Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018631.1 Corchorus olitorius cultivar O-4 contig18664, 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: 56282
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:2322 original size:27 final size:26
Alignment explanation
Indices: 2292--2347 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
2282 AAATACTTTA
2292 ATTAATTA-ATTAATTGTATAATGGCAT
1 ATTAATTATA-TAATTGTATAATGGC-T
* *
2319 ATTAATTGTATAATTGTATATTGGCT
1 ATTAATTATATAATTGTATAATGGCT
2345 ATT
1 ATT
2348 TGAGTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (26 bp):
ATTAATTATATAATTGTATAATGGCT
Found at i:7417 original size:9 final size:8
Alignment explanation
Indices: 7403--7431 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
7393 TGCAAAATTA
7403 ACAAAAAC
1 ACAAAAAC
7411 ACAAAAAC
1 ACAAAAAC
7419 ACAAAAA-
1 ACAAAAAC
7426 ACAAAA
1 ACAAAA
7432 TACGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (8 bp):
ACAAAAAC
Found at i:11972 original size:2 final size:2
Alignment explanation
Indices: 11967--12007 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
11957 TCTCTCTCTC
*
11967 TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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 TA TA TA T
12008 CTAGTAGCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13792 original size:102 final size:103
Alignment explanation
Indices: 13607--13807 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
13597 CAAAAACTAA
* *
13607 GAAAAAAATATATCTCACACATATAAGCTAAACAACAATTTCTATTAAAAAACAATTTTAAAAAT
1 GAAAAAAATAAATCTCACACATATAAGCTAAACAACAATTTCCATTAAAAAACAATTTTAAAAAT
13672 AAAGAAAAGGAAAAACAGCTTCACATGATCTACAGTTT
66 AAAGAAAAGGAAAAACAGCTTCACATGATCTACAGTTT
*
13710 GAAAAAAATAAATCTCACACATATAAGCTAAACAACAATTTCCATTAAAAAA-AGTTTTAAAAAT
1 GAAAAAAATAAATCTCACACATATAAGCTAAACAACAATTTCCATTAAAAAACAATTTTAAAAAT
*
13774 AAAGAAAAGGAAAAACAGCTTCATATGATCTACA
66 AAAGAAAAGGAAAAACAGCTTCACATGATCTACA
13808 AAGCGTTAAC
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 44 0.47
103 50 0.53
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (103 bp):
GAAAAAAATAAATCTCACACATATAAGCTAAACAACAATTTCCATTAAAAAACAATTTTAAAAAT
AAAGAAAAGGAAAAACAGCTTCACATGATCTACAGTTT
Found at i:14209 original size:41 final size:41
Alignment explanation
Indices: 14153--14241 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
14143 TCATCATAAT
* *
14153 ATATCCTTAAAAAATAAATCTTTTA-AAGAATACATTTTTAA
1 ATATCCTCAAAAAATAAATCCTTTAGAA-AATACATTTTTAA
* *
14194 ATATCCTCCAAAAATAAATCCTTTAGAAAATATATTTTTAA
1 ATATCCTCAAAAAATAAATCCTTTAGAAAATACATTTTTAA
14235 ATATCCT
1 ATATCCT
14242 TCAACAACGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 41 0.95
42 2 0.05
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.38
Consensus pattern (41 bp):
ATATCCTCAAAAAATAAATCCTTTAGAAAATACATTTTTAA
Found at i:15055 original size:21 final size:21
Alignment explanation
Indices: 15022--15065 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
15012 AATTATGTAC
* * *
15022 ATGTACATTTCATAGAATATT
1 ATGTACATATCATACAAAATT
*
15043 ATGTATATATCATACAAAATT
1 ATGTACATATCATACAAAATT
15064 AT
1 AT
15066 CAGTTATGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (21 bp):
ATGTACATATCATACAAAATT
Found at i:15129 original size:21 final size:21
Alignment explanation
Indices: 15100--15144 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
15090 TTATGTACAC
* *
15100 ATGTGCATGGCATAGAAAATT
1 ATGTACATGCCATAGAAAATT
15121 ATGTACATGCCATAGAAAATT
1 ATGTACATGCCATAGAAAATT
15142 ATG
1 ATG
15145 CATTGTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (21 bp):
ATGTACATGCCATAGAAAATT
Found at i:15520 original size:28 final size:28
Alignment explanation
Indices: 15469--15527 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
15459 CTGTTGGCCC
*
15469 CAAAACCCTAAACTGAAGCGGCCGACCT
1 CAAAACCCTAAACTGAAGCAGCCGACCT
* * * *
15497 CAAAATCCTAAATTGAGGCAGCCGGCCT
1 CAAAACCCTAAACTGAAGCAGCCGACCT
15525 CAA
1 CAA
15528 GCAAAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.14
Consensus pattern (28 bp):
CAAAACCCTAAACTGAAGCAGCCGACCT
Found at i:15533 original size:32 final size:31
Alignment explanation
Indices: 15497--15557 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
15487 CGGCCGACCT
*
15497 CAAAATCCTAAATTGAGGCAGCCGGCCTCAAG
1 CAAAAT-CTAAATTGAGGCAGACGGCCTCAAG
* * *
15529 CAAAATTTCAATTGAGGCCGACGGCCTCA
1 CAAAATCTAAATTGAGGCAGACGGCCTCA
15558 CTTCTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (31 bp):
CAAAATCTAAATTGAGGCAGACGGCCTCAAG
Found at i:16781 original size:17 final size:18
Alignment explanation
Indices: 16745--16786 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
16735 TAATTATTAC
16745 TTTG-ATTAAAAAATAGA
1 TTTGAATTAAAAAATAGA
16762 TTT-AATTATAAAAATA-A
1 TTTGAATTA-AAAAATAGA
16779 TTTGAATT
1 TTTGAATT
16787 TAGAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (18 bp):
TTTGAATTAAAAAATAGA
Found at i:19956 original size:34 final size:34
Alignment explanation
Indices: 19917--19987 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
19907 GTGTTTGTTA
*
19917 TAGAAAGTAGATCAAAAGATTATGTTGTGAGAAG
1 TAGAAAGTAGATCAAAAGATTATGCTGTGAGAAG
19951 TAGAAAGTAGATCAAAAGATTATGCTGTGAGAAG
1 TAGAAAGTAGATCAAAAGATTATGCTGTGAGAAG
19985 TAG
1 TAG
19988 TTGAAAGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (34 bp):
TAGAAAGTAGATCAAAAGATTATGCTGTGAGAAG
Found at i:23924 original size:30 final size:30
Alignment explanation
Indices: 23890--23946 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
23880 GCATCTCTTT
* * *
23890 TGATGCGCCCAAGGCTTATCATGGAATGGA
1 TGATGCACCAAAGACTTATCATGGAATGGA
23920 TGATGCACCAAAGACTTATCATGGAAT
1 TGATGCACCAAAGACTTATCATGGAAT
23947 TGAAGATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (30 bp):
TGATGCACCAAAGACTTATCATGGAATGGA
Found at i:26888 original size:15 final size:14
Alignment explanation
Indices: 26868--26901 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
26858 TTTGGGGGAA
26868 AAAGAAAGATAGTT
1 AAAGAAAGATAGTT
*
26882 CAAAGAAAGTTAGTT
1 -AAAGAAAGATAGTT
26897 AAAGA
1 AAAGA
26902 GTGTATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGAAAGATAGTT
Found at i:27280 original size:30 final size:30
Alignment explanation
Indices: 27244--27302 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
27234 CAAGGGGGAG
*
27244 GGAATGATGTGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
27274 GGAATGATGCGCCAAGGACTTATCATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
27303 CTTGAAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:27369 original size:18 final size:19
Alignment explanation
Indices: 27346--27383 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
27336 GTGCATGGGC
*
27346 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
27364 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
27383 T
1 T
27384 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:30671 original size:30 final size:30
Alignment explanation
Indices: 30614--30672 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
30604 CAGGGGGGAG
* *
30614 GGAATGATGCGCCCAAGGCTTATCATGGAA
1 GGAATGATGCGCCCAAGACTTACCATGGAA
30644 GGAATGATGCG-CCAAGAACTTACCATGGA
1 GGAATGATGCGCCCAAG-ACTTACCATGGA
30673 CTTGAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (30 bp):
GGAATGATGCGCCCAAGACTTACCATGGAA
Found at i:32996 original size:22 final size:23
Alignment explanation
Indices: 32969--33033 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 23
32959 TCAAATTGAA
32969 AGAGTAAAATGGTAATCAGTAAT
1 AGAGTAAAATGGTAATCAGTAAT
32992 A-AGT--AATGGTAATCAGTAA-
1 AGAGTAAAATGGTAATCAGTAAT
33011 AGAGTAAAATGGTAATCAGTAAT
1 AGAGTAAAATGGTAATCAGTAAT
33034 TAAAATTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 18 0.47
22 18 0.47
23 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.26
Consensus pattern (23 bp):
AGAGTAAAATGGTAATCAGTAAT
Found at i:33057 original size:55 final size:53
Alignment explanation
Indices: 32996--33233 Score: 200
Period size: 55 Copynumber: 4.3 Consensus size: 53
32986 AGTAATAAGT
*
32996 AATGGTAATCAGTAAAGAGTAAAATGGTAATCAGTAATTAAAATTCAAAAAGTAA
1 AATGGTAATCAGTAAA-AGTAAAAGGGTAATCAGTAATT-AAATTCAAAAAGTAA
*
33051 AATGGTAAT---T---AGTAAAAGGGTAATCAGTAATTCAATTCAAAAAGTAA
1 AATGGTAATCAGTAAAAGTAAAAGGGTAATCAGTAATTAAATTCAAAAAGTAA
* ** *
33098 GATGGTAATCAGTAAAAGGTAAAAAGGGTAATCAACAATTAAATTCAAAGAGTAAAATGGTA
1 AATGGTAATCAGTAAAA-GT-AAAAGGGTAATCAGTAATTAAATTCAAAAAGT---A----A
* * *
33160 AATGGTAATTCAATTCAAAGAGTAAAATGGTAAATCAGTAATTCAATTCAAAAAGTAA
1 AATGGTAA-TC-AGT-AAA-AGTAAAAGGGT-AATCAGTAATTAAATTCAAAAAGTAA
33218 AATGGTAAATCAGTAA
1 AATGGT-AATCAGTAA
33234 TCAAATTCAA
Statistics
Matches: 147, Mismatches: 15, Indels: 41
0.72 0.07 0.20
Matches are distributed among these distances:
47 22 0.15
48 21 0.14
50 1 0.01
52 1 0.01
53 1 0.01
54 2 0.01
55 37 0.25
56 2 0.01
57 2 0.01
58 10 0.07
59 2 0.01
62 9 0.06
63 2 0.01
64 9 0.06
65 25 0.17
66 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (53 bp):
AATGGTAATCAGTAAAAGTAAAAGGGTAATCAGTAATTAAATTCAAAAAGTAA
Found at i:33066 original size:15 final size:15
Alignment explanation
Indices: 33046--33080 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33036 AAATTCAAAA
* *
33046 AGTAAAATGGTAATT
1 AGTAAAAGGGTAATC
33061 AGTAAAAGGGTAATC
1 AGTAAAAGGGTAATC
33076 AGTAA
1 AGTAA
33081 TTCAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (15 bp):
AGTAAAAGGGTAATC
Found at i:33097 original size:32 final size:32
Alignment explanation
Indices: 33061--33265 Score: 182
Period size: 32 Copynumber: 6.6 Consensus size: 32
33051 AATGGTAATT
*
33061 AGTAAAAGGGTAATCAGTAATTCAATTCAAAA
1 AGTAAAATGGTAATCAGTAATTCAATTCAAAA
* *
33093 AGTAAGATGGTAATCAGTAA---AAGGT-AAAA
1 AGTAAAATGGTAATCAGTAATTCAA-TTCAAAA
** * *
33122 AG------GGTAATCAACAATTAAATTCAAAG
1 AGTAAAATGGTAATCAGTAATTCAATTCAAAA
* *
33148 AGTAAAATGGTAAAT-GGTAATTCAATTCAAAG
1 AGTAAAATGGT-AATCAGTAATTCAATTCAAAA
33180 AGTAAAATGGTAAATCAGTAATTCAATTCAAAA
1 AGTAAAATGGT-AATCAGTAATTCAATTCAAAA
*
33213 AGTAAAATGGTAAATCAGTAA-TCAAATTCAAAG
1 AGTAAAATGGT-AATCAGTAATTC-AATTCAAAA
*
33246 AGTAAAATGGTAATTAGTAA
1 AGTAAAATGGTAATCAGTAA
33266 AAGGGTAATC
Statistics
Matches: 144, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.07
25 1 0.01
26 7 0.05
29 8 0.06
30 1 0.01
32 59 0.41
33 58 0.40
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (32 bp):
AGTAAAATGGTAATCAGTAATTCAATTCAAAA
Found at i:33105 original size:47 final size:48
Alignment explanation
Indices: 33013--33116 Score: 165
Period size: 47 Copynumber: 2.2 Consensus size: 48
33003 ATCAGTAAAG
* *
33013 AGTAAAATGGTAATCAGTAATTAAAATTCAAAAAGTAAAATGGTAATT
1 AGTAAAAGGGTAATCAGTAATTAAAATTCAAAAAGTAAAATGGTAATC
* *
33061 AGTAAAAGGGTAATCAGTAATT-CAATTCAAAAAGTAAGATGGTAATC
1 AGTAAAAGGGTAATCAGTAATTAAAATTCAAAAAGTAAAATGGTAATC
33108 AGTAAAAGG
1 AGTAAAAGG
33117 TAAAAAGGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 31 0.60
48 21 0.40
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (48 bp):
AGTAAAAGGGTAATCAGTAATTAAAATTCAAAAAGTAAAATGGTAATC
Found at i:33196 original size:65 final size:66
Alignment explanation
Indices: 33119--33258 Score: 196
Period size: 65 Copynumber: 2.2 Consensus size: 66
33109 GTAAAAGGTA
* * *
33119 AAAAGGGT-AATCAACAATTAAATTCAAAGAGTAAAATGGTAAAT-GGTAATTC-AATTCAAAGA
1 AAAATGGTAAATCAACAATTAAATTCAAAAAGTAAAATGGTAAATCAGTAA-TCAAATTCAAAGA
33181 GT
65 GT
** *
33183 AAAATGGTAAATCAGTAATTCAATTCAAAAAGTAAAATGGTAAATCAGTAATCAAATTCAAAGAG
1 AAAATGGTAAATCAACAATTAAATTCAAAAAGTAAAATGGTAAATCAGTAATCAAATTCAAAGAG
33248 T
66 T
33249 AAAATGGTAA
1 AAAATGGTAA
33259 TTAGTAAAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 7 0.10
65 34 0.51
66 26 0.39
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (66 bp):
AAAATGGTAAATCAACAATTAAATTCAAAAAGTAAAATGGTAAATCAGTAATCAAATTCAAAGAG
T
Found at i:33201 original size:33 final size:33
Alignment explanation
Indices: 33134--33258 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
33124 GGTAATCAAC
* *
33134 AATTAAATTCAAAGAGTAAAATGGTAAAT-GGT
1 AATTCAATTCAAAGAGTAAAATGGTAAATCAGT
33166 AATTCAATTCAAAGAGTAAAATGGTAAATCAGT
1 AATTCAATTCAAAGAGTAAAATGGTAAATCAGT
*
33199 AATTCAATTCAAAAAGTAAAATGGTAAATCAGT
1 AATTCAATTCAAAGAGTAAAATGGTAAATCAGT
33232 AA-TCAAATTCAAAGAGTAAAATGGTAA
1 AATTC-AATTCAAAGAGTAAAATGGTAA
33259 TTAGTAAAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
32 30 0.34
33 57 0.66
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.26
Consensus pattern (33 bp):
AATTCAATTCAAAGAGTAAAATGGTAAATCAGT
Found at i:33265 original size:65 final size:65
Alignment explanation
Indices: 33134--33258 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
33124 GGTAATCAAC
* *
33134 AATTAAATTCAAAGAGTAAAATGGTAAATGGTAATTCAATTCAAAGAGTAAAATGGTAAATCAGT
1 AATTAAATTCAAAAAGTAAAATGGTAAATAGTAATTCAATTCAAAGAGTAAAATGGTAAATCAGT
*
33199 AATTCAATTCAAAAAGTAAAATGGTAAATCAGTAA-TCAAATTCAAAGAGTAAAATGGTAA
1 AATTAAATTCAAAAAGTAAAATGGTAAAT-AGTAATTC-AATTCAAAGAGTAAAATGGTAA
33259 TTAGTAAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
65 29 0.53
66 26 0.47
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.26
Consensus pattern (65 bp):
AATTAAATTCAAAAAGTAAAATGGTAAATAGTAATTCAATTCAAAGAGTAAAATGGTAAATCAGT
Found at i:33266 original size:15 final size:15
Alignment explanation
Indices: 33246--33280 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33236 AAATTCAAAG
* *
33246 AGTAAAATGGTAATT
1 AGTAAAAGGGTAATC
33261 AGTAAAAGGGTAATC
1 AGTAAAAGGGTAATC
33276 AGTAA
1 AGTAA
33281 TCAAGTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (15 bp):
AGTAAAAGGGTAATC
Found at i:33283 original size:47 final size:46
Alignment explanation
Indices: 33213--33310 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 46
33203 CAATTCAAAA
* * *
33213 AGTAAAATGGTAAATCAGTAATCAAATTCAAAGAGTAAAATGGTAATT
1 AGTAAAAGGGTAAATCAGTAATCAAATTCAAAAAGT--AATGGTAATC
*
33261 AGTAAAAGGGT-AATCAGTAATCAAGTTCAAAAAGTAATGGTAATC
1 AGTAAAAGGGTAAATCAGTAATCAAATTCAAAAAGTAATGGTAATC
33306 AGTAA
1 AGTAA
33311 TAAAGTTAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 14 0.30
47 22 0.48
48 10 0.22
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (46 bp):
AGTAAAAGGGTAAATCAGTAATCAAATTCAAAAAGTAATGGTAATC
Found at i:33303 original size:30 final size:31
Alignment explanation
Indices: 33269--33426 Score: 133
Period size: 35 Copynumber: 4.8 Consensus size: 31
33259 TTAGTAAAAG
*
33269 GGTAATCAGTAATCAAGTTCAAAAAGT-AAT
1 GGTAATCAGTAATAAAGTTCAAAAAGTAAAT
33299 GGTAATCAGTAATAAAGTT-AGAAAGAGTAAAAAT
1 GGTAATCAGTAATAAAGTTCA-AAA-AGT--AAAT
* * *
33333 GGTATTCAGTAATTAAGGTCAAAAAGTAAAAT
1 GGTAATCAGTAATAAAGTTCAAAAAGT-AAAT
*
33365 GGTATTCAGTAATTAAAGTT-AAGAAGAGTAAAAAT
1 GGTAATCAGTAA-TAAAGTTCAA-AA-AGT--AAAT
* *
33400 GGTATTCAGTAATTAAAGTTTAAAAAG
1 GGTAATCAGTAA-TAAAGTTCAAAAAG
33427 AGTAAAAATG
Statistics
Matches: 111, Mismatches: 6, Indels: 18
0.82 0.04 0.13
Matches are distributed among these distances:
29 1 0.01
30 21 0.19
31 3 0.03
32 19 0.17
33 10 0.09
34 27 0.24
35 28 0.25
36 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (31 bp):
GGTAATCAGTAATAAAGTTCAAAAAGTAAAT
Found at i:33377 original size:103 final size:109
Alignment explanation
Indices: 33270--33494 Score: 242
Period size: 103 Copynumber: 2.1 Consensus size: 109
33260 TAGTAAAAGG
*
33270 GTAATCAGTAATCAAGTTCAA-AA-AGT-AATGGTAATCAGTAA-TAAAG-TTAGAAAGAGTAAA
1 GTAATCAGTAA--AAGTT-AAGAAGAGTAAATGGTAATCAGTAATTAAAGTTTAAAAAGAGTAAA
* *
33330 AATGGTATTCAGTAATT-AAGGT-CAAAA-AGTAAAA-TGGTATTCA
63 AATGGTATTCAATAATTAAAGGTAAAAAAGAGTAAAATTGGTATTCA
*
33373 GTAAT---T-AAAGTTAAGAAGAGTAAAAATGGTATTCAGTAATTAAAGTTTAAAAAGAGTAAAA
1 GTAATCAGTAAAAGTTAAGAAGAGT--AAATGGTAATCAGTAATTAAAGTTTAAAAAGAGTAAAA
**
33434 ATGGTATTCAATAATTAAATTTAAAAAAAAGAGTAAAATTGGTATTCA
64 ATGGTATTCAATAATTAAAGGT--AAAAAAGAGTAAAATTGGTATTCA
33482 GTAATCAGTAAAA
1 GTAATCAGTAAAA
33495 AAAAGGGGGA
Statistics
Matches: 99, Mismatches: 6, Indels: 24
0.77 0.05 0.19
Matches are distributed among these distances:
96 2 0.02
97 7 0.07
98 3 0.03
99 1 0.01
100 1 0.01
101 14 0.14
102 5 0.05
103 34 0.34
104 3 0.03
107 4 0.04
108 7 0.07
109 14 0.14
112 1 0.01
113 3 0.03
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (109 bp):
GTAATCAGTAAAAGTTAAGAAGAGTAAATGGTAATCAGTAATTAAAGTTTAAAAAGAGTAAAAAT
GGTATTCAATAATTAAAGGTAAAAAAGAGTAAAATTGGTATTCA
Found at i:33398 original size:67 final size:67
Alignment explanation
Indices: 33264--33486 Score: 256
Period size: 67 Copynumber: 3.3 Consensus size: 67
33254 GGTAATTAGT
* * * *
33264 AAAAGGGTAATCAGTAATCAAGTTCAAAAAGT--AATGGTAATCAGTAA-TAAAGTT-AGAAAGA
1 AAAATGGTATTCAGTAATTAAGTTCAAAAAGTAAAATGGTATTCAGTAATTAAAGTTAAG-AAGA
33325 GTA
65 GTA
*
33328 AAAATGGTATTCAGTAATTAAGGTCAAAAAGTAAAATGGTATTCAGTAATTAAAGTTAAGAAGAG
1 AAAATGGTATTCAGTAATTAAGTTCAAAAAGTAAAATGGTATTCAGTAATTAAAGTTAAGAAGAG
33393 TA
66 TA
* * *
33395 AAAATGGTATTCAGTAATTAAAGTTTAAAAAGAGTAAAAATGGTATTCAATAATTAAATTTAAAA
1 AAAATGGTATTCAGTAATT-AAG-TTCAAAA-AGT-AAAATGGTATTCAGTAATTAAAGTT---A
*
33460 AAAAGAGTA
59 AGAAGAGTA
*
33469 AAATTGGTATTCAGTAAT
1 AAAATGGTATTCAGTAAT
33487 CAGTAAAAAA
Statistics
Matches: 137, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
64 28 0.20
66 14 0.10
67 33 0.24
68 5 0.04
69 5 0.04
70 3 0.02
71 23 0.17
74 26 0.19
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (67 bp):
AAAATGGTATTCAGTAATTAAGTTCAAAAAGTAAAATGGTATTCAGTAATTAAAGTTAAGAAGAG
TA
Found at i:33399 original size:35 final size:35
Alignment explanation
Indices: 33296--33486 Score: 246
Period size: 36 Copynumber: 5.5 Consensus size: 35
33286 TTCAAAAAGT
* *
33296 AATGGTAATCAGTAA-TAAAGTTAGAAAGAGTAAA
1 AATGGTATTCAGTAATTAAAGTTAAAAAGAGTAAA
* *
33330 AATGGTATTCAGTAATT-AAGGTCAAAA-AGT-AA
1 AATGGTATTCAGTAATTAAAGTTAAAAAGAGTAAA
*
33362 AATGGTATTCAGTAATTAAAGTTAAGAAGAGTAAA
1 AATGGTATTCAGTAATTAAAGTTAAAAAGAGTAAA
33397 AATGGTATTCAGTAATTAAAGTTTAAAAAGAGTAAA
1 AATGGTATTCAGTAATTAAAG-TTAAAAAGAGTAAA
* *
33433 AATGGTATTCAATAATTAAATTTAAAAAAAAGAGTAAA
1 AATGGTATTCAGTAATTAAAGTT---AAAAAGAGTAAA
*
33471 ATTGGTATTCAGTAAT
1 AATGGTATTCAGTAAT
33487 CAGTAAAAAA
Statistics
Matches: 137, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
32 19 0.14
33 10 0.07
34 24 0.18
35 26 0.19
36 32 0.23
38 26 0.19
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (35 bp):
AATGGTATTCAGTAATTAAAGTTAAAAAGAGTAAA
Found at i:33498 original size:38 final size:36
Alignment explanation
Indices: 33320--33499 Score: 135
Period size: 35 Copynumber: 5.1 Consensus size: 36
33310 ATAAAGTTAG
* * *
33320 AAAGAGTAAAAATGGTATTCAGTAATTAAGGT---CA
1 AAAGAGTAAAAATGGTATTCAATAATTAA-ATAAAAA
* *
33354 AAA-AGT-AAAATGGTATTCAGTAATTAAAGT--TAA
1 AAAGAGTAAAAATGGTATTCAATAATTAAA-TAAAAA
* * **
33387 GAAGAGTAAAAATGGTATTCAGTAATTAAAGT-TTAA
1 AAAGAGTAAAAATGGTATTCAATAATTAAA-TAAAAA
33423 AAAGAGTAAAAATGGTATTCAATAATTAAATTTAAAAA
1 AAAGAGTAAAAATGGTATTCAATAATTAAA--TAAAAA
* * * *
33461 AAAGAGTAAAATTGGTATTCAGTAA-TCAGTAAAAA
1 AAAGAGTAAAAATGGTATTCAATAATTAAATAAAAA
33496 AAAG
1 AAAG
33500 GGGGAGGGGG
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
32 22 0.17
33 6 0.05
34 6 0.05
35 34 0.27
36 31 0.24
37 3 0.02
38 25 0.20
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.28
Consensus pattern (36 bp):
AAAGAGTAAAAATGGTATTCAATAATTAAATAAAAA
Found at i:33592 original size:36 final size:33
Alignment explanation
Indices: 33521--33667 Score: 131
Period size: 36 Copynumber: 4.5 Consensus size: 33
33511 GTAAGGCAAG
*
33521 GGTAATCAGTAATTAAGTTAAAATAGTAAAAAT
1 GGTAATCAGTAATTAAGTTAAAAGAGTAAAAAT
33554 GGTAATCAGTAATTTAAGTTAAAGAAGAGTAAAAAT
1 GGTAATCAGTAA-TTAAGTT-AA-AAGAGTAAAAAT
* * * * **
33590 GGTAATCAATCATTAAATTCAATCAGT-AAAA-
1 GGTAATCAGTAATTAAGTTAAAAGAGTAAAAAT
* ***
33621 GGTAAT-GGTAATTAAGAGCAAAGAGT-AAAAT
1 GGTAATCAGTAATTAAGTTAAAAGAGTAAAAAT
*
33652 GGTAATCAATAATTAA
1 GGTAATCAGTAATTAA
33668 ATTCAGTAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
30 16 0.17
31 12 0.13
32 11 0.12
33 16 0.17
34 8 0.09
35 8 0.09
36 21 0.23
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (33 bp):
GGTAATCAGTAATTAAGTTAAAAGAGTAAAAAT
Found at i:33652 original size:62 final size:64
Alignment explanation
Indices: 33578--33756 Score: 187
Period size: 62 Copynumber: 2.8 Consensus size: 64
33568 TAAGTTAAAG
* *
33578 AAGAGTAAAAATGGTAATCAATCATTAAATTCAATCAGTAAAAGGTAATGGTAAT-TAA-GAGCA
1 AAGAGT-AAAATGGTAATCAATAATTAAATTCAATCAGTAAAAGGTAATGGTAATATAATCAGCA
33641 AAGAGTAAAATGGTAATCAATAATTAAA-T---TCAGT-AAAGAGTAAATGGTAATGATAATCAG
1 AAGAGTAAAATGGTAATCAATAATTAAATTCAATCAGTAAAAG-GT-AATGGTAAT-ATAATCAG
33701 CA
63 CA
* **
33703 AAGAGT--AATGGTAATCAGTAATTAAATTCAGTAAAGAGTAAAAGGTAATGGTAA
1 AAGAGTAAAATGGTAATCAATAATTAAATTC---AATCAGTAAAAGGTAATGGTAA
33757 AAATGGTAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 23
0.78 0.04 0.18
Matches are distributed among these distances:
57 4 0.04
58 7 0.07
59 9 0.09
60 19 0.19
61 5 0.05
62 31 0.32
63 6 0.06
66 8 0.08
67 5 0.05
68 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (64 bp):
AAGAGTAAAATGGTAATCAATAATTAAATTCAATCAGTAAAAGGTAATGGTAATATAATCAGCA
Found at i:33691 original size:27 final size:27
Alignment explanation
Indices: 33661--33751 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
33651 TGGTAATCAA
33661 TAATTAAATTCAGTAAAGAGTAAATGG
1 TAATTAAATTCAGTAAAGAGTAAATGG
* * *
33688 TAATGATAA-TCAGCAAAGAGTAATGGTAATCAG
1 TAATTA-AATTCAGTAAAGAGT-A----AAT-GG
*
33721 TAATTAAATTCAGTAAAGAGTAAAAGG
1 TAATTAAATTCAGTAAAGAGTAAATGG
33748 TAAT
1 TAAT
33752 GGTAAAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
27 21 0.43
28 5 0.10
32 6 0.12
33 17 0.35
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.27
Consensus pattern (27 bp):
TAATTAAATTCAGTAAAGAGTAAATGG
Found at i:33731 original size:60 final size:61
Alignment explanation
Indices: 33586--33752 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 61
33576 AGAAGAGTAA
* ** * *
33586 AAATGGTAATCAATCATTAAATTC---AATCAGTAAAAGGTAATGGTAATTAAGAGCAAAGAGT
1 AAATGGTAATCAATAATTAAATTCAGTAAAGAGTAAAAGGTAATGATAA-T--CAGCAAAGAGT
*
33647 AAAATGGTAATCAATAATTAAATTCAGTAAAGAGTAAATGGTAATGATAATCAGCAAAGAGT
1 -AAATGGTAATCAATAATTAAATTCAGTAAAGAGTAAAAGGTAATGATAATCAGCAAAGAGT
*
33709 -AATGGTAATCAGTAATTAAATTCAGTAAAGAGTAAAAGGTAATG
1 AAATGGTAATCAATAATTAAATTCAGTAAAGAGTAAAAGGTAATG
33753 GTAAAAATGG
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
60 42 0.45
62 33 0.35
64 1 0.01
65 18 0.19
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (61 bp):
AAATGGTAATCAATAATTAAATTCAGTAAAGAGTAAAAGGTAATGATAATCAGCAAAGAGT
Found at i:33810 original size:26 final size:26
Alignment explanation
Indices: 33755--33820 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
33745 AGGTAATGGT
**
33755 AAAAATGGTAATCAGTAAAAAAGAGT
1 AAAAATGGTAATCAGTAAAAAAGACA
** *
33781 AAAAATGGTAATCAGTAAGTAAGTCA
1 AAAAATGGTAATCAGTAAAAAAGACA
33807 AAAAA-GAGTAATCA
1 AAAAATG-GTAATCA
33821 ATACTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 1 0.03
26 33 0.97
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (26 bp):
AAAAATGGTAATCAGTAAAAAAGACA
Found at i:35059 original size:1 final size:1
Alignment explanation
Indices: 35021--35045 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35011 CTTCATTCCT
35021 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
35046 GCAACTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38148 original size:2 final size:2
Alignment explanation
Indices: 38141--38188 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
38131 TTATTATTAT
38141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
38182 TA TA TA T
1 TA TA TA T
38189 TTACAAGGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39160 original size:402 final size:399
Alignment explanation
Indices: 38416--39170 Score: 875
Period size: 402 Copynumber: 1.9 Consensus size: 399
38406 TGTTTGAGTG
* * * *
38416 TAAGATGAATGGGGTTACTAGATACACTGAGGTTATACTTAAAGAGGCGATGATACCGATTTTAG
1 TAAGATGAATGGGGCTACTAGATACACTGAGGTTATACTAAAAGAGGCGATAATACCGATGTTAG
* *
38481 TGGTTCAAACAATTTTAAAAGTGAAAAACATCTTCACGTGATCTATAAAACGTTACCCAATAGAA
66 TGGTTCAAACAATTTTAAAAGTGAAAAACATCTTCACGTGATCTATAAAACGTTAACCAACAGAA
* * ** *
38546 TTTCTTTTTCAAAATTGGAGAATTCATCATCACGTGACGTGTGAGCGTTACTATCAAATAAATAT
131 TTTATATTTCAAAATTGGAGAA-TCATCATCACGTGACGTGAAAGCGTTACTATCAAATAAATAA
* * * * * * *
38611 TTTGACTCAAATTTTCAAAATCAGACAAACTTTGTCATGTGACATTTTTAGGCGTTACTATATCT
195 TTTGACTCAAATTCTCAAAATCACACAAAATTTATCATGTGACACTTTAAGGCGTTACTATATCC
* * *
38676 AAATGTTTAATGCCAAAATCATTATGTTGACACTTAGTGGAATAGTTTCTAAAAAAATGTTTATT
260 AAATGTTTAATGCCAAAATAATTATGTTGACACTTAGTGGAATAATTTCTAAAAAAA--TCTATT
*
38741 TCCTTTTTCAAAAAATATGTATTATGTGGTGATGGAAAAATTAATAAATATCTAAATTTTGATTG
323 TCCTTTTTCAAAAAATATGAATTATGTGGTGATGGAAAAATTAATAAATATCTAAATTTTGATTG
38806 TTTATTTGCATA
388 TTTATTTGCATA
* * * * * *
38818 TAAGATGAATGTGGCTATTAGATTCAGTGAGGTTATACTAAAAGAGGTGATAATATCGATGTTAG
1 TAAGATGAATGGGGCTACTAGATACACTGAGGTTATACTAAAAGAGGCGATAATACCGATGTTAG
* * **
38883 TGGTTTAAACAATTTTTAAAATAAGGAAAATGAAAACCATCTTCACGTGATCTATAAAGTGTTAA
66 TGGTTCAAACAA-TTTT--AA-AA-G----TGAAAAACATCTTCACGTGATCTATAAAACGTTAA
* *
38948 CCAACATAATTTATATTTCAAAATTGGA-AA-CATCATCACGTGACGT-AAAGTGTTACTA-CGA
122 CCAACAGAATTTATATTTCAAAATTGGAGAATCATCATCACGTGACGTGAAAGCGTTACTATC-A
* * * *
39009 AATATATAATTTGACTCGAGTTCTCAAAATCATCA-AAAATTTATCATGTTAC-CTTTAAGG-GT
186 AATAAATAATTTGACTCAAATTCTCAAAATCA-CACAAAATTTATCATGTGACACTTTAAGGCGT
* * * * * *
39071 TACTGA-ATCCAATTTTTTAATGCCAAATTTAATT-TGTTGACTCTTAGTGGAATAATTTCTTAG
250 TACT-ATATCCAAATGTTTAATGCCAAA-ATAATTATGTTGACACTTAGTGGAATAATTTCTAAA
*
39134 GAAA-CTATTTCCTCTTTTC-AAAAATATGAATTATGTG
313 AAAATCTATTTCCT-TTTTCAAAAAATATGAATTATGTG
39171 ATACTACTTT
Statistics
Matches: 294, Mismatches: 45, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
402 91 0.31
403 9 0.03
405 54 0.18
406 14 0.05
407 52 0.18
408 17 0.06
410 2 0.01
411 55 0.19
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (399 bp):
TAAGATGAATGGGGCTACTAGATACACTGAGGTTATACTAAAAGAGGCGATAATACCGATGTTAG
TGGTTCAAACAATTTTAAAAGTGAAAAACATCTTCACGTGATCTATAAAACGTTAACCAACAGAA
TTTATATTTCAAAATTGGAGAATCATCATCACGTGACGTGAAAGCGTTACTATCAAATAAATAAT
TTGACTCAAATTCTCAAAATCACACAAAATTTATCATGTGACACTTTAAGGCGTTACTATATCCA
AATGTTTAATGCCAAAATAATTATGTTGACACTTAGTGGAATAATTTCTAAAAAAATCTATTTCC
TTTTTCAAAAAATATGAATTATGTGGTGATGGAAAAATTAATAAATATCTAAATTTTGATTGTTT
ATTTGCATA
Found at i:44104 original size:17 final size:17
Alignment explanation
Indices: 44082--44119 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
44072 AAATACAAAG
44082 AACTATCTAGTATAACA
1 AACTATCTAGTATAACA
* *
44099 AACTATCTGGTGTAACA
1 AACTATCTAGTATAACA
44116 AACT
1 AACT
44120 TTACAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (17 bp):
AACTATCTAGTATAACA
Found at i:44867 original size:28 final size:28
Alignment explanation
Indices: 44820--44873 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
44810 TTCATAGAAT
* * *
44820 ATTATGTATATATCATACAAATTTATTA
1 ATTATGTACATATCAAACAAAATTATTA
*
44848 ATTATGTACATGTCAAACAAAATTAT
1 ATTATGTACATATCAAACAAAATTAT
44874 GTACACATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (28 bp):
ATTATGTACATATCAAACAAAATTATTA
Found at i:49583 original size:151 final size:151
Alignment explanation
Indices: 49324--49603 Score: 533
Period size: 151 Copynumber: 1.9 Consensus size: 151
49314 TACAAGGTTA
*
49324 CTTCGACGGAGGAGAAGAGAACTGTTGAAAAAATTGGGGATTTTCAATTTAGGGTTTGAAAAAGG
1 CTTCGACGGAGGAGAAGAGAACTGTTAAAAAAATTGGGGATTTTCAATTTAGGGTTTGAAAAAGG
*
49389 GGAAAGGTGAAAACGAACAGAGAGAAGATAAGAAGAAGAGAGGAGGCGGAAGAATAGAAAAAAAA
66 GGAAAAGTGAAAACGAACAGAGAGAAGATAAGAAGAAGAGAGGAGGCGGAAGAATAGAAAAAAAA
49454 AGATGGAAGGTTACTTCGAGT
131 AGATGGAAGGTTACTTCGAGT
*
49475 CTTCGACGGAGGAGAAGAGAACTGTTAAAAAAATTGGGGATTTTCAATTTAGGGTTTGAAAAGGG
1 CTTCGACGGAGGAGAAGAGAACTGTTAAAAAAATTGGGGATTTTCAATTTAGGGTTTGAAAAAGG
49540 GGAAAAGTGAAAACGAACAGAGAGAAGATAAGAAGAAGAGAGGAGGCGGAAGAATAGAAAAAAA
66 GGAAAAGTGAAAACGAACAGAGAGAAGATAAGAAGAAGAGAGGAGGCGGAAGAATAGAAAAAAA
49604 TGGGTTGAGG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 126 1.00
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.16
Consensus pattern (151 bp):
CTTCGACGGAGGAGAAGAGAACTGTTAAAAAAATTGGGGATTTTCAATTTAGGGTTTGAAAAAGG
GGAAAAGTGAAAACGAACAGAGAGAAGATAAGAAGAAGAGAGGAGGCGGAAGAATAGAAAAAAAA
AGATGGAAGGTTACTTCGAGT
Found at i:53479 original size:2 final size:2
Alignment explanation
Indices: 53472--53503 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
53462 AAATATTAAC
53472 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
53504 AAAGTACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55071 original size:21 final size:21
Alignment explanation
Indices: 55047--55088 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55037 AGGGAGATTA
55047 ACAAAATCTCATAGGAAGGTT
1 ACAAAATCTCATAGGAAGGTT
* *
55068 ACAAAATTTTATAGGAAGGTT
1 ACAAAATCTCATAGGAAGGTT
55089 TATTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
ACAAAATCTCATAGGAAGGTT
Found at i:55119 original size:22 final size:22
Alignment explanation
Indices: 55048--55212 Score: 117
Period size: 22 Copynumber: 7.5 Consensus size: 22
55038 GGGAGATTAA
*
55048 CAAAATCTCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
*
55069 CAAAATTTTATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
** * **
55092 TTAAATTTTATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
** *
55114 CAAAATTTCATATAAAGTTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
55136 CACAATTTCATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
*
55157 CAAAATTTCATA--ACGTGATTAT
1 CAAAATTTCATAGGAAG-G-TTAT
* *
55179 CAAAATTTAATAGGATA-GTAAT
1 CAAAATTTCATAGGA-AGGTTAT
55201 CAAAATTTCATA
1 CAAAATTTCATA
55213 AAAATATTCA
Statistics
Matches: 112, Mismatches: 22, Indels: 19
0.73 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
21 31 0.28
22 62 0.55
23 17 0.15
24 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:55163 original size:43 final size:45
Alignment explanation
Indices: 55110--55220 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 45
55100 TATAGTTAGG
* *
55110 TTATCAAAATTTCATATAAAGT-TTATCACAATTTCATAGG-TAA
1 TTATCAAAATTTCATATAAAGTATTATCAAAATTTAATAGGATAA
* *
55153 TTATCAAAATTTC--ATAACGTGATTATCAAAATTTAATAGGATAG
1 TTATCAAAATTTCATATAAAGT-ATTATCAAAATTTAATAGGATAA
* *
55197 TAATCAAAATTTCATA-AAAATATT
1 TTATCAAAATTTCATATAAAGTATT
55221 CAATTGAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 6 0.11
43 29 0.52
44 17 0.30
45 3 0.05
46 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATATAAAGTATTATCAAAATTTAATAGGATAA
Done.