Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000222.1 Hibiscus syriacus cultivar Beakdansim tig00000392_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: 107274
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5107 original size:24 final size:24
Alignment explanation
Indices: 5072--5118 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5062 CTGTAGTTTC
5072 AAAGAATGCTACAAATTTAGCGTT
1 AAAGAATGCTACAAATTTAGCGTT
*
5096 AAAGAATTCTACAAATTTAGCGT
1 AAAGAATGCTACAAATTTAGCGT
5119 CCATAGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (24 bp):
AAAGAATGCTACAAATTTAGCGTT
Found at i:9525 original size:24 final size:24
Alignment explanation
Indices: 9498--9613 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
9488 TTCGATTTGA
*
9498 ATTCTAATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
9522 ATTCTGATCTGATA-TCTGACATGA
1 ATTCTGATCTGATACT-TGACATGG
9546 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
9570 ATTCTGATCTGATACTTGAC-TTG
1 ATTCTGATCTGATACTTGACATGG
*
9593 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
9614 CTGATTTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 4 0.05
24 79 0.94
25 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:9547 original size:48 final size:48
Alignment explanation
Indices: 9495--9613 Score: 186
Period size: 48 Copynumber: 2.5 Consensus size: 48
9485 ATTTTCGATT
*
9495 TGAATTCTAATCTGATACTTGACATGGATTCTGATCTGATA-TCTGACA
1 TGAATTCTGATCTGATACTTGACATGGATTCTGATCTGATACT-TGACA
*
9543 TGAATTCTGATCTGATACTTGACATGGATTCTGATCTGATACTTGACT
1 TGAATTCTGATCTGATACTTGACATGGATTCTGATCTGATACTTGACA
* *
9591 TGATTTCTGATATGATACTTGAC
1 TGAATTCTGATCTGATACTTGAC
9614 CTGATTTATG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
48 65 0.98
49 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (48 bp):
TGAATTCTGATCTGATACTTGACATGGATTCTGATCTGATACTTGACA
Found at i:13246 original size:35 final size:36
Alignment explanation
Indices: 13193--13298 Score: 146
Period size: 38 Copynumber: 2.9 Consensus size: 36
13183 ATTAATCTTC
*
13193 AATAAG-AAAATACTCAAATTTCATATGAAACCTT-T
1 AATAAGAAAAATAC-CAAATTTCTTATGAAACCTTAT
13228 AATAAGAAAAATACCAAATTTCTTATGAAACCTTTCAT
1 AATAAGAAAAATACCAAATTTCTTATGAAACC-TT-AT
13266 AATAA-AAAAATACCCAAATTTCTTATGAAACCT
1 AATAAGAAAAATA-CCAAATTTCTTATGAAACCT
13299 AAATTGGTGA
Statistics
Matches: 65, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
35 23 0.35
36 9 0.14
37 8 0.12
38 25 0.38
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (36 bp):
AATAAGAAAAATACCAAATTTCTTATGAAACCTTAT
Found at i:15828 original size:18 final size:18
Alignment explanation
Indices: 15805--15843 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
15795 TAAATTGAAA
15805 AAAAATA-AATTTGAAGTT
1 AAAAATAGAA-TTGAAGTT
15823 AAAAATAGTAATTGAAGTT
1 AAAAATAG-AATTGAAGTT
15842 AA
1 AA
15844 TTTTATAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 10 0.53
20 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (18 bp):
AAAAATAGAATTGAAGTT
Found at i:20827 original size:23 final size:23
Alignment explanation
Indices: 20801--20846 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20791 GCCTTATTCT
20801 TTTAAGTGTTTATATTATAATCA
1 TTTAAGTGTTTATATTATAATCA
20824 TTTAAGTGTTTATATTATAATCA
1 TTTAAGTGTTTATATTATAATCA
20847 AGATGGAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (23 bp):
TTTAAGTGTTTATATTATAATCA
Found at i:31099 original size:17 final size:17
Alignment explanation
Indices: 31077--31111 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
31067 CTGAACTTTA
31077 CTCTCTCTTATTTCACT
1 CTCTCTCTTATTTCACT
31094 CTCTCTCTTATTTCACT
1 CTCTCTCTTATTTCACT
31111 C
1 C
31112 ATTGTATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.51
Consensus pattern (17 bp):
CTCTCTCTTATTTCACT
Found at i:34191 original size:30 final size:30
Alignment explanation
Indices: 34155--34222 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
34145 CAAGATACAT
*
34155 AACTTTTCAAAATTACACTTTTGGTCTATA
1 AACTTTTCAAAATTACACTTTTGGTCCATA
* * *
34185 AACTTTTGAAAATTACCCTTTTGGTCCCTA
1 AACTTTTCAAAATTACACTTTTGGTCCATA
34215 AACTTTTC
1 AACTTTTC
34223 CAATCTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTCAAAATTACACTTTTGGTCCATA
Found at i:39002 original size:24 final size:24
Alignment explanation
Indices: 38964--39023 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
38954 AACACTTCTC
38964 AAACATTTTTCAAAA-TTCTTTCATA
1 AAACA-TTTTCAAAACTTC-TTCATA
*
38989 AAACATTTTCAAAACTTCTTCATC
1 AAACATTTTCAAAACTTCTTCATA
*
39013 AAACTTTTTCA
1 AAACATTTTCA
39024 CCTTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACATTTTCAAAACTTCTTCATA
Found at i:39508 original size:33 final size:34
Alignment explanation
Indices: 39470--39588 Score: 114
Period size: 37 Copynumber: 3.4 Consensus size: 34
39460 TCACTCTAGA
*
39470 CCTTCTTAGGATC-GTCTAGAAATTCATTTTAGT
1 CCTTCTTAGGATCTCTCTAGAAATTCATTTTAGT
* * ** *
39503 CCTTCTTAGGATCATTTTTCTAAAAATTTGTTTGAGT
1 CCTTCTTAGGATC---TCTCTAGAAATTCATTTTAGT
*
39540 CTTTCTTAGGATCATTTCTCTAGAAATTCATTTTAGT
1 CCTTCTTAGGATC---TCTCTAGAAATTCATTTTAGT
39577 CCTTCTTAGGAT
1 CCTTCTTAGGAT
39589 TGTTTCTCTA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 13 0.19
37 57 0.81
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (34 bp):
CCTTCTTAGGATCTCTCTAGAAATTCATTTTAGT
Found at i:39546 original size:37 final size:37
Alignment explanation
Indices: 39484--39625 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 37
39474 CTTAGGATCG
* * *
39484 TCTAGAAATTCATTTTAGTCCTTCTTAGGATCATTTT
1 TCTAAAAATTCATTTGAGTCCTTCTTAGGATCATTTC
** *
39521 TCTAAAAATTTGTTTGAGTCTTTCTTAGGATCATTTC
1 TCTAAAAATTCATTTGAGTCCTTCTTAGGATCATTTC
* * **
39558 TCTAGAAATTCATTTTAGTCCTTCTTAGGATTGTTTC
1 TCTAAAAATTCATTTGAGTCCTTCTTAGGATCATTTC
* * * * *
39595 TCTAGAAATTTATTAGATTCCTTTTTAGGAT
1 TCTAAAAATTCATTTGAGTCCTTCTTAGGAT
39626 TGTTTCTCCA
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 87 1.00
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.49
Consensus pattern (37 bp):
TCTAAAAATTCATTTGAGTCCTTCTTAGGATCATTTC
Found at i:39604 original size:74 final size:74
Alignment explanation
Indices: 39484--39676 Score: 217
Period size: 74 Copynumber: 2.6 Consensus size: 74
39474 CTTAGGATCG
** * * * *
39484 TCTAGAAATTCATTTTAGTCCTTCTTAGGATCATTTTTCTAAAAATTTGTTTGAGT-CTTTCTTA
1 TCTAGAAATTCATTTTAGTCCTTCTTAGGATTGTTTCTCTAGAAATTTATTAGAGTCCTTT-TTA
39548 GGATCATTTC
65 GGATCATTTC
*
39558 TCTAGAAATTCATTTTAGTCCTTCTTAGGATTGTTTCTCTAGAAATTTATTAGATTCCTTTTTAG
1 TCTAGAAATTCATTTTAGTCCTTCTTAGGATTGTTTCTCTAGAAATTTATTAGAGTCCTTTTTAG
**
39623 GATTGTTTC
66 GATCATTTC
* * * ** * * *
39632 TCCATAATTTTGTTTTAGTCATTCTCAGGATTGTTTCCCTAGAAA
1 TCTAGAAATTCATTTTAGTCCTTCTTAGGATTGTTTCTCTAGAAA
39677 CCTCAACTTG
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 97 0.96
75 4 0.04
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (74 bp):
TCTAGAAATTCATTTTAGTCCTTCTTAGGATTGTTTCTCTAGAAATTTATTAGAGTCCTTTTTAG
GATCATTTC
Found at i:39751 original size:45 final size:45
Alignment explanation
Indices: 39683--39999 Score: 363
Period size: 45 Copynumber: 7.0 Consensus size: 45
39673 GAAACCTCAA
** * * *
39683 CTTGACTTTTCTCACGAAGATGAGTCAATTTTTTGGTGATGTTATT
1 CTTGAC-TTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
* *
39729 CTTGACTTTCTCGTGAATATGAGTCAATATTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
* * *
39774 CTTGACTTTCTCGTAAAGAGGAGTCAATCTTTTAGTGATGTCCTT
1 CTTGACTTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
*
39819 CTTTACTTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
* * *
39864 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTAAGTGTTGTCATT
1 CTTGACTTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
* * * *
39909 CTTGACTTTCTCACGAGAA-A-GAGTCAATCTTTTAGTGTTTTCCTT
1 CTTGACTTTCT--CGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
* * * *
39954 ATTGACTTTATTGCGAAGA-GAAGTCAA-CTTTCTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGATG-AGTCAATCTTT-TAGTGATGTCATT
39999 C
1 C
40000 AAGCAAAGCA
Statistics
Matches: 235, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.02
44 6 0.03
45 213 0.91
46 7 0.03
47 5 0.02
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGATGAGTCAATCTTTTAGTGATGTCATT
Found at i:41984 original size:37 final size:37
Alignment explanation
Indices: 41942--42132 Score: 140
Period size: 37 Copynumber: 5.2 Consensus size: 37
41932 TAGGATCGTA
* *
41942 TAGAAATTCATGTTAGTTC-TTCCTAGGATTGTTTTTC
1 TAGAAATTCATGTTAG-TCATTCTTAGGATTGTTTCTC
* * *
41979 TAGAAATTTAT-TTGAGTCTTTCTTAGGCTTGTTTCTC
1 TAGAAATTCATGTT-AGTCATTCTTAGGATTGTTTCTC
* * *
42016 TAGAAATTAATTTTAGTCATTCTTAGGATCGTTTCTC
1 TAGAAATTCATGTTAGTCATTCTTAGGATTGTTTCTC
* * *
42053 TAGAAATTC--GTTAGATTCCTTCTTAGGACTGTTTTTC
1 TAGAAATTCATGTTAG--TCATTCTTAGGATTGTTTCTC
* * ** * * *
42090 CATAAATTTGTTTTAGTCCTTCTTAGGAATGTTTC-C
1 TAGAAATTCATGTTAGTCATTCTTAGGATTGTTTCTC
42126 TTAGAAA
1 -TAGAAA
42133 CCTCAACTTG
Statistics
Matches: 124, Mismatches: 22, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
35 4 0.03
36 5 0.04
37 109 0.88
38 2 0.02
39 4 0.03
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (37 bp):
TAGAAATTCATGTTAGTCATTCTTAGGATTGTTTCTC
Found at i:42124 original size:74 final size:74
Alignment explanation
Indices: 41943--42132 Score: 179
Period size: 74 Copynumber: 2.6 Consensus size: 74
41933 AGGATCGTAT
* * * * * * * * *
41943 AGAAATTCATGTTAGTTCTTCCTAGGATTGTTTTTCTAGAAATTTATTTGAGTCTTTCTTAGGCT
1 AGAAATTAATTTTAGTCCTTCTTAGGAATGTTTCTCTAGAAATTCATTAGAGTCCTTCTTAGGCT
*
42008 TGTTTCTCT
66 TGTTTCTCC
* * *
42017 AGAAATTAATTTTAGTCATTCTTAGG-ATCGTTTCTCTAGAAATTCGTTAGATTCCTTCTTAGGA
1 AGAAATTAATTTTAGTCCTTCTTAGGAAT-GTTTCTCTAGAAATTCATTAGAGTCCTTCTTAGG-
*
42081 C-TGTTTTTCC
64 CTTGTTTCTCC
* **
42091 ATAAATTTGTTTTAGTCCTTCTTAGGAATGTTTC-CTTAGAAA
1 AGAAATTAATTTTAGTCCTTCTTAGGAATGTTTCTC-TAGAAA
42133 CCTCAACTTG
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
73 2 0.02
74 89 0.95
75 3 0.03
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (74 bp):
AGAAATTAATTTTAGTCCTTCTTAGGAATGTTTCTCTAGAAATTCATTAGAGTCCTTCTTAGGCT
TGTTTCTCC
Found at i:42208 original size:45 final size:45
Alignment explanation
Indices: 42139--42722 Score: 625
Period size: 45 Copynumber: 13.0 Consensus size: 45
42129 GAAACCTCAA
* * * * *
42139 CTTGACTTTCTCGCGAAGATGAGTCAATTTTTTGGTGATGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* * *
42184 CTTGACTTTCTCGTGAAGACGAGTCAATCTTTTAGTGATATAATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* *
42229 CTTGACTTTCTTGTAAAGAGGAGTCAATCTTTTAGTGATGTTC-TT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATG-TCATT
* *
42274 CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGATGTCTTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* *
42319 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGCTATCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
** * * * *
42364 CTTGACTTTCTCACGAGGAGGAGTCAATATTTTATTGTTGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
** * * * * *
42409 CTTGACTTTCTCACGAAGAGAAATCAACCTTCTAGTGATGTAATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* * * * *
42454 CTTGACTTTCTCCTGAAGAGGAATTAATCTTTTAGTGTTGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* * * * * * * * *
42499 CCTGACTTTTTCGCGAAAAAGAATCAATCTCTTAGTGTTATCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* * ** *
42544 CTTAACTTTTTCGCAAAGAGGAGTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* *
42589 CTTGACTTTCTCGTGAAGAGGAGACAATCTTTTAGTGATGTCTTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
* * *
42634 CTTGACTTTCCCGTGAAGAGGAGTTAA-CATTTTAATGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGATGTCATT
* * * *
42679 CTTAACTTTCTCATGGAGATGAGTCAA-CTTTTTAGTGATGTCAT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGATGTCAT
42723 CTTCAATCTG
Statistics
Matches: 454, Mismatches: 82, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
44 3 0.01
45 450 0.99
46 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGATGTCATT
Found at i:45972 original size:43 final size:43
Alignment explanation
Indices: 45880--46099 Score: 174
Period size: 43 Copynumber: 5.1 Consensus size: 43
45870 ACAAAATTGT
* ** * * * * *
45880 TCTATAGCGGCGTTTGGGGAAAAAAAGCCGCAATATGTCTAGA
1 TCTATAGCAGCGTTTTTGGAACAAATGCCGCAAAAGGTCGAGA
* * * * *
45923 TTTATAGTAGTGCTTTTGGAACAAATGCCGCAACAGGTCGAGA
1 TCTATAGCAGCGTTTTTGGAACAAATGCCGCAAAAGGTCGAGA
* * *
45966 TCTATAGCGGCGTTTTTGGAGA-AAACGCCGCAAAAGGTTGAGA
1 TCTATAGCAGCGTTTTTGGA-ACAAATGCCGCAAAAGGTCGAGA
* * *
46009 TCTATAGCAGCGTTTTTGGAGCAAATACCGCAAAAGGT-TAGA
1 TCTATAGCAGCGTTTTTGGAACAAATGCCGCAAAAGGTCGAGA
* * * * * * *
46051 TCTATAACGGCATTTTTAGAACAAACGCTGCAAAAAGTCGAGA
1 TCTATAGCAGCGTTTTTGGAACAAATGCCGCAAAAGGTCGAGA
*
46094 TATATA
1 TCTATA
46100 ACGGCGAAAA
Statistics
Matches: 138, Mismatches: 36, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
42 32 0.23
43 105 0.76
44 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (43 bp):
TCTATAGCAGCGTTTTTGGAACAAATGCCGCAAAAGGTCGAGA
Found at i:46026 original size:86 final size:84
Alignment explanation
Indices: 45880--46099 Score: 208
Period size: 86 Copynumber: 2.6 Consensus size: 84
45870 ACAAAATTGT
** * * * * * *
45880 TCTATAGCGGCGTTTGGGGAAAAAAAGCCGCAATATGTCT-AGATTTATAGTAGTGCTTTTGGAA
1 TCTATAGCGGCGTTTTTGG-AAAAACGCCGCAAAAAGT-TGAGATATATAGCAGCGCTTTTGGAA
* *
45944 CAAATGCCGCAACAGGTCGAGA
64 CAAATACCGCAAAAGGT-GAGA
* * * *
45966 TCTATAGCGGCGTTTTTGGAGAAAACGCCGCAAAAGGTTGAGATCTATAGCAGCGTTTTTGGAGC
1 TCTATAGCGGCGTTTTTGGA-AAAACGCCGCAAAAAGTTGAGATATATAGCAGCGCTTTTGGAAC
*
46031 AAATACCGCAAAAGGTTAGA
65 AAATACCGCAAAAGGTGAGA
* * * * *
46051 TCTATAACGGCATTTTTAGAACAAACGCTGCAAAAAGTCGAGATATATA
1 TCTATAGCGGCGTTTTTGGAA-AAACGCCGCAAAAAGTTGAGATATATA
46100 ACGGCGAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
84 1 0.01
85 45 0.41
86 65 0.59
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (84 bp):
TCTATAGCGGCGTTTTTGGAAAAACGCCGCAAAAAGTTGAGATATATAGCAGCGCTTTTGGAACA
AATACCGCAAAAGGTGAGA
Found at i:46084 original size:85 final size:86
Alignment explanation
Indices: 45936--46099 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 86
45926 ATAGTAGTGC
* * * * *
45936 TTTTGGAACAAATGCCGCAACAGGTCGAGATCTATAGCGGCGTTTTTGGAGAAAACGCCGCAAAA
1 TTTTGGAACAAATACCGCAAAAGGTCGAGATCTATAACGGCATTTTTAGAGAAAACGCCGCAAAA
* * *
46001 GGTTGAGATCTATAGCAGCGT
66 AGTCGAGATATATAGCAGCGT
* * *
46022 TTTTGGAGCAAATACCGCAAAAGGT-TAGATCTATAACGGCATTTTTAGA-ACAAACGCTGCAAA
1 TTTTGGAACAAATACCGCAAAAGGTCGAGATCTATAACGGCATTTTTAGAGA-AAACGCCGCAAA
46085 AAGTCGAGATATATA
65 AAGTCGAGATATATA
46100 ACGGCGAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.02
85 43 0.65
86 22 0.33
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (86 bp):
TTTTGGAACAAATACCGCAAAAGGTCGAGATCTATAACGGCATTTTTAGAGAAAACGCCGCAAAA
AGTCGAGATATATAGCAGCGT
Found at i:49951 original size:79 final size:76
Alignment explanation
Indices: 49856--50035 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 76
49846 AAAATCAAGT
* * *
49856 CTATAGCGGCGTTTTTATAAAAACGCCGCTACAGTATTATTCTTTAGC-GACATTTGTCAAAAAA
1 CTATTGCGGCGTTTTTATAAAAACGCCGCTACAATATTACTCTTTAGCAG-CATTTGTCAAAAAA
*
49920 CAACTATACATGAC
65 -AACCA-ACATGAC
* *
49934 ACTATTGCGGCATTTTTATAAAAACGCCGCTACAATATTACTCTTTAGCAGCGTTTGTCAAAAAA
1 -CTATTGCGGCGTTTTTATAAAAACGCCGCTACAATATTACTCTTTAGCAGCATTTGTCAAAAAA
*
49999 AGCCAACATGAC
65 AACCAACATGAC
*
50011 CTTATTGCGACGTTTTTATAAAAAC
1 C-TATTGCGGCGTTTTTATAAAAAC
50036 CCACCAAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
76 1 0.01
77 28 0.31
78 3 0.03
79 57 0.63
80 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (76 bp):
CTATTGCGGCGTTTTTATAAAAACGCCGCTACAATATTACTCTTTAGCAGCATTTGTCAAAAAAA
ACCAACATGAC
Found at i:50712 original size:28 final size:29
Alignment explanation
Indices: 50637--50716 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 29
50627 TTAGTTCTAT
* * *
50637 TATATGGTC-GACTCTGTCGCCTAATTGA
1 TATATGGTCGGTCTATGCCGCCTAATTGA
*
50665 TATATGGTCGGT-TATACCGCCTGAA-TGA
1 TATATGGTCGGTCTATGCCGCCT-AATTGA
50693 TATATGGTCGGTCT-TGCCGCCTAA
1 TATATGGTCGGTCTATGCCGCCTAA
50717 GTATTATTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.05
28 38 0.86
29 4 0.09
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (29 bp):
TATATGGTCGGTCTATGCCGCCTAATTGA
Found at i:51890 original size:20 final size:23
Alignment explanation
Indices: 51865--51907 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
51855 AAGAAAATTA
51865 AAATTT-TGGA-CC-CCACTTAT
1 AAATTTCTGGATCCGCCACTTAT
51885 AAATTTCTGGATCCGCCACTTAT
1 AAATTTCTGGATCCGCCACTTAT
51908 GCCCACATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 4 0.20
22 2 0.10
23 8 0.40
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (23 bp):
AAATTTCTGGATCCGCCACTTAT
Found at i:54536 original size:19 final size:19
Alignment explanation
Indices: 54512--54554 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
54502 TTGGTATATT
*
54512 TGTTTTTTTTTCCTTTCTC
1 TGTTTTTTTTTCCGTTCTC
54531 TGTTTTTTTTTCCGTTCTC
1 TGTTTTTTTTTCCGTTCTC
54550 TGTTT
1 TGTTT
54555 CTGTCTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.00, C:0.19, G:0.09, T:0.72
Consensus pattern (19 bp):
TGTTTTTTTTTCCGTTCTC
Found at i:55054 original size:3 final size:3
Alignment explanation
Indices: 55046--55140 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
55036 AATATATATT
* *
55046 TAA TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
55094 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55141 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55516 original size:40 final size:41
Alignment explanation
Indices: 55472--55574 Score: 163
Period size: 40 Copynumber: 2.5 Consensus size: 41
55462 AAGTTGAACA
* *
55472 AGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGAT-G
1 AGTTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGATAG
55512 AGTTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGATGACG
1 AGTTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGAT-A-G
55555 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
55575 CTACCTGGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
40 37 0.64
43 21 0.36
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (41 bp):
AGTTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGATAG
Found at i:55912 original size:227 final size:226
Alignment explanation
Indices: 55514--56027 Score: 956
Period size: 227 Copynumber: 2.3 Consensus size: 226
55504 TTCAGATGAG
* *
55514 TTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
*
55579 CTGGCAATGTTGATCCATCAAATGATGAATTCCAGCAAAAGATTGAACAAGTTCTTCTCATTATG
63 CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATG
*
55644 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAAATAATCC
128 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGG-AAAAAATAATCC
55709 ATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
192 ATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
55744 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
55809 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
55874 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAAATAATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAAATAATCCATCA
55939 AGTGATAGATTTGAGCAAAAGGTTGAACAAA
196 AGTGATAGATTTGAGCAAAAGGTTGAACAAA
55970 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
56028 TTCTCTGAAA
Statistics
Matches: 280, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
226 105 0.38
227 140 0.50
230 35 0.12
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (226 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAAATAATCCATCA
AGTGATAGATTTGAGCAAAAGGTTGAACAAA
Found at i:56063 original size:113 final size:113
Alignment explanation
Indices: 55514--56066 Score: 772
Period size: 113 Copynumber: 4.9 Consensus size: 113
55504 TTCAGATGAG
* *
55514 TTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TAC
* *** * * ** *
55579 -CTGGCAATGTTGATCCATCAAATGAT-GAATTCCAGCAAAAGATTGAACAAG
62 TCTGGAAAAAATAATCCATCAAGTGATAG-ATTTGAGCAAAAGATTGAACAAA
*
55630 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTG
*
55695 GAAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 G-AAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGATTGAACAAA
55744 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCT
* *** * * ** *
55808 GGCAATGTTGATCCATCAAATGAT-GAATTCAAGCAAAAGATTGAACAAG
65 GGAAAAAATAATCCATCAAGTGATAG-ATTTGAGCAAAAGATTGAACAAA
*
55857 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTG
*
55922 GAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGATTGAACAAA
*
55970 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTG
*
56035 AAAAAAATAATCCATCAAGTGATAGATTTGAG
66 GAAAAAATAATCCATCAAGTGATAGATTTGAG
56067 TCTTTGCTAA
Statistics
Matches: 393, Mismatches: 37, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
112 5 0.01
113 252 0.64
114 98 0.25
115 3 0.01
116 35 0.09
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTG
GAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGATTGAACAAA
Found at i:56869 original size:84 final size:84
Alignment explanation
Indices: 56757--57117 Score: 643
Period size: 84 Copynumber: 4.3 Consensus size: 84
56747 GATCATGCAG
* * *
56757 TTCATCTT-TTAATTCCAACGATTGGTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCC
1 TTCATCTTCTAAATT-CAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
56821 AGAAGATGCTATTGAGCACA
65 AGAAGATGCTATTGAGCACA
* *
56841 TTCATCTTCTAAATTCAATGATTAGTTCTGTCCAACCAGATCAGATAACTTAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
56906 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
*
56925 TTCATCTTCTAAATTCAATGATTGGTTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
56990 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
57009 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
57074 GAAGATGCTATTGAGCACA
66 GAAGATGCTATTGAGCACA
*
57093 TTCATCTTCCAAATTCAATGATTGG
1 TTCATCTTCTAAATTCAATGATTGG
57118 ACTAAGATAT
Statistics
Matches: 266, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
84 261 0.98
85 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (84 bp):
TTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGAGCACA
Found at i:58139 original size:1 final size:1
Alignment explanation
Indices: 58135--58217 Score: 94
Period size: 1 Copynumber: 83.0 Consensus size: 1
58125 CTTGACCCCC
* * * * * *
58135 TTTTTCTTTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTCTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
58200 TTTTTTTTCTTTCTTTTT
1 TTTTTTTTTTTTTTTTTT
58218 CTTCAAGCAT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:58147 original size:9 final size:9
Alignment explanation
Indices: 58134--58220 Score: 104
Period size: 9 Copynumber: 9.3 Consensus size: 9
58124 CCTTGACCCC
*
58134 CTTTTTCTT
1 CTTTTTTTT
58143 -TTTTTTTT
1 CTTTTTTTT
58151 CTTTTTTTCTT
1 C-TTTTTT-TT
*
58162 TTTTTTTTT
1 CTTTTTTTT
*
58171 TTTTTTTTT
1 CTTTTTTTT
58180 CTTTTTTTTT
1 C-TTTTTTTT
58190 CTTTTTTTT
1 CTTTTTTTT
58199 CTTTTTTTT
1 CTTTTTTTT
58208 CTTTCTTTTT
1 CTTT-TTTTT
58218 CTT
1 CTT
58221 CAAGCATAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
8 7 0.10
9 32 0.46
10 29 0.41
11 2 0.03
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:58159 original size:19 final size:19
Alignment explanation
Indices: 58135--58216 Score: 112
Period size: 19 Copynumber: 4.3 Consensus size: 19
58125 CTTGACCCCC
58135 TTTTTCTTTTTTTTTTCTT
1 TTTTTCTTTTTTTTTTCTT
*
58154 TTTTTCTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTCTT
*
58173 TTTTTTTCTTTTTTTTTCTT
1 TTTTTCT-TTTTTTTTTCTT
*
58193 TTTTT-TCTTTTTTTTCTT
1 TTTTTCTTTTTTTTTTCTT
58211 TCTTTT
1 T-TTTT
58217 TCTTCAAGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.21
19 29 0.51
20 16 0.28
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTTCTT
Found at i:58184 original size:40 final size:40
Alignment explanation
Indices: 58135--58217 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
58125 CTTGACCCCC
* *
58135 TTTTTCTTTTTTTTT-TCTTTTTTTCTTTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTCT-TTTTTTTCTTTTTTTTCTTTCTT
58175 TTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTTCTTTCTT
1 TTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTTCTTTCTT
58215 TTT
1 TTT
58218 CTTCAAGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (40 bp):
TTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTTCTTTCTT
Found at i:58218 original size:28 final size:27
Alignment explanation
Indices: 58134--58220 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 27
58124 CCTTGACCCC
*
58134 CTTTTTCTTTTTTTTTTCTTTTTTTCTTT
1 CTTTTTTTTTTTTTTTTC-TTTTTT-TTT
*
58163 TTTTTTTTTTTTTTTTTCTTTTTTTTT
1 CTTTTTTTTTTTTTTTTCTTTTTTTTT
*
58190 CTTTTTTTTCTTTTTTTTCTTTCTTTTT
1 CTTTTTTTT-TTTTTTTTCTTTTTTTTT
58218 CTT
1 CTT
58221 CAAGCATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 11 0.21
28 26 0.49
29 16 0.30
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (27 bp):
CTTTTTTTTTTTTTTTTCTTTTTTTTT
Found at i:60720 original size:11 final size:12
Alignment explanation
Indices: 60703--60736 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
60693 CTGACCACAA
60703 ATCCCAAAAGTT
1 ATCCCAAAAGTT
60715 -TCCCAAAAGTT
1 ATCCCAAAAGTT
*
60726 ACCCCAAAAGT
1 ATCCCAAAAGT
60737 GCATTTAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (12 bp):
ATCCCAAAAGTT
Found at i:69579 original size:22 final size:21
Alignment explanation
Indices: 69554--69596 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
69544 TTTATTATAT
**
69554 ATATTTATGAATATATATAAAA
1 ATATTTAACAATATA-ATAAAA
69576 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
69597 GAAAAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:70515 original size:20 final size:20
Alignment explanation
Indices: 70490--70531 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
70480 GGTATATTTG
*
70490 TTTTTTTTTCCTTTCTCTGT
1 TTTTTTTTTCCGTTCTCTGT
70510 TTTTTTTTTCCGTTCTCTGT
1 TTTTTTTTTCCGTTCTCTGT
70530 TT
1 TT
70532 CTGTCTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (20 bp):
TTTTTTTTTCCGTTCTCTGT
Found at i:71031 original size:3 final size:3
Alignment explanation
Indices: 71023--71111 Score: 115
Period size: 3 Copynumber: 29.7 Consensus size: 3
71013 AATATATATT
** * * *
71023 TAA TAA TAA TAA TAA TAA CGA TGA TGA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
71071 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
71112 TGGATAAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:73053 original size:7 final size:7
Alignment explanation
Indices: 73041--73097 Score: 60
Period size: 7 Copynumber: 8.1 Consensus size: 7
73031 GATTACACCA
73041 TAAACCC
1 TAAACCC
*
73048 TAAACCT
1 TAAACCC
*
73055 TAAACCA
1 TAAACCC
*
73062 TAAGCCC
1 TAAACCC
*
73069 TAAACAC
1 TAAACCC
**
73076 TAAACAT
1 TAAACCC
73083 TAAACCC
1 TAAACCC
73090 TAAACCC
1 TAAACCC
73097 T
1 T
73098 TAATTCGATT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:73062 original size:21 final size:21
Alignment explanation
Indices: 73037--73100 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
73027 TTTAGATTAC
73037 ACCATAAACCCTAAACCTTAA
1 ACCATAAACCCTAAACCTTAA
*
73058 ACCATAAGCCCTAAACAC-TAA
1 ACCATAAACCCTAAAC-CTTAA
73079 A-CATTAAACCCTAAACCCTTAA
1 ACCA-TAAACCCTAAA-CCTTAA
73101 TTCGATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 2 0.05
21 30 0.81
22 5 0.14
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.19
Consensus pattern (21 bp):
ACCATAAACCCTAAACCTTAA
Found at i:84997 original size:37 final size:37
Alignment explanation
Indices: 84922--85005 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
84912 TGTTATCTTG
* * *
84922 TATAAATTTGGATATGTTGTCATATTTGTCATCTTTT
1 TATAAATTTAGATATGTTGTCATATTTGTAAACTTTT
*
84959 TATAAATTTAGATGTGTTGTCATATTTTGTAAACTTTT
1 TATAAATTTAGATATGTTGTCATA-TTTGTAAACTTTT
* *
84997 AATACATTT
1 TATAAATTT
85006 GAAGTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 22 0.55
38 18 0.45
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (37 bp):
TATAAATTTAGATATGTTGTCATATTTGTAAACTTTT
Found at i:89273 original size:59 final size:59
Alignment explanation
Indices: 89200--89317 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
89190 GGCAAAGATG
* *
89200 AGTTACTTATTTGAGCTGTGCTTAACAAACGATCAACTTCTACGTTGAATTTGATGTTA
1 AGTTACGTATTTGAGCTGTGCTTAACAAACGATCAACTTCTACGCTGAATTTGATGTTA
89259 AGTTACGTATTTGAGCTGTGCTTAACAAACGATCAACTTCTACGCTGAATTTGATGTTA
1 AGTTACGTATTTGAGCTGTGCTTAACAAACGATCAACTTCTACGCTGAATTTGATGTTA
89318 CGTTTTGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (59 bp):
AGTTACGTATTTGAGCTGTGCTTAACAAACGATCAACTTCTACGCTGAATTTGATGTTA
Found at i:96752 original size:39 final size:39
Alignment explanation
Indices: 96693--96782 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
96683 AAGCAGTAAA
*
96693 TTATTTGAATTAGTAATTTAGATTAACTATAACTCTAT-
1 TTATTTGATTTAGTAATTTAGATTAACTATAACTCTATC
*
96731 TCTATTTGATTTAGTAGTTTAGATTAACTATAACTCTATC
1 T-TATTTGATTTAGTAATTTAGATTAACTATAACTCTATC
96771 TTATTTGTATTT
1 TTATTTG-ATTT
96783 CTCATCTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
38 1 0.02
39 41 0.87
40 5 0.11
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (39 bp):
TTATTTGATTTAGTAATTTAGATTAACTATAACTCTATC
Done.