATTTTGTTCTGATA
1 TTATTTTGTTCTGATA
1020509 T
1 T
1020510 AATCAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.64
Consensus pattern (16 bp):
TTATTTTGTTCTGATA
Found at i:1020757 original size:26 final size:26
Alignment explanation
Indices: 1020688--1020748 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
1020678 TAAACTTATC
*
1020688 AAATGGAGTAAGACTTTTAATTTTGTA
1 AAATGG-GTAAGAATTTTAATTTTGTA
1020715 AAATGGGTAAGAATTTTAATTTTGTA
1 AAATGGGTAAGAATTTTAATTTTGTA
1020741 AAATGGGT
1 AAATGGGT
1020749 TTGTTTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 27 0.82
27 6 0.18
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (26 bp):
AAATGGGTAAGAATTTTAATTTTGTA
Found at i:1022706 original size:38 final size:38
Alignment explanation
Indices: 1022658--1022733 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
1022648 TCACTCAATC
1022658 GATGATTATTAGTGAAATTTTGACTATTAGTTTTGCAT
1 GATGATTATTAGTGAAATTTTGACTATTAGTTTTGCAT
* *
1022696 GATGATTATTAGTTAAATTTTTACTATTAGTTTTGCAT
1 GATGATTATTAGTGAAATTTTGACTATTAGTTTTGCAT
1022734 TTAAGGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (38 bp):
GATGATTATTAGTGAAATTTTGACTATTAGTTTTGCAT
Found at i:1024970 original size:32 final size:30
Alignment explanation
Indices: 1024923--1025024 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
1024913 TATTTATCTA
* **
1024923 ATATAACTATAAATTAAAGTATTTATTTAAATGT
1 ATATAA-T-TAAATTAAAATAAATATTTAAA--T
1024957 ATATAATTAAATTAAAATAAATATTTAAAT
1 ATATAATTAAATTAAAATAAATATTTAAAT
* * * *
1024987 ATACAATTAAATTTAAATAAAAATTTATAT
1 ATATAATTAAATTAAAATAAATATTTAAAT
*
1025017 ATTTAATT
1 ATATAATT
1025025 GTACAAAACC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 33 0.56
32 19 0.32
33 1 0.02
34 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (30 bp):
ATATAATTAAATTAAAATAAATATTTAAAT
Found at i:1026764 original size:155 final size:160
Alignment explanation
Indices: 1026496--1026926 Score: 478
Period size: 168 Copynumber: 2.7 Consensus size: 160
1026486 ATAATTCTTC
** * *
1026496 GACCTATTCCTAAACCCAAGCCTAAAGCCTAGAATTATATAATTGAGTCT----A-TAATGTA--
1 GACCTATTCCTAAACCCAATTCTAAAGCCCAAAATTATATAATTGAGTCTAAAAAGTAAT-TATG
* * * *
1026554 -AC-TAAGG-ACACATGATAAACAAATTAAGTGACCTATATTCACCTTCTTTAGGGTAAAATTAA
65 GACACAAGGAATACATGATAAACAAATTAAGTGACCTATATTCAACTTCTTTAAGGTAAAATTAA
*
1026616 TTATAGACATGC-CA-A-A-T-CAATTATGT
130 TTATAGACATGCAAATAGAGTACAATTATGT
* * * *
1026642 GACCTCTTCCTAAACCCAATTCTAAAGCCTAAATTTATATAATTTAGTCTAAAAAGTAATTATGG
1 GACCTATTCCTAAACCCAATTCTAAAGCCCAAAATTATATAATTGAGTCTAAAAAGTAATTATGG
*
1026707 ACACAAGGAATACATGATAAACAAATTAAATGACCTATATTCAACTTCTTTAAGGTAAAATTAAT
66 ACACAAGGAATACATGATAAACAAATTAAGTGACCTATATTCAACTTCTTTAAGGTAAAATTAAT
* * *
1026772 TATTGACTTGCAAAATTATGAGTTGAAAGTAATTATGT
131 TATAGACATGC-AAA-TA-GAG-T---A-CAATTATGT
*
1026810 GACCTATTCCTAAACCCAATTCTAAAGCCCAAAATTATATAATTGAGTCTAAATAGTAATTATGG
1 GACCTATTCCTAAACCCAATTCTAAAGCCCAAAATTATATAATTGAGTCTAAAAAGTAATTATGG
* * * *
1026875 ACACAAGGACTATATGATAAACAAATTAAGTGACTTATATTCAGCTTCTTTA
66 ACACAAGGAATACATGATAAACAAATTAAGTGACCTATATTCAACTTCTTTA
1026927 TGATAAAAGT
Statistics
Matches: 237, Mismatches: 25, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
146 44 0.19
150 3 0.01
151 4 0.02
153 2 0.01
154 4 0.02
155 61 0.26
157 1 0.00
159 1 0.00
161 1 0.00
163 1 0.00
168 115 0.49
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (160 bp):
GACCTATTCCTAAACCCAATTCTAAAGCCCAAAATTATATAATTGAGTCTAAAAAGTAATTATGG
ACACAAGGAATACATGATAAACAAATTAAGTGACCTATATTCAACTTCTTTAAGGTAAAATTAAT
TATAGACATGCAAATAGAGTACAATTATGT
Found at i:1027481 original size:2 final size:2
Alignment explanation
Indices: 1027474--1027503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1027464 TTGCAATAAC
1027474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1027504 TTAGAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1027994 original size:20 final size:17
Alignment explanation
Indices: 1027955--1027992 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1027945 CATAACAATA
1027955 TGTTATTATAGAATAAT
1 TGTTATTATAGAATAAT
1027972 TGTTATTATAGAATAAT
1 TGTTATTATAGAATAAT
1027989 TGTT
1 TGTT
1027993 GTAAACCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (17 bp):
TGTTATTATAGAATAAT
Found at i:1028462 original size:31 final size:30
Alignment explanation
Indices: 1028417--1028474 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
1028407 GGCCCAATTT
* **
1028417 TTTTACCTACTTTTAAGGGACCTAAAAAAA
1 TTTTACCAACTTTTAAGAAACCTAAAAAAA
1028447 TTTTATCCAACTTTTAAGAAACCTAAAA
1 TTTTA-CCAACTTTTAAGAAACCTAAAA
1028475 CCCCATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (30 bp):
TTTTACCAACTTTTAAGAAACCTAAAAAAA
Found at i:1029494 original size:11 final size:11
Alignment explanation
Indices: 1029478--1029514 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1029468 AAAAGTTTAT
1029478 TTAATTACATA
1 TTAATTACATA
1029489 TTAATT--AT-
1 TTAATTACATA
1029497 TTAATTACATA
1 TTAATTACATA
1029508 TTAATTA
1 TTAATTA
1029515 TAATTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 2 0.09
11 13 0.57
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAATTACATA
Found at i:1029496 original size:19 final size:19
Alignment explanation
Indices: 1029474--1029515 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1029464 TTCTAAAAGT
1029474 TTATTTAATTACATATTAA
1 TTATTTAATTACATATTAA
1029493 TTATTTAATTACATATTAA
1 TTATTTAATTACATATTAA
1029512 TTAT
1 TTAT
1029516 AATTTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTTAATTACATATTAA
Found at i:1036001 original size:16 final size:17
Alignment explanation
Indices: 1035980--1036015 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1035970 GGTCAAGACT
1035980 AAAATTACA-AAACTAA
1 AAAATTACAGAAACTAA
*
1035996 AAAATTACAGGAACTAA
1 AAAATTACAGAAACTAA
1036013 AAA
1 AAA
1036016 TGATCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATTACAGAAACTAA
Found at i:1040272 original size:15 final size:15
Alignment explanation
Indices: 1040252--1040286 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1040242 TTTAATTATT
1040252 TATAAATTATAAAAA
1 TATAAATTATAAAAA
1040267 TATAAATTATAAAAA
1 TATAAATTATAAAAA
1040282 T-TAAA
1 TATAAA
1040287 ATTTCATCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TATAAATTATAAAAA
Found at i:1040288 original size:15 final size:15
Alignment explanation
Indices: 1040223--1040289 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
1040213 AATGCCCCCC
1040223 TAAAATTATAAAAAT
1 TAAAATTATAAAAAT
* * *
1040238 T-CAATT-TAATTATT
1 TAAAATTATAA-AAAT
1040252 TATAAATTATAAAAA-
1 TA-AAATTATAAAAAT
1040267 TATAAATTATAAAAAT
1 TA-AAATTATAAAAAT
1040283 TAAAATT
1 TAAAATT
1040290 TCATCCGGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
13 3 0.07
14 7 0.17
15 21 0.51
16 7 0.17
17 3 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATTATAAAAAT
Found at i:1040289 original size:30 final size:29
Alignment explanation
Indices: 1040223--1040289 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1040213 AATGCCCCCC
* * *
1040223 TAAAATTATAAAAATTCAATTTAATTATT
1 TAAAATTATAAAAATTAAATTTAATAAAT
1040252 TATAAATTATAAAAATATAAATTATAA-AAAT
1 TA-AAATTATAAAAAT-TAAATT-TAATAAAT
1040283 TAAAATT
1 TAAAATT
1040290 TCATCCGGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.06
30 18 0.56
31 9 0.28
32 3 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAATTATAAAAATTAAATTTAATAAAT
Found at i:1041281 original size:31 final size:31
Alignment explanation
Indices: 1041253--1041313 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1041243 AATAGTCATT
*
1041253 GAACTATTTAAAAATTTTCATTTAAGTCACC
1 GAACTATTCAAAAATTTTCATTTAAGTCACC
*
1041284 GAACTATTCAAAAATTTTTATTTAAGTCAC
1 GAACTATTCAAAAATTTTCATTTAAGTCAC
1041314 TAGGCTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (31 bp):
GAACTATTCAAAAATTTTCATTTAAGTCACC
Found at i:1050312 original size:44 final size:45
Alignment explanation
Indices: 1050222--1050350 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1050212 GACAGAACGA
*
1050222 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1050268 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1050312 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1050351 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1054790 original size:39 final size:39
Alignment explanation
Indices: 1054701--1054916 Score: 353
Period size: 39 Copynumber: 5.5 Consensus size: 39
1054691 ACAAAGCATG
* * *
1054701 CGGGACTTTAAGCCCGGATGTAATACCAGCAC-AAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
1054741 CAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1054780 CGGGACTTAGCCCGGGTATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1054819 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1054858 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
1054897 CGGGAATTAGCCCGGATATA
1 CGGGACTTAGCCCGGATATA
1054917 TATCTCACAC
Statistics
Matches: 167, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
38 20 0.12
39 142 0.85
40 5 0.03
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:1063543 original size:29 final size:30
Alignment explanation
Indices: 1063480--1063546 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
1063470 GATTGAACAA
* * **
1063480 AATTATT-AATTCGATAAATTAATTTTTTT
1 AATTATTAAATTCAATAAAATAATTTTAAT
*
1063509 ATTTATTAAATTCAATAAAATAA-TTTAAT
1 AATTATTAAATTCAATAAAATAATTTTAAT
1063538 AATTATTAA
1 AATTATTAA
1063547 GGAAAAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (30 bp):
AATTATTAAATTCAATAAAATAATTTTAAT
Found at i:1064593 original size:31 final size:30
Alignment explanation
Indices: 1064499--1064595 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 30
1064489 GTGTAATCTG
* *
1064499 ATACATGAATTTTAA-TTTGGTTAAATTAT
1 ATACATGAAATTTAATTTTGGTTCAATTAT
** * * * *
1064528 ATTTATGGAAATTTTATTGTGGTTCAAATGT
1 ATACAT-GAAATTTAATTTTGGTTCAATTAT
1064559 ATACATGAAACTTTAATTTTGGTTCAATTAT
1 ATACATGAAA-TTTAATTTTGGTTCAATTAT
1064590 ATACAT
1 ATACAT
1064596 TTATTTTTAT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 4 0.08
30 11 0.22
31 36 0.71
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (30 bp):
ATACATGAAATTTAATTTTGGTTCAATTAT
Found at i:1064775 original size:31 final size:29
Alignment explanation
Indices: 1064698--1064778 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
1064688 GAACTAGATC
* *
1064698 AAATCAAAATTTTATGTATGAAATTACACA
1 AAATCAAAA-TTTATATATAAAATTACACA
* *
1064728 AAATTAAAATTCATATATAAAATTACACA
1 AAATCAAAATTTATATATAAAATTACACA
1064757 TTAAATCAAAATTTATATATAA
1 --AAATCAAAATTTATATATAA
1064779 TTTTGAGACT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 17 0.40
30 8 0.19
31 18 0.42
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTACACA
Found at i:1064780 original size:29 final size:27
Alignment explanation
Indices: 1064698--1064780 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 27
1064688 GAACTAGATC
*
1064698 AAATCAAAATTTTATGTATGAAATTACACA
1 AAATCAAAA-TTTATATAT--AATTACACA
* *
1064728 AAATTAAAATTCATATATAAAATTACACA
1 AAATCAAAATT--TATATATAATTACACA
1064757 TTAAATCAAAATTTATATATAATT
1 --AAATCAAAATTTATATATAATT
1064781 TTGAGACTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
29 21 0.48
30 8 0.18
31 15 0.34
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.36
Consensus pattern (27 bp):
AAATCAAAATTTATATATAATTACACA
Found at i:1066092 original size:23 final size:22
Alignment explanation
Indices: 1066049--1066092 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1066039 AAATTATTGA
* **
1066049 TTTATTTTTAATATTTTATATG
1 TTTATTTTTAATAATACATATG
1066071 TTTATTTTATAATAATACATAT
1 TTTATTTT-TAATAATACATAT
1066093 TGCATCTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTATTTTTAATAATACATATG
Found at i:1074560 original size:2 final size:2
Alignment explanation
Indices: 1074553--1074579 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1074543 AGAGATTGCT
1074553 TA 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 TA T
1074580 GCAAGTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1077950 original size:150 final size:151
Alignment explanation
Indices: 1077680--1077975 Score: 524
Period size: 150 Copynumber: 2.0 Consensus size: 151
1077670 AGAATAGGGG
* *
1077680 CCCCCTCTTGCTCTCTGCCGCTAGCTTTGATGTGTCTTCAGTTGGCACAGGGTGAAGTAAATATA
1 CCCCCCCTTGCTCTCTGCCGCTAGCTTTGATGTGTCTTCAGTTGACACAGGGTGAAGTAAATATA
1077745 TAATTTACATACATGAGATTTAGTTTTAAAAAATATTTAGAATAAATATCAAAAA-TAAATTTGA
66 TAATTTACATACATGAGATTTAGTTTTAAAAAATATTTAGAATAAATATCAAAAATTAAATTTGA
*
1077809 ATTTTGATTCAATTTAAGGCC
131 ATTTTCATTCAATTTAAGGCC
*
1077830 CCCCCCCTTGCTCTCTGCCGCTAGCTTTGATGTGTTTTCAGTTGACACAGGGTGAAGTAAATATA
1 CCCCCCCTTGCTCTCTGCCGCTAGCTTTGATGTGTCTTCAGTTGACACAGGGTGAAGTAAATATA
*
1077895 TAATTTACATACGTGAGATTTAGTTTTAAAAAAATATTTAGAATAAATATC-AAAATTAAATTTG
66 TAATTTACATACATGAGATTTAGTTTT-AAAAAATATTTAGAATAAATATCAAAAATTAAATTTG
1077959 AATTTTCATTCAATTTA
130 AATTTTCATTCAATTTA
1077976 TAATTTTATA
Statistics
Matches: 139, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
150 92 0.66
151 47 0.34
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (151 bp):
CCCCCCCTTGCTCTCTGCCGCTAGCTTTGATGTGTCTTCAGTTGACACAGGGTGAAGTAAATATA
TAATTTACATACATGAGATTTAGTTTTAAAAAATATTTAGAATAAATATCAAAAATTAAATTTGA
ATTTTCATTCAATTTAAGGCC
Found at i:1081515 original size:15 final size:15
Alignment explanation
Indices: 1081491--1081520 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1081481 AAATTGTAAT
*
1081491 TTTATTATTTTATAA
1 TTTATAATTTTATAA
1081506 TTTATAATTTTATAA
1 TTTATAATTTTATAA
1081521 ATTTTAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATAATTTTATAA
Found at i:1081519 original size:8 final size:8
Alignment explanation
Indices: 1081487--1081526 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
1081477 CCATAAATTG
1081487 TAATTTTA
1 TAATTTTA
*
1081495 TTATTTTA
1 TAATTTTA
1081503 TAA-TTTA
1 TAATTTTA
1081510 TAATTTTA
1 TAATTTTA
1081518 TAAATTTTA
1 T-AATTTTA
1081527 AAAGAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAATTTTA
Found at i:1086459 original size:26 final size:27
Alignment explanation
Indices: 1086432--1086481 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1086422 CTAGTTTAAT
*
1086432 TTTGCTAT-TCAATT-ATTTTTAATAA
1 TTTGCTATCTCAATTAAGTTTTAATAA
*
1086457 TTTGGTATCTCAATTAAGTTTTAAT
1 TTTGCTATCTCAATTAAGTTTTAAT
1086482 GCTCACCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 6 0.29
27 8 0.38
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (27 bp):
TTTGCTATCTCAATTAAGTTTTAATAA
Found at i:1087049 original size:19 final size:19
Alignment explanation
Indices: 1087025--1087066 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1087015 ATTCAACATC
*
1087025 AATTAAATAAACAATTAAA
1 AATTAAATAAAAAATTAAA
*
1087044 AATT-AATAAAAAATTTAA
1 AATTAAATAAAAAATTAAA
1087062 AATTA
1 AATTA
1087067 TTTTACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAATAAAAAATTAAA
Found at i:1091432 original size:19 final size:19
Alignment explanation
Indices: 1091408--1091447 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1091398 GTTGAGATAG
1091408 TAAAAATTATGATTTTTTT
1 TAAAAATTATGATTTTTTT
1091427 TAAAAATTATGATTTTTTT
1 TAAAAATTATGATTTTTTT
1091446 TA
1 TA
1091448 TTCATATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TAAAAATTATGATTTTTTT
Found at i:1100183 original size:2 final size:2
Alignment explanation
Indices: 1100176--1100205 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1100166 AAGAGTTTTC
1100176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1100206 GTTTAACTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1107833 original size:24 final size:25
Alignment explanation
Indices: 1107797--1107843 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1107787 CTGTTGCTTA
*
1107797 TTTTTGCTTTCATT-TTTTGTGGAAT
1 TTTTTGCTATCATTATTTT-TGGAAT
1107822 TTTTTG-TATCATTATTTTTGGA
1 TTTTTGCTATCATTATTTTTGGA
1107844 TTAATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (25 bp):
TTTTTGCTATCATTATTTTTGGAAT
Found at i:1111424 original size:22 final size:23
Alignment explanation
Indices: 1111390--1111447 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1111380 TTAACAATTT
1111390 AATAATTTAAATAAAAAATT-TTA
1 AATAATTT-AATAAAAAATTATTA
*
1111413 AATAATTTAAT-AAAAATTATTG
1 AATAATTTAATAAAAAATTATTA
*
1111435 AATAGTTTAATAA
1 AATAATTTAATAA
1111448 TTATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.23
22 15 0.48
23 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (23 bp):
AATAATTTAATAAAAAATTATTA
Found at i:1113095 original size:2 final size:2
Alignment explanation
Indices: 1113088--1113114 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1113078 AGCTTTTAGA
1113088 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1113115 ACTACATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1115029 original size:22 final size:20
Alignment explanation
Indices: 1114992--1115034 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1114982 GAAATAGGAC
*
1114992 AAAAAAATAAAAAAAATACT
1 AAAAAAATAAAAAAAAAACT
*
1115012 AAAATAATACAAAGAAAAAACT
1 AAAAAAATA-AAA-AAAAAACT
1115034 A
1 A
1115035 TGTACCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAAATAAAAAAAAAACT
Found at i:1119521 original size:14 final size:15
Alignment explanation
Indices: 1119502--1119532 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1119492 TTACTTCTTG
1119502 TTCAAGCCTAT-TTT
1 TTCAAGCCTATATTT
1119516 TTCAAGCCTATATTT
1 TTCAAGCCTATATTT
1119531 TT
1 TT
1119533 ATCTAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (15 bp):
TTCAAGCCTATATTT
Found at i:1123170 original size:2 final size:2
Alignment explanation
Indices: 1123163--1123192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1123153 ACCCTAAGTT
1123163 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
1123193 ATTAACTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1125752 original size:29 final size:29
Alignment explanation
Indices: 1125700--1125763 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1125690 ATAAGTAGAT
1125700 ATAAGTTTTGTATAAAAAATTTTATACAAC
1 ATAAGTTTTGTATAAAAAATTTTATA-AAC
*
1125730 ATAA-TTTTGTATTATAAAA-TTTATAAAC
1 ATAAGTTTTGTA-TAAAAAATTTTATAAAC
*
1125758 AAAAGT
1 ATAAGT
1125764 AATTGTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 6 0.20
29 14 0.47
30 10 0.33
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (29 bp):
ATAAGTTTTGTATAAAAAATTTTATAAAC
Found at i:1125767 original size:32 final size:29
Alignment explanation
Indices: 1125700--1125767 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1125690 ATAAGTAGAT
* *
1125700 ATAAGTTTTGTATAAAAAATTTTATACAAC
1 ATAA-TTTTGTATAAAAAATTTTAAACAAA
*
1125730 ATAATTTTGTATTATAAAATTTATAAACAAA
1 ATAATTTTGTA-TAAAAAATTT-TAAACAAA
1125761 AGTAATT
1 A-TAATT
1125768 GTAAGTAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.22
30 13 0.41
31 7 0.22
32 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (29 bp):
ATAATTTTGTATAAAAAATTTTAAACAAA
Found at i:1125942 original size:18 final size:19
Alignment explanation
Indices: 1125901--1125950 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1125891 AACTGACTTA
* *
1125901 ATTTAATATATTTTTAATT
1 ATTTAAAATATATTTAATT
1125920 ATTTAAAATATATTTAA-T
1 ATTTAAAATATATTTAATT
1125938 ATTTAAAATATAT
1 ATTTAAAATATAT
1125951 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTAAAATATATTTAATT
Found at i:1127092 original size:46 final size:45
Alignment explanation
Indices: 1127024--1127191 Score: 191
Period size: 46 Copynumber: 3.6 Consensus size: 45
1127014 CCCGCCCCTA
*
1127024 AGTGAACTCGGACTTAACTCAACGAGTTCGGGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCAT
*
1127069 AGGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCAT
* * *
1127117 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCAT
1127162 AAGTGAACTCGGACTCAACTCAACGAGTTC
1 -AGTGAACTCGGACTCAACTCAACGAGTTC
1127192 AGATGCTCAA
Statistics
Matches: 104, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 3 0.03
46 55 0.53
47 28 0.27
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCAT
Found at i:1127186 original size:93 final size:93
Alignment explanation
Indices: 1127027--1127197 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
1127017 GCCCCTAAGT
* * * *
1127027 GAACTCGGACTTAACTCAACGAGTTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1127092 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
1127120 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1127185 CGAGTTCAGATGC
66 CGAGTTCAGATGC
1127198 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:1127213 original size:46 final size:45
Alignment explanation
Indices: 1127071--1127213 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 45
1127061 GCATCCATAG
*
1127071 GTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA
1 GTGAACTCGGACTCAACTCAACGAGTTCAGATGCTC-A---ACCATCT-A
* * * * * *
1127119 -CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AA
1 GTGAACTCGGACTCAACTCAACGAGTTC--AGATGCTCAACCATCTA
1127164 GTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCTA
1 GTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCAT-CTA
1127210 GTGA
1 GTGA
1127214 CATGTCACTT
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
44 10 0.13
45 1 0.01
46 31 0.41
47 29 0.38
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
GTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCTA
Found at i:1134623 original size:28 final size:29
Alignment explanation
Indices: 1134590--1134666 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
1134580 TTTACTTTTA
1134590 TAAAATTTGAAATTTAATTATTATA-TTT
1 TAAAATTTGAAATTTAATTATTATACTTT
** *
1134618 TAAAATTAAAAATTTAATTATTTTACTTT
1 TAAAATTTGAAATTTAATTATTATACTTT
*
1134647 T-CAATTTAGAAATCTTAATT
1 TAAAATTT-GAAAT-TTAATT
1134667 TAGTCATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 26 0.65
29 8 0.20
30 6 0.15
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (29 bp):
TAAAATTTGAAATTTAATTATTATACTTT
Found at i:1135133 original size:2 final size:2
Alignment explanation
Indices: 1135126--1135155 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1135116 TAAACTGGCT
1135126 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
1135156 AAGGGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1139476 original size:28 final size:29
Alignment explanation
Indices: 1139424--1139478 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1139414 TATTTTAGAT
*
1139424 AAAAATAAAAATAAAAAATTGATTTTTTA
1 AAAAATAAAAATAAAAAATTAATTTTTTA
1139453 AAAAATAAAAATAAAAAA-TAATTTTT
1 AAAAATAAAAATAAAAAATTAATTTTT
1139479 CATTAAGCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATAAAAATAAAAAATTAATTTTTTA
Found at i:1141924 original size:10 final size:10
Alignment explanation
Indices: 1141905--1141942 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1141895 ACAAAAATAG
1141905 AAAATATAAA
1 AAAATATAAA
*
1141915 AAAATCTAAA
1 AAAATATAAA
1141925 GAAAATATAAA
1 -AAAATATAAA
1141936 AAAATAT
1 AAAATAT
1141943 TTAAAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAATATAAA
Found at i:1142050 original size:15 final size:16
Alignment explanation
Indices: 1142030--1142074 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
1142020 TTAATTTGAA
1142030 CAATTTCACTCAA-TT
1 CAATTTCACTCAATTT
1142045 CAATTTCACTCAGAATTT
1 CAATTTCACTC--AATTT
1142063 C-ATTTCACTCAA
1 CAATTTCACTCAA
1142075 CTCGATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.48
17 11 0.41
18 3 0.11
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (16 bp):
CAATTTCACTCAATTT
Found at i:1142665 original size:2 final size:2
Alignment explanation
Indices: 1142658--1142692 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1142648 TAGTTTCAAG
*
1142658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1142693 AATAATCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1143549 original size:18 final size:18
Alignment explanation
Indices: 1143499--1143549 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
1143489 AGTTAAGCAA
*
1143499 AATTTAATTAAAATTGAATT
1 AATTTAATT--AATTGAAAT
*
1143519 AATTT-ATCGAATTGAAAT
1 AATTTAAT-TAATTGAAAT
1143537 AATTTAATTAATT
1 AATTTAATTAATT
1143550 TAATTCTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 17 0.65
19 4 0.15
20 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (18 bp):
AATTTAATTAATTGAAAT
Found at i:1147381 original size:76 final size:75
Alignment explanation
Indices: 1147245--1147393 Score: 237
Period size: 76 Copynumber: 2.0 Consensus size: 75
1147235 TTTTTTTGCC
* * *
1147245 AGTGTAAGACCATAGCTAAGCTATGGCAATGTGATAAATCATGTGATCATGGCAAGGCCATGATA
1 AGTGCAAGACCATAGCTAAGCTATGGCAATGTGATAAATCATGTGATAATGGCAAAGCCATGATA
1147310 AAATATGTGCA
66 AAA-ATGTGCA
*
1147321 AGTGCAAGACCATAGTTAAGCTATGGCAATGTGATAAAGT-ATGTGATAATGGCAAAGCCATGAT
1 AGTGCAAGACCATAGCTAAGCTATGGCAATGTGATAAA-TCATGTGATAATGGCAAAGCCATGAT
1147385 AAAAATGTG
65 AAAAATGTG
1147394 TGTAAAACCA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 5 0.07
76 62 0.91
77 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (75 bp):
AGTGCAAGACCATAGCTAAGCTATGGCAATGTGATAAATCATGTGATAATGGCAAAGCCATGATA
AAAATGTGCA
Found at i:1153583 original size:40 final size:39
Alignment explanation
Indices: 1153504--1153623 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 39
1153494 TTTTCATTTC
1153504 AAAAACTATACCAAAATTAT-AAGAGAATACCAAAAATTAT
1 AAAAA-TATACCAAAATTATGAAGA-AATACCAAAAATTAT
* * * * *
1153544 TAAAGTGTACCGAAAATTATGAAGAAATATCAAACATTAT
1 AAAAATATACC-AAAATTATGAAGAAATACCAAAAATTAT
* *
1153584 AAAAATATATCAATTATTATGAAGAAATACCAAAAATTAT
1 AAAAATATACCAA-AATTATGAAGAAATACCAAAAATTAT
1153624 GCTAAATATT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
39 7 0.11
40 54 0.83
41 4 0.06
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (39 bp):
AAAAATATACCAAAATTATGAAGAAATACCAAAAATTAT
Found at i:1153624 original size:20 final size:20
Alignment explanation
Indices: 1153511--1153624 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
1153501 TTCAAAAACT
1153511 ATACC-AAAATTAT-AAGAGA
1 ATACCAAAAATTATGAAGA-A
* *
1153530 ATACCAAAAATTATTAA-AGT
1 ATACCAAAAATTATGAAGA-A
* *
1153550 GTACCGAAAATTATGAAGAA
1 ATACCAAAAATTATGAAGAA
* * *
1153570 ATATCAAACATTAT-AAAAA
1 ATACCAAAAATTATGAAGAA
* **
1153589 TATATCAATTATTATGAAGAA
1 -ATACCAAAAATTATGAAGAA
1153610 ATACCAAAAATTATG
1 ATACCAAAAATTATG
1153625 CTAAATATTT
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 9 0.12
20 58 0.78
21 7 0.09
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (20 bp):
ATACCAAAAATTATGAAGAA
Found at i:1161683 original size:14 final size:14
Alignment explanation
Indices: 1161660--1161689 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1161650 TGAAAAATAT
1161660 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
1161674 GTTGATTTGGATTG
1 GTTGAATTGGATTG
1161688 GT
1 GT
1161690 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:1162698 original size:18 final size:16
Alignment explanation
Indices: 1162674--1162715 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
1162664 TTGGTTGATC
*
1162674 TTTTTAAATTTATTTCA
1 TTTTTAAATTT-TTTAA
1162691 TTTATTAAATTTTTTAA
1 TTT-TTAAATTTTTTAA
1162708 TTTTTAAA
1 TTTTTAAA
1162716 AGAATATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAATTTTTTAA
Found at i:1162736 original size:19 final size:19
Alignment explanation
Indices: 1162712--1162784 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
1162702 TTTTAATTTT
1162712 TAAAAGAATATCAAAATTA
1 TAAAAGAATATCAAAATTA
**
1162731 TAAAAGTGTATCGAAAATTA
1 TAAAAGAATATC-AAAATTA
* * *
1162751 TGAAGGAAGATCAAACATTA
1 TAAAAGAATATCAAA-ATTA
* *
1162771 TAAGAGTATATCAA
1 TAAAAGAATATCAA
1162785 TTATTATGAA
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (19 bp):
TAAAAGAATATCAAAATTA
Found at i:1162811 original size:40 final size:40
Alignment explanation
Indices: 1162724--1162811 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
1162714 AAAGAATATC
*
1162724 AAAATTATAAAAGTGTATCGAAAATTATGAAGGAAGATCA
1 AAAATTATAAAAGTATATCGAAAATTATGAAGGAAGATCA
* * *
1162764 AACATTATAAGAGTATATC-AATTATTATGAA-GAA-ATGCCA
1 AAAATTATAAAAGTATATCGAA-AATTATGAAGGAAGAT--CA
1162804 AAAATTAT
1 AAAATTAT
1162812 GCCAAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
38 2 0.05
39 5 0.12
40 33 0.82
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (40 bp):
AAAATTATAAAAGTATATCGAAAATTATGAAGGAAGATCA
Found at i:1170214 original size:2 final size:2
Alignment explanation
Indices: 1170207--1170232 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1170197 AAAATGATGA
1170207 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
1170233 TTGATTGTGT
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:1171609 original size:16 final size:17
Alignment explanation
Indices: 1171571--1171615 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1171561 TTTCTTTATA
*
1171571 ATTTTATAATTTTCTTAT
1 ATTTTATAATTTT-TAAT
*
1171589 TTTTTA-AATTTTTAAT
1 ATTTTATAATTTTTAAT
1171605 ATTTTATAATT
1 ATTTTATAATT
1171616 ATAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 10 0.43
18 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATAATTTTTAAT
Found at i:1171643 original size:24 final size:24
Alignment explanation
Indices: 1171593--1171639 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1171583 TCTTATTTTT
* * *
1171593 TAAATTTTTAATATTTTATAATTA
1 TAAAATTTTAAAAATTTATAATTA
1171617 TAAAATTTTAAAAATTTA-AATTA
1 TAAAATTTTAAAAATTTATAATTA
1171640 ATAATCAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAAAATTTTAAAAATTTATAATTA
Found at i:1171881 original size:26 final size:26
Alignment explanation
Indices: 1171845--1171937 Score: 150
Period size: 26 Copynumber: 3.6 Consensus size: 26
1171835 TATAAACAAG
1171845 CTATCATTATCAACAAGGGGAAATCT
1 CTATCATTATCAACAAGGGGAAATCT
*
1171871 CTATCCTTATCAACAAGGGGAAATCT
1 CTATCATTATCAACAAGGGGAAATCT
*
1171897 CTATCCTTATCAACAAGGGGAAATCT
1 CTATCATTATCAACAAGGGGAAATCT
* *
1171923 GTATCATTATTAACA
1 CTATCATTATCAACA
1171938 GGGATTAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (26 bp):
CTATCATTATCAACAAGGGGAAATCT
Found at i:1173417 original size:24 final size:23
Alignment explanation
Indices: 1173364--1173417 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1173354 TTTTTTTTCC
* *
1173364 ATTTT-TTTGTTTTTATTATTTA
1 ATTTTATTTGTTTATAATATTTA
*
1173386 TTTATTATTTGTTTATAATATTTTA
1 ATT-TTATTTGTTTATAATA-TTTA
1173411 ATTTTAT
1 ATTTTAT
1173418 ATTTTTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.08
23 2 0.08
24 15 0.60
25 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (23 bp):
ATTTTATTTGTTTATAATATTTA
Found at i:1173587 original size:17 final size:18
Alignment explanation
Indices: 1173554--1173596 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1173544 TTGTTTAATA
1173554 TTAT-TTTATAATATTTT
1 TTATATTTATAATATTTT
*
1173571 TTATATTTA-AATTTTTT
1 TTATATTTATAATATTTT
1173588 TTATCATTT
1 TTAT-ATTT
1173597 CAAGGCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATTTATAATATTTT
Found at i:1174578 original size:13 final size:13
Alignment explanation
Indices: 1174560--1174605 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1174550 TAATTAATTA
1174560 AATTTTTTAGATT
1 AATTTTTTAGATT
* *
1174573 AATTTTATAAATT
1 AATTTTTTAGATT
1174586 AAATTTTTTAGATT
1 -AATTTTTTAGATT
1174600 AATTTT
1 AATTTT
1174606 ATAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (13 bp):
AATTTTTTAGATT
Found at i:1174585 original size:27 final size:27
Alignment explanation
Indices: 1174555--1174610 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1174545 TTAAGTAATT
1174555 AATTAAATTTTTTAGATTAATTTTATA
1 AATTAAATTTTTTAGATTAATTTTATA
1174582 AATTAAATTTTTTAGATTAATTTTATA
1 AATTAAATTTTTTAGATTAATTTTATA
1174609 AA
1 AA
1174611 AAAAGGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
AATTAAATTTTTTAGATTAATTTTATA
Found at i:1174590 original size:14 final size:13
Alignment explanation
Indices: 1174555--1174610 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1174545 TTAAGTAATT
*
1174555 AATTAAATTTTTTA
1 AATT-AATTTTATA
*
1174569 GATTAATTTTATA
1 AATTAATTTTATA
*
1174582 AATTAAATTTTTTA
1 AATT-AATTTTATA
*
1174596 GATTAATTTTATA
1 AATTAATTTTATA
1174609 AA
1 AA
1174611 AAAAGGCATG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
13 20 0.59
14 14 0.41
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (13 bp):
AATTAATTTTATA
Found at i:1177375 original size:2 final size:2
Alignment explanation
Indices: 1177370--1177402 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1177360 ATATATATAT
1177370 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1177403 CCCGCGGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1178527 original size:24 final size:23
Alignment explanation
Indices: 1178496--1178540 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1178486 CTTCAGTGAC
1178496 TTTTACTTCTCTAC-TTTTTTTCA
1 TTTTACTTCTC-ACATTTTTTTCA
*
1178519 TTTTCACTTTTCACATTTTTTT
1 TTTT-ACTTCTCACATTTTTTT
1178541 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTACTTCTCACATTTTTTTCA
Found at i:1195439 original size:18 final size:18
Alignment explanation
Indices: 1195416--1195451 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1195406 ATCAAAATAT
*
1195416 TATTTTTTATAATATTTA
1 TATTTTTGATAATATTTA
*
1195434 TATTTTTGATTATATTTA
1 TATTTTTGATAATATTTA
1195452 ATTAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTTTTGATAATATTTA
Found at i:1196723 original size:29 final size:31
Alignment explanation
Indices: 1196646--1196723 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
1196636 TCTTAAAATT
*
1196646 ATACATAAACTTTGATTTAATGTGTAATATG
1 ATACATAAACTTTGATTTAATGTATAATATG
* *
1196677 ATACATAAATTTTAATTT-A-GTATAATTAT-
1 ATACATAAACTTTGATTTAATGTATAA-TATG
**
1196706 ATATTTAAACTTTGATTT
1 ATACATAAACTTTGATTT
1196724 TGGTTCATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 19 0.49
30 4 0.10
31 16 0.41
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (31 bp):
ATACATAAACTTTGATTTAATGTATAATATG
Found at i:1204627 original size:2 final size:2
Alignment explanation
Indices: 1204620--1204656 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1204610 TAACTGAATT
1204620 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1204657 GAGCTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1208655 original size:24 final size:23
Alignment explanation
Indices: 1208627--1208672 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1208617 GGTTTAATTT
1208627 TAATAAAATAAATTATTAAAAAAA
1 TAATAAAATAAA-TATTAAAAAAA
**
1208651 TAATAAAATTTATATTAAAAAA
1 TAATAAAATAAATATTAAAAAA
1208673 TGTTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAATAAAATAAATATTAAAAAAA
Done.