Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014208.1 Kokia drynarioides strain JFW-HI SEQ_129241, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 219927
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:10806 original size:29 final size:29
Alignment explanation
Indices: 10773--10831 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
10763 AAGTTAAGGG
10773 TTCCTATCTTGATACTCATTGATTTCTTA
1 TTCCTATCTTGATACTCATTGATTTCTTA
*
10802 TTCCTATTTTGATACTCATTGATTTCTTA
1 TTCCTATCTTGATACTCATTGATTTCTTA
10831 T
1 T
10832 AGTCACATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (29 bp):
TTCCTATCTTGATACTCATTGATTTCTTA
Found at i:17184 original size:15 final size:15
Alignment explanation
Indices: 17164--17192 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17154 GAAATGAGTC
17164 ATTAAATCAATTTAA
1 ATTAAATCAATTTAA
17179 ATTAAATCAATTTA
1 ATTAAATCAATTTA
17193 GCTAAAAATA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATCAATTTAA
Found at i:19279 original size:79 final size:81
Alignment explanation
Indices: 19147--19319 Score: 269
Period size: 80 Copynumber: 2.2 Consensus size: 81
19137 TAAATTTTTT
* * * *
19147 TTTTTAAGGAGGCGAATTTAAATTGTAATTTTTATGATAGTAAAAATGTAA-TTTTAAAAAATTA
1 TTTTTAAGGAGGCGAAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAAATAA
*
19211 AATCAAAATTTTATCA
66 AATAAAAATTTTATCA
*
19227 TTTTTAAGG-GGCGAAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAGATAA
1 TTTTTAAGGAGGCGAAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAAATAA
19291 AATAAAAATTTTATCA
66 AATAAAAATTTTATCA
*
19307 TTTTTAGGGAGGC
1 TTTTTAAGGAGGC
19320 TAAAATATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
79 38 0.45
80 43 0.51
81 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (81 bp):
TTTTTAAGGAGGCGAAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAAATAA
AATAAAAATTTTATCA
Found at i:22288 original size:15 final size:15
Alignment explanation
Indices: 22255--22288 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22245 ATATGTTTAT
*
22255 TTATTATTTAACTTA
1 TTATTATTTAACTCA
*
22270 TTATTATTTAACTCG
1 TTATTATTTAACTCA
22285 TTAT
1 TTAT
22289 AAGACCCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (15 bp):
TTATTATTTAACTCA
Found at i:23860 original size:26 final size:26
Alignment explanation
Indices: 23831--23883 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
23821 AGTTCTTGAG
23831 ATTGAGTCGATATCCATGGGAGATGT
1 ATTGAGTCGATATCCATGGGAGATGT
23857 ATTGAGTCGATATCCATGGGAGATGT
1 ATTGAGTCGATATCCATGGGAGATGT
23883 A
1 A
23884 GCATTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.30
Consensus pattern (26 bp):
ATTGAGTCGATATCCATGGGAGATGT
Found at i:27995 original size:21 final size:21
Alignment explanation
Indices: 27969--28015 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
27959 CTATAGGCAA
27969 AACTACCAGTACTTATTATGC
1 AACTACCAGTACTTATTATGC
*
27990 AACTACCGGTACTTATTATGC
1 AACTACCAGTACTTATTATGC
28011 AACTA
1 AACTA
28016 TCGATACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (21 bp):
AACTACCAGTACTTATTATGC
Found at i:40649 original size:26 final size:26
Alignment explanation
Indices: 40620--40674 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
40610 TACCCCCAAC
** * *
40620 AAAACTTTGATGATTTTACCCTTAGT
1 AAAACTTTGACAATTTCACCCCTAGT
*
40646 AAAATTTTGACAATTTCACCCCTAGT
1 AAAACTTTGACAATTTCACCCCTAGT
40672 AAA
1 AAA
40675 TTTTCAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (26 bp):
AAAACTTTGACAATTTCACCCCTAGT
Found at i:41616 original size:76 final size:76
Alignment explanation
Indices: 41477--41623 Score: 249
Period size: 76 Copynumber: 1.9 Consensus size: 76
41467 GTGTATGAGT
*
41477 CATGCGTTCATAGTCCTCCATCCACTCAAGATTTAGGTATGTCACACTACGAACATCATAAGTGA
1 CATGCGTTCATAGTCCTCCATCCACTCAAGATTTAGGTATGTCACACTACGAACATCACAAGTGA
41542 ATAAATTCGGC
66 ATAAATTCGGC
* * * *
41553 CATGCGTTCATAGTCCTCCATCCACTCAGGATTTAGGTATGTTACACTATGAACGTCACAAGTGA
1 CATGCGTTCATAGTCCTCCATCCACTCAAGATTTAGGTATGTCACACTACGAACATCACAAGTGA
41618 ATAAAT
66 ATAAAT
41624 CCATAAACAG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (76 bp):
CATGCGTTCATAGTCCTCCATCCACTCAAGATTTAGGTATGTCACACTACGAACATCACAAGTGA
ATAAATTCGGC
Found at i:44921 original size:10 final size:10
Alignment explanation
Indices: 44896--44942 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
44886 TTTAACACAA
44896 CACATATTAAT
1 CACAT-TTAAT
44907 CACATTTAAT
1 CACATTTAAT
* *
44917 TACATATAAT
1 CACATTTAAT
44927 CACATTTAAT
1 CACATTTAAT
44937 CACATT
1 CACATT
44943 AGTAACATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 27 0.84
11 5 0.16
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (10 bp):
CACATTTAAT
Found at i:44928 original size:20 final size:21
Alignment explanation
Indices: 44896--44941 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
44886 TTTAACACAA
44896 CACATATTAATCACATTTAAT
1 CACATATTAATCACATTTAAT
*
44917 TACATA-TAATCACATTTAAT
1 CACATATTAATCACATTTAAT
44937 CACAT
1 CACAT
44942 TAGTAACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
CACATATTAATCACATTTAAT
Found at i:44966 original size:78 final size:77
Alignment explanation
Indices: 44850--44994 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 77
44840 CATTCTTTTA
* * *
44850 CACATTAATCGCATTAATCACATGAGTAATTAAGCATTTAACACAACACATATTAATCACATTTA
1 CACATTAATCACATTAATAACATGAATAATTAAGCATTTAACACAACACATATTAATCACATTTA
44915 ATTACATATAAT
66 ATTACATATAAT
* * * * *
44927 CACATTTAATCACATTAGTAACATGAATACTTCAA-CATTTATCACATCACATATTCATCACATT
1 CACA-TTAATCACATTAATAACATGAATAATT-AAGCATTTAACACAACACATATTAATCACATT
44991 TAAT
64 TAAT
44995 CACCTTGGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
77 4 0.07
78 52 0.90
79 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (77 bp):
CACATTAATCACATTAATAACATGAATAATTAAGCATTTAACACAACACATATTAATCACATTTA
ATTACATATAAT
Found at i:44993 original size:58 final size:58
Alignment explanation
Indices: 44918--45058 Score: 212
Period size: 58 Copynumber: 2.4 Consensus size: 58
44908 ACATTTAATT
44918 ACATA-TAATCACATTTAATCACATTAGTAACATGAATACTTCAACATTTATCACATC
1 ACATATTAATCACATTTAATCACATTAGTAACATGAATACTTCAACATTTATCACATC
* * * * * *
44975 ACATATTCATCACATTTAATCACCTTGGTCACATGAATATTTTAACATTTATCACATC
1 ACATATTAATCACATTTAATCACATTAGTAACATGAATACTTCAACATTTATCACATC
*
45033 ACATATTAATCACATTTAGTCACATT
1 ACATATTAATCACATTTAATCACATT
45059 TAATCACATT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
57 5 0.07
58 69 0.93
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (58 bp):
ACATATTAATCACATTTAATCACATTAGTAACATGAATACTTCAACATTTATCACATC
Found at i:45049 original size:25 final size:23
Alignment explanation
Indices: 45023--45121 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 23
45013 ATTTTAACAT
45023 TTATCACATCACATATTAATCACA
1 TTATCACATCACAT-TTAATCACA
*
45047 TT-T-A-GTCACATTTAATCACA
1 TTATCACATCACATTTAATCACA
45067 TT-T-A-ATCACATTTAATCACA
1 TTATCACATCACATTTAATCACA
* *
45087 TTAGTCACATGAATATTTAATCACA
1 TTA-TCACAT-CACATTTAATCACA
45112 TTAGTCACAT
1 TTA-TCACAT
45122 GTATATTTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
20 30 0.45
21 6 0.09
22 2 0.03
23 2 0.03
24 4 0.06
25 22 0.33
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.37
Consensus pattern (23 bp):
TTATCACATCACATTTAATCACA
Found at i:45057 original size:10 final size:10
Alignment explanation
Indices: 45030--45088 Score: 100
Period size: 10 Copynumber: 5.8 Consensus size: 10
45020 CATTTATCAC
45030 ATCACATATTA
1 ATCACAT-TTA
45041 ATCACATTTA
1 ATCACATTTA
*
45051 GTCACATTTA
1 ATCACATTTA
45061 ATCACATTTA
1 ATCACATTTA
45071 ATCACATTTA
1 ATCACATTTA
45081 ATCACATT
1 ATCACATT
45089 AGTCACATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
10 39 0.85
11 7 0.15
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (10 bp):
ATCACATTTA
Found at i:45063 original size:20 final size:20
Alignment explanation
Indices: 45031--45096 Score: 107
Period size: 20 Copynumber: 3.3 Consensus size: 20
45021 ATTTATCACA
45031 TCACATATTAATCACATTTAG
1 TCACAT-TTAATCACATTTAG
*
45052 TCACATTTAATCACATTTAA
1 TCACATTTAATCACATTTAG
45072 TCACATTTAATCACA-TTAG
1 TCACATTTAATCACATTTAG
45091 TCACAT
1 TCACAT
45097 GAATATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.21
20 28 0.65
21 6 0.14
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (20 bp):
TCACATTTAATCACATTTAG
Found at i:45074 original size:30 final size:30
Alignment explanation
Indices: 45030--45096 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
45020 CATTTATCAC
*
45030 ATCACATATTAATCACATTTAGTCACATTTA
1 ATCACATATTAATCACATTTAATCACA-TTA
45061 ATCACAT-TTAATCACATTTAATCACATTA
1 ATCACATATTAATCACATTTAATCACATTA
*
45090 GTCACAT
1 ATCACAT
45097 GAATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 9 0.26
30 18 0.53
31 7 0.21
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (30 bp):
ATCACATATTAATCACATTTAATCACATTA
Found at i:45122 original size:25 final size:25
Alignment explanation
Indices: 45076--45153 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
45066 ATTTAATCAC
45076 ATTTAATCACATTAGTCACATGAAT
1 ATTTAATCACATTAGTCACATGAAT
*
45101 ATTTAATCACATTAGTCACATGTAT
1 ATTTAATCACATTAGTCACATGAAT
* * *
45126 ATTTAAGCACA--AATCACATCAAT
1 ATTTAATCACATTAGTCACATGAAT
45149 ATTTA
1 ATTTA
45154 CTAACAGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.29
25 34 0.71
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (25 bp):
ATTTAATCACATTAGTCACATGAAT
Found at i:45779 original size:21 final size:21
Alignment explanation
Indices: 45752--45816 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
45742 ATTCTACTAG
45752 TACAACTAAGACTTCTATCGA
1 TACAACTAAGACTTCTATCGA
* * **
45773 TATAACTATGGGTTCTATCGA
1 TACAACTAAGACTTCTATCGA
** *
45794 TACAACTCGGACTTCTATTGA
1 TACAACTAAGACTTCTATCGA
45815 TA
1 TA
45817 GAACAGACTC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (21 bp):
TACAACTAAGACTTCTATCGA
Found at i:53136 original size:52 final size:51
Alignment explanation
Indices: 53070--53300 Score: 250
Period size: 52 Copynumber: 4.5 Consensus size: 51
53060 TCGATGACTC
* * *
53070 TGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAAGGTTC-GATGACA
1 TGTGTCATCGTGAGTATATGAATCCCTTACAGATTATAAGG-TCAGATGACA
* * **
53121 TCGTGCCATCATGAGTATATGAATCCCTTACAGATTATAAGGTCAGATGGTTA
1 T-GTGTCATCGTGAGTATATGAATCCCTTACAGATTATAAGGTCAGAT-GACA
* * * *
53174 TGTGTTATCGTGAGTATATGAATCTCTTACAGATTATAAGGTCTGATGGCTA
1 TGTGTCATCGTGAGTATATGAATCCCTTACAGATTATAAGGTCAGATGAC-A
** * *
53226 TGTGTCATCGTGAGTATATGAATCCCTTATGGATTATGAA-GTCCGATGATTA
1 TGTGTCATCGTGAGTATATGAATCCCTTACAGATTAT-AAGGTCAGATGA-CA
*
53278 TATGTCATCGTGAGTATATGAAT
1 TGTGTCATCGTGAGTATATGAAT
53301 GAAGTGAAAA
Statistics
Matches: 152, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
51 4 0.03
52 143 0.94
53 5 0.03
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (51 bp):
TGTGTCATCGTGAGTATATGAATCCCTTACAGATTATAAGGTCAGATGACA
Found at i:53250 original size:104 final size:104
Alignment explanation
Indices: 53070--53300 Score: 299
Period size: 104 Copynumber: 2.2 Consensus size: 104
53060 TCGATGACTC
*
53070 TGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAAGGTTCGATGACATCGTGCCATCATGA
1 TGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAAAGGTTCGATGACATCGTGCCATCATGA
*
53135 GTATATGAATCCCTTACAGATTAT-AAGGTCAGATGGTTA
66 GTATATGAATCCCTTACAGATTATGAA-GTCAGATGATTA
* * * * *
53174 TGTGTTATCGTGAGTATATGAAT-CTCTTACAGATTATAAGG-TCTGATGGCTAT-GTGTCATCG
1 TGTGTCATCGTGAGTATATGAATCCT-TTACAGATTAAAAGGTTC-GATGAC-ATCGTGCCATCA
** *
53236 TGAGTATATGAATCCCTTATGGATTATGAAGTCCGATGATTA
63 TGAGTATATGAATCCCTTACAGATTATGAAGTCAGATGATTA
*
53278 TATGTCATCGTGAGTATATGAAT
1 TGTGTCATCGTGAGTATATGAAT
53301 GAAGTGAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
103 4 0.04
104 103 0.93
105 4 0.04
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (104 bp):
TGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAAAGGTTCGATGACATCGTGCCATCATGA
GTATATGAATCCCTTACAGATTATGAAGTCAGATGATTA
Found at i:59738 original size:52 final size:51
Alignment explanation
Indices: 59650--59842 Score: 201
Period size: 52 Copynumber: 3.7 Consensus size: 51
59640 GTAAACGAAG
* * *
59650 AGGTCTGATGACTCTGTGTCATCGTAAGTATATGAATCCTTTACGGATTAA
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCCTTACGGATTAA
* * * * *
59701 CAGGTTTGATGACTTTGTGTCATCGTGAGTATTTGAATCCCTTACGGACTATG
1 -AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCCTTACGGATTA-A
* **
59754 AGGT-TCGAT-AGCTATGTGTTATCGTGAGTATATGAATCCCTTACAAATTATA
1 AGGTCT-GATGA-CTATGTGTCATCGTGAGTATATGAATCCCTTACGGATTA-A
* * *
59806 AGGTCTGATGGCTATGTGTCGTCGTGAGCATATGAAT
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAAT
59843 TATGTGGTCC
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
51 2 0.02
52 115 0.97
53 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (51 bp):
AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCCTTACGGATTAA
Found at i:61324 original size:22 final size:22
Alignment explanation
Indices: 61296--61339 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
61286 ACTTCTTCCA
61296 TCATGGGCCAAGAGATTACTAT
1 TCATGGGCCAAGAGATTACTAT
61318 TCATGGGCCAAGAGATTACTAT
1 TCATGGGCCAAGAGATTACTAT
61340 CTCAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (22 bp):
TCATGGGCCAAGAGATTACTAT
Found at i:62939 original size:21 final size:21
Alignment explanation
Indices: 62915--62982 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
62905 ATTCTACTAG
62915 TAGAACTAAGACTTCTACCGA
1 TAGAACTAAGACTTCTACCGA
* ** *
62936 TAGAACTATGGGTTCTACTGA
1 TAGAACTAAGACTTCTACCGA
* ** *
62957 TACAACTTGGACTTCTATCGA
1 TAGAACTAAGACTTCTACCGA
62978 TAGAA
1 TAGAA
62983 TAAACTCCAG
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (21 bp):
TAGAACTAAGACTTCTACCGA
Found at i:71345 original size:17 final size:18
Alignment explanation
Indices: 71313--71346 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
71303 AAAAAGAAAC
*
71313 CACAAATCATGTTGCAAA
1 CACAAATCATGATGCAAA
71331 CACAAA-CATGATGCAA
1 CACAAATCATGATGCAA
71347 TGCACCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (18 bp):
CACAAATCATGATGCAAA
Found at i:72148 original size:20 final size:19
Alignment explanation
Indices: 72124--72171 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
72114 CAAATCAACG
72124 ATCAACGGTCAAAGTCAACA
1 ATCAACGGTCAAAGTCAA-A
*
72144 GTCAACGGTCAAAGTCAAA
1 ATCAACGGTCAAAGTCAAA
72163 ATCAACGGT
1 ATCAACGGT
72172 TAACGGTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCAACGGTCAAAGTCAAA
Found at i:72213 original size:22 final size:22
Alignment explanation
Indices: 72168--72230 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
72158 TCAAAATCAA
*
72168 CGGTTAACGGTTGGTCAACAGC
1 CGGTTAATGGTTGGTCAACAGC
**
72190 CGGTTAATGGTTGGTCAATGGC
1 CGGTTAATGGTTGGTCAACAGC
* * *
72212 CGATCAATGATTGGTCAAC
1 CGGTTAATGGTTGGTCAAC
72231 GACTGGACTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (22 bp):
CGGTTAATGGTTGGTCAACAGC
Found at i:78402 original size:2 final size:2
Alignment explanation
Indices: 78395--78428 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
78385 TCATAGCAAT
78395 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
78429 ACTCAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79334 original size:7 final size:7
Alignment explanation
Indices: 79315--79368 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
79305 TTTTAGAAAA
79315 AGTCAAC
1 AGTCAAC
79322 -GATCAAC
1 AG-TCAAC
79329 AGTCAA-
1 AGTCAAC
79335 AGTCAAC
1 AGTCAAC
*
79342 GGTCAAC
1 AGTCAAC
79349 -GATCAA-
1 AG-TCAAC
79355 AGTCAAC
1 AGTCAAC
79362 AGTCAAC
1 AGTCAAC
79369 GATTAATCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
6 12 0.30
7 27 0.68
8 1 0.03
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.15
Consensus pattern (7 bp):
AGTCAAC
Found at i:79338 original size:20 final size:20
Alignment explanation
Indices: 79313--79371 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
79303 TTTTTTAGAA
79313 AAAGTCAACGATCAAC-AGTC
1 AAAGTCAACGATCAACGA-TC
*
79333 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGATCAACGATC
79353 AAAGTCAAC-AGTCAACGAT
1 AAAGTCAACGA-TCAACGAT
79372 TAATCAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGATCAACGATC
Found at i:79354 original size:27 final size:27
Alignment explanation
Indices: 79316--79369 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
79306 TTTAGAAAAA
79316 GTCAACGATCAACAGTCAA-AGTCAACG
1 GTCAACGATCAA-AGTCAACAGTCAACG
79343 GTCAACGATCAAAGTCAACAGTCAACG
1 GTCAACGATCAAAGTCAACAGTCAACG
79370 ATTAATCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.15
Consensus pattern (27 bp):
GTCAACGATCAAAGTCAACAGTCAACG
Found at i:79434 original size:15 final size:16
Alignment explanation
Indices: 79416--79450 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
79406 GGGTTTGGAC
79416 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
79431 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
79447 TTGG
1 TTGG
79451 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:80298 original size:19 final size:19
Alignment explanation
Indices: 80261--80299 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
80251 GAGTGTTACA
*
80261 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACAGTGG
* *
80280 ACAATTTTGATTATAGTGG
1 ACAAATTTGATTACAGTGG
80299 A
1 A
80300 TGACAGTGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (19 bp):
ACAAATTTGATTACAGTGG
Found at i:85115 original size:22 final size:22
Alignment explanation
Indices: 85087--85139 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
85077 AGTATGTTCG
85087 GTTCGTTTATGTCCACGAACAA
1 GTTCGTTTATGTCCACGAACAA
85109 GTTCGTTTATGTCCACGAACAA
1 GTTCGTTTATGTCCACGAACAA
85131 GTTCGTTTA
1 GTTCGTTTA
85140 AAAGTTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (22 bp):
GTTCGTTTATGTCCACGAACAA
Found at i:85174 original size:24 final size:24
Alignment explanation
Indices: 85147--85200 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
85137 TTAAAAGTTT
** *
85147 GTTTATAAGCTTGTTTATTGGCTC
1 GTTTATAAGCTCATTTATTGACTC
*
85171 GTTTATAAGCTCATTTATTGACTT
1 GTTTATAAGCTCATTTATTGACTC
85195 GTTTAT
1 GTTTAT
85201 GACTCGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
GTTTATAAGCTCATTTATTGACTC
Found at i:97303 original size:20 final size:21
Alignment explanation
Indices: 97271--97311 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
97261 CGGTGAAAGC
97271 TTTATAATATTTTTAT-TTTT
1 TTTATAATATTTTTATATTTT
97291 TTTACTAAT-TTTTTATATTTT
1 TTTA-TAATATTTTTATATTTT
97312 ATATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATAATATTTTTATATTTT
Found at i:98529 original size:73 final size:73
Alignment explanation
Indices: 98405--98552 Score: 199
Period size: 73 Copynumber: 2.0 Consensus size: 73
98395 TCTTCGTAGT
* ** * *
98405 GTTTACAGTGTCACTGTCGGTTCCGTATAGCTCCGCAGTGTTTACAATGTCATTGCTTATTCAGT
1 GTTTACAATGTCACTGTCGGTTCAATATAGCTCAGCAGTGTTTACAATGTCACTGCTTATTCAGT
98470 ATAACTTC
66 ATAACTTC
* * * *
98478 GTTTACAATGTCACTG-CGGGTTCAATATAGTTCAGCAGTGTTTATAGTGTCACTGCTTATTTAG
1 GTTTACAATGTCACTGTC-GGTTCAATATAGCTCAGCAGTGTTTACAATGTCACTGCTTATTCAG
98542 TATAACTTC
65 TATAACTTC
98551 GT
1 GT
98553 ATTGTATACA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
72 1 0.02
73 64 0.98
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (73 bp):
GTTTACAATGTCACTGTCGGTTCAATATAGCTCAGCAGTGTTTACAATGTCACTGCTTATTCAGT
ATAACTTC
Found at i:107330 original size:16 final size:16
Alignment explanation
Indices: 107309--107342 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
107299 CACTGTCTCA
107309 CATTGTACACA-TCATG
1 CATTGT-CACATTCATG
107325 CATTGTCACATTCATG
1 CATTGTCACATTCATG
107341 CA
1 CA
107343 AACATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (16 bp):
CATTGTCACATTCATG
Found at i:108291 original size:23 final size:23
Alignment explanation
Indices: 108265--108453 Score: 267
Period size: 23 Copynumber: 8.3 Consensus size: 23
108255 TTCATGAGTT
*
108265 TATTTACA-CATAAATCATATTAA
1 TATTTA-AGCATAAATCACATTAA
*
108288 TATTTAAGCATAAATTACATTAA
1 TATTTAAGCATAAATCACATTAA
*
108311 TATTTAAGCATAAATCATATTAA
1 TATTTAAGCATAAATCACATTAA
* *
108334 CATTTAATCATAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
108357 TATTTAAGCACAAATCACATT--
1 TATTTAAGCATAAATCACATTAA
*
108378 TATTTAAGCACAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
108401 TATTTAAGCATAAATCATATTAA
1 TATTTAAGCATAAATCACATTAA
*
108424 CATTTAAGCATAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
108447 TATTTAA
1 TATTTAA
108454 CACATTTAAT
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
21 21 0.14
22 1 0.01
23 126 0.85
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (23 bp):
TATTTAAGCATAAATCACATTAA
Found at i:108384 original size:90 final size:89
Alignment explanation
Indices: 108265--108457 Score: 305
Period size: 90 Copynumber: 2.1 Consensus size: 89
108255 TTCATGAGTT
* * * *
108265 TATTTACACATAAATCATATTAATATTTAAGCATAAATTACATTAATATTTAAGCATAAATCATA
1 TATTTA-ACACAAATCACATT--TATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATA
*
108330 TTAACATTTAATCATAAATCACATTAA
63 TTAACATTTAAGCATAAATCACATTAA
108357 TATTTAAGCACAAATCACATTTATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATATT
1 TATTTAA-CACAAATCACATTTATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATATT
108422 AACATTTAAGCATAAATCACATTAA
65 AACATTTAAGCATAAATCACATTAA
108447 TATTTAACACA
1 TATTTAACACA
108458 TTTAATGATA
Statistics
Matches: 95, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
89 4 0.04
90 73 0.77
91 1 0.01
92 17 0.18
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (89 bp):
TATTTAACACAAATCACATTTATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATATTA
ACATTTAAGCATAAATCACATTAA
Found at i:108900 original size:36 final size:36
Alignment explanation
Indices: 108847--109107 Score: 364
Period size: 36 Copynumber: 7.2 Consensus size: 36
108837 TTAGCACAAT
** * *
108847 ATATTTACTATAACATGGCATGAGTAACATACCTAC
1 ATATTTACTATCTCATGGCATGAATAACATACCCAC
108883 ATATTTACTATCTCATGGCATGAATAACATACCCAC
1 ATATTTACTATCTCATGGCATGAATAACATACCCAC
* * * *
108919 ATATTTACTGTCTCATGACATGAAAAATATACCCAC
1 ATATTTACTATCTCATGGCATGAATAACATACCCAC
*
108955 ATATTTACTATCTCATGGCATGAATAACAAACCCAC
1 ATATTTACTATCTCATGGCATGAATAACATACCCAC
108991 ATATTTACTATCTCAAT-GCATGAATAACATACCCAC
1 ATATTTACTATCTC-ATGGCATGAATAACATACCCAC
* * * *
109027 ATAATTACTGTCACATGGCATGGATAACATACCCAC
1 ATATTTACTATCTCATGGCATGAATAACATACCCAC
*
109063 ATATTTACTGTCTCATGGCATGAATAACATA-CCAGC
1 ATATTTACTATCTCATGGCATGAATAACATACCCA-C
109099 ATATTTACT
1 ATATTTACT
109108 TTCACAATAG
Statistics
Matches: 201, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
35 5 0.02
36 194 0.97
37 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (36 bp):
ATATTTACTATCTCATGGCATGAATAACATACCCAC
Found at i:115244 original size:6 final size:6
Alignment explanation
Indices: 115233--115264 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
115223 TCAAAATTAG
115233 AAATAA AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
115265 TAATAAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:115619 original size:9 final size:9
Alignment explanation
Indices: 115605--115631 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
115595 GTTTCTAGGA
115605 CCAAGATTT
1 CCAAGATTT
115614 CCAAGATTT
1 CCAAGATTT
115623 CCAAGATTT
1 CCAAGATTT
115632 AAAATATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (9 bp):
CCAAGATTT
Found at i:142437 original size:20 final size:20
Alignment explanation
Indices: 142399--142435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
142389 TGTTAATATG
*
142399 ATTTTGACTTAGTTTAAATT
1 ATTTTGACATAGTTTAAATT
142419 ATTTTGACAT-GTTTAAA
1 ATTTTGACATAGTTTAAA
142436 ATCGTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (20 bp):
ATTTTGACATAGTTTAAATT
Found at i:144414 original size:20 final size:20
Alignment explanation
Indices: 144374--144429 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
144364 AAGCCCGTGA
*
144374 TATCGATATTTTT-TCACAAG
1 TATCGATATTTTTAT-AAAAG
*
144394 TATTGATATTTTTATAAAAG
1 TATCGATATTTTTATAAAAG
*
144414 TATCGATAATTTTATA
1 TATCGATATTTTTATA
144430 TCGGTATCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (20 bp):
TATCGATATTTTTATAAAAG
Found at i:155122 original size:17 final size:17
Alignment explanation
Indices: 155100--155141 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
155090 GAATGTCACA
155100 CCATTAATGTGCTGGAC
1 CCATTAATGTGCTGGAC
155117 CCATTAATGTGCTGGAC
1 CCATTAATGTGCTGGAC
*
155134 GCATTAAT
1 CCATTAAT
155142 TGAGGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (17 bp):
CCATTAATGTGCTGGAC
Found at i:160523 original size:17 final size:17
Alignment explanation
Indices: 160484--160539 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
160474 TCCCTTTGAT
** *
160484 ATTGCATTTTAATTTTC
1 ATTGCATTTCCATTGTC
* *
160501 ACTGCATTTGCATTGTC
1 ATTGCATTTCCATTGTC
160518 ATTGCATTTCCATTTGTC
1 ATTGCATTTCCA-TTGTC
160536 ATTG
1 ATTG
160540 TAAATTAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50
Consensus pattern (17 bp):
ATTGCATTTCCATTGTC
Found at i:164657 original size:14 final size:15
Alignment explanation
Indices: 164631--164660 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
164621 ATTTTAGAAC
164631 ATAAAGTTAAAGGAA
1 ATAAAGTTAAAGGAA
164646 ATAAAG-TAAAGGAA
1 ATAAAGTTAAAGGAA
164660 A
1 A
164661 GAGATAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
ATAAAGTTAAAGGAA
Found at i:170109 original size:6 final size:6
Alignment explanation
Indices: 170094--170145 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
170084 TAACTTTGAA
* * * * * *
170094 ATTTTG ATTTTT ATTTTC ATTTTA ATTTTT GTTTTT AATTTT AATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
170142 ATTT
1 ATTT
170146 GTTTATGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:170129 original size:19 final size:18
Alignment explanation
Indices: 170093--170145 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
170083 TTAACTTTGA
*
170093 AATTTTGATTTTTATTTT
1 AATTTTAATTTTTATTTT
* *
170111 CATTTTAATTTTTGTTTTT
1 AATTTTAATTTTT-ATTTT
170130 AATTTTAA-TTTTATTT
1 AATTTTAATTTTTATTT
170146 GTTTATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.10
18 15 0.52
19 11 0.38
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (18 bp):
AATTTTAATTTTTATTTT
Found at i:175523 original size:23 final size:23
Alignment explanation
Indices: 175493--175580 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
175483 TTCATTTACA
*
175493 CATAAATCACATTAATATTGAAG
1 CATAAATCACATTAATATTTAAG
175516 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
175539 CAT--A-CACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
175559 CACAAATCACACTAATATTTAA
1 CATAAATCACATTAATATTTAA
175581 CACATTTAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.31
21 1 0.02
22 1 0.02
23 39 0.66
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:176021 original size:36 final size:36
Alignment explanation
Indices: 175974--176168 Score: 257
Period size: 36 Copynumber: 5.4 Consensus size: 36
175964 TTAGCATAAT
* *
175974 ATATTCATTGTCACATGGCATGAATAACATACCCGC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* * *
176010 ATATTTATTGTCTCATGGCGTGAATAACATACTCAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* *
176046 ATATTTACTATCACATGGCATGAATAACATACCCAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* *
176082 ATATTTATTGTCTCATGGTATGAATAACATACCCAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
* * * *
176118 ATATTTACTGTCTCATAGCATGAATAACATACCAAC
1 ATATTTATTGTCACATGGCATGAATAACATACCCAC
176154 ATATTTACTT-TCACA
1 ATATTTA-TTGTCACA
176169 ACAGTCATCA
Statistics
Matches: 138, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
36 137 0.99
37 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
ATATTTATTGTCACATGGCATGAATAACATACCCAC
Found at i:176107 original size:108 final size:108
Alignment explanation
Indices: 175974--176168 Score: 302
Period size: 108 Copynumber: 1.8 Consensus size: 108
175964 TTAGCATAAT
* * * *
175974 ATATTCATTGTCACATGGCATGAATAACATACCCGCATATTTATTGTCTCATGGCGTGAATAACA
1 ATATTCATTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
176039 TACTC-ACATATTTACTATCACATGGCATGAATAACATACCCAC
66 TAC-CAACATATTTACTATCACATGGCATGAATAACATACCCAC
* * *
176082 ATATTTATTGTCTCATGGTATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
1 ATATTCATTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
*
176147 TACCAACATATTTACTTTCACA
66 TACCAACATATTTACTATCACA
176169 ACAGTCATCA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 77 0.99
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (108 bp):
ATATTCATTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
TACCAACATATTTACTATCACATGGCATGAATAACATACCCAC
Found at i:189424 original size:28 final size:29
Alignment explanation
Indices: 189368--189432 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
189358 CCAAATATAT
*
189368 TATGTTATAAAAATATTATTTTAATTTTA
1 TATGTTATAAAAATATTATTATAATTTTA
189397 TATGTTA-AAAAATA--ATTATATATATTTA
1 TATGTTATAAAAATATTATTATA-AT-TTTA
189425 TAT-TTATA
1 TATGTTATA
189433 TTTATATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 5 0.16
27 5 0.16
28 15 0.47
29 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TATGTTATAAAAATATTATTATAATTTTA
Found at i:189428 original size:6 final size:6
Alignment explanation
Indices: 189417--189458 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
189407 AATAATTATA
189417 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
189459 AAATCACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:189547 original size:8 final size:8
Alignment explanation
Indices: 189534--189562 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
189524 AATCCAACCC
189534 AAAATATA
1 AAAATATA
189542 AAAATATA
1 AAAATATA
189550 AAAATATA
1 AAAATATA
189558 AAAAT
1 AAAAT
189563 TATATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:189905 original size:50 final size:50
Alignment explanation
Indices: 189830--189929 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
189820 ATCCACACTT
189830 GAAAAATTAATTTAAATATCTTGCATTGGCCCAACCCAACTCATGATGGG
1 GAAAAATTAATTTAAATATCTTGCATTGGCCCAACCCAACTCATGATGGG
*
189880 GAAAAATTGATTTAAATATCTTGCATTGGCCCAACCCAACTCATGATGGG
1 GAAAAATTAATTTAAATATCTTGCATTGGCCCAACCCAACTCATGATGGG
189930 ATATATTGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (50 bp):
GAAAAATTAATTTAAATATCTTGCATTGGCCCAACCCAACTCATGATGGG
Found at i:191320 original size:21 final size:21
Alignment explanation
Indices: 191296--191335 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
191286 ACATTTAAAC
191296 AATTTAAGATAAATAATATTT
1 AATTTAAGATAAATAATATTT
*
191317 AATTTAATATAAATAATAT
1 AATTTAAGATAAATAATAT
191336 GTAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AATTTAAGATAAATAATATTT
Found at i:191332 original size:25 final size:24
Alignment explanation
Indices: 191278--191332 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
191268 TAAATGTAAT
*
191278 AATAAATAACATTTAAACAATTTA
1 AATAAATAACATTTAAACAATATA
* **
191302 AGATAAATAATATTTAATTTAATATA
1 A-ATAAATAACATTTAA-ACAATATA
191328 AATAA
1 AATAA
191333 TATGTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 18 0.72
26 6 0.24
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAAATAACATTTAAACAATATA
Found at i:191993 original size:6 final size:6
Alignment explanation
Indices: 191983--192055 Score: 112
Period size: 6 Copynumber: 12.3 Consensus size: 6
191973 ATTAATTCAA
* * *
191983 AACTCA AACT-C AAATCC AAATCC AACTCC AACTCC AACTCC AACTCC
1 AACTCC AACTCC AACTCC AACTCC AACTCC AACTCC AACTCC AACTCC
192030 AACTCC AACTCC AACTCC AACTCC AA
1 AACTCC AACTCC AACTCC AACTCC AA
192056 ATCTAAAACA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
5 3 0.05
6 60 0.95
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (6 bp):
AACTCC
Found at i:194578 original size:24 final size:24
Alignment explanation
Indices: 194521--194606 Score: 58
Period size: 22 Copynumber: 3.7 Consensus size: 24
194511 ATAACTTATT
* *
194521 ATTGATATTTTAATATA-TAAAAT-
1 ATTGATA-TTAAATATATTTAAATA
* *
194544 ATTAATTTTAAATATATTTAAATA
1 ATTGATATTAAATATATTTAAATA
194568 ATTGATATT-AAT-TATTTACAA-A
1 ATTGATATTAAATATATTTA-AATA
*
194590 ATTTA-ATTAGAATATAT
1 ATTGATATTA-AATATAT
194607 AAAATTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 3 0.06
22 19 0.38
23 18 0.36
24 10 0.20
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (24 bp):
ATTGATATTAAATATATTTAAATA
Found at i:194623 original size:19 final size:21
Alignment explanation
Indices: 194587--194628 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
194577 AATTATTTAC
194587 AAAATTTAATTAGAATAT-AT
1 AAAATTTAATTAGAATATCAT
**
194607 AAAATTT-ATTATCATATCAT
1 AAAATTTAATTAGAATATCAT
194627 AA
1 AA
194629 TATTGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATTTAATTAGAATATCAT
Found at i:209639 original size:8 final size:8
Alignment explanation
Indices: 209597--209653 Score: 60
Period size: 9 Copynumber: 6.6 Consensus size: 8
209587 AAAGAATTGC
209597 AAAAAATAT
1 AAAAAAT-T
*
209606 AAAATATT
1 AAAAAATT
209614 ACAAAAATT
1 A-AAAAATT
*
209623 ATTAAAATT
1 A-AAAAATT
209632 AAAAAATT
1 AAAAAATT
209640 AAAAAATAT
1 AAAAAAT-T
209649 AAAAA
1 AAAAA
209654 TTTACTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
8 15 0.37
9 26 0.63
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAAATT
Found at i:209691 original size:24 final size:25
Alignment explanation
Indices: 209659--209710 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
209649 AAAAATTTAC
*
209659 TAAAAA-TTTTCATTATTTAAATAA
1 TAAAAATTTTTCATAATTTAAATAA
* *
209683 TAAATATTTTTTATAATTTAAATAA
1 TAAAAATTTTTCATAATTTAAATAA
209708 TAA
1 TAA
209711 GTAACATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAAAATTTTTCATAATTTAAATAA
Found at i:212424 original size:23 final size:23
Alignment explanation
Indices: 212397--212441 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
212387 GGGCCAACTT
*
212397 GGTTTGGGTTTAGATCTGTTTAG
1 GGTTTAGGTTTAGATCTGTTTAG
*
212420 GGTTTAGGTTTGGATCTGTTTA
1 GGTTTAGGTTTAGATCTGTTTA
212442 TATTTTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.04, G:0.33, T:0.49
Consensus pattern (23 bp):
GGTTTAGGTTTAGATCTGTTTAG
Found at i:212452 original size:23 final size:23
Alignment explanation
Indices: 212398--212453 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
212388 GGCCAACTTG
*
212398 GTTTGGGTTTAGATCTGTTTAGG
1 GTTTGGGTTTAGATCTGTTTAGA
* * *
212421 GTTTAGGTTTGGATCTGTTTATA
1 GTTTGGGTTTAGATCTGTTTAGA
*
212444 TTTTGGGTTT
1 GTTTGGGTTT
212454 TTGTAATTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.04, G:0.30, T:0.54
Consensus pattern (23 bp):
GTTTGGGTTTAGATCTGTTTAGA
Found at i:213225 original size:23 final size:23
Alignment explanation
Indices: 213199--213248 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
213189 CGGTAAAAGA
*
213199 TTGAAATCTTCAATCTACCTCTC
1 TTGAAATCTTCAATCTACCCCTC
213222 TTGAAATCTTCAATCTACCCCTC
1 TTGAAATCTTCAATCTACCCCTC
213245 TTGA
1 TTGA
213249 TTAAGGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.06, T:0.38
Consensus pattern (23 bp):
TTGAAATCTTCAATCTACCCCTC
Found at i:213263 original size:64 final size:64
Alignment explanation
Indices: 213162--213281 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
213152 AAAAGACTGG
*
213162 AATCTTCAATCTACCCTTCTTGATTAACGGTAAAAGATTGAAATCTTCAATCTACCTCTCTTGA
1 AATCTTCAATCTACCCCTCTTGATTAACGGTAAAAGATTGAAATCTTCAATCTACCTCTCTTGA
* *
213226 AATCTTCAATCTACCCCTCTTGATTAAGGGTAAAAGATTGGAATCTTCAATCTACC
1 AATCTTCAATCTACCCCTCTTGATTAACGGTAAAAGATTGAAATCTTCAATCTACC
213282 CCTTTTGATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (64 bp):
AATCTTCAATCTACCCCTCTTGATTAACGGTAAAAGATTGAAATCTTCAATCTACCTCTCTTGA
Found at i:213421 original size:44 final size:45
Alignment explanation
Indices: 213229--213440 Score: 258
Period size: 46 Copynumber: 4.8 Consensus size: 45
213219 CTCTTGAAAT
* *
213229 CTTCAATCTACCCCTCTTGA-TTAAGGGTAAAAGATTGGA-AT--
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAGATGG
* * *
213270 CTTCAATCTACCCCTTTTGA-TTAGGAGTAAAAGATTGGATGATGG
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGA-GATGG
* *
213315 CTGT-AATCTGCCCCTCTTGACTTAAGGGTAAAAGATTGGATGGTGG
1 CT-TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGA-GATGG
* * *
213361 CTTTAATTTGCCCCTCTTGACTTAGGGGTAATAGATTGGA-ATGG
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAGATGG
213405 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGAT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGAT
213441 CGGTGTGTCT
Statistics
Matches: 149, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
41 36 0.24
43 2 0.01
44 36 0.24
45 17 0.11
46 58 0.39
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAGATGG
Found at i:213421 original size:90 final size:86
Alignment explanation
Indices: 213229--213440 Score: 259
Period size: 90 Copynumber: 2.4 Consensus size: 86
213219 CTCTTGAAAT
* *
213229 CTTCAATCTACCCCTCTTGA-TTAAGGGTAAAAGATTGGAATCTTCAATCTACCCCTTTTGATTA
1 CTTCAATCTGCCCCTCTTGACTTAAGGGTAAAAGATTGGAATCTTCAATCTACCCCTCTTGATTA
213293 GGAGTAAAAGATTGGATGATGG
66 GGAGTAAAAGATTGGA-GATGG
* * * *
213315 CTGT-AATCTGCCCCTCTTGACTTAAGGGTAAAAGATTGGATGGTGGCTTTAATTTGCCCCTCTT
1 CT-TCAATCTGCCCCTCTTGACTTAAGGGTAAAAGATTGGA--AT--CTTCAATCTACCCCTCTT
* *
213379 GACTTAGGGGTAATAGATTGGA-ATGG
61 GA-TTAGGAGTAAAAGATTGGAGATGG
*
213405 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGAT
1 CTTCAATCTGCCCCTCTTGACTTAAGGGTAAAAGAT
213441 CGGTGTGTCT
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
86 17 0.16
87 20 0.18
89 2 0.02
90 37 0.34
91 16 0.15
92 17 0.16
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (86 bp):
CTTCAATCTGCCCCTCTTGACTTAAGGGTAAAAGATTGGAATCTTCAATCTACCCCTCTTGATTA
GGAGTAAAAGATTGGAGATGG
Done.