Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold469
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: 185253
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.33
Warning! 9277 characters in sequence are not A, C, G, or T
Found at i:84 original size:17 final size:17
Alignment explanation
Indices: 62--95 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52 ACGTGGCATG
62 TACCTAAGTAATGTATA
1 TACCTAAGTAATGTATA
*
79 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
96 GGGATTAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:1271 original size:43 final size:43
Alignment explanation
Indices: 1126--1273 Score: 117
Period size: 43 Copynumber: 3.5 Consensus size: 43
1116 GGTGTGATTT
* **
1126 CATGTAAAACCATATCTGGGACATTGGCATCGA-A-GTAAGAAAA
1 CATGTAAGACCATATCTGGGACATTGGCATCGATATGT--GTTAA
* * * * *
1169 CGTGTAAGATCATGTCTGAGACATTGGCATCGTATATG-ATT--
1 CATGTAAGACCATATCTGGGACATTGGCATCG-ATATGTGTTAA
* * * * *
1210 CGTATAAGACCTTGTCTGGGACAGTGGCATCGATATGTGTTAA
1 CATGTAAGACCATATCTGGGACATTGGCATCGATATGTGTTAA
1253 CATGTAAGACCATATCTGGGA
1 CATGTAAGACCATATCTGGGA
1274 TATGACATTG
Statistics
Matches: 81, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
40 5 0.06
41 29 0.36
43 44 0.54
44 1 0.01
45 1 0.01
46 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCATATCTGGGACATTGGCATCGATATGTGTTAA
Found at i:1903 original size:8 final size:7
Alignment explanation
Indices: 1871--1896 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1861 TCTAATTGGT
1871 AAAAAGA
1 AAAAAGA
1878 AAAAAGA
1 AAAAAGA
1885 AAAAAGA
1 AAAAAGA
1892 AAAAA
1 AAAAA
1897 ATGAAAATGA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:13212 original size:25 final size:25
Alignment explanation
Indices: 13165--13215 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
13155 GAATGAAATT
* *
13165 TCTTAAAATTTTATTGGGGGTAAAA
1 TCTTAAAATTTTACTGGGAGTAAAA
13190 TCTTAAAAATTTTACT-GGAGTAAAA
1 TCTT-AAAATTTTACTGGGAGTAAAA
13215 T
1 T
13216 TGGGATGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (25 bp):
TCTTAAAATTTTACTGGGAGTAAAA
Found at i:16700 original size:102 final size:103
Alignment explanation
Indices: 16536--16753 Score: 420
Period size: 102 Copynumber: 2.1 Consensus size: 103
16526 AAATACACTC
*
16536 AAATAATATAATTTATTTTAATTATAAAAGGGCATTTTTATAATTTTTCTAATCGAGTTGGTGGC
1 AAATAATATAAATTATTTTAATTATAAAAGGGCATTTTTATAATTTTTCTAATCGAGTTGGTGGC
16601 TCCGTTTAGAGTGACACTAACTAAATAAAACACTTAAT
66 TCCGTTTAGAGTGACACTAACTAAATAAAACACTTAAT
16639 AAATAATATAAATTA-TTTAATTATAAAAGGGCATTTTTATAATTTTTCTAATCGAGTTGGTGGC
1 AAATAATATAAATTATTTTAATTATAAAAGGGCATTTTTATAATTTTTCTAATCGAGTTGGTGGC
16703 TCCGTTTAGAGTGACACTAACTAAATAAAACACTTAAT
66 TCCGTTTAGAGTGACACTAACTAAATAAAACACTTAAT
16741 AAATAATATAAAT
1 AAATAATATAAAT
16754 ATGTTAAAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 100 0.88
103 14 0.12
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (103 bp):
AAATAATATAAATTATTTTAATTATAAAAGGGCATTTTTATAATTTTTCTAATCGAGTTGGTGGC
TCCGTTTAGAGTGACACTAACTAAATAAAACACTTAAT
Found at i:16764 original size:16 final size:15
Alignment explanation
Indices: 16745--16786 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
16735 CTTAATAAAT
16745 AATATAAATATGTTAA
1 AATATAAATAT-TTAA
*
16761 AATATATATATTTAA
1 AATATAAATATTTAA
16776 AAT-T-AATATTT
1 AATATAAATATTT
16787 CTCAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.25
14 1 0.04
15 7 0.29
16 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATAAATATTTAA
Found at i:20855 original size:59 final size:59
Alignment explanation
Indices: 20735--20894 Score: 162
Period size: 59 Copynumber: 2.7 Consensus size: 59
20725 TTTTAGGACC
* * * * * *
20735 TGAATTTAGCAACTATTCTCACATCAGAGTTTGAACTTTTTTTTAACCAAGTTAAGTCT
1 TGAAATTAGCAATTATTCTCACATTAGGGTCTGAACTTTTTTTTAACCAAGTTAAGCCT
* * * * * *
20794 TGAAATTGGCAATTGTTTTCACATTGGGGTCTGAACTTTTTTTTATCCAA-TTTAGACCT
1 TGAAATTAGCAATTATTCTCACATTAGGGTCTGAACTTTTTTTTAACCAAGTTAAG-CCT
* * *
20853 TGAACTTAGCAATTATTCTCATATTAGGGTTTGAA-TTTTTTT
1 TGAAATTAGCAATTATTCTCACATTAGGGTCTGAACTTTTTTT
20895 GGTCCAAATT
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
58 11 0.14
59 70 0.86
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.44
Consensus pattern (59 bp):
TGAAATTAGCAATTATTCTCACATTAGGGTCTGAACTTTTTTTTAACCAAGTTAAGCCT
Found at i:26192 original size:2 final size:2
Alignment explanation
Indices: 26185--26223 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
26175 ATAAGAATGA
26185 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
26224 AGTAATAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28388 original size:28 final size:27
Alignment explanation
Indices: 28357--28409 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
28347 AAATAATTAG
*
28357 ATTTTTTTATATTTTTACAATATTTATC
1 ATTTTTATATATTTTT-CAATATTTATC
*
28385 ATTTTTATATATTTTTTAATATTTA
1 ATTTTTATATATTTTTCAATATTTA
28410 ACAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTTATATATTTTTCAATATTTATC
Found at i:28484 original size:21 final size:21
Alignment explanation
Indices: 28460--28503 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28450 GTTAATCTTA
*
28460 GTCTGCCAAATGGCACGTTTT
1 GTCTGCCAAATAGCACGTTTT
* *
28481 GTCTGCTAAATAGCTCGTTTT
1 GTCTGCCAAATAGCACGTTTT
28502 GT
1 GT
28504 TTTAGGACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (21 bp):
GTCTGCCAAATAGCACGTTTT
Found at i:31751 original size:50 final size:50
Alignment explanation
Indices: 31678--31868 Score: 242
Period size: 50 Copynumber: 3.9 Consensus size: 50
31668 ACATTAAGAG
31678 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* *
31726 GATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * *
31776 GATAAGAGGTCCCCCGTAAGACCATTTCTGGGACATGGCATAGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * *
31826 TATGAGAACTCACATGTAAGACCATATCTGGGATATGGCATTG
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTG
31869 CAGTACAAGA
Statistics
Matches: 121, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
48 7 0.06
50 114 0.94
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:39985 original size:21 final size:20
Alignment explanation
Indices: 39935--39987 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
39925 TTTTTATATA
* *
39935 TAAGCTTTTTTAATATATTTT
1 TAAG-TTTTTTAATTTAATTT
*
39956 TAA-TATTTTATATTTAATTT
1 TAAGTTTTTTA-ATTTAATTT
39976 TAAGTTTTTTAA
1 TAAGTTTTTTAA
39988 ATTTGTTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TAAGTTTTTTAATTTAATTT
Found at i:39991 original size:21 final size:21
Alignment explanation
Indices: 39935--39991 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
39925 TTTTTATATA
* *
39935 TAAGCTTTTTT-AATATATTTT
1 TAAG-TTTTTTAAATTTAATTT
* *
39956 TAA-TATTTTATATTTAATTT
1 TAAGTTTTTTAAATTTAATTT
39976 TAAGTTTTTTAAATTT
1 TAAGTTTTTTAAATTT
39992 GTTTAGAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 5 0.18
20 10 0.36
21 13 0.46
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TAAGTTTTTTAAATTTAATTT
Found at i:52067 original size:16 final size:16
Alignment explanation
Indices: 52030--52069 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
52020 TTAATGAAAT
* *
52030 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
52046 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
52062 TAAAATTA
1 TAAAATTA
52070 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:53579 original size:23 final size:24
Alignment explanation
Indices: 53553--53599 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
53543 TAAATCAAAC
*
53553 TTAAAATAAAAACTAT-TATATTT
1 TTAAAATAAAAAATATATATATTT
53576 TTAAAATAAAAAATATATATATTT
1 TTAAAATAAAAAATATATATATTT
53600 AATATATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAATAAAAAATATATATATTT
Found at i:56087 original size:10 final size:9
Alignment explanation
Indices: 56072--56114 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
56062 GGTTCCTCTA
56072 AAAAAATTAC
1 AAAAAATT-C
56082 AAAAAATTC
1 AAAAAATTC
*
56091 AAAATAATTTT
1 AAAA-AA-TTC
56102 AAAAAATTC
1 AAAAAATTC
56111 AAAA
1 AAAA
56115 TATTTAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 11 0.38
10 12 0.41
11 6 0.21
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAAATTC
Found at i:56099 original size:20 final size:20
Alignment explanation
Indices: 56071--56116 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
56061 TGGTTCCTCT
*
56071 AAAAAAATTACAAAAAATTC
1 AAAATAATTACAAAAAATTC
**
56091 AAAATAATTTTAAAAAATTC
1 AAAATAATTACAAAAAATTC
56111 AAAATA
1 AAAATA
56117 TTTAAGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATTACAAAAAATTC
Found at i:56134 original size:20 final size:21
Alignment explanation
Indices: 56111--56151 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
56101 TAAAAAATTC
* *
56111 AAAATATTTAAGAAAT-CTAA
1 AAAATATATAAAAAATGCTAA
56131 AAAATATATAAAAAATGCTAA
1 AAAATATATAAAAAATGCTAA
56152 CTTATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAATATATAAAAAATGCTAA
Found at i:56272 original size:2 final size:2
Alignment explanation
Indices: 56265--56296 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56255 GAGTTTTCAA
56265 AT 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 AT
56297 TTTGTGTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61821 original size:160 final size:160
Alignment explanation
Indices: 61557--61872 Score: 533
Period size: 160 Copynumber: 2.0 Consensus size: 160
61547 ACACGGATAC
* *
61557 TTCAAGAAAAGTAGAGTCAGAGTAACATAGGTAGCACCTGATTGAACTGTTCAATCATGTCAAAG
1 TTCAAGAAAAGTAGAGTCAGAGCAACATAGGTAGCACCTGATTAAACTGTTCAATCATGTCAAAG
* * *
61622 TTTTAGATGATGAATAGCCGTTGAAAGCAACTAAATCTGTGTCCAACAATTATTTTTTGTTGGCT
66 TTTTAGATGATGAATACCCGTTGAAAGCAACTAAATCTGTGTCCAACAATTATCTTTTATTGGCT
61687 TTACTTCGTATGGTAAAAGATTTTGGATTG
131 TTACTTCGTATGGTAAAAGATTTTGGATTG
** *
61717 TTCAAGAAAAGTAGAGTTGGAGCAACATTGGTAGCACCTGATTAAACTGTTCAATCATGTCAAAG
1 TTCAAGAAAAGTAGAGTCAGAGCAACATAGGTAGCACCTGATTAAACTGTTCAATCATGTCAAAG
* *
61782 TTTTAGATGATGAATACCCTTTGAAAGCAATTAAATCTGTGTCCAACAATTATCTTTTATTGGCT
66 TTTTAGATGATGAATACCCGTTGAAAGCAACTAAATCTGTGTCCAACAATTATCTTTTATTGGCT
*
61847 TTACTTTGTATGGTAAAAGATTTTGG
131 TTACTTCGTATGGTAAAAGATTTTGG
61873 CTCGATTGTA
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
160 145 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (160 bp):
TTCAAGAAAAGTAGAGTCAGAGCAACATAGGTAGCACCTGATTAAACTGTTCAATCATGTCAAAG
TTTTAGATGATGAATACCCGTTGAAAGCAACTAAATCTGTGTCCAACAATTATCTTTTATTGGCT
TTACTTCGTATGGTAAAAGATTTTGGATTG
Found at i:63329 original size:2 final size:2
Alignment explanation
Indices: 63322--63351 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
63312 AACATCATAC
*
63322 GT GT GT GT GT GT GT GT AT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
63352 ATGCATACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:63344 original size:14 final size:14
Alignment explanation
Indices: 63325--63354 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
63315 ATCATACGTG
63325 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
63339 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
63353 TG
1 TG
63355 CATACCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (14 bp):
TGTGTGTGTGTGTA
Found at i:69484 original size:13 final size:12
Alignment explanation
Indices: 69456--69491 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
69446 TTTATCAGTG
69456 AAAAATATACAT
1 AAAAATATACAT
*
69468 AAAAATATCCAT
1 AAAAATATACAT
69480 AAAAA-ATACAT
1 AAAAATATACAT
69491 A
1 A
69492 TGACAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATATACAT
Found at i:69754 original size:19 final size:19
Alignment explanation
Indices: 69716--69756 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
69706 ACCATATATA
* * *
69716 ATTTCAATACATCATGCTT
1 ATTTCAATAAACCATACTT
69735 ATTTCAATAAACCATACTT
1 ATTTCAATAAACCATACTT
69754 ATT
1 ATT
69757 GTACATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTCAATAAACCATACTT
Found at i:88462 original size:39 final size:40
Alignment explanation
Indices: 88419--88523 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
88409 TTCCATTATG
88419 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
88458 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
88503 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
88524 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:88517 original size:45 final size:44
Alignment explanation
Indices: 88417--88526 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
88407 TTTTCCATTA
88417 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
88456 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
88501 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
88527 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:88526 original size:16 final size:16
Alignment explanation
Indices: 88505--88537 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
88495 TTGATTTGCT
*
88505 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
88521 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
88537 A
1 A
88538 ATTCAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:91296 original size:3 final size:3
Alignment explanation
Indices: 91288--91313 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
91278 ACACTGACAG
91288 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
91314 TAAAAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:94905 original size:103 final size:102
Alignment explanation
Indices: 94772--95222 Score: 624
Period size: 103 Copynumber: 4.4 Consensus size: 102
94762 AAGGAAAAGG
94772 AAAAAAAAATTTGGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTT
1 AAAAAAAAATTT-GGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTT
* *
94837 TTGTGTCAGAATCAGATATTAGTATACGAAAAAAGTAAA
65 TTGTGTCAGAATCAGATATCAATATACGAAAAAAGT-AA
*
94876 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTTT
* *
94941 TGTGTCAGAATCAGATATTAGTATACGAAAAAAGT-A
66 TGTGTCAGAATCAGATATCAATATACGAAAAAAGTAA
* * ****
94977 AAAAAAAAATTTGGGTGTTGGCCTGTCAATGGCCGGTACCCAGTACAA--TTTAAAAA-AAAATT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTTT
* * *
95039 CGTGTCAGAATCAGATATCAATATACGAAAAAAAT-T
66 TGTGTCAGAATCAGATATCAATATACGAAAAAAGTAA
* **
95075 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCCTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTT-TTAAAAA----TT
*
95140 TTTTTTCGCGTCAGAATCAGATATCAATATACGAAAAAAGTAA
61 TTTTTT-GTGTCAGAATCAGATATCAATATACGAAAAAAGTAA
*
95183 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACC
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACC
95223 AAATTTATCA
Statistics
Matches: 309, Mismatches: 28, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
98 78 0.25
99 8 0.03
100 1 0.00
101 51 0.17
103 87 0.28
104 12 0.04
106 2 0.01
107 32 0.10
108 38 0.12
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (102 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTTT
TGTGTCAGAATCAGATATCAATATACGAAAAAAGTAA
Found at i:95079 original size:98 final size:100
Alignment explanation
Indices: 94772--95222 Score: 532
Period size: 98 Copynumber: 4.4 Consensus size: 100
94762 AAGGAAAAGG
***
94772 AAAAAAAAATTTGGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTT
1 AAAAAAAAATTT-GGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTTTAAAAATAAATT
* * * *
94837 TTGTGTCAGAATCAGATATTAGTATACGAAAAAAGTAAA
64 TCGTGTCAGAATCAGATATCAATATACGAAAAAA--ATA
* ***
94876 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTACAATTTTTAAAAATTTTTTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTTTAAAAATAAATTT
* * * *
94941 TGTGTCAGAATCAGATATTAGTATACGAAAAAAGTA
65 CGTGTCAGAATCAGATATCAATATACGAAAAAAATA
* * *
94977 AAAAAAAAATTTGGGTGTTGGCCTGTCAATGGCCGGTACCCAGTACAA-TTTAAAAA-AAAATTC
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAATAAATTTC
*
95040 GTGTCAGAATCAGATATCAATATACGAAAAAAATT
66 GTGTCAGAATCAGATATCAATATACGAAAAAAATA
*
95075 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTACAA-TTTAAAAA-AAATTCC
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAATAAA----
* *
95138 TTTTTTTTCGCGTCAGAATCAGATATCAATATACGAAAAAAGTAA
62 -----TTTCGTGTCAGAATCAGATATCAATATACGAAAAAAAT-A
*
95183 AAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACC
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACC
95223 AAATTTATCA
Statistics
Matches: 313, Mismatches: 24, Indels: 16
0.89 0.07 0.05
Matches are distributed among these distances:
98 89 0.28
99 8 0.03
101 46 0.15
103 85 0.27
104 12 0.04
107 35 0.11
108 38 0.12
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (100 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAATAAATTTC
GTGTCAGAATCAGATATCAATATACGAAAAAAATA
Found at i:95830 original size:43 final size:44
Alignment explanation
Indices: 95766--95877 Score: 156
Period size: 44 Copynumber: 2.5 Consensus size: 44
95756 GAATTGAATT
*
95766 AAATGAAATTCAGAAAAGTGAGTCAAA-ATAAATTGG-ATAGAAAC
1 AAATGAAATT-TGAAAAGTGAGTCAAAGATAAA-TGGAATAGAAAC
* *
95810 AAATGAAATTTGAAAAGTGAGTCAAAGATAGATGGAATAGAAAT
1 AAATGAAATTTGAAAAGTGAGTCAAAGATAAATGGAATAGAAAC
*
95854 AAATGAAATTTGAAAAGTTAGTCA
1 AAATGAAATTTGAAAAGTGAGTCA
95878 GAACAATTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
43 18 0.29
44 44 0.71
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.23
Consensus pattern (44 bp):
AAATGAAATTTGAAAAGTGAGTCAAAGATAAATGGAATAGAAAC
Found at i:97189 original size:104 final size:104
Alignment explanation
Indices: 96876--98465 Score: 2510
Period size: 104 Copynumber: 15.4 Consensus size: 104
96866 ATTACAAGGT
* * * * * * * *
96876 GGTGTCGGCCATTAACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
* *
96941 TTCTGACAC-----AA-AATCTTTTTTTAAATTGTACTGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTA-TGG
* * * * * *
96975 GG-GCCGGCCATTGATAGGCCGGCACCCAAAATTTTTTTTTTACTTTTTTCGTATACTG-GTATC
1 GGTGCCGGCTATTGACAAGCCAGCACCC-AAA-TTTTTTTTTATTTTTTTCGTATTCTGAG-ATC
* ** *
97038 TGATT-TTTCACCTAAAAAAATAA------TTTAAATTGTACT-G
63 TTATTCTGACA-C-AAAAAAATAATTTTTTTTTAATTTGTA-TGG
97075 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97140 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97179 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97244 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97283 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97348 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97387 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97452 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97491 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97556 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97595 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97660 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97699 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97764 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97803 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97868 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
97907 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
97972 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
98011 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
98076 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
98115 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
*
98180 TTCTGACACAAAAAAATAATTTTTTTTTAAATTGTACT-G
66 TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTA-TGG
* * * * * * *
98219 GGTGCCGGCCATTGATAGGCCAGTACCCAAATTTTTTTTTTTACTTTTTTCGTATACTGATATCT
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAA--TTTTTTTTTATTTTTTTCGTATTCTGAGATCT
* * *
98284 GATTTTGACACTAAAAAAATAA------TTTAAATTGTACT-G
64 TATTCTGACAC-AAAAAAATAATTTTTTTTTAATTTGTA-TGG
* * * * * * *
98320 GGTGCCGGCCATTGATAGGCCGGCACCCAAAATTTTTTTTTTACTTTTTTCGTATACTGATATCT
1 GGTGCCGGCTATTGACAAGCCAGCACCC-AAA-TTTTTTTTTATTTTTTTCGTATTCTGAGATCT
* *
98385 GATTCTGACACAAAAAAATAATTTTTTTTTAAATTGTACT-G
64 TATTCTGACACAAAAAAATAATTTTTTTTTAATTTGTA-TGG
98426 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTT
1 GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTT
98466 CCTTTTTCTT
Statistics
Matches: 1425, Mismatches: 34, Indels: 59
0.94 0.02 0.04
Matches are distributed among these distances:
98 31 0.02
99 40 0.03
100 55 0.04
101 117 0.08
102 3 0.00
103 1 0.00
104 1084 0.76
105 4 0.00
106 78 0.05
107 12 0.01
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (104 bp):
GGTGCCGGCTATTGACAAGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTCTGAGATCTTA
TTCTGACACAAAAAAATAATTTTTTTTTAATTTGTATGG
Found at i:98479 original size:16 final size:16
Alignment explanation
Indices: 98458--98489 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
98448 GCACCCAAAT
98458 TTTTTTTTCCTTTTTC
1 TTTTTTTTCCTTTTTC
98474 TTTTTTTTCCTTTTTC
1 TTTTTTTTCCTTTTTC
98490 ATATATCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCCTTTTTC
Found at i:99613 original size:32 final size:33
Alignment explanation
Indices: 99568--99634 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
99558 AAATGCCAAT
99568 TTACTTTTATCTATTTACTTAATATTTT-ATTA
1 TTACTTTTATCTATTTACTTAATATTTTCATTA
* **
99600 TTACTTGTT-TCTATTTTCTTTTTATTTTCATTA
1 TTACTT-TTATCTATTTACTTAATATTTTCATTA
99633 TT
1 TT
99635 TTATTATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.67
Consensus pattern (33 bp):
TTACTTTTATCTATTTACTTAATATTTTCATTA
Found at i:107031 original size:14 final size:17
Alignment explanation
Indices: 106994--107036 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 17
106984 AAATTAATTC
106994 TAATGTATATTATTAAAT
1 TAAT-TATATTATTAAAT
107012 TAATTATATTA-TAAA-
1 TAATTATATTATTAAAT
107027 T-ATTATATTA
1 TAATTATATTA
107037 AGAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.36
15 1 0.04
16 4 0.16
17 7 0.28
18 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAATTATATTATTAAAT
Found at i:111003 original size:32 final size:32
Alignment explanation
Indices: 110964--111034 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
110954 ATTTTAGAGG
* *
110964 TTGATTAATACAAATCATTGGAGAAATTAAGA
1 TTGATTAATACAAACCATTGAAGAAATTAAGA
*
110996 TTGATTAATACAAACCCTTGAAGAAATTAAGA
1 TTGATTAATACAAACCATTGAAGAAATTAAGA
111028 TTGATTA
1 TTGATTA
111035 GAAATTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGATTAATACAAACCATTGAAGAAATTAAGA
Found at i:116222 original size:27 final size:27
Alignment explanation
Indices: 116184--116237 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
116174 CCCCATCTAA
116184 ACTCCAATTTGGGCGGAGTAGACGAGG
1 ACTCCAATTTGGGCGGAGTAGACGAGG
*
116211 ACTCCGATTTGGGCGGAGTAGACGAGG
1 ACTCCAATTTGGGCGGAGTAGACGAGG
116238 GCTTCGTCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (27 bp):
ACTCCAATTTGGGCGGAGTAGACGAGG
Found at i:123892 original size:6 final size:6
Alignment explanation
Indices: 123881--123932 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
123871 TTTTTGAGCT
* * * * *
123881 TATATG TATATG TCTATG TCTATG TCTATG TCTATG TACATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
123929 TATA
1 TATA
123933 ATTCTGAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:123910 original size:18 final size:18
Alignment explanation
Indices: 123883--123929 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
123873 TTTGAGCTTA
123883 TATGTATATGTCTATGTC
1 TATGTATATGTCTATGTC
*
123901 TATGTCTATGTCTATGTAC
1 TATGTATATGTCTATGT-C
123920 -ATGTATATGT
1 TATGTATATGT
123930 ATAATTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (18 bp):
TATGTATATGTCTATGTC
Found at i:128688 original size:14 final size:15
Alignment explanation
Indices: 128665--128701 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
128655 ATTATTAAAT
128665 AAAT-TTTTAAAG-A
1 AAATATTTTAAAGAA
128678 AAATATTTTAAAGATA
1 AAATATTTTAAAGA-A
128694 AAATATTT
1 AAATATTT
128702 CCTTTATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 8 0.38
16 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (15 bp):
AAATATTTTAAAGAA
Found at i:131545 original size:74 final size:75
Alignment explanation
Indices: 131446--131601 Score: 305
Period size: 74 Copynumber: 2.1 Consensus size: 75
131436 TAATAAGTTG
131446 TTTAATTTTGATTTTCAAAATATTTAAAATATTAATATTAAAGATTATAATTTTCAATATTAATA
1 TTTAATTTTGATTTTCAAAATATTTAAAATATTAATATTAAAGATTATAATTTTCAATATTAATA
131511 AAAATACATA
66 AAAATACATA
131521 TTTAATTTTG-TTTTCAAAATATTTAAAATATTAATATTAAAGATTATAATTTTCAATATTAATA
1 TTTAATTTTGATTTTCAAAATATTTAAAATATTAATATTAAAGATTATAATTTTCAATATTAATA
131585 AAAATACATA
66 AAAATACATA
131595 TTTAATT
1 TTTAATT
131602 ATTTATATTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 71 0.88
75 10 0.12
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (75 bp):
TTTAATTTTGATTTTCAAAATATTTAAAATATTAATATTAAAGATTATAATTTTCAATATTAATA
AAAATACATA
Found at i:133497 original size:17 final size:17
Alignment explanation
Indices: 133475--133509 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
133465 ATTTTTTCTT
* *
133475 TTTTTTAATAATTTTTA
1 TTTTTTAAAAAATTTTA
133492 TTTTTTAAAAAATTTTA
1 TTTTTTAAAAAATTTTA
133509 T
1 T
133510 AAAATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTAAAAAATTTTA
Found at i:133533 original size:10 final size:11
Alignment explanation
Indices: 133493--133536 Score: 58
Period size: 10 Copynumber: 4.3 Consensus size: 11
133483 TAATTTTTAT
133493 TTTTTA-AAAA
1 TTTTTATAAAA
*
133503 ATTTTATAAAA
1 TTTTTATAAAA
133514 -TTTTATAAAA
1 TTTTTATAAAA
133524 TTTTTA-AAAA
1 TTTTTATAAAA
133534 TTT
1 TTT
133537 ATTTAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTTATAAAA
Found at i:133656 original size:73 final size:74
Alignment explanation
Indices: 133548--133694 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
133538 TTTAATTAAA
133548 ACCAAACCTAAAAACCAATGAAACCGAAACTGGGATATTCTGACCGGTTCCATGGTTCTGTTTTA
1 ACCAAACCTAAAAACCAATGAAACCGAAACTGGGATATTCTGACCGGTTCCATGGTTCTGTTTTA
133613 AAAAAACAT
66 AAAAAACAT
133622 ACCAAACCT-AAAACCAATGAAACCGAAACTGGGATATTCTGACCGGTTCCATGGTTCTGTTTTA
1 ACCAAACCTAAAAACCAATGAAACCGAAACTGGGATATTCTGACCGGTTCCATGGTTCTGTTTTA
133686 AAAAAACAT
66 AAAAAACAT
133695 TGAACAATCC
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 64 0.88
74 9 0.12
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (74 bp):
ACCAAACCTAAAAACCAATGAAACCGAAACTGGGATATTCTGACCGGTTCCATGGTTCTGTTTTA
AAAAAACAT
Found at i:137052 original size:7 final size:7
Alignment explanation
Indices: 137040--137154 Score: 167
Period size: 7 Copynumber: 15.9 Consensus size: 7
137030 CATGCCATAG
137040 CCCTAAA
1 CCCTAAA
137047 CCCTAAA
1 CCCTAAA
137054 CCCTAAA
1 CCCTAAA
137061 CCCTAAA
1 CCCTAAA
137068 CCCTAAAA
1 CCCT-AAA
137076 CCCTAAA
1 CCCTAAA
137083 CCCTAAA
1 CCCTAAA
137090 CCCTAAA
1 CCCTAAA
*
137097 CCCCAAA
1 CCCTAAA
137104 CCCCTAAAA
1 -CCCT-AAA
137113 CCCTAAA
1 CCCTAAA
*
137120 CCCCAAAA
1 -CCCTAAA
137128 CCCTAAA
1 CCCTAAA
*
137135 CCTTAAA
1 CCCTAAA
137142 CCCTAAA
1 CCCTAAA
137149 CCCTAA
1 CCCTAA
137155 TACTCACATT
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
7 75 0.77
8 20 0.20
9 3 0.03
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.13
Consensus pattern (7 bp):
CCCTAAA
Found at i:137079 original size:29 final size:28
Alignment explanation
Indices: 137040--137154 Score: 167
Period size: 29 Copynumber: 4.0 Consensus size: 28
137030 CATGCCATAG
137040 CCCTAAACCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAACCCTAAA
137068 CCCTAAAACCCTAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAACCCTAAA
* *
137097 CCCCAAACCCCTAAAACCCTAAACCCCAAAA
1 CCCTAAA-CCCT-AAACCCTAAA-CCCTAAA
*
137128 CCCTAAACCTTAAACCCTAAACCCTAA
1 CCCTAAACCCTAAACCCTAAACCCTAA
137155 TACTCACATT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
28 12 0.15
29 41 0.53
30 13 0.17
31 12 0.15
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.13
Consensus pattern (28 bp):
CCCTAAACCCTAAACCCTAAACCCTAAA
Found at i:138426 original size:5 final size:6
Alignment explanation
Indices: 138411--138435 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
138401 AAATTCATAA
138411 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
138436 TTCAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:139042 original size:25 final size:25
Alignment explanation
Indices: 138990--139043 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
138980 AATGAATTGA
*
138990 TTTAATTTTTATTTATTATTACATT
1 TTTAATTTTTATTTATTATTACAAT
* *
139015 TTTAA-TTTTATTTTTTTTTACCAAT
1 TTTAATTTTTATTTATTATTA-CAAT
139040 TTTA
1 TTTA
139044 GTCCTACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTAATTTTTATTTATTATTACAAT
Found at i:143904 original size:47 final size:45
Alignment explanation
Indices: 143795--143902 Score: 139
Period size: 43 Copynumber: 2.4 Consensus size: 45
143785 CTTTACCATT
* * *
143795 TTGATATATTTGATATATTGAGTATGTTCGGTATGTTTTTGTATATC
1 TTGATATTTTTTATATATTGAGTATGTT--GTATGTTATTGTATATC
*
143842 TTGGTATTTTTTATATATTGAGTATG-T-TATGTTATTGTATATC
1 TTGATATTTTTTATATATTGAGTATGTTGTATGTTATTGTATATC
*
143885 TTGATATTTTTTTTATAT
1 TTGATATTTTTTATATAT
143903 ATTTGATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 31 0.56
46 1 0.02
47 23 0.42
ACGTcount: A:0.23, C:0.03, G:0.16, T:0.58
Consensus pattern (45 bp):
TTGATATTTTTTATATATTGAGTATGTTGTATGTTATTGTATATC
Found at i:144741 original size:29 final size:30
Alignment explanation
Indices: 144703--144760 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
144693 TGATATAACC
*
144703 TTGATAGTTTAGGGAT-ATAATTAGAATGAT
1 TTGATAGTTTAAGGATCA-AATTAGAATGAT
*
144733 TTGA-AGTTTAAGGATCAATTTAGAATGA
1 TTGATAGTTTAAGGATCAAATTAGAATGA
144761 ACTCATAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
TTGATAGTTTAAGGATCAAATTAGAATGAT
Found at i:144979 original size:14 final size:13
Alignment explanation
Indices: 144960--144989 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
144950 CCCTTTCTTC
144960 CTCTTCTCCTCCTT
1 CTCTTCTCC-CCTT
144974 CTCTTCTCCCCTT
1 CTCTTCTCCCCTT
144987 CTC
1 CTC
144990 CGGTCCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (13 bp):
CTCTTCTCCCCTT
Found at i:147638 original size:24 final size:24
Alignment explanation
Indices: 147581--147632 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
147571 TTTTTAAAAG
* * *
147581 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
147605 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
147629 ATTT
1 ATTT
147633 GACATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:147643 original size:24 final size:24
Alignment explanation
Indices: 147598--147644 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
147588 ATTTATGAGT
*
147598 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTAATTAGC
147622 ATAATATATTT-GACATTAATTAG
1 ATAATATATTTAG-CATTAATTAG
147645 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTAATTAGC
Found at i:148732 original size:9 final size:9
Alignment explanation
Indices: 148715--148745 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
148705 TCGAGTTGAT
148715 TCGAATAAC
1 TCGAATAAC
*
148724 TCGATTAAC
1 TCGAATAAC
148733 TCGAATAAC
1 TCGAATAAC
148742 TCGA
1 TCGA
148746 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:170793 original size:27 final size:26
Alignment explanation
Indices: 170740--170801 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
170730 AGAAAACAAC
* * *
170740 AAAAAGAGAATCTATTCTAAAAAGAA
1 AAAAAGAAAACCTAATCTAAAAAGAA
170766 AAAAAGAAAACCTAATCTAAAAATGAA
1 AAAAAGAAAACCTAATCTAAAAA-GAA
170793 AAAAAGAAA
1 AAAAAGAAA
170802 GAAAGAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.68, C:0.08, G:0.10, T:0.15
Consensus pattern (26 bp):
AAAAAGAAAACCTAATCTAAAAAGAA
Found at i:175653 original size:28 final size:28
Alignment explanation
Indices: 175621--175685 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
175611 TATCAAAAAT
175621 ATCAATAAAAATTTTTAAGTGTAGAGAC
1 ATCAATAAAAATTTTTAAGTGTAGAGAC
* *
175649 ATCAATAAAATTTTTTAAGTGTAGAGAT
1 ATCAATAAAAATTTTTAAGTGTAGAGAC
175677 ATCAATAAA
1 ATCAATAAA
175686 TATCAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (28 bp):
ATCAATAAAAATTTTTAAGTGTAGAGAC
Found at i:177235 original size:12 final size:12
Alignment explanation
Indices: 177218--177243 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
177208 AAAGAAAATG
177218 TATTATTATTTT
1 TATTATTATTTT
177230 TATTATTATTTT
1 TATTATTATTTT
177242 TA
1 TA
177244 AATATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:182068 original size:83 final size:83
Alignment explanation
Indices: 181975--182140 Score: 269
Period size: 83 Copynumber: 2.0 Consensus size: 83
181965 AACTAATTCC
* * * *
181975 TAATTTATCTCATAAATTCCAACTCAATGGTTCTATTCACAAATTCCATATCAATGGTCTCATCT
1 TAATTGATCTCACAAATTCCAACTCAATAGTTCAATTCACAAATTCCATATCAATGGTCTCATCT
*
182040 TTTACCTACTTAAAAAAT
66 TTTACCTACATAAAAAAT
* *
182058 TAATTGATCTCACAAATTCCAACTCAATAGTTCAATTCACAAATTTCATATCAATGGTCTTATCT
1 TAATTGATCTCACAAATTCCAACTCAATAGTTCAATTCACAAATTCCATATCAATGGTCTCATCT
182123 TTTACCTACATAAAAAAT
66 TTTACCTACATAAAAAAT
182141 AAAAAATTAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (83 bp):
TAATTGATCTCACAAATTCCAACTCAATAGTTCAATTCACAAATTCCATATCAATGGTCTCATCT
TTTACCTACATAAAAAAT
Found at i:182657 original size:14 final size:14
Alignment explanation
Indices: 182638--182667 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
182628 TGACCTTGTT
182638 CAGTTGTGCTGTCC
1 CAGTTGTGCTGTCC
*
182652 CAGTTGTGTTGTCC
1 CAGTTGTGCTGTCC
182666 CA
1 CA
182668 TCAATGACAG
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:0.10, C:0.27, G:0.27, T:0.37
Consensus pattern (14 bp):
CAGTTGTGCTGTCC
Found at i:182967 original size:5 final size:5
Alignment explanation
Indices: 182957--182982 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
182947 TGAGCATTCG
182957 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
182983 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:183628 original size:30 final size:29
Alignment explanation
Indices: 183594--183651 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
183584 AGAGGTGGGA
*
183594 TGGGAAGAAAATAAAAGTTTTAGGGGAAAC
1 TGGG-AGAAAATAAAAATTTTAGGGGAAAC
* * *
183624 TGGGAGGAAGTAAAAATTTTGGGGGAAA
1 TGGGAGAAAATAAAAATTTTAGGGGAAA
183652 ATAAAATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.34, T:0.21
Consensus pattern (29 bp):
TGGGAGAAAATAAAAATTTTAGGGGAAAC
Done.