Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008362.1 Hibiscus syriacus cultivar Beakdansim tig00111101_pilon, 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: 636979
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 1 of 3
Found at i:3178 original size:15 final size:16
Alignment explanation
Indices: 3150--3181 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3140 AAAATCTTTC
3150 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
3166 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
3181 T
1 T
3182 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:3955 original size:16 final size:16
Alignment explanation
Indices: 3931--3963 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3921 TATCGCCGAC
*
3931 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3947 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3963 C
1 C
3964 TATTCACGTG
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:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:4392 original size:12 final size:12
Alignment explanation
Indices: 4375--4414 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
4365 TACAGCAGCC
4375 CCCCCTTAGCAG
1 CCCCCTTAGCAG
4387 CCCCCTTAGCAG
1 CCCCCTTAGCAG
4399 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
4412 CCC
1 CCC
4415 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:4403 original size:13 final size:13
Alignment explanation
Indices: 4368--4414 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
4358 AAAAAATTAC
4368 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
4382 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
4394 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
4407 AGCAGCCC
1 AGCAGCCC
4415 ATGTGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.38
13 15 0.47
14 5 0.16
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:5350 original size:27 final size:27
Alignment explanation
Indices: 5312--5365 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5302 TAAATTTATT
*
5312 TAAAAAATTATTAATTTAATTTAATAA
1 TAAAAAATTATTAATTTAATATAATAA
* * *
5339 TAAAATATTATTATTTTAGTATAATAA
1 TAAAAAATTATTAATTTAATATAATAA
5366 ATTTAACCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TAAAAAATTATTAATTTAATATAATAA
Found at i:6130 original size:12 final size:12
Alignment explanation
Indices: 6112--6164 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
6102 ACTATACGGT
6112 ATGAACAATACC
1 ATGAACAATACC
* *
6124 GTGAACAGTA--
1 ATGAACAATACC
*
6134 ATGAACAATATC
1 ATGAACAATACC
6146 ATGAACAATACC
1 ATGAACAATACC
6158 ATGAACA
1 ATGAACA
6165 GTGCTATAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.24
12 26 0.76
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:7039 original size:22 final size:22
Alignment explanation
Indices: 7009--7098 Score: 126
Period size: 22 Copynumber: 4.1 Consensus size: 22
6999 GGCATGTGAA
* *
7009 ATTTATCCCAAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
7031 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
* * *
7053 ATTTTTCACGAAGGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
*
7075 ATTTGTCCCGAATGACCTCTGT
1 ATTTGTCCCGAATGACCTATGT
7097 AT
1 AT
7099 ACTGTATATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:12099 original size:15 final size:15
Alignment explanation
Indices: 12066--12107 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
12056 CTAAAACTCC
12066 AATTATTTTT-TATA
1 AATTATTTTTATATA
* *
12080 TATTATTTTTATTTA
1 AATTATTTTTATATA
*
12095 AATTACTTTTATA
1 AATTATTTTTATA
12108 AAAACGATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTATTTTTATATA
Found at i:14699 original size:3 final size:3
Alignment explanation
Indices: 14693--14726 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
14683 TCAGAAGAAG
14693 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
14727 AGTCTTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:18577 original size:3 final size:3
Alignment explanation
Indices: 18569--18630 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
18559 AGCTTTCACT
18569 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18617 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
18631 GCTTTTATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18991 original size:17 final size:17
Alignment explanation
Indices: 18969--19008 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
18959 TGATGAGAGT
18969 GGGAGTGTAAGGGAACA
1 GGGAGTGTAAGGGAACA
18986 GGGAGTGTAAGGGAACA
1 GGGAGTGTAAGGGAACA
19003 GGGAGT
1 GGGAGT
19009 TTCGGAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.50, T:0.12
Consensus pattern (17 bp):
GGGAGTGTAAGGGAACA
Found at i:21891 original size:2 final size:2
Alignment explanation
Indices: 21886--21942 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
21876 TTATTTTTTT
21886 TA 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 TA
21928 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
21943 TATCGAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23521 original size:90 final size:87
Alignment explanation
Indices: 23367--23623 Score: 318
Period size: 90 Copynumber: 3.0 Consensus size: 87
23357 CGAACCAAAC
* * *
23367 ATGAACACCTTTAAAAATAAACAACGAATACAAACATAACCTTATTCGTTCAAGCCCGAATCATT
1 ATGAACACCTTTAAAAATAAACAACGAATACGAACATAACCTTATTCGTTCAAACTC-AATCATT
23432 TACACTCCTAAAATACAACTGGG
65 TACACTCCTAAAATACAACTGGG
*
23455 ATTTGAACACCTTTAAAAATAAACAACGAATACGAACATAACCTTATTCGTTCAAACTTAATTCA
1 A--TGAACACCTTTAAAAATAAACAACGAATACGAACATAACCTTATTCGTTCAAACTCAA-TCA
23520 TTTACACTCCTAAAATACAAC----
63 TTTACACTCCTAAAATACAACTGGG
* * * * *
23541 ----ACA--TTTAAAAATAAACAACGAATACGAACATAACCTTGTTAGTTCAAGCTCGACTCTTT
1 ATGAACACCTTTAAAAATAAACAACGAATACGAACATAACCTTATTCGTTCAAACTC-AATCATT
23600 TACACTCCTAAAATACAACTGGG
65 TACACTCCTAAAATACAACTGGG
23623 A
1 A
23624 ATATTTGAAC
Statistics
Matches: 150, Mismatches: 10, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
78 67 0.45
79 1 0.01
80 3 0.02
88 1 0.01
89 2 0.01
90 76 0.51
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (87 bp):
ATGAACACCTTTAAAAATAAACAACGAATACGAACATAACCTTATTCGTTCAAACTCAATCATTT
ACACTCCTAAAATACAACTGGG
Found at i:23602 original size:78 final size:78
Alignment explanation
Indices: 23460--23618 Score: 246
Period size: 78 Copynumber: 2.0 Consensus size: 78
23450 CTGGGATTTG
* * * *
23460 AACACCTTTAAAAATAAACAACGAATACGAACATAACCTTATTCGTTCAAACTTAATTCATTTAC
1 AACACATTTAAAAATAAACAACGAATACGAACATAACCTTATTAGTTCAAACTCAACTCATTTAC
23525 ACTCCTAAAATAC
66 ACTCCTAAAATAC
* * * *
23538 AACACATTTAAAAATAAACAACGAATACGAACATAACCTTGTTAGTTCAAGCTCGACTCTTTTAC
1 AACACATTTAAAAATAAACAACGAATACGAACATAACCTTATTAGTTCAAACTCAACTCATTTAC
23603 ACTCCTAAAATAC
66 ACTCCTAAAATAC
23616 AAC
1 AAC
23619 TGGGAATATT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (78 bp):
AACACATTTAAAAATAAACAACGAATACGAACATAACCTTATTAGTTCAAACTCAACTCATTTAC
ACTCCTAAAATAC
Found at i:28002 original size:2 final size:2
Alignment explanation
Indices: 27995--28026 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27985 CGAAATAATG
27995 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
28027 CGATAATACT
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:34582 original size:21 final size:22
Alignment explanation
Indices: 34556--34600 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
34546 TAAATAAATA
*
34556 AATAATTTAAAAT-ATTTTTAT
1 AATAATTTAAAATAAATTTTAT
*
34577 AATAATTTAATATAAATTTTAT
1 AATAATTTAAAATAAATTTTAT
34599 AA
1 AA
34601 AATAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTAAAATAAATTTTAT
Found at i:44404 original size:29 final size:26
Alignment explanation
Indices: 44371--44425 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 26
44361 CTAATTTTTG
*
44371 CTTTTGGTTTGTGATGGCATCTCTTATTC
1 CTTTTGGTTTGGGAT--C-TCTCTTATTC
*
44400 CTTTTGTTTTGGGATCTCTCTTATTC
1 CTTTTGGTTTGGGATCTCTCTTATTC
44426 ACACCATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 1 0.04
29 13 0.54
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.55
Consensus pattern (26 bp):
CTTTTGGTTTGGGATCTCTCTTATTC
Found at i:50855 original size:176 final size:178
Alignment explanation
Indices: 50510--50863 Score: 630
Period size: 176 Copynumber: 2.0 Consensus size: 178
50500 TGAACAAATC
50510 ATTGCAGGAAGATGTCCAAGTTAATCAGGGCATAGGATGGAGATAGTGTTAATCGGGTTTCTTCC
1 ATTGCAGGAAGATGTCCAAGTTAATCAGGGCATAGGATGGAGATAGTGTTAATCGGGTTTCTTCC
50575 ACTTCAAGCACAAATGAGGTTACCACCATAGTATCAATACAAAACAGGCAATTAACCACCAGATT
66 ACTTCAAGCACAAATGAGGTTACCACCATAGTATCAATACAAAACAGGCAATTAACCACCAGATT
50640 CACAGAGTCTGTATCTGTTTCTAGTCCAGATTCTCGCATTTTCTCTGA
131 CACAGAGTCTGTATCTGTTTCTAGTCCAGATTCTCGCATTTTCTCTGA
50688 ATTGCAGGAAGATGTCCAAGTTAATCAGGGCAT-GGATGGAGATAGTGTTAATCGGGTTTCTT-C
1 ATTGCAGGAAGATGTCCAAGTTAATCAGGGCATAGGATGGAGATAGTGTTAATCGGGTTTCTTCC
50751 -C-TC-AGCACAAATGAGGTTAACCACCATAGTATCAAATAC-AAACAGGCAATTAAACCACCAG
66 ACTTCAAGCACAAATGAGGTT-ACCACCATAGTATC-AATACAAAACAGGCAATT-AACCACCAG
50812 ATTCACAGAGTTCTGTATCTGTTTCTAGTCCAGATTCTCGCATTTTCTCTGA
128 ATTCACAGAG-TCTGTATCTGTTTCTAGTCCAGATTCTCGCATTTTCTCTGA
50864 TAAACTCAAT
Statistics
Matches: 172, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
173 15 0.09
174 28 0.16
175 25 0.15
176 42 0.24
177 29 0.17
178 33 0.19
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (178 bp):
ATTGCAGGAAGATGTCCAAGTTAATCAGGGCATAGGATGGAGATAGTGTTAATCGGGTTTCTTCC
ACTTCAAGCACAAATGAGGTTACCACCATAGTATCAATACAAAACAGGCAATTAACCACCAGATT
CACAGAGTCTGTATCTGTTTCTAGTCCAGATTCTCGCATTTTCTCTGA
Found at i:62426 original size:86 final size:87
Alignment explanation
Indices: 62229--62449 Score: 282
Period size: 86 Copynumber: 2.6 Consensus size: 87
62219 ATTGCTATGT
* * * * * *
62229 TATTTAGGTTTGATTCTTCGATCATTTATTGATTCTAACTATGAAGAACATTATAGTATTGTTTG
1 TATTTAGGTTTGATTCTTCAATCATCTATTCATTCTAACCATGAAGAACACTATAGTATCGTTTG
* * *
62294 ATTGTTGCTGTCATTGTTATAG
66 ATTGTCGCTGTCACTATTATAG
* * * *
62316 TATATGGGTTTGATTCTTCCATCATCTATTCATTCTAGCCATGAAGAACACTATAGT-TCGTTTG
1 TATTTAGGTTTGATTCTTCAATCATCTATTCATTCTAACCATGAAGAACACTATAGTATCGTTTG
* *
62380 GTTGTCGCTTTCACTATTATAG
66 ATTGTCGCTGTCACTATTATAG
* *
62402 TATTTAGGTTTGATTCTTCAATCATCTATTCATTCCAACTATGAAGAA
1 TATTTAGGTTTGATTCTTCAATCATCTATTCATTCTAACCATGAAGAA
62450 TGTATAGTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 65 0.57
87 49 0.43
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.44
Consensus pattern (87 bp):
TATTTAGGTTTGATTCTTCAATCATCTATTCATTCTAACCATGAAGAACACTATAGTATCGTTTG
ATTGTCGCTGTCACTATTATAG
Found at i:63871 original size:13 final size:13
Alignment explanation
Indices: 63853--63877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63843 TTAATATCAT
63853 TTTTAAATTTAAC
1 TTTTAAATTTAAC
63866 TTTTAAATTTAA
1 TTTTAAATTTAA
63878 AGATATATAT
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAATTTAAC
Found at i:64034 original size:83 final size:81
Alignment explanation
Indices: 63899--64061 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 81
63889 ATTAGAAAAT
63899 TTTTGAATAAATAAGTTAGTCTATTATGGTTTATTGAAAAGATATATATATATATGACTAAAATT
1 TTTTGAATAAATAAGTTAGTCTATTATGGTTTATTGAAAAG--ATATATATATATGACTAAAATT
63964 AGTTTACAAAACTTACCA
64 AGTTTACAAAACTTACCA
*
63982 TTTTGAATAAATAAGTTAGTTTATTATGGTTTATTGAAAAGATATATATATATGACTAAAATTAG
1 TTTTGAATAAATAAGTTAGTCTATTATGGTTTATTGAAAAGATATATATATATGACTAAAATTAG
64047 TTTACAAAACTTACC
66 TTTACAAAACTTACC
64062 TAAGTATTTA
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
81 39 0.49
83 40 0.51
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (81 bp):
TTTTGAATAAATAAGTTAGTCTATTATGGTTTATTGAAAAGATATATATATATGACTAAAATTAG
TTTACAAAACTTACCA
Found at i:74374 original size:55 final size:55
Alignment explanation
Indices: 74288--74424 Score: 168
Period size: 55 Copynumber: 2.5 Consensus size: 55
74278 TCATACTTGG
* * * **
74288 GGGTATCGGTATACTCCCCAGTGTATAGATACACAAAT-AACACTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGAA-ACTCGATGTTTTGA
* * *
74343 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTTGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGAAACTCGATGTTTTGA
* *
74398 GGGTATTGATACACTCATCAGTGTACC
1 GGGTATCGATACACTCCTCAGTGTACC
74425 AGTACACTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 70 0.99
56 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGAAACTCGATGTTTTGA
Found at i:78552 original size:6 final size:6
Alignment explanation
Indices: 78543--78574 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
78533 CCTTCACCTT
78543 CACCCA CACCCA CACCCA CACCCA CACCCA CA
1 CACCCA CACCCA CACCCA CACCCA CACCCA CA
78575 ATTGAAGCAC
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:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCA
Found at i:80433 original size:2 final size:2
Alignment explanation
Indices: 80426--80494 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
80416 GAACTATTTG
80426 AT AT AT AT AT 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 AT AT AT AT AT
80468 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
80495 CAAATTATTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:91046 original size:2 final size:2
Alignment explanation
Indices: 91039--91063 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91029 TTAATAGATA
91039 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 A
91064 AGGTGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91224 original size:24 final size:23
Alignment explanation
Indices: 91195--91240 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
91185 TTTTTCTGGA
91195 TATATTTGATTAATAAATTATAAT
1 TATATTTGATTAATAAA-TATAAT
* *
91219 TATATTTTATTATTAAATATAA
1 TATATTTGATTAATAAATATAA
91241 CTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTTGATTAATAAATATAAT
Found at i:92193 original size:5 final size:5
Alignment explanation
Indices: 92183--92236 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
92173 TATTCATTAT
* *
92183 TTTTA TTTTA TTTTA TTTTA TTATA TTGTA TCTTTA -TTT- TTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA -TTTTA
92233 TTTT
1 TTTT
92237 TTAGCAACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 6 0.14
5 28 0.67
6 8 0.19
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:92288 original size:22 final size:20
Alignment explanation
Indices: 92263--92308 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
92253 TATGACATAA
92263 TTTTTTCTACTTTTATGACACG
1 TTTTTTCTAC-TTT-TGACACG
* *
92285 TTTTTTTTTCTTTTGACACG
1 TTTTTTCTACTTTTGACACG
92305 TTTT
1 TTTT
92309 CAATTGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.63
Consensus pattern (20 bp):
TTTTTTCTACTTTTGACACG
Found at i:92848 original size:28 final size:29
Alignment explanation
Indices: 92789--92849 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
92779 AATTATGAAA
*
92789 AATAATTAGTTTTATGAAAAAAATATTTT
1 AATAATTAGTTTTATGAAAAAAATATTAT
* ** *
92818 AATAATTATTTTTATTTAAAAAGT-TTAT
1 AATAATTAGTTTTATGAAAAAAATATTAT
92846 AATA
1 AATA
92850 TTTAATACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
AATAATTAGTTTTATGAAAAAAATATTAT
Found at i:93484 original size:20 final size:20
Alignment explanation
Indices: 93459--93532 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
93449 ACTAATGAAA
93459 GAAGAAGAAATGAGTTTATG
1 GAAGAAGAAATGAGTTTATG
93479 GAAGAAGAACACATGAGTTTATG
1 GAAGAAG-A-A-ATGAGTTTATG
* *
93502 GAAGAAGAAA-CATGTTTGTG
1 GAAGAAGAAATGA-GTTTATG
93522 GAAGAA-AAATG
1 GAAGAAGAAATG
93533 GGTATGAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.09
20 20 0.43
21 2 0.04
22 2 0.04
23 18 0.39
ACGTcount: A:0.46, C:0.04, G:0.28, T:0.22
Consensus pattern (20 bp):
GAAGAAGAAATGAGTTTATG
Found at i:93487 original size:23 final size:23
Alignment explanation
Indices: 93457--93510 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
93447 ATACTAATGA
*
93457 AAGAAGAAGAAATGAGTTTATGG
1 AAGAAGAACAAATGAGTTTATGG
*
93480 AAGAAGAACACATGAGTTTATGG
1 AAGAAGAACAAATGAGTTTATGG
93503 AAGAAGAA
1 AAGAAGAA
93511 ACATGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.19
Consensus pattern (23 bp):
AAGAAGAACAAATGAGTTTATGG
Found at i:93637 original size:18 final size:18
Alignment explanation
Indices: 93614--93665 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
93604 AAAAAATAGG
93614 TTTATGGAAGAAGAAGTA
1 TTTATGGAAGAAGAAGTA
* *
93632 TTTAT-GAAGAAGAAAATG
1 TTTATGGAAGAAG-AAGTA
*
93650 TTTATGGAAAAAGAAG
1 TTTATGGAAGAAGAAG
93666 AATGGTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.25
18 15 0.54
19 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (18 bp):
TTTATGGAAGAAGAAGTA
Found at i:94011 original size:18 final size:19
Alignment explanation
Indices: 93974--94016 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
93964 TAGTTTACCC
* *
93974 TATAAAAAATTTGATGAAT
1 TATAAAAAAATTGATAAAT
93993 TATAAAAAAATT-ATAAAT
1 TATAAAAAAATTGATAAAT
94011 TA-AAAA
1 TATAAAA
94017 TTAAAATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
19 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
TATAAAAAAATTGATAAAT
Found at i:99595 original size:6 final size:6
Alignment explanation
Indices: 99569--99617 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
99559 TTTGAATAAT
*
99569 TATTTA T-TTTA TTAATTA TATTTA TATTTA TATTT- TATTTA TA-TTA
1 TATTTA TATTTA -TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
99615 TAT
1 TAT
99618 CATACAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 14 0.38
6 20 0.54
7 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:100983 original size:13 final size:11
Alignment explanation
Indices: 100945--100984 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
100935 TTATATGCCG
100945 AAAATTTATAA
1 AAAATTTATAA
*
100956 AAAATTTATAT
1 AAAATTTATAA
100967 AAAATTATCATAA
1 AAAATT-T-ATAA
100980 AAAAT
1 AAAAT
100985 ATTAATAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 16 0.64
12 1 0.04
13 8 0.32
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:113309 original size:24 final size:22
Alignment explanation
Indices: 113260--113309 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
113250 ACGAAGTAAT
*
113260 ATTAAAAATTTAAGGGTACGAG
1 ATTAAAAATTTAAGGGTACGAA
* *
113282 ATTACAAAATTTCAGAGGTGCGAA
1 ATTA-AAAATTTAAG-GGTACGAA
113306 ATTA
1 ATTA
113310 TATCGTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 9 0.39
24 10 0.43
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTAAAAATTTAAGGGTACGAA
Found at i:129372 original size:15 final size:15
Alignment explanation
Indices: 129352--129381 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
129342 TGTATATCCA
129352 ACTTTTTATACTTTT
1 ACTTTTTATACTTTT
129367 ACTTTTTATACTTTT
1 ACTTTTTATACTTTT
129382 CTGTTATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
ACTTTTTATACTTTT
Found at i:132154 original size:31 final size:32
Alignment explanation
Indices: 132082--132157 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
132072 GACATAGCCG
*
132082 AGGGACTAAAATCGAATGGAAGTTAACGATTA
1 AGGGACTAAAATCGAATGGAAGGTAACGATTA
* *
132114 AAGGACTAAAATCGAAT-GAATCGGTAATG-TT-
1 AGGGACTAAAATCGAATGGAA--GGTAACGATTA
132145 AGGGACTAAAATC
1 AGGGACTAAAATC
132158 AAAGAGATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 15 0.39
32 18 0.47
33 5 0.13
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (32 bp):
AGGGACTAAAATCGAATGGAAGGTAACGATTA
Found at i:132659 original size:2 final size:2
Alignment explanation
Indices: 132652--132680 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
132642 CTATTTTCAC
132652 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 A
132681 ACAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137130 original size:20 final size:21
Alignment explanation
Indices: 137105--137149 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
137095 TATTTTTTAA
*
137105 TTTTTAATAA-TAAAAAATAT
1 TTTTTAAAAACTAAAAAATAT
137125 TTTTTAAAAACTTAAAAAATAT
1 TTTTTAAAAAC-TAAAAAATAT
137147 TTT
1 TTT
137150 ATTTGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTTAAAAACTAAAAAATAT
Found at i:141689 original size:3 final size:3
Alignment explanation
Indices: 141681--141754 Score: 80
Period size: 3 Copynumber: 24.3 Consensus size: 3
141671 TTAAATAAGA
* * *
141681 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
141727 AAT AAAT AAT AAT AAT -AT AAT AAT AAT A
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
141755 TATATATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 4 0.07
3 47 0.78
4 9 0.15
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:141726 original size:37 final size:37
Alignment explanation
Indices: 141674--141772 Score: 121
Period size: 37 Copynumber: 2.6 Consensus size: 37
141664 AAAATAATTA
*
141674 AATAAGAAATAATAATAATAAATAA-AATAATTACAAT
1 AATAATAAATAATAATAATAAATAATAATAA-TACAAT
* *
141711 AATAATAAATGATAATAATAAATAATAATAATATAAT
1 AATAATAAATAATAATAATAAATAATAATAATACAAT
*
141748 AATAATATATATATAA-ATATAAATA
1 AATAATAAATA-ATAATA-ATAAATA
141773 TTTTAAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
37 38 0.70
38 16 0.30
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (37 bp):
AATAATAAATAATAATAATAAATAATAATAATACAAT
Found at i:141874 original size:44 final size:44
Alignment explanation
Indices: 141819--141913 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
141809 TTTTTGAAAT
141819 TATATAATATATAGATTTTAAAA-AATATTTAAAAAA-TATATATA
1 TATATAATATATA-ATTTTAAAATAATATTTAAAAAACTATATA-A
* * * *
141863 TATATATTATATATTTTTAAAATATTTTTTAAAAAACTATATAA
1 TATATAATATATAATTTTAAAATAATATTTAAAAAACTATATAA
141907 TATATAA
1 TATATAA
141914 ATGTTTTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
43 8 0.18
44 30 0.68
45 6 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (44 bp):
TATATAATATATAATTTTAAAATAATATTTAAAAAACTATATAA
Found at i:141904 original size:37 final size:37
Alignment explanation
Indices: 141861--141998 Score: 115
Period size: 37 Copynumber: 3.7 Consensus size: 37
141851 AAAATATATA
* * *
141861 TATATATATTATATATTTTTAAAATATTTTTTAAAAAAC
1 TATATATA-TATAAATTTTCAAAATATTTTTT-CAAAAC
*
141900 TATATAATATATAAATGTTTTC-AAA-ATGTTTTCAAAAC
1 TATAT-ATATATAAA--TTTTCAAAATATTTTTTCAAAAC
* *
141938 TATATATCATATAAATTTCCAAAAT-GTTTTTCAAAAC
1 TATATAT-ATATAAATTTTCAAAATATTTTTTCAAAAC
**
141975 TATAT-T-TATATGTTTTCAAAATAT
1 TATATATATATAAATTTTCAAAATAT
141999 ATATATATTA
Statistics
Matches: 81, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
34 13 0.16
36 5 0.06
37 20 0.25
38 17 0.21
39 16 0.20
40 6 0.07
41 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATATATATAAATTTTCAAAATATTTTTTCAAAAC
Found at i:141904 original size:39 final size:39
Alignment explanation
Indices: 141819--141985 Score: 105
Period size: 37 Copynumber: 4.3 Consensus size: 39
141809 TTTTTGAAAT
* * * *
141819 TATATA-ATATATAGAT-TTTAAAAAAT-ATTTAAAAAA
1 TATATATATATATAAATGTTTTAAAAATGTTTTAAAAAC
* *
141855 TATATATATATATATTATATATTTTTAAAATATTTTTTAAAAAAC
1 TATATATATATATA--A-AT-GTTTTAAAA-ATGTTTT-AAAAAC
* *
141900 TATATA-ATATATAAATGTTTTCAAAATGTTTTCAAAAC
1 TATATATATATATAAATGTTTTAAAAATGTTTTAAAAAC
* ** *
141938 TATATAT-CATATAAA--TTTCCAAAATGTTTTTCAAAAC
1 TATATATATATATAAATGTTTTAAAAATG-TTTTAAAAAC
*
141975 TATATTTATAT
1 TATATATATAT
141986 GTTTTCAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
36 16 0.15
37 23 0.21
38 20 0.19
39 6 0.06
40 9 0.08
41 2 0.02
42 8 0.07
43 2 0.02
44 10 0.09
45 11 0.10
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (39 bp):
TATATATATATATAAATGTTTTAAAAATGTTTTAAAAAC
Found at i:141928 original size:11 final size:11
Alignment explanation
Indices: 141912--141936 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
141902 TATAATATAT
141912 AAATGTTTTCA
1 AAATGTTTTCA
141923 AAATGTTTTCA
1 AAATGTTTTCA
141934 AAA
1 AAA
141937 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:142005 original size:21 final size:22
Alignment explanation
Indices: 141965--142006 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
141955 TCCAAAATGT
*
141965 TTTTCAAAACTATATTTATATG
1 TTTTCAAAACTATATATATATG
141987 TTTTCAAAA-TATATATATAT
1 TTTTCAAAACTATATATATAT
142007 TATATACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTCAAAACTATATATATATG
Found at i:142027 original size:39 final size:37
Alignment explanation
Indices: 141984--142088 Score: 129
Period size: 37 Copynumber: 2.7 Consensus size: 37
141974 CTATATTTAT
141984 ATGTTTTCAAAATATATATATATTATATACATTTTCAAA
1 ATGTTTTCAAAA-A-ATATATATTATATACATTTTCAAA
* * * *
142023 ATGTTTTCAAAGACTATATATTATATATATTTTTAAA
1 ATGTTTTCAAAAAATATATATTATATACATTTTCAAA
*
142060 ATGTTTTCGAAAAAAACATATATTATATA
1 ATGTTTTC--AAAAAATATATATTATATA
142089 TCATATAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 29 0.51
38 1 0.02
39 27 0.47
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
ATGTTTTCAAAAAATATATATTATATACATTTTCAAA
Found at i:142101 original size:99 final size:98
Alignment explanation
Indices: 141917--142102 Score: 223
Period size: 99 Copynumber: 1.9 Consensus size: 98
141907 TATATAAATG
** * *
141917 TTTTCAAAATGTTTTCAAAACTATATATCATATAAATTTCCAAAATGTTTTTCAAAACTATATTT
1 TTTTCAAAATGTTTTCAAAACTATATATCATATAAATTTCCAAAATGTTTTTCAAAAAAACATAT
* *
141982 ATATGTTTTCAAAATATATATATATTATATACA
66 ATATGATATCAAAATATATATATATTATATACA
* * **
142015 TTTTCAAAATGTTTTCAAAGACTATATATTATATATATTTTTAAAATG-TTTTCGAAAAAAACAT
1 TTTTCAAAATGTTTTCAAA-ACTATATATCATATAAATTTCCAAAATGTTTTTC-AAAAAAACAT
142079 ATATTAT-ATATCATATAATATATA
64 ATA-TATGATATCA-A-AATATATA
142103 CTTTTCAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
98 24 0.33
99 37 0.51
100 4 0.05
101 8 0.11
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (98 bp):
TTTTCAAAATGTTTTCAAAACTATATATCATATAAATTTCCAAAATGTTTTTCAAAAAAACATAT
ATATGATATCAAAATATATATATATTATATACA
Found at i:146739 original size:19 final size:19
Alignment explanation
Indices: 146715--146753 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
146705 CCGTTGCATG
*
146715 CATAAGAGTCTATTGTATT
1 CATAAGAGTCCATTGTATT
146734 CATAAGAGTCCATTGTATT
1 CATAAGAGTCCATTGTATT
146753 C
1 C
146754 CCACGGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (19 bp):
CATAAGAGTCCATTGTATT
Found at i:151385 original size:62 final size:62
Alignment explanation
Indices: 151309--151426 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
151299 AGGTTGAATT
* * * * *
151309 TTTTTTTTTAAAAAATTTGGTTTCGGGTCGGGTTTTTTTAAGTTTGATATTCGGGTTGTGTG
1 TTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAAGTTTGATATTCGGGTTGTGTG
*
151371 TTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAATTTTGATATTCGGGT
1 TTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAAGTTTGATATTCGGGT
151427 CAGATTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (62 bp):
TTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAAGTTTGATATTCGGGTTGTGTG
Found at i:151424 original size:28 final size:28
Alignment explanation
Indices: 151392--151448 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
151382 AAAATTCGGG
* * *
151392 TTCGGATCGGATTTTTTTAATTTTGATA
1 TTCGGATCAGATTTTTTTAAGTGTGATA
*
151420 TTCGGGTCAGATTTTTTTAAGTGTGATA
1 TTCGGATCAGATTTTTTTAAGTGTGATA
151448 T
1 T
151449 ACGAGTTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.51
Consensus pattern (28 bp):
TTCGGATCAGATTTTTTTAAGTGTGATA
Found at i:151437 original size:62 final size:61
Alignment explanation
Indices: 151306--151437 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 61
151296 ATCAGGTTGA
* * * * * *
151306 ATTTTTTTTTTTAAAAAATTTGGTTTCGGGTCGGGTTTTTTTAAGTTTGATATTCGGGTTG
1 ATTTTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAAGTTTGATATTCGGGTAG
*
151367 -TGTGTTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAATTTTGATATTCGGGTCAG
1 AT-T-TTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAAGTTTGATATTCGGGT-AG
151430 ATTTTTTT
1 ATTTTTTT
151438 AAGTGTGATA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
60 1 0.02
61 1 0.02
62 55 0.92
63 2 0.03
64 1 0.02
ACGTcount: A:0.20, C:0.06, G:0.21, T:0.53
Consensus pattern (61 bp):
ATTTTTTTTTTAAAAAAATTCGGGTTCGGATCGGATTTTTTTAAGTTTGATATTCGGGTAG
Found at i:154236 original size:3 final size:3
Alignment explanation
Indices: 154228--154317 Score: 180
Period size: 3 Copynumber: 30.0 Consensus size: 3
154218 TTTACAAACC
154228 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
154276 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
154318 GATGGTTTCA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:158799 original size:23 final size:22
Alignment explanation
Indices: 158754--158799 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
158744 ATTAAAATAC
**
158754 TAAAAATAAAATTAATATTATT
1 TAAAAATAAAATTAATACCATT
*
158776 TAAAAATAATATATAATACCATT
1 TAAAAATAAAAT-TAATACCATT
158799 T
1 T
158800 CTTAAGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAATAAAATTAATACCATT
Found at i:160647 original size:129 final size:129
Alignment explanation
Indices: 160386--160676 Score: 311
Period size: 129 Copynumber: 2.3 Consensus size: 129
160376 CATTTTCAGG
* *
160386 TTGAGCACGACTCAAAATGATGAA-ACCCTAATTTCAAGTCGAACTCAATTTGTAAAAGTAAAAC
1 TTGAGCACGACTCAATATGAT-AACACCCTAATTTCAAGTCGAACTAAATTTGTAAAAGTAAAAC
* * ** * * * * * *
160450 TTAATACTTAATCAAGATTCGAATTTCAAGTTATGCTTGACCTTTTAAGCTTAAGCTTTGATTTC
65 TTAATACTCAATCAAGATTCGAATTTCAAGTCATGCTCAAACTGTCAAGCTCAAGCTTTGACTGC
* * ***
160515 TTGAGCACAACTCAATATGATTACACCCTAATTTTGGGTCGAACTTAAATTT-TAAAAGTAAAAC
1 TTGAGCACGACTCAATATGATAACACCCTAATTTCAAGTCGAAC-TAAATTTGTAAAAGTAAAAC
* * * *
160579 TTAATACTCGATCAAGATTC-AATTTCGAGTCGTGCTCAAACTGTC-AGACTCAAGCTTCTTACT
65 TTAATACTCAATCAAGATTCGAATTTCAAGTCATGCTCAAACTGTCAAG-CTCAAGCTT-TGACT
160642 GC
128 GC
* *
160644 TTGAGCACGACTCAATAAGAAAACACCCTAATT
1 TTGAGCACGACTCAATATGATAACACCCTAATT
160677 ACATGTAAGC
Statistics
Matches: 133, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
127 2 0.02
128 26 0.20
129 99 0.74
130 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (129 bp):
TTGAGCACGACTCAATATGATAACACCCTAATTTCAAGTCGAACTAAATTTGTAAAAGTAAAACT
TAATACTCAATCAAGATTCGAATTTCAAGTCATGCTCAAACTGTCAAGCTCAAGCTTTGACTGC
Found at i:167720 original size:21 final size:20
Alignment explanation
Indices: 167634--167791 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
167624 AAATGACCAA
**
167634 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
167653 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
167673 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
167693 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
167714 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
167735 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
167755 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
167776 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
167792 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:167820 original size:20 final size:20
Alignment explanation
Indices: 167758--167951 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
167748 CGATTTTCCA
* ** *
167758 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
167778 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
167798 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
167818 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
167838 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
167858 AAATCGCAATGCGTATCTGT
1 AAATCGCAACGCGTATCCGT
*
167878 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
167898 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
*
167918 AAAATCACAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
167939 AAATCGCAACGCG
1 AAATCGCAACGCG
167952 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:167842 original size:60 final size:60
Alignment explanation
Indices: 167758--167951 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
167748 CGATTTTCCA
* ** * *
167758 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** * *
167818 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCTGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* ** *
167878 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCACAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
167939 AAATCGCAACGCG
1 AAATCGCAACGCG
167952 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 80 0.73
61 29 0.27
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:168373 original size:33 final size:33
Alignment explanation
Indices: 168334--168404 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
168324 TTCACTTAGA
*
168334 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
168367 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
168400 TTTCA
1 TTTCA
168405 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:168541 original size:41 final size:41
Alignment explanation
Indices: 168483--168560 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
168473 TTGCAGAAGA
*
168483 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
168524 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
168561 CACAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:168557 original size:21 final size:21
Alignment explanation
Indices: 168484--168559 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
168474 TGCAGAAGAG
*
168484 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
168505 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
168525 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
168546 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
168560 TCACAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:168601 original size:19 final size:19
Alignment explanation
Indices: 168579--168772 Score: 131
Period size: 19 Copynumber: 11.1 Consensus size: 19
168569 GAAACCAAAA
*
168579 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
168598 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
168612 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
168631 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
168645 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
168664 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
168678 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
168697 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
168711 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
168731 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
168751 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
168771 TC
1 TC
168773 AACCAAAAGA
Statistics
Matches: 139, Mismatches: 14, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
14 40 0.29
16 12 0.09
17 12 0.09
19 42 0.30
20 19 0.14
21 14 0.10
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:168620 original size:14 final size:14
Alignment explanation
Indices: 168601--168723 Score: 84
Period size: 14 Copynumber: 7.7 Consensus size: 14
168591 TTTCATTTCG
168601 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
168615 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
168634 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
168648 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
168667 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
168681 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
168700 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
168714 CGTTGCGATT
1 CGTTGCGATT
168724 TTCATTTCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
14 40 0.45
16 9 0.10
17 9 0.10
19 30 0.34
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:168626 original size:33 final size:33
Alignment explanation
Indices: 168584--168772 Score: 297
Period size: 33 Copynumber: 5.5 Consensus size: 33
168574 CAAAATCGCA
168584 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
168617 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
168650 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
168683 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
168716 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
168757 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
168773 AACCAAAAGA
Statistics
Matches: 147, Mismatches: 1, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
33 111 0.76
34 2 0.01
35 6 0.04
37 1 0.01
38 1 0.01
39 3 0.02
40 2 0.01
41 21 0.14
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:168734 original size:21 final size:21
Alignment explanation
Indices: 168708--168772 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
168698 CGCGTTGCGA
168708 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
168729 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
168749 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
168770 TTC
1 TTC
168773 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:170624 original size:93 final size:93
Alignment explanation
Indices: 170465--170840 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
170455 TAGATTGCTT
*
170465 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
170530 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
170558 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
170623 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
170651 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
170716 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
170744 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
170809 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
170836 AGTAA
1 AGTAA
170841 TGCAATCCAT
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 276 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:170928 original size:19 final size:19
Alignment explanation
Indices: 170888--171016 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
170878 TAGTTTACTT
* *
170888 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
170908 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
170927 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
170946 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
170960 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
170979 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
170993 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
171012 TCGCA
1 TCGCA
171017 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:170967 original size:33 final size:32
Alignment explanation
Indices: 170924--171016 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
170914 CGCGAAACCA
**
170924 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
170956 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
170989 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
171017 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:171014 original size:52 final size:52
Alignment explanation
Indices: 170888--171016 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
170878 TAGTTTACTT
**
170888 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
170940 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
170993 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
171017 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:171034 original size:19 final size:19
Alignment explanation
Indices: 171012--171165 Score: 121
Period size: 19 Copynumber: 8.6 Consensus size: 19
171002 GAAACCAAAA
*
171012 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
171031 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
171047 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
171064 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
**
171080 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
171097 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
171116 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
* *
171135 TCGCGTTGTGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
171155 TCGTGTTGCGA
1 TCGCGTTGCGA
171166 AAGTAAACTA
Statistics
Matches: 108, Mismatches: 16, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
14 15 0.14
16 10 0.09
17 11 0.10
19 61 0.56
20 11 0.10
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:171053 original size:14 final size:14
Alignment explanation
Indices: 171034--171090 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
171024 TTTCATTTCG
171034 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
171048 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
171065 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
171081 CGTTGCGATT
1 CGTTGCGATT
171091 TTGGTTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:171059 original size:33 final size:33
Alignment explanation
Indices: 171017--171147 Score: 154
Period size: 33 Copynumber: 3.8 Consensus size: 33
171007 CAAAATCGCA
171017 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* *
171050 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
** *
171083 TTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TT--CTT-TCG
* *
171121 TTGCGATTATCATTTCGCGTTGTGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
171148 TTAAGTTTCG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
33 53 0.65
35 2 0.02
36 2 0.02
37 1 0.01
38 24 0.29
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:173112 original size:14 final size:14
Alignment explanation
Indices: 173093--173128 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
173083 ATTGTTTAAT
173093 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
173107 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
173121 TGATTTGT
1 TGATTTGT
173129 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:173294 original size:33 final size:33
Alignment explanation
Indices: 173252--173370 Score: 166
Period size: 33 Copynumber: 3.4 Consensus size: 33
173242 GCGAAATGAA
173252 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
173285 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAG
173324 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
173358 AATCGCAATGCGA
1 AATCGCAATGCGA
173371 TTTTAATTTC
Statistics
Matches: 77, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
33 29 0.38
34 13 0.17
35 2 0.03
36 1 0.01
37 1 0.01
38 2 0.03
39 13 0.17
40 16 0.21
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:173321 original size:20 final size:19
Alignment explanation
Indices: 173234--173351 Score: 174
Period size: 19 Copynumber: 6.4 Consensus size: 19
173224 CAAAATGACT
173234 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
173253 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
173272 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
173286 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
173305 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
173325 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
173345 ATCGCAA
1 ATCGCAA
173352 CGAGAGAATC
Statistics
Matches: 91, Mismatches: 2, Indels: 11
0.88 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 39 0.43
20 36 0.40
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:173383 original size:73 final size:72
Alignment explanation
Indices: 173234--173370 Score: 258
Period size: 73 Copynumber: 1.9 Consensus size: 72
173224 CAAAATGACT
173234 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
173298 AATGAAA
66 AATGAAA
173305 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCG
173370 A
65 A
173371 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 10 0.16
72 19 0.30
73 35 0.55
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAAA
Found at i:173388 original size:19 final size:19
Alignment explanation
Indices: 173360--173510 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
173350 AACGAGAGAA
* *
173360 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
173379 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
173395 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
173412 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
173431 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
173447 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
173464 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
173482 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
173498 TCGCATTGCGATT
1 TCGCATTGCGATT
173511 CTCTCGTTGC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
14 23 0.21
16 16 0.15
17 12 0.11
18 3 0.03
19 42 0.39
20 12 0.11
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:173423 original size:52 final size:52
Alignment explanation
Indices: 173360--173479 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
173350 AACGAGAGAA
*
173360 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
173412 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
173464 TCCGCATTGCGATTTT
1 T-CGCATTGCGATTTT
173480 CATGTTGGGA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 51 0.78
53 14 0.22
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:173532 original size:33 final size:33
Alignment explanation
Indices: 173417--173524 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
173407 TCATTTCGCA
173417 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
173450 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
173484 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
173517 TTGCGATT
1 TTGCGATT
173525 GTAATTTCCG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:175823 original size:12 final size:12
Alignment explanation
Indices: 175806--175830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
175796 TCTTCGGGGA
175806 CTTTTTCTTCTT
1 CTTTTTCTTCTT
175818 CTTTTTCTTCTT
1 CTTTTTCTTCTT
175830 C
1 C
175831 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:176039 original size:24 final size:24
Alignment explanation
Indices: 176005--176051 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
175995 CTGAAACATC
176005 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
176029 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
176052 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:176933 original size:20 final size:20
Alignment explanation
Indices: 176733--176962 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
176723 AAATTTCAGT
* * * *
176733 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
176753 GTTACGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
176773 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
176793 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
176813 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
176833 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
176853 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
176873 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
176893 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
176913 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
176933 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
176953 GTTGCGATTT
1 GTTGCGATTT
176963 TGGAAAATCG
Statistics
Matches: 178, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.02
20 172 0.97
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:176979 original size:21 final size:21
Alignment explanation
Indices: 176949--177031 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
176939 ATTTTCATAT
*
176949 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
176970 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
176991 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
177012 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
177032 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:177022 original size:42 final size:43
Alignment explanation
Indices: 176929--177027 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
176919 ATTTATGTGT
* *
176929 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
176970 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
177012 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
177028 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:183343 original size:2 final size:2
Alignment explanation
Indices: 183338--183362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
183328 AATGATATTT
183338 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
183363 TTGATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:183947 original size:16 final size:16
Alignment explanation
Indices: 183926--183956 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
183916 AATTCAATTT
*
183926 TTAAAATAAAATATAC
1 TTAAAACAAAATATAC
183942 TTAAAACAAAATATA
1 TTAAAACAAAATATA
183957 TAAATGTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAACAAAATATAC
Found at i:195078 original size:20 final size:20
Alignment explanation
Indices: 195050--195100 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
195040 ATATATATAT
*
195050 ATATAATTTTTTAATAAAA-A
1 ATATTATTTTTTAA-AAAAGA
195070 ATATTA-TTTTTAAAAAAGA
1 ATATTATTTTTTAAAAAAGA
195089 A-ATTAATTTTTT
1 ATATT-ATTTTTT
195101 TTAATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.26
19 10 0.37
20 10 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATTATTTTTTAAAAAAGA
Found at i:195086 original size:18 final size:20
Alignment explanation
Indices: 195057--195099 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
195047 TATATATAAT
195057 TTTTTAATAAAA-AATATT-A
1 TTTTTAATAAAAGAA-ATTAA
195076 TTTTTAA-AAAAGAAATTAA
1 TTTTTAATAAAAGAAATTAA
195095 TTTTT
1 TTTTT
195100 TTTAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTTAATAAAAGAAATTAA
Found at i:196100 original size:56 final size:55
Alignment explanation
Indices: 195968--196111 Score: 198
Period size: 56 Copynumber: 2.6 Consensus size: 55
195958 CAGGGCCTCA
*
195968 AAAAATACGGGCCTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAATAAGGG-CTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
* * *
196024 AAAAATAAAGGCTCCAAAATCGAGTATATGTATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAATAAGGGCT-CGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
* * *
196080 ACAAATAGGGGTCTCGAAATCGAATATATCTA
1 AAAAATAAGGG-CTCGAAATCGAGTATATCTA
196112 GAAAATAGAG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
55 2 0.03
56 72 0.95
57 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (55 bp):
AAAAATAAGGGCTCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
Found at i:198780 original size:27 final size:27
Alignment explanation
Indices: 198750--198835 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
198740 TAATTATTAA
198750 TGTAAATTATATATTACATTAACTCAT
1 TGTAAATTATATATTACATTAACTCAT
* * *
198777 TGT-AATCTAATTTATTA-ATAAACTAAT
1 TGTAAAT-T-ATATATTACATTAACTCAT
*
198804 T-TAAATTATATATTACATTAATTCAT
1 TGTAAATTATATATTACATTAACTCAT
198830 TGTAAA
1 TGTAAA
198836 ATAATCTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 7 0.15
26 13 0.28
27 20 0.43
28 7 0.15
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (27 bp):
TGTAAATTATATATTACATTAACTCAT
Found at i:199594 original size:13 final size:13
Alignment explanation
Indices: 199576--199600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
199566 TGTCTTTTAT
199576 TAAAAAATAAAAA
1 TAAAAAATAAAAA
199589 TAAAAAATAAAA
1 TAAAAAATAAAA
199601 CAAAATATTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:202968 original size:19 final size:20
Alignment explanation
Indices: 202931--202978 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
202921 GTGATGCTAA
202931 ATTTTCCAC-TTGAATTTGCT
1 ATTTT-CACTTTGAATTTGCT
202951 ATTTTCACTTTGAA-TTGCT
1 ATTTTCACTTTGAATTTGCT
202970 ATTTTCACT
1 ATTTTCACT
202979 AATGTTCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (20 bp):
ATTTTCACTTTGAATTTGCT
Found at i:207805 original size:21 final size:21
Alignment explanation
Indices: 207779--207823 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
207769 GATTTCTGGG
* *
207779 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
207800 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
207821 CAA
1 CAA
207824 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:208420 original size:17 final size:17
Alignment explanation
Indices: 208398--208430 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
208388 TAGGAGATTT
208398 GAACATA-AATGATAAGA
1 GAACATATAA-GATAAGA
208415 GAACATATAAGATAAG
1 GAACATATAAGATAAG
208431 CTAGATGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GAACATATAAGATAAGA
Found at i:208522 original size:20 final size:21
Alignment explanation
Indices: 208481--208527 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
208471 ACATGGGTTG
208481 TATAT-AGAAAATTATGAAGT
1 TATATGAGAAAATTATGAAGT
* *
208501 TATATGAGAAGATTAT-AGGT
1 TATATGAGAAAATTATGAAGT
208521 TATATGA
1 TATATGA
208528 AATTGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (21 bp):
TATATGAGAAAATTATGAAGT
Found at i:209413 original size:143 final size:141
Alignment explanation
Indices: 209253--209520 Score: 457
Period size: 145 Copynumber: 1.9 Consensus size: 141
209243 GAGACATATG
209253 TATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACAC-ACTTGATCCCTAACATATGTATATGA
1 TATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAACTTGATCCCTAACATATGTATATGA
* *
209317 TTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAATTCTATGC
66 TTCTTAAAGAATTCTACGTGGTCCTTATGGAC---ATCATATGGCACTACGGTGCAATTCTATGC
209382 GGTTCTTCGGGACA
128 GGTTCTTCGGGACA
* *
209396 TATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATACTTGATCCCTAGCATATGTATATG
1 TATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACA-ACTTGATCCCTAACATATGTATATG
209461 ATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATATGGCACTACGGTGCAATTCTA
65 ATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATATGGCACTACGGTGCAATTCTA
209521 CGGGGCACTT
Statistics
Matches: 119, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
142 26 0.22
143 37 0.31
145 56 0.47
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (141 bp):
TATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAACTTGATCCCTAACATATGTATATGA
TTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATATGGCACTACGGTGCAATTCTATGCGGT
TCTTCGGGACA
Found at i:212393 original size:11 final size:11
Alignment explanation
Indices: 212377--212406 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
212367 CAATAAGATA
212377 AAGGAATTATG
1 AAGGAATTATG
212388 AAGGAATTATG
1 AAGGAATTATG
212399 AAGGAATT
1 AAGGAATT
212407 TGCAATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (11 bp):
AAGGAATTATG
Found at i:212947 original size:242 final size:236
Alignment explanation
Indices: 212494--212974 Score: 876
Period size: 242 Copynumber: 2.0 Consensus size: 236
212484 ATCTAATTAA
212494 GAAGTATGAAGTGTAGAATTGGAATTAGAACACATTGAAAATTTGGTATGATTTTTGAATCTCAT
1 GAAGTATGAAGTGTAGAATTGGAATTAGAACACATTGAAAATTTGGTATGATTTTTGAATCTCAT
212559 ATGGAATAGGATTTTGAGGTTTAAGAAAATAAATGAATATAATTGGTTTAAGTATGTGTACTAGA
66 ATGGAATAGGATTTTGAGGTTTAAGAAAATAAATGAATATAATTGGTTTAAGTATGTGTACTAGA
212624 GTTAAGAATGAAAAAGGGGATGATATGAAGTGTTTGAGAGGAAATGAGGTAATTTTCGGGCTGAA
131 GTTAAGAATGAAAAAGGGGATGATATGAAGTGTTTGAGAGGAAATGAGGTAATTTTCGGGCTGAA
212689 ATATGATTTCTGGGCAAGGGGAATCGGTACCCA-TCAAGGG
196 ATATGATTTCTGGGCAAGGGGAATCGGTACCCATTCAAGGG
212729 GAAGTATGAAGTGTTAGAATTGGAATTAGAACACATTGAAAATTTGGTATGATTTTTGAATCTCA
1 GAAGTATGAAGTG-TAGAATTGGAATTAGAACACATTGAAAATTTGGTATGATTTTTGAATCTCA
212794 TATGGAATATAGGATTTTGAGGTTTAAGATGAAATAAATGAATATAAATTGGTTTAAGTATGTGT
65 TATGG-A-ATAGGATTTTGAGGTTTAAGA--AAATAAATGAATAT-AATTGGTTTAAGTATGTGT
212859 A-TAGAGTTAAGAATGAAAAAGGGGATGATATATGAAGTGTTTGAGAGGAAATGAGGTAATTTTC
125 ACTAGAGTTAAGAATGAAAAAGGGGATG--ATATGAAGTGTTTGAGAGGAAATGAGGTAATTTTC
212923 GGGCTGAAATATGATTTCTGGGCAAGGGGAATCGGTACCCATTCAAGGG
188 GGGCTGAAATATGATTTCTGGGCAAGGGGAATCGGTACCCATTCAAGGG
212972 GAA
1 GAA
212975 CCGATACCCC
Statistics
Matches: 237, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
235 13 0.05
236 56 0.24
237 1 0.00
238 21 0.09
240 40 0.17
241 20 0.08
242 76 0.32
243 10 0.04
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (236 bp):
GAAGTATGAAGTGTAGAATTGGAATTAGAACACATTGAAAATTTGGTATGATTTTTGAATCTCAT
ATGGAATAGGATTTTGAGGTTTAAGAAAATAAATGAATATAATTGGTTTAAGTATGTGTACTAGA
GTTAAGAATGAAAAAGGGGATGATATGAAGTGTTTGAGAGGAAATGAGGTAATTTTCGGGCTGAA
ATATGATTTCTGGGCAAGGGGAATCGGTACCCATTCAAGGG
Found at i:212971 original size:21 final size:21
Alignment explanation
Indices: 212945--212989 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
212935 GATTTCTGGG
* *
212945 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
212966 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
212987 CAA
1 CAA
212990 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:213586 original size:18 final size:18
Alignment explanation
Indices: 213563--213597 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
213553 CTAGGAGATT
213563 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
213581 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
213598 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:213683 original size:21 final size:22
Alignment explanation
Indices: 213654--213697 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
213644 GTTGTATGAT
213654 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
213675 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
213697 A
1 A
213698 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:214581 original size:150 final size:149
Alignment explanation
Indices: 214396--214700 Score: 556
Period size: 150 Copynumber: 2.0 Consensus size: 149
214386 GAGTCGAGGG
214396 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
214461 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
214526 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
214545 TCTATGCGGTTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 TCTACGCGG-TTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACA
214610 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATT
214675 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
214695 TCTACG
1 TCTACG
214701 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
149 8 0.05
150 141 0.95
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:214723 original size:23 final size:23
Alignment explanation
Indices: 214679--214723 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
214669 ATCATTATAT
*
214679 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
214702 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
214724 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:220799 original size:2 final size:2
Alignment explanation
Indices: 220792--220826 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
220782 ACTTCTTAAT
220792 TA TA TA TA 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 TA TA TA TA T
220827 TGTGTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229697 original size:2 final size:2
Alignment explanation
Indices: 229690--229721 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
229680 TTCAACATGA
*
229690 AT AT AT AT AT AT AT AC 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
229722 TCTATCTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:232653 original size:36 final size:36
Alignment explanation
Indices: 232604--232745 Score: 178
Period size: 36 Copynumber: 4.0 Consensus size: 36
232594 TGAATACGAA
*
232604 GAACGTAAGGAAGCATCGACACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* * * *
232640 GAACGGAATGAAGCATTGACACTTTCAATTCAAGAC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
** * *
232676 GAATAGAAGGAAACATCGACACTTTCGATTCAAGTT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* *
232712 GAACGGAATGAGGCATC-ACACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
232746 TTTCATCTTT
Statistics
Matches: 88, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 17 0.19
36 71 0.81
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
Found at i:232696 original size:72 final size:71
Alignment explanation
Indices: 232610--232744 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 71
232600 CGAAGAACGT
* *
232610 AAGGAAGCATCGACACTTTCGATTCAAGTCGAACGGAATGAAGCATTGACACTTTCAATTCAAGA
1 AAGGAAACATCGACACTTTCGATTCAAGTCGAACGGAATGAAGCA-TCACACTTTCAATTCAAGA
232675 CGAATAG
65 CGAATAG
* * *
232682 AAGGAAACATCGACACTTTCGATTCAAGTTGAACGGAATGAGGCATCACACTTTCGATTCAAG
1 AAGGAAACATCGACACTTTCGATTCAAGTCGAACGGAATGAAGCATCACACTTTCAATTCAAG
232745 TTTTCATCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
71 16 0.28
72 42 0.72
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (71 bp):
AAGGAAACATCGACACTTTCGATTCAAGTCGAACGGAATGAAGCATCACACTTTCAATTCAAGAC
GAATAG
Found at i:232826 original size:26 final size:27
Alignment explanation
Indices: 232797--232849 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
232787 GTTAGACTGC
*
232797 TGTTAAAGA-ACATGCACGTGTATTGA
1 TGTTAAAGACACATGCACATGTATTGA
*
232823 TGTTAAAGACATATGCACATGTATTGA
1 TGTTAAAGACACATGCACATGTATTGA
232850 ATAAGCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (27 bp):
TGTTAAAGACACATGCACATGTATTGA
Found at i:236939 original size:32 final size:34
Alignment explanation
Indices: 236903--237011 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 34
236893 GTGGTAAGAA
* *
236903 ATTATTTTTATGTTAGTAT-TTT-T-TAAATAGTT
1 ATTATTTTTATATTAATATATTTATGTAAATA-TT
236935 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATTA-TTTTTATATTAATATATTTATGTAAATATT
* * *
236970 ATT-TTTTTAT-TAAAATAATATTTATATAATTATT
1 ATTATTTTTATAT-TAAT-ATATTTATGTAAATATT
237004 ATTTATTT
1 A-TTATTT
237012 AGAATTATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
32 5 0.08
33 23 0.36
34 19 0.30
35 8 0.12
36 9 0.14
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (34 bp):
ATTATTTTTATATTAATATATTTATGTAAATATT
Found at i:236989 original size:36 final size:34
Alignment explanation
Indices: 236934--237012 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
236924 TTTAAATAGT
*
236934 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
236966 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
237000 TATTATTTATTTA
1 TATTATTTTTTTA
237013 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:238758 original size:21 final size:21
Alignment explanation
Indices: 238728--238775 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
238718 GCAGGGGTAC
* *
238728 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
238749 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
238770 ATGCCA
1 ATGCCA
238776 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:238805 original size:21 final size:21
Alignment explanation
Indices: 238779--238872 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
238769 TATGCCATCT
* *
238779 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
238800 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
238821 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
*
238842 CCACCA-GGTTACATGCCTAGC
1 CC-GCAGGGTTACATGCCTAGC
238863 CCGCAGGGTT
1 CCGCAGGGTT
238873 TTATACCATA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
20 2 0.03
21 62 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:238832 original size:42 final size:42
Alignment explanation
Indices: 238749--238866 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
238739 TCCACTTCAT
* * * *
238749 ATGCCAAGCCCACCAGTTTATATGCC-ATCTCCG-CAGGGTTAC
1 ATGCCGAGCCCACCAGGTTACATGCCTAGC-CCGCCA-GGTTAC
* * *
238791 ATTCCGAGCCC-GCAGGGTTACATTCCTAGCCCGCCAGGTTAC
1 ATGCCGAGCCCACCA-GGTTACATGCCTAGCCCGCCAGGTTAC
*
238833 ATGCCTAGCCCACCAGGTTACATGCCTAGCCCGC
1 ATGCCGAGCCCACCAGGTTACATGCCTAGCCCGC
238867 AGGGTTTTAT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
41 2 0.03
42 53 0.87
43 6 0.10
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (42 bp):
ATGCCGAGCCCACCAGGTTACATGCCTAGCCCGCCAGGTTAC
Found at i:239495 original size:34 final size:30
Alignment explanation
Indices: 239393--239495 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 30
239383 ATAAATGTTT
*
239393 TTAAAATACAAATTATATTTTCGAAATTTAAA
1 TTAAAATA-AAATTATATATTC-AAATTTAAA
* *
239425 ATAAAATAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAATTATA-TATTCAAATTTAAA
239456 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATA-AAATTATA-TATTC-AAATTTAA-A
239491 TTAAA
1 TTAAA
239496 TTTCAACTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 16 0.27
32 18 0.30
33 12 0.20
34 13 0.22
35 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (30 bp):
TTAAAATAAAATTATATATTCAAATTTAAA
Found at i:240578 original size:128 final size:128
Alignment explanation
Indices: 239879--240760 Score: 1702
Period size: 128 Copynumber: 6.9 Consensus size: 128
239869 AGTTATTCAA
239879 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
239944 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
240007 ACTGATATATCTAGTGTCCCCGAGGGACATGA--GACATAATAGGGCAATGATAACATGTTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
240070 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
240133 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
240198 GACG-AATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
240259 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
240324 GACGAAATAATGGAAGGCGCGCCCCC-GGAACGCGCCTTCATGTGAATAGTAAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
240386 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
240451 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
240514 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
240579 GATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
240642 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
240707 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
240761 CCGATTATAG
Statistics
Matches: 743, Mismatches: 6, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
126 235 0.32
127 158 0.21
128 350 0.47
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:240841 original size:8 final size:8
Alignment explanation
Indices: 240828--240868 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
240818 TCACAATCTT
240828 TCAAATTC
1 TCAAATTC
240836 TCAAATTC
1 TCAAATTC
* *
240844 CCAAACTC
1 TCAAATTC
240852 T-AAATTC
1 TCAAATTC
240859 TCAAATTC
1 TCAAATTC
240867 TC
1 TC
240869 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:252005 original size:18 final size:17
Alignment explanation
Indices: 251960--252008 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
251950 TTTTTTTTAA
*
251960 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
251978 ATAATTTATAATATTAT
1 AAAATATATAATATTAT
251995 ACAAATATATAATA
1 A-AAATATATAATA
252009 AGGATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:258016 original size:2 final size:2
Alignment explanation
Indices: 258009--258034 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
257999 CCATCATAGA
258009 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
258035 CAATTCCACT
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:265945 original size:3 final size:3
Alignment explanation
Indices: 265931--265969 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
265921 ATATATTTAT
* *
265931 TTA TTC TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
265970 AATAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Done.