Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 101 of 130
Found at i:19780684 original size:85 final size:85
Alignment explanation
Indices: 19780422--19780709 Score: 293
Period size: 85 Copynumber: 3.4 Consensus size: 85
19780412 AGAATGATCT
* * *
19780422 CATTTTATTTTTTAAAATTTTCAAAGCCTCAGTTATGGGGGAGCATTTTACTTTTTCAAAG-TTC
1 CATTTTATTTTTTCAAAGTTTCAAAGCCTCAGTTGTGGGGGAGCATTTTAC-TTTTCAAAGTTTC
* * *
19780486 TAAAACCTCAGTTGTAGGGGAG
65 -AAAGCCTAAGTTGTGGGGGAG
* *
19780508 CATTTTACTTTTTCAAAG-TTCTAAAGCCTCAGTTGTGGGGGA-CATTTTACTTTTCCAAAGTTC
1 CATTTTATTTTTTCAAAGTTTC-AAAGCCTCAGTTGTGGGGGAGCATTTTACTTTT-CAAAGTTT
* * **
19780571 CAAAGCC-ACAATTATGAAGGAG
64 CAAAGCCTA-AGTTGTGGGGGAG
* * * *
19780593 TATTTTATTTTTTCAAAGTTTCATAGCCTCAGTTGTGAGTGAGCATTTTA-TTTTCAAAAGTTTC
1 CATTTTATTTTTTCAAAGTTTCAAAGCCTCAGTTGTGGGGGAGCATTTTACTTTTC-AAAGTTTC
*
19780657 AAAGCCTAAGTTGTGGGGGAA
65 AAAGCCTAAGTTGTGGGGGAG
* *
19780678 CGTTTTA--TTTTCAAAAGTTCCAAAGCCTCAGT
1 CATTTTATTTTTTC-AAAGTTTCAAAGCCTCAGT
19780710 CATAGGAGAG
Statistics
Matches: 166, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
83 5 0.03
84 22 0.13
85 92 0.55
86 47 0.28
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (85 bp):
CATTTTATTTTTTCAAAGTTTCAAAGCCTCAGTTGTGGGGGAGCATTTTACTTTTCAAAGTTTCA
AAGCCTAAGTTGTGGGGGAG
Found at i:19780805 original size:42 final size:42
Alignment explanation
Indices: 19780740--19780848 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 42
19780730 TTTTCAAAAA
**
19780740 TTTATTTTCCAAAAGTTCCAAAGCCTCAATTGTGGGAGAACAT
1 TTTATTTT-CAAAAGTTTTAAAGCCTCAATTGTGGGAGAACAT
* * *
19780783 TTTATTTTCAAAAGTTTTAAAGCCTCAGTTGTGGGGGAGCAT
1 TTTATTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAGAACAT
*
19780825 TTTATTTTTCAAAAATTTTAAAGC
1 TTTA-TTTTCAAAAGTTTTAAAGC
19780849 TTTAGTTCTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 33 0.56
43 26 0.44
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (42 bp):
TTTATTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAGAACAT
Found at i:19780833 original size:102 final size:99
Alignment explanation
Indices: 19780639--19780842 Score: 266
Period size: 102 Copynumber: 2.0 Consensus size: 99
19780629 GAGTGAGCAT
* * *
19780639 TTTATTTTCAAAAGTTTCAAAGCCTAAGTTGTGGGGGAACGTTTTATTTTCAAAAGTTCCAAAGC
1 TTTATTTTCAAAAGTTCCAAAGCCTAAGTTGTGGGAGAACATTTTATTTTCAAAAGTTCCAAAGC
* *
19780704 CTCAGTCATAGGAGAGCTTTTTTTTTTTTTCAAAAA
66 CTCAGTCATAGGAGAGC--ATTTTATTTTTCAAAAA
**
19780740 TTTATTTTCCAAAAGTTCCAAAGCCTCAA-TTGTGGGAGAACATTTTATTTTCAAAAGTTTTAAA
1 TTTATTTT-CAAAAGTTCCAAAGCCT-AAGTTGTGGGAGAACATTTTATTTTCAAAAGTTCCAAA
** * *
19780804 GCCTCAGTTGTGGGGGAGCATTTTATTTTTCAAAAA
64 GCCTCAGTCATAGGAGAGCATTTTATTTTTCAAAAA
19780840 TTT
1 TTT
19780843 TAAAGCTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
100 18 0.20
101 8 0.09
102 62 0.69
103 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (99 bp):
TTTATTTTCAAAAGTTCCAAAGCCTAAGTTGTGGGAGAACATTTTATTTTCAAAAGTTCCAAAGC
CTCAGTCATAGGAGAGCATTTTATTTTTCAAAAA
Found at i:19780848 original size:43 final size:43
Alignment explanation
Indices: 19780740--19780870 Score: 165
Period size: 43 Copynumber: 3.1 Consensus size: 43
19780730 TTTTCAAAAA
* ** * *
19780740 TTTATTTTCCAAAAGTTCCAAAGCCTCAATTGTGGGAGAACAT
1 TTTATTTTTCAAAAGTTTTAAAGCCTCAGTTGTGGGAGAGCAT
*
19780783 TTTA-TTTTCAAAAGTTTTAAAGCCTCAGTTGTGGGGGAGCAT
1 TTTATTTTTCAAAAGTTTTAAAGCCTCAGTTGTGGGAGAGCAT
* * * *
19780825 TTTATTTTTCAAAAATTTTAAAGCTTTAGTTCTGGGAGAGCAT
1 TTTATTTTTCAAAAGTTTTAAAGCCTCAGTTGTGGGAGAGCAT
19780868 TTT
1 TTT
19780871 TTAAAAAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 36 0.47
43 40 0.53
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (43 bp):
TTTATTTTTCAAAAGTTTTAAAGCCTCAGTTGTGGGAGAGCAT
Found at i:19781824 original size:21 final size:20
Alignment explanation
Indices: 19781799--19781840 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
19781789 TATTTAATTG
*
19781799 TATATTTATTTGCATGATTTA
1 TATATTTAATTGCATG-TTTA
*
19781820 TATATTTAATTGTATGTTTA
1 TATATTTAATTGCATGTTTA
19781840 T
1 T
19781841 TTGCATGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (20 bp):
TATATTTAATTGCATGTTTA
Found at i:19781826 original size:33 final size:33
Alignment explanation
Indices: 19781719--19781852 Score: 157
Period size: 32 Copynumber: 4.1 Consensus size: 33
19781709 TTGTGTAACT
* *
19781719 TTTATATATTTAATTGCATGTCTAATTGCATGA
1 TTTATATATTTAATTGTATGTTTAATTGCATGA
* * * *
19781752 -TTAT-TAATTTATTTATTTGTGTAATTGCATGA
1 TTTATAT-ATTTAATTGTATGTTTAATTGCATGA
* *
19781784 -TTATATATTTAATTGTATATTTATTTGCATGA
1 TTTATATATTTAATTGTATGTTTAATTGCATGA
*
19781816 TTTATATATTTAATTGTATGTTTATTTGCATGA
1 TTTATATATTTAATTGTATGTTTAATTGCATGA
19781849 TTTA
1 TTTA
19781853 CATTGTTAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
31 1 0.01
32 49 0.57
33 36 0.42
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.55
Consensus pattern (33 bp):
TTTATATATTTAATTGTATGTTTAATTGCATGA
Found at i:19781864 original size:33 final size:33
Alignment explanation
Indices: 19781719--19781852 Score: 143
Period size: 33 Copynumber: 4.1 Consensus size: 33
19781709 TTGTGTAACT
* * * *
19781719 TTTATATATTTAATTGCATGTCTAATTGCATGA
1 TTTATATATTTAATTGTATATTTATTTGCATGA
* *
19781752 -TTAT-TAATTT-ATT-TATTTGTGTAATTGCATGA
1 TTTATAT-ATTTAATTGTATAT-T-TATTTGCATGA
19781784 -TTATATATTTAATTGTATATTTATTTGCATGA
1 TTTATATATTTAATTGTATATTTATTTGCATGA
*
19781816 TTTATATATTTAATTGTATGTTTATTTGCATGA
1 TTTATATATTTAATTGTATATTTATTTGCATGA
19781849 TTTA
1 TTTA
19781853 CATTGTTAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
30 3 0.03
31 4 0.05
32 37 0.42
33 40 0.45
34 4 0.05
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.55
Consensus pattern (33 bp):
TTTATATATTTAATTGTATATTTATTTGCATGA
Found at i:19783442 original size:144 final size:145
Alignment explanation
Indices: 19783243--19783534 Score: 319
Period size: 144 Copynumber: 2.0 Consensus size: 145
19783233 AAAGCTCCAA
* * * ** * *
19783243 ATCATGATTTTATAATATTTGATGATTTTTAGATTTTTGAAAACTTTGACTGTACCTTGAA-AGC
1 ATCATGATTTTATAATATTTGATAATTTTTAGATATTAGAAAACTACGACAGTACC-CGAAGAGC
* * * * *
19783307 TTTGAAATTACCAAAATACC-TTTTGGGGGTATCTTT-GTAATTTGATCTTCCCAATGTCG-ATT
65 TGTGAAATTACCAAAATACCTTTTTAGGGGTAT-TTTCATAATTTGACCTTCCCAAGGTCGAATT
19783369 TTCAT-AAAACTTTTTCAG
129 TTCATGAAAA--TTTTCAG
*
19783387 ATCATGATTTTATAATATTTGATAATTTTT-GATGCATTAGAAATC-ACGACAGTACCCGAAGAG
1 ATCATGATTTTATAATATTTGATAATTTTTAGAT--ATTAGAAAACTACGACAGTACCCGAAGAG
* * * * *
19783450 GTGTGTAATTATCAAAATACCTTTTTAGGGGTATTTTCATAATTTGACCTTCCTAAGGTTGAATT
64 CTGTGAAATTACCAAAATACCTTTTTAGGGGTATTTTCATAATTTGACCTTCCCAAGGTCGAATT
19783515 TTCATGAAAATTTTCAG
129 TTCATGAAAATTTTCAG
19783532 ATC
1 ATC
19783535 CTAATTTCCT
Statistics
Matches: 123, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
143 6 0.05
144 59 0.48
145 46 0.37
146 8 0.07
147 4 0.03
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (145 bp):
ATCATGATTTTATAATATTTGATAATTTTTAGATATTAGAAAACTACGACAGTACCCGAAGAGCT
GTGAAATTACCAAAATACCTTTTTAGGGGTATTTTCATAATTTGACCTTCCCAAGGTCGAATTTT
CATGAAAATTTTCAG
Found at i:19786260 original size:25 final size:25
Alignment explanation
Indices: 19786232--19786358 Score: 136
Period size: 25 Copynumber: 5.2 Consensus size: 25
19786222 GTTTGCTTTA
19786232 CATTTCATGCATATTTTAATTATGT
1 CATTTCATGCATATTTTAATTATGT
* *
19786257 CA-TTCAATGCATACTTTAATAATGT
1 CATTTC-ATGCATATTTTAATTATGT
* * *
19786282 CATTTCATGCATATTGTAACTACGT
1 CATTTCATGCATATTTTAATTATGT
* *
19786307 TATTTCATG--T-TTTTAATTTTGT
1 CATTTCATGCATATTTTAATTATGT
* *
19786329 CATTTCATACATATCTTAATTATGT
1 CATTTCATGCATATTTTAATTATGT
19786354 CATTT
1 CATTT
19786359 ACTATATATT
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
22 15 0.19
23 1 0.01
24 4 0.05
25 58 0.72
26 3 0.04
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (25 bp):
CATTTCATGCATATTTTAATTATGT
Found at i:19788733 original size:25 final size:25
Alignment explanation
Indices: 19788701--19788753 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
19788691 TTGTCTTAAG
19788701 AAACATAGTAGTTATCAATTTTTTT
1 AAACATAGTAGTTATCAATTTTTTT
*
19788726 AAACATAGTAGTTATTAATTTTTTT
1 AAACATAGTAGTTATCAATTTTTTT
19788751 AAA
1 AAA
19788754 GGAACTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (25 bp):
AAACATAGTAGTTATCAATTTTTTT
Found at i:19789706 original size:9 final size:9
Alignment explanation
Indices: 19789694--19789731 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
19789684 CAACATCAGG
*
19789694 ATCATCATT
1 ATCACCATT
19789703 ATCACCATT
1 ATCACCATT
19789712 ATCACCATT
1 ATCACCATT
19789721 ATCACCATT
1 ATCACCATT
19789730 AT
1 AT
19789732 TGGTTTCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (9 bp):
ATCACCATT
Found at i:19790427 original size:21 final size:21
Alignment explanation
Indices: 19790382--19790447 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
19790372 TACAATAATT
* * *
19790382 AAATACATCAAATAAAATAAG
1 AAATACATCAAATAATAGAAA
19790403 AAATACATCAAATAATAGAAA
1 AAATACATCAAATAATAGAAA
* *
19790424 AAATATATAAAATAATAGAAA
1 AAATACATCAAATAATAGAAA
19790445 AAA
1 AAA
19790448 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.70, C:0.06, G:0.05, T:0.20
Consensus pattern (21 bp):
AAATACATCAAATAATAGAAA
Found at i:19796560 original size:29 final size:28
Alignment explanation
Indices: 19796512--19796569 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
19796502 CATAAAACAA
*
19796512 AAAATAAAAAAACCTAAACCCAAAATAAG
1 AAAATAAAAAAACCTAAA-CCAAAAAAAG
19796541 AAAATAAAAGTAAA-CT-AACCAAAAAAAG
1 AAAATAAAA--AAACCTAAACCAAAAAAAG
19796569 A
1 A
19796570 TACAGATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 10 0.38
29 11 0.42
30 2 0.08
31 3 0.12
ACGTcount: A:0.71, C:0.14, G:0.05, T:0.10
Consensus pattern (28 bp):
AAAATAAAAAAACCTAAACCAAAAAAAG
Found at i:19806720 original size:26 final size:26
Alignment explanation
Indices: 19806672--19806725 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
19806662 ATAGCAATTC
* *
19806672 AATATAAACAATAATGCTCTTATTAA
1 AATATAAACAATAATACTCTTATAAA
* *
19806698 AATATATACAATAATACTGTTATAAA
1 AATATAAACAATAATACTCTTATAAA
19806724 AA
1 AA
19806726 AGGTGATGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (26 bp):
AATATAAACAATAATACTCTTATAAA
Found at i:19812629 original size:29 final size:29
Alignment explanation
Indices: 19812585--19812670 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
19812575 AAATTATTGT
*
19812585 TAAATTATAATAAAATATTTAATTTAATCTA
1 TAAATTAT-A-AAAATATTTAATTTAATATA
* * * *
19812616 TAAATTTTAAAAATTTTTAATTTGATATT
1 TAAATTATAAAAATATTTAATTTAATATA
*
19812645 TAAATTATAAATATA-TTAA-TTAATAT
1 TAAATTATAAAAATATTTAATTTAATAT
19812671 GATATTTATC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.13
28 4 0.09
29 28 0.61
30 1 0.02
31 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAATTATAAAAATATTTAATTTAATATA
Found at i:19812712 original size:24 final size:24
Alignment explanation
Indices: 19812685--19812734 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
19812675 TTTATCTGTA
19812685 ATATAAATAATTTTAAATAATAAT
1 ATATAAATAATTTTAAATAATAAT
* *
19812709 ATATAATTAATTTTAAATAATGAT
1 ATATAAATAATTTTAAATAATAAT
19812733 AT
1 AT
19812735 GTGATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATAAATAATTTTAAATAATAAT
Found at i:19818470 original size:20 final size:19
Alignment explanation
Indices: 19818414--19818471 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
19818404 TTTCAGACAA
19818414 AAAATATAAT-TTTTATAT
1 AAAATATAATATTTTATAT
**
19818432 AAAATATAATATAAATATAT
1 AAAATATAATAT-TTTATAT
*
19818452 AAATTATGAATATTTTATAT
1 AAAATAT-AATATTTTATAT
19818472 CATATAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 10 0.31
19 1 0.03
20 16 0.50
21 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AAAATATAATATTTTATAT
Found at i:19820083 original size:35 final size:35
Alignment explanation
Indices: 19820032--19820102 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
19820022 ATTCATGAGA
*
19820032 AAAATTTAATGCAATAAGATTTCTTTAAATACTCT
1 AAAACTTAATGCAATAAGATTTCTTTAAATACTCT
19820067 AAAACTTAATGCAATAAGATTTCTTTAAATACTCT
1 AAAACTTAATGCAATAAGATTTCTTTAAATACTCT
19820102 A
1 A
19820103 TCATCTAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.38
Consensus pattern (35 bp):
AAAACTTAATGCAATAAGATTTCTTTAAATACTCT
Found at i:19820304 original size:15 final size:15
Alignment explanation
Indices: 19820273--19820363 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 15
19820263 AGAATTTTGA
*
19820273 ATTTTAAGGCTTT-GG
1 ATTTT-AGGGTTTAGG
19820288 ATTTTAGGGTTTAGG
1 ATTTTAGGGTTTAGG
* *
19820303 A-TTTAGGATTTTGG
1 ATTTTAGGGTTTAGG
*
19820317 ATTTT-GGGATTAGG
1 ATTTTAGGGTTTAGG
* *
19820331 GTTTT-GAGTTTTA-G
1 ATTTTAG-GGTTTAGG
*
19820345 ATTTTGGGGTTTA-G
1 ATTTTAGGGTTTAGG
19820359 ATTTT
1 ATTTT
19820364 TTATTTTAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
14 45 0.74
15 16 0.26
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.51
Consensus pattern (15 bp):
ATTTTAGGGTTTAGG
Found at i:19820342 original size:28 final size:28
Alignment explanation
Indices: 19820283--19820352 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
19820273 ATTTTAAGGC
*
19820283 TTTGGATTTTAGGGTTTAGGATTTAGGAT
1 TTTGGATTTT-GGGATTAGGATTTAGGAT
* *
19820312 TTTGGATTTTGGGATTAGGGTTT-TGAGT
1 TTTGGATTTTGGGATTAGGATTTAGGA-T
*
19820340 TTTAGATTTTGGG
1 TTTGGATTTTGGG
19820353 GTTTAGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.06
28 24 0.67
29 10 0.28
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (28 bp):
TTTGGATTTTGGGATTAGGATTTAGGAT
Found at i:19820363 original size:28 final size:28
Alignment explanation
Indices: 19820287--19820372 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
19820277 TAAGGCTTTG
* *
19820287 GATTTTAGGGTTTAGGATTTAGGATTTTG
1 GATTTT-GGGTTTAGGATTTTGGATTTTA
* *
19820316 GATTTTGGGATTAGGGTTTT-GAGTTTTA
1 GATTTTGGGTTTAGGATTTTGGA-TTTTA
**
19820344 GATTTTGGGGTTTA-GATTTTTTATTTTA
1 GATTTT-GGGTTTAGGATTTTGGATTTTA
19820372 G
1 G
19820373 GGTTTGAAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
27 2 0.04
28 32 0.68
29 13 0.28
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (28 bp):
GATTTTGGGTTTAGGATTTTGGATTTTA
Found at i:19820364 original size:22 final size:21
Alignment explanation
Indices: 19820326--19820377 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
19820316 GATTTTGGGA
*
19820326 TTAGGGTTTTGAGTTTTAGATT
1 TTAGGGTTTAGAGTTTT-GATT
* * *
19820348 TTGGGGTTTAGATTTTTTATT
1 TTAGGGTTTAGAGTTTTGATT
19820369 TTAGGGTTT
1 TTAGGGTTT
19820378 GAAGTTTGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTTGATT
Found at i:19820412 original size:21 final size:21
Alignment explanation
Indices: 19820388--19820455 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
19820378 GAAGTTTGAG
*
19820388 GTTTTGATTTCAGGGTTTAAT
1 GTTTCGATTTCAGGGTTTAAT
* * **
19820409 GTTTGGAGTTTCA-GTTTTAGG
1 GTTTCGA-TTTCAGGGTTTAAT
*
19820430 GTTTCGATTTTAGGGTTTATAT
1 GTTTCGATTTCAGGGTTTA-AT
19820452 GTTT
1 GTTT
19820456 AAAGTTTGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
20 4 0.11
21 22 0.63
22 9 0.26
ACGTcount: A:0.16, C:0.04, G:0.26, T:0.53
Consensus pattern (21 bp):
GTTTCGATTTCAGGGTTTAAT
Found at i:19820559 original size:28 final size:29
Alignment explanation
Indices: 19820512--19820571 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
19820502 GTTTAGAGGG
*
19820512 TTTAGGGTTTGAAGGGTTTAGAGATTT-GT
1 TTTAGGGTTTGAAGAGTTTAGAG-TTTAGT
19820541 TTTAGGGTTTG-AGAGTTTAGAGTTTAGT
1 TTTAGGGTTTGAAGAGTTTAGAGTTTAGT
19820569 TTT
1 TTT
19820572 GAAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 3 0.10
28 15 0.52
29 11 0.38
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (29 bp):
TTTAGGGTTTGAAGAGTTTAGAGTTTAGT
Found at i:19820593 original size:21 final size:22
Alignment explanation
Indices: 19820540--19820593 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
19820530 TAGAGATTTG
*
19820540 TTTTAGGGTTTGAGAGTTTAGA
1 TTTTAGGGTTTGAAAGTTTAGA
* * *
19820562 GTTTA-GTTTTGAAATTTTA-A
1 TTTTAGGGTTTGAAAGTTTAGA
19820582 TTTTAGGGTTTG
1 TTTTAGGGTTTG
19820594 GAGGATTTAG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (22 bp):
TTTTAGGGTTTGAAAGTTTAGA
Found at i:19820604 original size:16 final size:15
Alignment explanation
Indices: 19820583--19820637 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
19820573 AAATTTTAAT
19820583 TTTAGGGTTTGGAGG
1 TTTAGGGTTTGGAGG
* *
19820598 ATTTAGGATTT--AGT
1 -TTTAGGGTTTGGAGG
*
19820612 TTTGGGGTTTGGAAGG
1 TTTAGGGTTTGG-AGG
19820628 TTTAGGGTTT
1 TTTAGGGTTT
19820638 AGATTTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
16 20 0.67
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.45
Consensus pattern (15 bp):
TTTAGGGTTTGGAGG
Found at i:19820614 original size:29 final size:29
Alignment explanation
Indices: 19820577--19820644 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
19820567 GTTTTGAAAT
*
19820577 TTTAATTTTAGGGTTTGG-AGGATTTAGGA
1 TTTAGTTTTAGGGTTTGGAAGG-TTTAGGA
* *
19820606 TTTAGTTTTGGGGTTTGGAAGGTTTAGGG
1 TTTAGTTTTAGGGTTTGGAAGGTTTAGGA
19820635 TTTAGATTTT
1 TTTAG-TTTT
19820645 TTAATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (29 bp):
TTTAGTTTTAGGGTTTGGAAGGTTTAGGA
Found at i:19820657 original size:71 final size:70
Alignment explanation
Indices: 19820512--19820657 Score: 172
Period size: 71 Copynumber: 2.1 Consensus size: 70
19820502 GTTTAGAGGG
*
19820512 TTTAGGGTTTGAAGGGTTTAGAGATTTGTTTTAGGGTTTGAGAGTTTAGAGTTTAGTTTTGAAAT
1 TTTAGGGTTTGAAGGATTTAGAGATTTGTTTTAGGGTTTGAGAGTTTAGAGTTTAGTTTTGAAAT
19820577 TTTAAT
66 TTT-AT
* * * *
19820583 TTTAGGGTTTGGAGGATTTAG-GATTTAGTTTTGGGGTTTG-GAAGGTTTAGGGTTTAGATTTTT
1 TTTAGGGTTTGAAGGATTTAGAGATTT-GTTTTAGGGTTTGAG-A-GTTTAGAGTTTAG-TTTTG
*
19820646 TAATTTT-T
62 AAATTTTAT
19820654 TTTA
1 TTTA
19820658 AAAATACGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
70 6 0.09
71 37 0.57
72 12 0.18
73 10 0.15
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (70 bp):
TTTAGGGTTTGAAGGATTTAGAGATTTGTTTTAGGGTTTGAGAGTTTAGAGTTTAGTTTTGAAAT
TTTAT
Found at i:19821961 original size:35 final size:35
Alignment explanation
Indices: 19821914--19821995 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
19821904 CTGACCTTCT
*
19821914 GGATTCTCTGGTTTGGTAGAGCAAGGTGTCTGTGTG
1 GGATT-TCTGGTTTGGGAGAGCAAGGTGTCTGTGTG
* *
19821950 GGATTTTTGGTTTGGGAGAGCAGGGTGTCTGTGTG
1 GGATTTCTGGTTTGGGAGAGCAAGGTGTCTGTGTG
*
19821985 GGGTTTCTGGT
1 GGATTTCTGGT
19821996 GTTTTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 36 0.88
36 5 0.12
ACGTcount: A:0.11, C:0.09, G:0.43, T:0.38
Consensus pattern (35 bp):
GGATTTCTGGTTTGGGAGAGCAAGGTGTCTGTGTG
Found at i:19822752 original size:17 final size:18
Alignment explanation
Indices: 19822732--19822775 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
19822722 AAAAGAAAAT
*
19822732 TTTTTAAAAAAT-TAAAC
1 TTTTAAAAAAATCTAAAC
19822749 TTTTAAAAAAATCTAAA-
1 TTTTAAAAAAATCTAAAC
19822766 -TTTAAAAAAA
1 TTTTAAAAAAA
19822776 CCAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
17 11 0.44
18 4 0.16
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTTAAAAAAATCTAAAC
Found at i:19822769 original size:16 final size:16
Alignment explanation
Indices: 19822737--19822775 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
19822727 AAAATTTTTT
19822737 AAAAAATTAAACTTTTA
1 AAAAAATTAAAC-TTTA
19822754 AAAAAATCTAAA-TTTA
1 AAAAAAT-TAAACTTTA
19822770 AAAAAA
1 AAAAAA
19822776 CCAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATTAAACTTTA
Found at i:19822782 original size:26 final size:27
Alignment explanation
Indices: 19822753--19822803 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
19822743 TTAAACTTTT
* *
19822753 AAAAAAATCTAAATTTAA-AAAAACCA
1 AAAAAAATCAAAAATTAAGAAAAACCA
*
19822779 AAAAAATTCAAAAATTAAGAAAAAC
1 AAAAAAATCAAAAATTAAGAAAAAC
19822804 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.18
Consensus pattern (27 bp):
AAAAAAATCAAAAATTAAGAAAAACCA
Found at i:19822918 original size:16 final size:14
Alignment explanation
Indices: 19822897--19822931 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
19822887 AAACAAATTG
19822897 AAAATTTAATAAAAT
1 AAAATTTAA-AAAAT
19822912 CAAAATTTAAAAAAT
1 -AAAATTTAAAAAAT
19822927 AAAAT
1 AAAAT
19822932 AAAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 5 0.26
16 9 0.47
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTTAAAAAAT
Found at i:19822992 original size:36 final size:36
Alignment explanation
Indices: 19822952--19823038 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
19822942 AAAAGACCAT
* *
19822952 AAAAATCTGAAAAATT-AAAAATA-CCCTAAAATTTAA
1 AAAAAT-T-AAAAATTAAAAAACATCCCCAAAATTTAA
*
19822988 AAAAAATAAAAATTAAAAAACATCCCCAAAATTTAA
1 AAAAATTAAAAATTAAAAAACATCCCCAAAATTTAA
19823024 AAGAAATTCAAAAAT
1 AA-AAATT-AAAAAT
19823039 AAATTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
34 7 0.16
35 7 0.16
36 19 0.44
37 4 0.09
38 6 0.14
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.22
Consensus pattern (36 bp):
AAAAATTAAAAATTAAAAAACATCCCCAAAATTTAA
Found at i:19826233 original size:52 final size:52
Alignment explanation
Indices: 19826103--19826248 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 52
19826093 AAACTTGTCC
* ** ** ** *
19826103 ATTAAAAATCCCTCCCCTCTTAGAATTCTTCTCCTATAAGTCAAACTTGCCT
1 ATTAAGAATCCCTTTCCTCTTAGAATTCTTCTTTTGCAAGTCAAACTTACCT
*
19826155 ATTAAGAATCCCTTTCCTTTTAGAATTCTTCTTTTGCAAGTCAAACTTACCT
1 ATTAAGAATCCCTTTCCTCTTAGAATTCTTCTTTTGCAAGTCAAACTTACCT
* *
19826207 ATTAAGAATCCTCTTT-CTCTTGGAATTCTTCTTTTGTAAGTC
1 ATTAAGAATCC-CTTTCCTCTTAGAATTCTTCTTTTGCAAGTC
19826249 TTCTTATCCA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 77 0.95
53 4 0.05
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
ATTAAGAATCCCTTTCCTCTTAGAATTCTTCTTTTGCAAGTCAAACTTACCT
Found at i:19826289 original size:11 final size:11
Alignment explanation
Indices: 19826273--19826303 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
19826263 GCAATATCTG
19826273 ACAAATCTCAA
1 ACAAATCTCAA
19826284 ACAAATCTCAA
1 ACAAATCTCAA
19826295 ACAAATCTC
1 ACAAATCTC
19826304 TTATGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:19826682 original size:31 final size:31
Alignment explanation
Indices: 19826644--19826727 Score: 134
Period size: 30 Copynumber: 2.7 Consensus size: 31
19826634 TTCGAACCTT
* *
19826644 CAGCTCTGATACCACTTGTTGGGGATCACCA
1 CAGCTCTGATACCATTTGTTGGGGAACACCA
*
19826675 CAGCTCTGATACCATTTGTT-GAGAACACCA
1 CAGCTCTGATACCATTTGTTGGGGAACACCA
19826705 CAGCTCTGATACCATTTGTTGGG
1 CAGCTCTGATACCATTTGTTGGG
19826728 CTAAAGCCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 28 0.58
31 20 0.42
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (31 bp):
CAGCTCTGATACCATTTGTTGGGGAACACCA
Found at i:19827279 original size:52 final size:52
Alignment explanation
Indices: 19827212--19827336 Score: 160
Period size: 52 Copynumber: 2.4 Consensus size: 52
19827202 TATAACCATA
* * * *
19827212 CAAACTTGCCCATTAAAAATCCCTCTCCTCTTAGAATTATTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTATTCTCCTGCAAAT
* * * * *
19827264 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAAT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTATTCTCCTGCAAAT
*
19827316 CAAACTTACCTATTAAGAATC
1 CAAACTTGCCTATTAAGAATC
19827337 ATCTTTCTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTATTCTCCTGCAAAT
Found at i:19827354 original size:52 final size:52
Alignment explanation
Indices: 19827212--19827365 Score: 152
Period size: 52 Copynumber: 3.0 Consensus size: 52
19827202 TATAACCATA
* * * * * * * * *
19827212 CAAACTTGCCCATTAAAAATCCCTCTCCTCTT-AGAATTATTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCTCTTTCCT-TTGAGAATTCTTCTCTTGCAAAT
* *
19827264 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAAT
1 CAAACTTACCTATTAAGAATCTCTTTCCTTTGAGAATTCTTCTCTTGCAAAT
*
19827316 CAAACTTACCTATTAAGAATCATCTTT-CTCTTGA-AATTCTTCTTTTGCAA
1 CAAACTTACCTATTAAGAATC-TCTTTCCT-TTGAGAATTCTTCTCTTGCAA
19827366 GTCTTTTTGT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 2 0.02
52 78 0.89
53 8 0.09
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.40
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCTCTTTCCTTTGAGAATTCTTCTCTTGCAAAT
Found at i:19827409 original size:11 final size:11
Alignment explanation
Indices: 19827393--19827434 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
19827383 GCAATATCTG
19827393 ACAAATCTCAA
1 ACAAATCTCAA
19827404 ACAAATCTCAA
1 ACAAATCTCAA
19827415 ACAAATCTCAA
1 ACAAATCTCAA
19827426 ACAAATCTC
1 ACAAATCTC
19827435 TTATGAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:19827809 original size:31 final size:31
Alignment explanation
Indices: 19827771--19827855 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
19827761 TTCGAACCTT
* *
19827771 CAGCTCTGATACCACTTGTTGGGGATCACCA
1 CAGCTCTGATACCATTTGTTGGGGAACACCA
* * *
19827802 CAGCTCTGATATCATTTGTTGAGTAACACCA
1 CAGCTCTGATACCATTTGTTGGGGAACACCA
*
19827833 TAGCTCTGATACCATTTGTTGGG
1 CAGCTCTGATACCATTTGTTGGG
19827856 CTAAAAGCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (31 bp):
CAGCTCTGATACCATTTGTTGGGGAACACCA
Found at i:19828430 original size:52 final size:52
Alignment explanation
Indices: 19828340--19828484 Score: 175
Period size: 52 Copynumber: 2.8 Consensus size: 52
19828330 TATAACCATA
* * * * *
19828340 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
* * * *
19828392 CAAACTTGTCTATTAGGAATCTCTTTCCTTTTAAAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
* *
19828444 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTGAAATTCTT
1 CAAACTTGCCTATTAAGAAT-CTCTTTCCTCTTAAAATTCTT
19828485 TTTTTGCAAG
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
52 72 0.92
53 6 0.08
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
Found at i:19832241 original size:22 final size:22
Alignment explanation
Indices: 19832215--19832265 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
19832205 AATTTATTTA
19832215 TTTTATTTTAA-ATTATTAGA-AT
1 TTTTATTTTAATATT-TTA-ATAT
*
19832237 TTTTAATTTAATATTTTAATAT
1 TTTTATTTTAATATTTTAATAT
19832259 TTTTATT
1 TTTTATT
19832266 AGATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 21 0.84
23 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTATTTTAATATTTTAATAT
Found at i:19833107 original size:13 final size:14
Alignment explanation
Indices: 19833089--19833120 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
19833079 TTGTGTACTT
19833089 AAAAACAAAAAA-A
1 AAAAACAAAAAACA
19833102 AAAAACAAAAAACA
1 AAAAACAAAAAACA
19833116 AAAAA
1 AAAAA
19833121 TGAAGAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAACA
Found at i:19833671 original size:15 final size:15
Alignment explanation
Indices: 19833651--19833681 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19833641 AATCTGGCAC
19833651 TCAGTTTCAATCCAT
1 TCAGTTTCAATCCAT
19833666 TCAGTTTCAATCCAT
1 TCAGTTTCAATCCAT
19833681 T
1 T
19833682 TTAACTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (15 bp):
TCAGTTTCAATCCAT
Found at i:19854761 original size:58 final size:59
Alignment explanation
Indices: 19854645--19854858 Score: 200
Period size: 58 Copynumber: 3.5 Consensus size: 59
19854635 TTGCAAACAC
* * * ****
19854645 CAAACTCCAACATTAAACAATAAAGCATCATCCAAGAATTTTGATATCATCCAAAGTTTT
1 CAAACTCCAACATTAAACATTAAAACATCATCCAAGACTAAAAATATCATCCAAAG-TTT
19854705 CAAA-TCCAACATTAAACATTAAAACATCAT-CAAGACTAAAAATATCATCCAAAGTTT
1 CAAACTCCAACATTAAACATTAAAACATCATCCAAGACTAAAAATATCATCCAAAGTTT
* * * * * *
19854762 CACA-TGTCAACATTAAACATGACAAGATCATCCAACACTTGAAATAATAAAATCATCCAAAGTT
1 CAAACT-CCAACATTAAACATTAAAACATCATCCAAGAC-T-AAA-AAT---ATCATCCAAAGTT
19854826 T
59 T
*
19854827 CAAACTCTAAACATTAAACATTAAAACATCAT
1 CAAACTC-CAACATTAAACATTAAAACATCAT
19854859 GTTTTACAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
57 7 0.06
58 40 0.32
59 29 0.23
60 5 0.04
61 3 0.02
62 3 0.02
65 17 0.14
66 21 0.17
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (59 bp):
CAAACTCCAACATTAAACATTAAAACATCATCCAAGACTAAAAATATCATCCAAAGTTT
Found at i:19856922 original size:2 final size:2
Alignment explanation
Indices: 19856915--19856940 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19856905 AGTGTTACAG
19856915 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
19856941 AACTAAGTTA
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):
TA
Found at i:19868443 original size:13 final size:13
Alignment explanation
Indices: 19868427--19868451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19868417 TTAAAACTAC
19868427 AAACAAAAAAAAA
1 AAACAAAAAAAAA
19868440 AAACAAAAAAAA
1 AAACAAAAAAAA
19868452 GAACAAGAGG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAAAAAAAAA
Found at i:19870461 original size:2 final size:2
Alignment explanation
Indices: 19870454--19870518 Score: 105
Period size: 2 Copynumber: 32.5 Consensus size: 2
19870444 TAATTTAAAA
19870454 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
19870496 AG AG AG AG AG CA- AG AG AA AG AG A
1 AG AG AG AG AG -AG AG AG AG AG AG A
19870519 TCGAAACCTC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.97
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19872039 original size:28 final size:29
Alignment explanation
Indices: 19872003--19872057 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
19871993 TTAATTTAAG
*
19872003 ATATGAATT-TAATAAAATATTATATTTTT
1 ATATGAATTAAAATAAAAT-TTATATTTTT
*
19872032 ATAT-AATTAAAATATAATTTATATTT
1 ATATGAATTAAAATAAAATTTATATTT
19872058 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATGAATTAAAATAAAATTTATATTTTT
Found at i:19872059 original size:18 final size:18
Alignment explanation
Indices: 19872033--19872067 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19872023 TATATTTTTA
*
19872033 TATAATTAAAATATAATT
1 TATAATTAAAAAATAATT
*
19872051 TATATTTAAAAAATAAT
1 TATAATTAAAAAATAAT
19872068 ATTTTATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAATTAAAAAATAATT
Found at i:19875497 original size:134 final size:134
Alignment explanation
Indices: 19875061--19875533 Score: 519
Period size: 134 Copynumber: 3.6 Consensus size: 134
19875051 TACGACCATC
* * ** * * *
19875061 TTAGCAGCGTTTTTATCTTTGAAACGCCTCTAAATTAGTTGCATTTTTATGAGAAAAACG-CTAT
1 TTAGCAGCATTTGTATCTTTGAAACATCGCTAATTTAGTGGCATTTTTATGAGAAAAACGTC-AT
** * * * * *
19875125 TGCTTTTATGGCATTTATAACTGAAAATGCAACTACTTTAGGGGCATTTGTATCTGAAAATACCT
65 TGCTTTGGTGGCATTTATAACTGAAAATGCTATTACTTTAGAGGTATTTGTATTTGAAAATACCT
19875190 CTATA
130 CTATA
* * * * *
19875195 TTAACAACATTTGTATCTTTGATACATCGCTAATTTAGTGACA-TTTTATGAGAAAAACGTCGTT
1 TTAGCAGCATTTGTATCTTTGAAACATCGCTAATTTAGTGGCATTTTTATGAGAAAAACGTCATT
* * *
19875259 GCTTTGGTGGCATTTATAACTG-AAATG-TCTTACTTTAAAGGTGTTTGTATCTT-AAAATACCT
66 GCTTTGGTGGCATTTATAACTGAAAATGCTATTACTTTAGAGGTATTTGTAT-TTGAAAATACCT
*
19875321 CTATT
130 CTATA
* * * *
19875326 TTAGC-G-ATGTTTGTATCTTTGAGACACCACTAATTTAGTGGCGTTTTTATGAGAAAAACGTCA
1 TTAGCAGCA--TTTGTATCTTTGAAACATCGCTAATTTAGTGGCATTTTTATGAGAAAAACGTCA
* * *
19875389 TTGTTTTGGTGGCATTTGTAAATGAAAATGCTATTACTTTAGAGGTATTTGTATTTGAAAATACC
64 TTGCTTTGGTGGCATTTATAACTGAAAATGCTATTACTTTAGAGGTATTTGTATTTGAAAATACC
19875454 TCTATA
129 TCTATA
* * * *** **
19875460 TTAGCAGCATTTGTATCTTTGAAACGTCGTTACTTTAGTATTATTTTTATGAGAAAAACACCATT
1 TTAGCAGCATTTGTATCTTTGAAACATCGCTAATTTAGTGGCATTTTTATGAGAAAAACGTCATT
19875525 GCTTTGGTG
66 GCTTTGGTG
19875534 ATGTTTGTAT
Statistics
Matches: 278, Mismatches: 51, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
129 1 0.00
131 62 0.22
132 45 0.16
133 45 0.16
134 123 0.44
135 1 0.00
136 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (134 bp):
TTAGCAGCATTTGTATCTTTGAAACATCGCTAATTTAGTGGCATTTTTATGAGAAAAACGTCATT
GCTTTGGTGGCATTTATAACTGAAAATGCTATTACTTTAGAGGTATTTGTATTTGAAAATACCTC
TATA
Found at i:19878902 original size:14 final size:14
Alignment explanation
Indices: 19878885--19878919 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
19878875 TAATCAAGAA
19878885 AAATTCACAAGTGT
1 AAATTCACAAGTGT
19878899 AAATTCACAAGTGT
1 AAATTCACAAGTGT
19878913 AAATTCA
1 AAATTCA
19878920 TACTAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (14 bp):
AAATTCACAAGTGT
Found at i:19885037 original size:80 final size:80
Alignment explanation
Indices: 19884904--19885145 Score: 304
Period size: 80 Copynumber: 3.0 Consensus size: 80
19884894 TTAAATATTG
* * *
19884904 TGATTTGCTGAACCTTGTTGTATGATATTTTTTTGCTGAATGGTATTATATGATATTGAGGGGCT
1 TGATTTGCTGAACCTTGTTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGAGGGGTT
19884969 GAATCGTATGCTGAA
66 GAATCGTATGCTGAA
* * * * *
19884984 TGATTTGCTGAATCTTGTTGTATGATATTGTATTACCGAATGGTATTGTATGATATTGAGGGGTT
1 TGATTTGCTGAACCTTGTTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGAGGGGTT
* * *
19885049 GAATCATATACTAAA
66 GAATCGTATGCTGAA
** * * * * *
19885064 TTTTTTGCTGAACCTTATTGTCTGATATTATTTTGTTGAATGGTTTTGTATGATATTAAGGGGTT
1 TGATTTGCTGAACCTTGTTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGAGGGGTT
* *
19885129 GAATTGTATGTTGAA
66 GAATCGTATGCTGAA
19885144 TG
1 TG
19885146 GTGTTTCAGA
Statistics
Matches: 134, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 134 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.45
Consensus pattern (80 bp):
TGATTTGCTGAACCTTGTTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGAGGGGTT
GAATCGTATGCTGAA
Found at i:19890730 original size:2 final size:2
Alignment explanation
Indices: 19890723--19890768 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
19890713 AATAATCATC
* * *
19890723 AT AT AT AT AA AT AT AT AT GT AA 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
19890765 AT AT
1 AT AT
19890769 TACAAGGTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19890768 original size:12 final size:12
Alignment explanation
Indices: 19890723--19890767 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
19890713 AATAATCATC
19890723 ATATATATAAAT
1 ATATATATAAAT
*
19890735 ATATATGTAAAT
1 ATATATATAAAT
*
19890747 ATATATATATAT
1 ATATATATAAAT
19890759 ATATATATA
1 ATATATATA
19890768 TTACAAGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:19891185 original size:18 final size:18
Alignment explanation
Indices: 19891144--19891184 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19891134 AGCATAGAGT
*
19891144 TAAAATACTTTTATATTT
1 TAAAATACTTTTATATTC
*
19891162 TAAAATACTTTTGCTATTC
1 TAAAATACTTTT-ATATTC
19891181 TAAA
1 TAAA
19891185 TTATAAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAAATACTTTTATATTC
Found at i:19893035 original size:21 final size:22
Alignment explanation
Indices: 19893009--19893058 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
19892999 GTGGTAGCTG
*
19893009 TGAGATTAG-TTACTGTAATAA
1 TGAGATTAGAATACTGTAATAA
**
19893030 TGAGATT-GAATACTGTAATGG
1 TGAGATTAGAATACTGTAATAA
19893051 TGAGATTA
1 TGAGATTA
19893059 AAATTAGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (22 bp):
TGAGATTAGAATACTGTAATAA
Found at i:19894031 original size:18 final size:18
Alignment explanation
Indices: 19893993--19894030 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19893983 AAAATTTTTA
* *
19893993 TTTAAATTATTTTTAATT
1 TTTAAAATATTTATAATT
19894011 TTTAAAATATTTAT-ATT
1 TTTAAAATATTTATAATT
19894028 TTT
1 TTT
19894031 TCTACATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAAAATATTTATAATT
Found at i:19896074 original size:11 final size:11
Alignment explanation
Indices: 19896018--19896080 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 11
19896008 TTAAAAAAAA
19896018 AATGATTCTTG
1 AATGATTCTTG
* * *
19896029 -GTAATTTTTG
1 AATGATTCTTG
19896039 AA-GATTCTT-
1 AATGATTCTTG
* *
19896048 AAAGTTTCTT-
1 AATGATTCTTG
19896058 AATGATTCTTG
1 AATGATTCTTG
19896069 AATGATTCTTG
1 AATGATTCTTG
19896080 A
1 A
19896081 TCATATTATG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
9 2 0.05
10 26 0.65
11 12 0.30
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.48
Consensus pattern (11 bp):
AATGATTCTTG
Found at i:19896138 original size:18 final size:19
Alignment explanation
Indices: 19896100--19896138 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19896090 GGATAGTTGA
*
19896100 GATTTTCTTGAAAGTTCTT
1 GATTTTCTTGAAAGATCTT
*
19896119 GATTTTTTTGAAA-ATCTT
1 GATTTTCTTGAAAGATCTT
19896137 GA
1 GA
19896139 AATTCAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (19 bp):
GATTTTCTTGAAAGATCTT
Found at i:19900978 original size:12 final size:12
Alignment explanation
Indices: 19900961--19901000 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
19900951 GCATAAAATT
19900961 TATTATTATTAA
1 TATTATTATTAA
19900973 TATTATTATTAA
1 TATTATTATTAA
*
19900985 TAATATTATTATA
1 TATTATTATTA-A
19900998 TAT
1 TAT
19901001 ATTTTTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:19900980 original size:15 final size:15
Alignment explanation
Indices: 19900960--19900996 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
19900950 TGCATAAAAT
*
19900960 TTATTATTATTAATA
1 TTATTATTAATAATA
19900975 TTATTATTAATAATA
1 TTATTATTAATAATA
19900990 TTATTAT
1 TTATTAT
19900997 ATATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTAATAATA
Found at i:19902124 original size:144 final size:145
Alignment explanation
Indices: 19901933--19902238 Score: 352
Period size: 145 Copynumber: 2.1 Consensus size: 145
19901923 CAAGCTTAAG
** ***
19901933 AAGGTCAAATTACGAAAACACCCCTAAAAGGGTAATTTGTTAATTTCACACTTCCT-GGGTATTG
1 AAGGTCAAATTACGAAAACACCCCTAAAAGGGTAATTTAATAATTTCACACTTCCTAGGGTACCA
* * * *
19901997 CTATGATTTCAAATGCACAAAAAATCACAAAATATTATGATAGTAAGATCTAAAAAGTTTTACAA
66 CTATGATTTCAAATACACAAAAAATCACAAAATATTATGAAAGTAAAATCTAAAAAGTTTCACAA
19902062 AAATCTTAGCTCGAA
131 AAATCTTAGCTCGAA
* * * * * **
19902077 AAGGTTAAATTATGAAAATACCCCT-AAAGGTGTATTTTAATATTTTCACACTTTTTAGGGTACC
1 AAGGTCAAATTACGAAAACACCCCTAAAAGG-GTAATTTAATAATTTCACACTTCCTAGGGTACC
* * ** *
19902141 ATTATGATTTTAAATACACAAAAAATCATGAAATATTATGAAATTAAAATCTAAAAAGTTTCACA
65 ACTATGATTTCAAATACACAAAAAATCACAAAATATTATGAAAGTAAAATCTAAAAAGTTTCACA
*
19902206 AAAAT-TTGAGCT-TAGA
130 AAAATCTT-AGCTCGA-A
19902222 AAGGTCAAATTAC-AAAA
1 AAGGTCAAATTACGAAAA
19902239 TTACTCCTAA
Statistics
Matches: 134, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
143 5 0.04
144 48 0.36
145 81 0.60
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (145 bp):
AAGGTCAAATTACGAAAACACCCCTAAAAGGGTAATTTAATAATTTCACACTTCCTAGGGTACCA
CTATGATTTCAAATACACAAAAAATCACAAAATATTATGAAAGTAAAATCTAAAAAGTTTCACAA
AAATCTTAGCTCGAA
Found at i:19902225 original size:145 final size:143
Alignment explanation
Indices: 19901872--19902238 Score: 368
Period size: 144 Copynumber: 2.5 Consensus size: 143
19901862 TGAAAGCACC
* ** **
19901872 AAAAATCATGAAATATTAT-AGAATTGAGATCTGAAAAA-TTTCATGAAAATCCAAGCTTA-AGA
1 AAAAATCATGAAATATTATGA-AATTAAGATCT-AAAAAGTTTCACAAAAAT-TTAGCTTAGA-A
** ***
19901934 AGGTCAAATTACGAAAACACCCCTAAAAGGGTAATTTGTTAATTTCACACTTCCTGGGTATTGCT
62 AGGTCAAATTACGAAAACACCCCTAAAAGGGTAATTTAATAATTTCACACTTCCTGGGTACCACT
*
19901999 ATGATTTCAAATGCACA
127 ATGATTTCAAATACACA
** * * * *
19902016 AAAAATCACAAAATATTATGATAGTAAGATCTAAAAAGTTTTACAAAAATCTTAGC-TCGAAAAG
1 AAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCACAAAAAT-TTAGCTTAG-AAAG
* * * * * ** *
19902080 GTTAAATTATGAAAATACCCCT-AAAGGTGTATTTTAATATTTTCACACTTTTTAGGGTACCATT
64 GTCAAATTACGAAAACACCCCTAAAAGG-GTAATTTAATAATTTCACACTTCCT-GGGTACCACT
*
19902144 ATGATTTTAAATACACA
127 ATGATTTCAAATACACA
*
19902161 AAAAATCATGAAATATTATGAAATTAAAATCTAAAAAGTTTCACAAAAATTTGAGCTTAGAAAGG
1 AAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCACAAAAATTT-AGCTTAGAAAGG
19902226 TCAAATTAC-AAAA
65 TCAAATTACGAAAA
19902239 TTACTCCTAA
Statistics
Matches: 180, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
143 11 0.06
144 85 0.47
145 82 0.46
146 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (143 bp):
AAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCACAAAAATTTAGCTTAGAAAGGT
CAAATTACGAAAACACCCCTAAAAGGGTAATTTAATAATTTCACACTTCCTGGGTACCACTATGA
TTTCAAATACACA
Found at i:19910957 original size:104 final size:105
Alignment explanation
Indices: 19910825--19911020 Score: 279
Period size: 104 Copynumber: 1.9 Consensus size: 105
19910815 AAAAGTTAAC
* *
19910825 CATGAATATGATTTTCATGCATACATCACCTAACACATTGTTTCTTTTTAAATTTAATAAAAACA
1 CATGAATATGATTTTCATGAATACATCACCTAACACATTATTTCTTTTTAAATTTAATAAAAACA
19910890 ATGTATC-AGATGTA-ATTTAAAAAAATGTAATTAAGTAAG
66 ATGTATCAAG-TGTAGATTTAAAAAAATGTAATTAAGTAAG
* * ** * *
19910929 CATGGATATGATTTTCATGAATATATCACCTAATGCATTATTTCTTTTTATATTTAATAAAAATA
1 CATGAATATGATTTTCATGAATACATCACCTAACACATTATTTCTTTTTAAATTTAATAAAAACA
* *
19910994 ATGTGTCAAGTGTAGTTTTAAAAAAAT
66 ATGTATCAAGTGTAGATTTAAAAAAAT
19911021 AATTTAGTGA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
104 67 0.84
105 13 0.16
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39
Consensus pattern (105 bp):
CATGAATATGATTTTCATGAATACATCACCTAACACATTATTTCTTTTTAAATTTAATAAAAACA
ATGTATCAAGTGTAGATTTAAAAAAATGTAATTAAGTAAG
Found at i:19911115 original size:21 final size:20
Alignment explanation
Indices: 19911091--19911145 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
19911081 TTGAGTTTGT
19911091 TAATTAATTATTCAATAACAA
1 TAATTAATTATTCAAT-ACAA
* * *
19911112 TAATTTATTA-T-AATGCGA
1 TAATTAATTATTCAATACAA
19911130 TAATTAATTATTCAAT
1 TAATTAATTATTCAAT
19911146 TAATTAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 11 0.39
19 4 0.14
20 4 0.14
21 9 0.32
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATTAATTATTCAATACAA
Found at i:19918222 original size:16 final size:16
Alignment explanation
Indices: 19918201--19918235 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19918191 CAAAGCATCC
19918201 CAAAAGGCTTTAATCA
1 CAAAAGGCTTTAATCA
*
19918217 CAAAAGGCTTTAATGA
1 CAAAAGGCTTTAATCA
19918233 CAA
1 CAA
19918236 CATAGTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (16 bp):
CAAAAGGCTTTAATCA
Found at i:19919870 original size:143 final size:143
Alignment explanation
Indices: 19919610--19919876 Score: 333
Period size: 143 Copynumber: 1.9 Consensus size: 143
19919600 TCAAGTTATC
* * *
19919610 AAGCTTGACAACTTGCAAGCGTAGGAACTTAGTTGTCAAGCTTGATGACTTGCAAAGCTTGGATC
1 AAGCTTAACAACTTGCAAGCGTAGGAACTTAGTTGTCAAGCTTGATGACTGGCAAAGCTAGGATC
* * *
19919675 AGGCTTGCCTACATAAAAAATATGGTAAGGCTTTAGTTATCAACCCTTGGCACATTTCAGACTCC
66 AGGCTTACCTACATAAAAAATATGGTAAAGCTTTAGTTATCAACCCTCGGCACATTTCAGACTCC
19919740 GACTCAGGCTGTT
131 GACTCAGGCTGTT
* * * * * *
19919753 AAGCTTAACAACTTGCAAGCTTAGGAATTTAGTTGTCAAGGTTGCTTACTGGCAAAGCATAGAGT
1 AAGCTTAACAACTTGCAAGCGTAGGAACTTAGTTGTCAAGCTTGATGACTGGCAAAGC-TAG-GA
* ** * *
19919818 TGAGGCTTACCTAC-TTGAAAAT-TCGGTAAAGCTTTAGTTATCAA-GCTCGGCACCTTTCA
64 TCAGGCTTACCTACATAAAAAATAT-GGTAAAGCTTTAGTTATCAACCCTCGGCACATTTCA
19919877 AGCCTAAAAC
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
143 64 0.62
144 27 0.26
145 13 0.12
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (143 bp):
AAGCTTAACAACTTGCAAGCGTAGGAACTTAGTTGTCAAGCTTGATGACTGGCAAAGCTAGGATC
AGGCTTACCTACATAAAAAATATGGTAAAGCTTTAGTTATCAACCCTCGGCACATTTCAGACTCC
GACTCAGGCTGTT
Found at i:19920018 original size:105 final size:106
Alignment explanation
Indices: 19919891--19920107 Score: 260
Period size: 105 Copynumber: 2.1 Consensus size: 106
19919881 TAAAACTTAT
* * *
19919891 GTTGTCAAAGCTTGACAACTTGCAAGCTTAGAGACTTAATTGGT-AAGTTGGCATCTTGCAAACT
1 GTTGTCAAAGCTTGACAACTTGCAAGCTTAAAGACTTAATT-GTCAAATTGGCATCTCGCAAACT
** * * * *
19919955 AAGCTTTCAAGCTTGTTTACTTGTAAATTCAGTAGTGCCTAA
65 AAAATTTCAAGCTTGTCTACTTGTAAATCCAGTAATGCATAA
* * **
19919997 GTTGTC-AAGCTTGATC-ACTTGCAAGCTTAAAGAGTTAATTGTCAAATTGGTATCTCGTGAACT
1 GTTGTCAAAGCTTGA-CAACTTGCAAGCTTAAAGACTTAATTGTCAAATTGGCATCTCGCAAACT
* *
19920060 AAAATTTTAAGCTTGTCTACTTGTAAATCCGGTAATGCATAA
65 AAAATTTCAAGCTTGTCTACTTGTAAATCCAGTAATGCATAA
19920102 GTTGTC
1 GTTGTC
19920108 TAGTTGTGAT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
104 2 0.02
105 85 0.90
106 7 0.07
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (106 bp):
GTTGTCAAAGCTTGACAACTTGCAAGCTTAAAGACTTAATTGTCAAATTGGCATCTCGCAAACTA
AAATTTCAAGCTTGTCTACTTGTAAATCCAGTAATGCATAA
Found at i:19920828 original size:17 final size:17
Alignment explanation
Indices: 19920808--19920859 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
19920798 ATTAGTTTAC
19920808 TTAATAAATAAATATAT
1 TTAATAAATAAATATAT
* *
19920825 TTAATAATTTAATTATAT
1 TTAATAA-ATAAATATAT
19920843 TTATTATAAAATAAATA
1 TTA--AT-AAATAAATA
19920860 AAATGTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.26
18 11 0.41
20 7 0.26
21 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATAAATAAATATAT
Found at i:19921222 original size:17 final size:17
Alignment explanation
Indices: 19921201--19921239 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
19921191 AATATTGAAA
19921201 ATTTTTCAAT-AATTTT
1 ATTTTTCAATGAATTTT
**
19921217 ATTTTTCAATGTGTTTT
1 ATTTTTCAATGAATTTT
19921234 ATTTTT
1 ATTTTT
19921240 TTCATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (17 bp):
ATTTTTCAATGAATTTT
Found at i:19929182 original size:10 final size:10
Alignment explanation
Indices: 19929167--19929192 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19929157 TAGGCCTTAC
19929167 AAAAAAAGAA
1 AAAAAAAGAA
19929177 AAAAAAAGAA
1 AAAAAAAGAA
19929187 AAAAAA
1 AAAAAA
19929193 TTAATTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:19933664 original size:149 final size:147
Alignment explanation
Indices: 19933234--19933758 Score: 486
Period size: 149 Copynumber: 3.5 Consensus size: 147
19933224 TAGAATCCCA
* * * * * *
19933234 AGAATTTAAGAAAGTAGATTACTAAAGATGAAGTCAAATATTTCAAAAAAAATTAAAAAATAACA
1 AGAATTTAAGAAAGTAGAATGCTAAAAATGAAGTCAAATGTTT-AAAAAAAA--AAGAAA-AGCA
* ** * *
19933299 AAGAAAGAAAGACATACACATAAAAAATGAGAGTCTAGGGTAAAAAGTGAATAAAGCTTCAGTTA
62 AAGAAAGAAAGACATGCACATTGAAAATGAGAGTCTAGGGCAAAAAGTGAATAAAGCATCAGTTA
19933364 GAA-TCTCAAGTGAAAAAAAAAGAT
127 GAATTC-CAAGT---AAAAAAAGAT
* * * * * * * *
19933388 AGAATTCAAGAAACTAGAATGCTAAAATTGAAGTTAGATGTTTTTAAAAAAGAA-AAAAGCAAAA
1 AGAATTTAAGAAAGTAGAATGCTAAAAATGAAGTCAAATG-TTTAAAAAAAAAAGAAAAGCAAAG
* * * * * * * * * * * *
19933452 AAATAAATACAGGCACCTTGGAGATAAGAATCTATGGCAAAAGGTGAATAAA-AATTTAGTTAGA
65 AAAGAAAGACATGCACATTGAAAATGAGAGTCTAGGGCAAAAAGTGAATAAAGCA-TCAGTTAGA
*
19933516 ATTCCAAGTAAAAAAATGGT
129 ATTCCAAGTAAAAAAA-GAT
*
19933536 AGAATTTAAGAAAGTAAAATGCTAAAAATGAAGTCAAATGTTTAAAAGAAAAAAGAAAAGCAAAG
1 AGAATTTAAGAAAGTAGAATGCTAAAAATGAAGTCAAATGTTTAAAA-AAAAAAGAAAAGCAAAG
* * *
19933601 AAAGAAAGACATGCACATTGAAAACGAGAGTTTAGGGCAAAAAGTGAATAAAGCATCAATTAGAA
65 AAAGAAAGACATGCACATTGAAAATGAGAGTCTAGGGCAAAAAGTGAATAAAGCATCAGTTAGAA
*
19933666 TCCCAAGTAAAAAGAAGAT
130 TTCCAAGTAAAAA-AAGAT
** * * * * *
19933685 AGAATTTAAGAAAACAGAATGCTAAAATTGAAGTTAAATGTTCCAAAAAAGAAAG--AA-TAAAG
1 AGAATTTAAGAAAGTAGAATGCTAAAAATGAAGTCAAATGTT-TAAAAAAAAAAGAAAAGCAAAG
19933747 AAAGAAAGACAT
65 AAAGAAAGACAT
19933759 ATGGCTTTTC
Statistics
Matches: 297, Mismatches: 65, Indels: 26
0.77 0.17 0.07
Matches are distributed among these distances:
146 16 0.05
147 15 0.05
148 41 0.14
149 114 0.38
150 64 0.22
151 5 0.02
152 2 0.01
154 37 0.12
155 3 0.01
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.20
Consensus pattern (147 bp):
AGAATTTAAGAAAGTAGAATGCTAAAAATGAAGTCAAATGTTTAAAAAAAAAAGAAAAGCAAAGA
AAGAAAGACATGCACATTGAAAATGAGAGTCTAGGGCAAAAAGTGAATAAAGCATCAGTTAGAAT
TCCAAGTAAAAAAAGAT
Found at i:19934976 original size:26 final size:26
Alignment explanation
Indices: 19934918--19934977 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
19934908 TTACATCATC
** *
19934918 TACATCATAATCAAGGCATTTGTAAT
1 TACATCATAAGAAAGACATTTGTAAT
* *
19934944 TATATCATAAGAAAGACATTTGTATT
1 TACATCATAAGAAAGACATTTGTAAT
*
19934970 TGCATCAT
1 TACATCAT
19934978 TGCATTTGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (26 bp):
TACATCATAAGAAAGACATTTGTAAT
Found at i:19935414 original size:18 final size:18
Alignment explanation
Indices: 19935393--19935436 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19935383 AAAAAAATTT
*
19935393 AAAAAA-AAAAATAGCAA
1 AAAAAAGAAAAAAAGCAA
*
19935410 AAAAAAGAAAAAAAGTAA
1 AAAAAAGAAAAAAAGCAA
19935428 AAAAAAGAA
1 AAAAAAGAA
19935437 GAAGAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (18 bp):
AAAAAAGAAAAAAAGCAA
Found at i:19936502 original size:53 final size:53
Alignment explanation
Indices: 19936428--19936549 Score: 124
Period size: 53 Copynumber: 2.3 Consensus size: 53
19936418 ATGTTTTAAA
* * * * *
19936428 TTTTGAAAGTTCCAAAGCCTCT-TTTATAG-GGAGCAATTTTTAGGCAAGATT-
1 TTTTTAAAGTTTCAAAACCTCTATTT-TAGAGGAGCAATTTTCAAGCAAGATTC
* * *
19936479 TATTTCTAAAGTTTCAAAACCTCTATTTTTGAGGTGCAATTTTCAAGTAAGATTC
1 T-TTT-TAAAGTTTCAAAACCTCTATTTTAGAGGAGCAATTTTCAAGCAAGATTC
19936534 TTTTTAAAGTTTCAAA
1 TTTTTAAAGTTTCAAA
19936550 GCCTTTGATT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
51 1 0.02
52 3 0.05
53 29 0.50
54 24 0.41
55 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (53 bp):
TTTTTAAAGTTTCAAAACCTCTATTTTAGAGGAGCAATTTTCAAGCAAGATTC
Found at i:19936897 original size:20 final size:19
Alignment explanation
Indices: 19936853--19936919 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
19936843 TAAATTTGTT
19936853 AAAAAAAAAACAAAAATCA
1 AAAAAAAAAACAAAAATCA
*
19936872 AGAAAACAAAACATAAAA-CA
1 A-AAAAAAAAACA-AAAATCA
**
19936892 AAAAAAAAGAA-AAAACCCA
1 AAAAAAAA-AACAAAAATCA
19936911 AAAAAAAAA
1 AAAAAAAAA
19936920 TTTTGAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 15 0.37
21 4 0.10
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAACAAAAATCA
Found at i:19940517 original size:71 final size:71
Alignment explanation
Indices: 19940401--19940557 Score: 217
Period size: 71 Copynumber: 2.2 Consensus size: 71
19940391 TGACACTTTC
* *
19940401 TAAAGGTTCAATTGACTATAATTCAGAGATTAATTGATTCAATTTTTTCATGTGACTAGATTTCA
1 TAAAGGTTCAATTGACTATAATTCAGAGATTAATTGATTCAATTTTGTCATGTAACTAGATTTCA
19940466 TCCAAT
66 TCCAAT
* * * *
19940472 TAAAGGCTCAATTGACTATAATTTAGAGATTTACTT-ATTCAATTTTGTCATGTAACTAGATTTT
1 TAAAGGTTCAATTGACTATAATTCAGAGA-TTAATTGATTCAATTTTGTCATGTAACTAGATTTC
* **
19940536 GTTTAAT
65 ATCCAAT
19940543 TAAAGGTTCAATTGA
1 TAAAGGTTCAATTGA
19940558 GTTTAAATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
71 70 0.93
72 5 0.07
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (71 bp):
TAAAGGTTCAATTGACTATAATTCAGAGATTAATTGATTCAATTTTGTCATGTAACTAGATTTCA
TCCAAT
Found at i:19942980 original size:19 final size:19
Alignment explanation
Indices: 19942942--19942980 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19942932 TTTGAAAATA
** *
19942942 TTTTTAAAAAATTAATTTT
1 TTTTTAAAAAAGAAAATTT
19942961 TTTTTAAAAAAGAAAATTT
1 TTTTTAAAAAAGAAAATTT
19942980 T
1 T
19942981 ATCAACATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAAAGAAAATTT
Found at i:19943048 original size:56 final size:56
Alignment explanation
Indices: 19942980--19943088 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 56
19942970 AAGAAAATTT
19942980 TATCAACATATTT-AAGAATTTTAAACTTTAAAAATAAATTTAG-AAATAAAAAAACC
1 TATCAACATATTTGAAG-ATTTTAAACTTTAAAAAT-AATTTAGAAAATAAAAAAACC
* * * *
19943036 TATCAATATATTTGAAGGTTTTAAATTTTAAAAATAATTTTGAAAATAAAAAA
1 TATCAACATATTTGAAGATTTTAAACTTTAAAAATAATTTAGAAAATAAAAAA
19943089 CTTTACCAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
55 6 0.13
56 38 0.81
57 3 0.06
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (56 bp):
TATCAACATATTTGAAGATTTTAAACTTTAAAAATAATTTAGAAAATAAAAAAACC
Found at i:19943189 original size:24 final size:25
Alignment explanation
Indices: 19943162--19943208 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
19943152 TATTAAAAGG
*
19943162 TTTTTGAGATTTT-AAAAAATAATA
1 TTTTTGAAATTTTGAAAAAATAATA
*
19943186 TTTTTGAAATTTTGGAAAAATAA
1 TTTTTGAAATTTTGAAAAAATAA
19943209 AATCTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (25 bp):
TTTTTGAAATTTTGAAAAAATAATA
Found at i:19944383 original size:46 final size:46
Alignment explanation
Indices: 19944330--19944418 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
19944320 ATCTCTAAAG
**
19944330 TTTTGAATATGAATATTTGA-GTTTTGGATGTAAATCTCTTAAAAAT
1 TTTTGAATACAAATATTTGATGTTTTGG-TGTAAATCTCTTAAAAAT
* * *
19944376 TTTTGAATGCAAATCTTTGATTTTTTGGTGTAAATCTCTTAAA
1 TTTTGAATACAAATATTTGATGTTTTGGTGTAAATCTCTTAAA
19944419 TTTCTCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 31 0.84
47 6 0.16
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (46 bp):
TTTTGAATACAAATATTTGATGTTTTGGTGTAAATCTCTTAAAAAT
Found at i:19944421 original size:23 final size:23
Alignment explanation
Indices: 19944351--19944421 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 23
19944341 AATATTTGAG
*
19944351 TTTTGGATGTAAATCTCTTAAAAAT
1 TTTTGG-TGTAAATCTCTT-AAATT
* * *
19944376 TTTTGAATGCAAATCT-TT-GATT
1 TTTTG-GTGTAAATCTCTTAAATT
19944398 TTTTGGTGTAAATCTCTTAAATT
1 TTTTGGTGTAAATCTCTTAAATT
19944421 T
1 T
19944422 CTCAAATGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
21 8 0.22
22 9 0.25
23 4 0.11
24 2 0.06
25 13 0.36
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTTGGTGTAAATCTCTTAAATT
Found at i:19944445 original size:46 final size:46
Alignment explanation
Indices: 19944339--19944485 Score: 115
Period size: 45 Copynumber: 3.2 Consensus size: 46
19944329 GTTTTGAATA
* **
19944339 TGAATATTTGA-GTTTTGGATGTAAATCTCTTAAAAATTTTTGAATG
1 TGAATATTTGATTTTTTGGATGTAAATCTCTT-AAAATTTTCAAATG
** *
19944385 CAAATCTTTGATTTTTTGG-TGTAAATCTCTT-AAATTTCTCAAATG
1 TGAATATTTGATTTTTTGGATGTAAATCTCTTAAAATTT-TCAAATG
* * * *
19944430 TGAATATTTGA-ATTTTAGATTTGAATCT-TTAAAATTTCTCTCAAATG
1 TGAATATTTGATTTTTTGGATGTAAATCTCTTAAAA-TT-T-TCAAATG
*
19944477 CGAATATTT
1 TGAATATTT
19944486 AAATTTTATA
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
44 13 0.16
45 23 0.28
46 22 0.27
47 23 0.28
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (46 bp):
TGAATATTTGATTTTTTGGATGTAAATCTCTTAAAATTTTCAAATG
Found at i:19944485 original size:47 final size:47
Alignment explanation
Indices: 19944421--19944606 Score: 166
Period size: 47 Copynumber: 4.0 Consensus size: 47
19944411 CTCTTAAATT
* *
19944421 TCTCAAATGTGAATATTTGAATTTTAGATTTGAATCTTTAAAATTTC
1 TCTCAAATGCGAATATTTGAATTTTAGATATGAATCTTTAAAATTTC
* * * *
19944468 TCTCAAATGCGAATATTTAAATTTT--ATATGTAAGTCTTCAAAGTTCC
1 TCTCAAATGCGAATATTTGAATTTTAGATATG-AA-TCTTTAAAATTTC
* * * * *
19944515 TTTCAAATGCGAATATTGGAATTTTAAATAGGAATCTTTAAAAAATT-
1 TCTCAAATGCGAATATTTGAATTTTAGATATGAATCTTT-AAAATTTC
* * * * *
19944562 T-TCAAATGTGAATTTTTGAAATTTAGATATAAATC-TTGAAATTTC
1 TCTCAAATGCGAATATTTGAATTTTAGATATGAATCTTTAAAATTTC
19944607 ATTTGTGAAT
Statistics
Matches: 110, Mismatches: 23, Indels: 14
0.75 0.16 0.10
Matches are distributed among these distances:
44 5 0.05
45 6 0.05
46 29 0.26
47 60 0.55
48 6 0.05
49 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (47 bp):
TCTCAAATGCGAATATTTGAATTTTAGATATGAATCTTTAAAATTTC
Found at i:19944724 original size:20 final size:20
Alignment explanation
Indices: 19944593--19944734 Score: 70
Period size: 20 Copynumber: 7.3 Consensus size: 20
19944583 TTTAGATATA
19944593 AATC-TTGAAATTTCATTTGTG
1 AATCTTTGAAA-TT-ATTTGTG
* * **
19944614 AATCTTAGAAAATATTTGCA
1 AATCTTTGAAATTATTTGTG
*
19944634 AATCTTT-AAA--A-TAGTG
1 AATCTTTGAAATTATTTGTG
*
19944650 AAT-TTTTAAATTTATTTGTG
1 AATCTTTGAAA-TTATTTGTG
**
19944670 AATCTTT-AAA--A-TTGCA
1 AATCTTTGAAATTATTTGTG
*
19944686 AAACTTTGAAATTTTATTTGTG
1 AATCTTTGAAA--TTATTTGTG
**
19944708 AATCTTTGAAATTATTTACG
1 AATCTTTGAAATTATTTGTG
19944728 AATCTTT
1 AATCTTT
19944735 ACAATTGCAA
Statistics
Matches: 91, Mismatches: 17, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
15 3 0.03
16 17 0.19
17 5 0.05
19 4 0.04
20 35 0.38
21 9 0.10
22 18 0.20
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (20 bp):
AATCTTTGAAATTATTTGTG
Found at i:19944731 original size:58 final size:58
Alignment explanation
Indices: 19944647--19944771 Score: 164
Period size: 58 Copynumber: 2.2 Consensus size: 58
19944637 CTTTAAAATA
* **
19944647 GTGAAT-TTTTAAATTTATTTGTGAATCTTTAAAATTGCAAAACTTTGAAATTTTATTT
1 GTGAATCTTTGAAATTTATTTACGAATCTTTAAAATTGCAAAACTTTG-AATTTTATTT
* *
19944705 GTGAATCTTTGAAA-TTATTTACGAATCTTTACAATTGCAAATCTTTGAATTTTATTT
1 GTGAATCTTTGAAATTTATTTACGAATCTTTAAAATTGCAAAACTTTGAATTTTATTT
**
19944762 GAAAATCTTT
1 GTGAATCTTT
19944772 ATAATTGCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 18 0.31
58 35 0.59
59 6 0.10
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (58 bp):
GTGAATCTTTGAAATTTATTTACGAATCTTTAAAATTGCAAAACTTTGAATTTTATTT
Found at i:19944793 original size:95 final size:94
Alignment explanation
Indices: 19944597--19944874 Score: 313
Period size: 95 Copynumber: 2.9 Consensus size: 94
19944587 GATATAAATC
* * * * * * ** *
19944597 TTGAAATTTCATTTGTGAATCTTAGAAAATATTTGCAAATCTTTAAAATAGTGAATTTTTAAATT
1 TTGAAATTTCATTTGTGAATCTTTGAAATTATTTACGAATCTTTACAATTGCAAATTTTGAAATT
**
19944662 TATTTGTGAATCTTTAAAATTGCAAAACT
66 TATTTGAAAATCTTTAAAATTGCAAAACT
* *
19944691 TTGAAATTTTATTTGTGAATCTTTGAAATTATTTACGAATCTTTACAATTGCAAATCTTTGAATT
1 TTGAAATTTCATTTGTGAATCTTTGAAATTATTTACGAATCTTTACAATTGCAAAT-TTTGAAAT
*
19944756 TTATTTGAAAATCTTTATAATTGCAAAACT
65 TTATTTGAAAATCTTTAAAATTGCAAAACT
* * ** **
19944786 TTGAAATTTCATTTGTGAATCTGTGATATTATTTTTGAATCTTTACAATTTTTAAAATTTTGAAA
1 TTGAAATTTCATTTGTGAATCTTTGAAATTATTTACGAATCTTTACAA--TTGCAAATTTTGAAA
** *
19944851 TTTCATTTGTGAATTTTTAAAATT
64 TTT-ATTTGAAAATCTTTAAAATT
19944875 ATTTACGAAT
Statistics
Matches: 154, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
94 47 0.31
95 76 0.49
96 9 0.06
97 22 0.14
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (94 bp):
TTGAAATTTCATTTGTGAATCTTTGAAATTATTTACGAATCTTTACAATTGCAAATTTTGAAATT
TATTTGAAAATCTTTAAAATTGCAAAACT
Found at i:19944807 original size:38 final size:37
Alignment explanation
Indices: 19944711--19944807 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
19944701 ATTTGTGAAT
*
19944711 CTTTGAAA-TTATTT-ACGAATCTTTACAATTGCAAAT
1 CTTTGAAATTTATTTGA-GAATCTTTACAATTGCAAAA
* * *
19944747 CTTTGAATTTTATTTGAAAATCTTTATAATTGCAAAA
1 CTTTGAAATTTATTTGAGAATCTTTACAATTGCAAAA
*
19944784 CTTTGAAATTTCATTTGTGAATCT
1 CTTTGAAATTT-ATTTGAGAATCT
19944808 GTGATATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
36 7 0.14
37 33 0.65
38 11 0.22
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (37 bp):
CTTTGAAATTTATTTGAGAATCTTTACAATTGCAAAA
Found at i:19944874 original size:154 final size:154
Alignment explanation
Indices: 19944661--19944989 Score: 480
Period size: 154 Copynumber: 2.1 Consensus size: 154
19944651 ATTTTTAAAT
* * *
19944661 TTATTTGTGAATCTTTA-AAATTGCAAAACTTTGAAATTTTATTTGTGAATCTTTGAAATTATTT
1 TTATTTGTGAATCTTTACAATTTGCAAAACTTTGAAATTTCATTTGTGAATCTTTAAAATTATTT
* * * * * *
19944725 ACGAATCTTTACAATTGCAAATCTTTGAATTTTATTTGAAAATCTTTATAATTGCAAAACTTTGA
66 ACGAATCTTCACAATTGCAAATCATTGAATTTTATTTGAAAATATTCAAAATTACAAAACTTTGA
*
19944790 AATTTCATTTGTGAATCTGTGATA
131 AATTTCATTTGTGAATCTGTGAAA
* ** * *
19944814 TTATTTTTGAATCTTTACAATTTTTAAAATTTTGAAATTTCATTTGTGAATTTTTAAAATTATTT
1 TTATTTGTGAATCTTTACAATTTGCAAAACTTTGAAATTTCATTTGTGAATCTTTAAAATTATTT
* * *
19944879 ACGAATCTTCACAATTGTAAATCATTGAATTTTGTTTGCAAATATTCAAAATTACAAAACTTTGA
66 ACGAATCTTCACAATTGCAAATCATTGAATTTTATTTGAAAATATTCAAAATTACAAAACTTTGA
*
19944944 AATTTCATTTGTGAATCTTTGAAA
131 AATTTCATTTGTGAATCTGTGAAA
19944968 TTATTTGTGAATCTTTACAATT
1 TTATTTGTGAATCTTTACAATT
19944990 GTGAATCTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
153 16 0.10
154 139 0.90
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (154 bp):
TTATTTGTGAATCTTTACAATTTGCAAAACTTTGAAATTTCATTTGTGAATCTTTAAAATTATTT
ACGAATCTTCACAATTGCAAATCATTGAATTTTATTTGAAAATATTCAAAATTACAAAACTTTGA
AATTTCATTTGTGAATCTGTGAAA
Found at i:19944876 original size:59 final size:59
Alignment explanation
Indices: 19944780--19944894 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
19944770 TTATAATTGC
* * ** *
19944780 AAAACTTTGAAATTTCATTTGTGAATCTGTGATATTATTTTTGAATCTTTACAATTTTT
1 AAAACTTTGAAATTTCATTTGTGAATCTGTAAAATTATTTACGAATCTTCACAATTTTT
* * *
19944839 AAAATTTTGAAATTTCATTTGTGAATTTTTAAAATTATTTACGAATCTTCACAATT
1 AAAACTTTGAAATTTCATTTGTGAATCTGTAAAATTATTTACGAATCTTCACAATT
19944895 GTAAATCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (59 bp):
AAAACTTTGAAATTTCATTTGTGAATCTGTAAAATTATTTACGAATCTTCACAATTTTT
Found at i:19944975 original size:20 final size:22
Alignment explanation
Indices: 19944938--19944983 Score: 78
Period size: 20 Copynumber: 2.2 Consensus size: 22
19944928 AATTACAAAA
19944938 CTTTGAAATTTCATTTGTGAAT
1 CTTTGAAATTTCATTTGTGAAT
19944960 CTTTGAAA-TT-ATTTGTGAAT
1 CTTTGAAATTTCATTTGTGAAT
19944980 CTTT
1 CTTT
19944984 ACAATTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.58
21 2 0.08
22 8 0.33
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (22 bp):
CTTTGAAATTTCATTTGTGAAT
Found at i:19944993 original size:16 final size:15
Alignment explanation
Indices: 19944972--19945019 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
19944962 TTGAAATTAT
19944972 TTGTGAATCTTTACAA
1 TTGTGAATCTTTA-AA
19944988 TTGTGAATC-TTATAA
1 TTGTGAATCTTTA-AA
*
19945003 TTGCGAATCTTTAAA
1 TTGTGAATCTTTAAA
19945018 TT
1 TT
19945020 TTATTTGCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (15 bp):
TTGTGAATCTTTAAA
Found at i:19945027 original size:21 final size:21
Alignment explanation
Indices: 19945003--19945078 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
19944993 AATCTTATAA
19945003 TTGCGAATCTTTAAATTTTAT
1 TTGCGAATCTTTAAATTTTAT
*
19945024 TTGCGAATCTCTAAA----AT
1 TTGCGAATCTTTAAATTTTAT
*
19945041 TT-CGAATCTTTGAATTTTAT
1 TTGCGAATCTTTAAATTTTAT
19945061 TTGTC-AATCTTTATAATT
1 TTG-CGAATCTTTA-AATT
19945079 GAAAATCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
16 10 0.23
17 4 0.09
20 4 0.09
21 21 0.48
22 5 0.11
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (21 bp):
TTGCGAATCTTTAAATTTTAT
Found at i:19945086 original size:37 final size:37
Alignment explanation
Indices: 19944988--19945079 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
19944978 ATCTTTACAA
*
19944988 TTGTGAATC-TTATAATTGCGAATCTTTAAATTTTAT
1 TTGTCAATCTTTATAATTGCGAATCTTTAAATTTTAT
* * * *
19945024 TTG-CGAATCTCTAAAATTTCGAATCTTTGAATTTTAT
1 TTGTC-AATCTTTATAATTGCGAATCTTTAAATTTTAT
19945061 TTGTCAATCTTTATAATTG
1 TTGTCAATCTTTATAATTG
19945080 AAAATCTATA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
36 7 0.16
37 37 0.82
38 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (37 bp):
TTGTCAATCTTTATAATTGCGAATCTTTAAATTTTAT
Found at i:19945165 original size:21 final size:20
Alignment explanation
Indices: 19945141--19945187 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
19945131 ATTTTTTAAC
*
19945141 TCTTTTCCAAATCTTTGGATT
1 TCTTTTCC-AATCTTAGGATT
*
19945162 TCTTTGGCCAATCTTAGGATT
1 TCTTT-TCCAATCTTAGGATT
19945183 T-TTTT
1 TCTTTT
19945188 TGGTGAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.14
21 17 0.77
22 2 0.09
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (20 bp):
TCTTTTCCAATCTTAGGATT
Found at i:19945228 original size:21 final size:21
Alignment explanation
Indices: 19945192--19945257 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
19945182 TTTTTTTGGT
*
19945192 GAATCTTTGAAC-TCTTTTGC
1 GAATCTTTAAACTTCTTTTGC
19945212 GAATCTTTAAACTTCTTTTGC
1 GAATCTTTAAACTTCTTTTGC
* *
19945233 AAATCTTTAAATCTT-TTTTGT
1 GAATCTTTAAA-CTTCTTTTGC
19945254 GAAT
1 GAAT
19945258 TTTGAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.28
21 26 0.65
22 3 0.08
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (21 bp):
GAATCTTTAAACTTCTTTTGC
Found at i:19945228 original size:63 final size:62
Alignment explanation
Indices: 19945119--19945263 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 62
19945109 TATTTATTTA
* * ** * * *
19945119 TTTTTTTGGTAAATTTTTTAACTCTTTTCCAAATCTTTGGATTTCTTTGGCCAATC-TTAGGAT
1 TTTTTTTGGTGAA-TTTTGAACTCTTTTCCAAATCTTTAAACTTCTTTGGCAAATCTTTA-AAT
* * *
19945182 TTTTTTTGGTGAATCTTTGAACTCTTTTGCGAATCTTTAAACTTCTTTTGCAAATCTTTAAAT
1 TTTTTTTGGTGAAT-TTTGAACTCTTTTCCAAATCTTTAAACTTCTTTGGCAAATCTTTAAAT
*
19945245 CTTTTTT-GTGAATTTTGAA
1 TTTTTTTGGTGAATTTTGAA
19945264 TATTTACGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
61 6 0.09
62 7 0.10
63 53 0.77
64 3 0.04
ACGTcount: A:0.22, C:0.13, G:0.12, T:0.52
Consensus pattern (62 bp):
TTTTTTTGGTGAATTTTGAACTCTTTTCCAAATCTTTAAACTTCTTTGGCAAATCTTTAAAT
Found at i:19945818 original size:1 final size:1
Alignment explanation
Indices: 19945773--19945799 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
19945763 AGGAAAAATG
19945773 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
19945800 CGAAAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19947519 original size:16 final size:16
Alignment explanation
Indices: 19947498--19947555 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
19947488 TGGTAATGTA
19947498 AAAAAAATATTATTAT
1 AAAAAAATATTATTAT
*
19947514 AAAAAAATAATT-TTAA
1 AAAAAAAT-ATTATTAT
* * *
19947530 ACAAAAAATGTTAATGT
1 A-AAAAAATATTATTAT
19947547 AAAAAAATA
1 AAAAAAATA
19947556 AGAGTAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAAAAATATTATTAT
Found at i:19949228 original size:16 final size:15
Alignment explanation
Indices: 19949196--19949225 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19949186 AAAAAAATAG
19949196 TATTATAAATAAAAA
1 TATTATAAATAAAAA
*
19949211 TATTCTAAATAAAAA
1 TATTATAAATAAAAA
19949226 ATAAGTGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TATTATAAATAAAAA
Found at i:19949434 original size:18 final size:18
Alignment explanation
Indices: 19949394--19949445 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
19949384 TTAAATTGAC
19949394 AAATAAAAAAATATTATTAT
1 AAATAAAAAAATA--ATTAT
*
19949414 AAATAAAAAAATAATTCT
1 AAATAAAAAAATAATTAT
**
19949432 AAATGTAAAAATAA
1 AAATAAAAAAATAA
19949446 GTGTTAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.55
20 13 0.45
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAAAAAAATAATTAT
Found at i:19949441 original size:19 final size:19
Alignment explanation
Indices: 19949419--19949463 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
19949409 ATTATAAATA
*
19949419 AAAAAATAATTCTAAATGT
1 AAAAAATAAGTCTAAATGT
* *
19949438 -AAAAATAAGTGTTAATGT
1 AAAAAATAAGTCTAAATGT
19949456 AAAAAATA
1 AAAAAATA
19949464 TGAGAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (19 bp):
AAAAAATAAGTCTAAATGT
Found at i:19949748 original size:285 final size:282
Alignment explanation
Indices: 19949247--19949767 Score: 676
Period size: 285 Copynumber: 1.8 Consensus size: 282
19949237 AGTAAAAAAA
* * * * * *
19949247 TAAAAATAATCGTAAAATTGGTATAATTTGGTGGAAAATATGTTTGAAGTGTCATAATATTTAAG
1 TAAAAATAATCATAAAATTAGTATAATTTGGTGGAAAATATGTTAGAACTATCATAACATTTAAG
* * ** *
19949312 AAAAAGTTATGATAATTCTAAATATAATAAAATTAGGAACAAACGTAACAAATTTTATTGTAATG
66 AAAAAGTTATGATAATTCTAAATATAATAAAATTAAGAACAAACGTAAAAAAAATTATTGTAACG
19949377 TAAATAATTAAATTGACAAATAAAAAAATATTATTATAAATAAAAAAATAATTCTAAATGTAAAA
131 TAAATAATTAAATTGACAAATAAAAAAATATTATTATAAATAAAAAAATAATTC-AAA-GTAAAA
* * *
19949442 ATAAGTGTTAATGTAAAAAATATGAGAATAATCATAAAATTGGTGTAATTTAACGTAAAATATGT
194 AAAAATATTAATGTAAAAAATATGAGAATAATCATAAAATTGGTGTAATTTAACGTAAAATATGT
19949507 TAAAAGTATCGTAACATAATGAGG
259 TAAAAGTATCGTAACATAATGAGG
* * * *
19949531 TAAAAATCATCATAAAATTAGTATCATTTGGTGTAAAATATGTTAGGACTAT-AGTAACATTCTA
1 TAAAAATAATCATAAAATTAGTATAATTTGGTGGAAAATATGTTAGAACTATCA-TAACATT-TA
* * * * * *
19949595 AGGAAGAGTTATGATAATTCTAAA-AGTAATGAAATATAAGAATAAGCGTAAAAAAAATTATTTT
64 AGAAAAAGTTATGATAATTCTAAATA-TAATAAAAT-TAAGAACAAACGTAAAAAAAATTATTGT
19949659 AACGTAAATAATTAAATTGACAACATAAAAGAATTATTATTATTATAAAT-AAAAAATAATTC-A
127 AACGTAAATAATTAAATTGACAA-ATAAAA-AA--A-TATTATTATAAATAAAAAAATAATTCAA
*
19949722 A-TAAAAAAAAATATTTATGT-AAAAATATGAGAATAATCATAAAATT
187 AGTAAAAAAAAATATTAATGTAAAAAATATGAGAATAATCATAAAATT
19949768 TGTATCATTT
Statistics
Matches: 203, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
283 1 0.00
284 50 0.25
285 58 0.29
286 58 0.29
287 6 0.03
288 4 0.02
290 13 0.06
291 13 0.06
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (282 bp):
TAAAAATAATCATAAAATTAGTATAATTTGGTGGAAAATATGTTAGAACTATCATAACATTTAAG
AAAAAGTTATGATAATTCTAAATATAATAAAATTAAGAACAAACGTAAAAAAAATTATTGTAACG
TAAATAATTAAATTGACAAATAAAAAAATATTATTATAAATAAAAAAATAATTCAAAGTAAAAAA
AAATATTAATGTAAAAAATATGAGAATAATCATAAAATTGGTGTAATTTAACGTAAAATATGTTA
AAAGTATCGTAACATAATGAGG
Found at i:19952399 original size:18 final size:18
Alignment explanation
Indices: 19952368--19952424 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
19952358 TTCTTCTACT
19952368 TAAATAAT-AATAATAAA
1 TAAATAATAAATAATAAA
19952385 TAAATAATAAATAATAAAA
1 TAAATAATAAATAAT-AAA
*
19952404 TTACA-AA-AAATAATAAA
1 -TAAATAATAAATAATAAA
19952421 TAAA
1 TAAA
19952425 CTTTTCTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 11 0.31
18 13 0.37
19 5 0.14
20 3 0.09
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAATAAATAATAAA
Found at i:19956608 original size:3 final size:3
Alignment explanation
Indices: 19956600--19956634 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19956590 CATTAAGTTC
19956600 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19956635 AAGAAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19965042 original size:48 final size:49
Alignment explanation
Indices: 19964938--19965042 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 49
19964928 ATTAAGATCA
* *
19964938 ATTTTTTTAAAAGTTGTCAAGCCTTTAACGAGAGGAGGTTTGTAGTAAG
1 ATTTTTTTAAAAGTTGTCAAGCCTTTAACAAGAGGAGCTTTGTAGTAAG
* *
19964987 ATATTTTT-AAAGTT-TCCAAG-CTTCTAACAAGAGGAGCTTT-TCAGTCAG
1 ATTTTTTTAAAAGTTGT-CAAGCCTT-TAACAAGAGGAGCTTTGT-AGTAAG
19965035 ATTTTTTT
1 ATTTTTTT
19965043 TTTAGTTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
47 5 0.10
48 36 0.75
49 7 0.15
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (49 bp):
ATTTTTTTAAAAGTTGTCAAGCCTTTAACAAGAGGAGCTTTGTAGTAAG
Found at i:19965109 original size:46 final size:48
Alignment explanation
Indices: 19965046--19965159 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
19965036 TTTTTTTTTT
* * * *
19965046 AGTTTTCAAGCCACTAATGAAAAGAG-CTTTTA-TGTCAGATTTTTAA
1 AGTTGTCAAGCCTCTAATGAAAAGAGCCTTTCATTATCAGATTTTTAA
* **
19965092 AGTTGTCAAGCCTCTAATGAAAGGAGCCTTTCATTATTTGATTTTTAA
1 AGTTGTCAAGCCTCTAATGAAAAGAGCCTTTCATTATCAGATTTTTAA
*
19965140 AGTTGTCAAGCCTTTAATGA
1 AGTTGTCAAGCCTCTAATGA
19965160 GAGGAGCATT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 23 0.40
47 5 0.09
48 30 0.52
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (48 bp):
AGTTGTCAAGCCTCTAATGAAAAGAGCCTTTCATTATCAGATTTTTAA
Found at i:19965438 original size:3 final size:3
Alignment explanation
Indices: 19965430--19965459 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19965420 CCTAAGCTTT
19965430 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19965460 CAAAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19967238 original size:17 final size:17
Alignment explanation
Indices: 19967216--19967258 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
19967206 ATTTTTTTAA
*
19967216 AAAATATAATAATAAAT
1 AAAATAAAATAATAAAT
19967233 AAAATAAAATAATAAAT
1 AAAATAAAATAATAAAT
19967250 -AAATAAAAT
1 AAAATAAAAT
19967259 GTATGCACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAAAATAATAAAT
Found at i:19968146 original size:64 final size:64
Alignment explanation
Indices: 19968065--19968185 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
19968055 TTTTGAGAAA
* * *
19968065 TAAATTCATAAATTCCTATCAAA-ATATTAGAGGATTTTATAAGTTTAAAAATAATTTGTAATGT
1 TAAATTCATAAAATCCTAT-AAACATATTAGAGGATATTATAAGTTCAAAAATAATTTGTAATGT
* **
19968129 TAAATTCATAAAATCCTATAAACTTATTAGAGGATATTATGGGTTCAAAAATAATTT
1 TAAATTCATAAAATCCTATAAACATATTAGAGGATATTATAAGTTCAAAAATAATTT
19968186 TTGAAATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
63 3 0.06
64 47 0.94
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (64 bp):
TAAATTCATAAAATCCTATAAACATATTAGAGGATATTATAAGTTCAAAAATAATTTGTAATGT
Found at i:19968196 original size:64 final size:64
Alignment explanation
Indices: 19968046--19968197 Score: 164
Period size: 64 Copynumber: 2.4 Consensus size: 64
19968036 CATGAGTTTA
** * * * *
19968046 AAAAATAGCTTTTGAGAAATAAATTCATAAATTCCTATCAAAATATTAGAGGATTTTATAAGTTT
1 AAAAATAATTTTTGA-AATTAAATTCATAAAATCCTATCAAAATATTAGAGGATATTATAAGTTC
* * * **
19968111 AAAAATAATTTGT-AATGTTAAATTCATAAAATCCTAT-AAACTTATTAGAGGATATTATGGGTT
1 AAAAATAATTTTTGAA-ATTAAATTCATAAAATCCTATCAAA-ATATTAGAGGATATTATAAGTT
19968174 C
64 C
19968175 AAAAATAATTTTTGAAATTAAAT
1 AAAAATAATTTTTGAAATTAAAT
19968198 ACTTTAGATC
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
63 4 0.06
64 55 0.77
65 12 0.17
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (64 bp):
AAAAATAATTTTTGAAATTAAATTCATAAAATCCTATCAAAATATTAGAGGATATTATAAGTTC
Found at i:19969358 original size:16 final size:15
Alignment explanation
Indices: 19969310--19969362 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
19969300 GAAAATGTAA
19969310 AAAATAATATATTTT
1 AAAATAATATATTTT
* *
19969325 ATTAAATATTATAATTT
1 A--AAATAATATATTTT
19969342 AAAATAAATATATTTT
1 AAAAT-AATATATTTT
19969358 AAAAT
1 AAAAT
19969363 TGTCTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 5 0.16
16 13 0.42
17 13 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATAATATATTTT
Found at i:19969432 original size:100 final size:95
Alignment explanation
Indices: 19969314--19969558 Score: 267
Period size: 100 Copynumber: 2.5 Consensus size: 95
19969304 ATGTAAAAAA
* * * *
19969314 TAATATATTTTATTAAATATTATAATTTAAAATAAATATATTTTAAAATTGTCTATTTAATAAGT
1 TAATATATTTTATCAAATATTATAATTTAAAATAAATAAATATCAAAATTGTCTATTT--TAA-T
**
19969379 TTTTTTTTTTATTTTTAAAATATAACATAAAATTT
63 GGTTTTTTTT-TTTTTAAAATATAACAT-AAATTT
** * *
19969414 TAATATATTAAATCAAATATTATAATTTAAAATAAATAAATATCAAAGTTTTCTATTTTAATGGT
1 TAATATATTTTATCAAATATTATAATTTAAAATAAATAAATATCAAAATTGTCTATTTTAATGGT
* * *
19969479 TTTTTTTTTTTTCAAATATAATATAGATTT
66 TTTTTTTTTTTTAAAATATAACATAAATTT
* * * * *
19969509 TAA-ATATTTTTACCAAATATTATAATTTAAGATAAAGAAATTTCATAATT
1 TAATATA-TTTTATCAAATATTATAATTTAAAATAAATAAATATCAAAATT
19969559 TTTTTATTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
94 3 0.02
95 43 0.35
96 15 0.12
97 9 0.07
98 3 0.02
100 50 0.41
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (95 bp):
TAATATATTTTATCAAATATTATAATTTAAAATAAATAAATATCAAAATTGTCTATTTTAATGGT
TTTTTTTTTTTTAAAATATAACATAAATTT
Found at i:19975294 original size:16 final size:16
Alignment explanation
Indices: 19975275--19975305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19975265 CTTTGAAAAA
*
19975275 GTTGTTCTATGAAGGT
1 GTTGTTCTATAAAGGT
19975291 GTTGTTCTATAAAGG
1 GTTGTTCTATAAAGG
19975306 AGTTATTCAT
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:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (16 bp):
GTTGTTCTATAAAGGT
Found at i:19975397 original size:46 final size:46
Alignment explanation
Indices: 19975322--19975411 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
19975312 TCATTGGATA
* * *
19975322 ATTGTTTCGTGAAAGAGTTGTTCTTTGAATATTTGTTTTGTAAACT
1 ATTGTTTCGTGAAAGAGTTGTTCTCTGAATATTTATTTTATAAACT
*
19975368 ATTG-TTCTGTGAAAGAGTTATT-TCCTGAATATTTATTTTATAAA
1 ATTGTTTC-GTGAAAGAGTTGTTCT-CTGAATATTTATTTTATAAA
19975412 ATAACTTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 4 0.11
46 34 0.89
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.49
Consensus pattern (46 bp):
ATTGTTTCGTGAAAGAGTTGTTCTCTGAATATTTATTTTATAAACT
Found at i:19976313 original size:36 final size:35
Alignment explanation
Indices: 19976226--19976318 Score: 136
Period size: 35 Copynumber: 2.6 Consensus size: 35
19976216 TTTAACTTTT
*
19976226 TTTTATATTCTATTTTTTCAAACCAAAGTTTATAA
1 TTTTATATTTTATTTTTTCAAACCAAAGTTTATAA
19976261 TTTTATATTTTATTTTTTCAAACCAAAGTTTATAA
1 TTTTATATTTTATTTTTTCAAACCAAAGTTTATAA
19976296 GTATTTCA-ATTTT-TTTTTTCAAA
1 -T-TTT-ATATTTTATTTTTTCAAA
19976319 AAAACAATTA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
35 34 0.63
36 11 0.20
37 8 0.15
38 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTTATATTTTATTTTTTCAAACCAAAGTTTATAA
Found at i:19979291 original size:71 final size:72
Alignment explanation
Indices: 19979208--19979409 Score: 191
Period size: 71 Copynumber: 2.8 Consensus size: 72
19979198 TAAGAAAGTA
* * *
19979208 TTCATCACTTATTCTTCTATTTTTAAGGGAAACATTCTTATTAATTGTTTTTTATTTTTTTTGAA
1 TTCATTACTTATTCTACTATTTTTAAGGGAAACA-TCTTATTAATTGTTTTTTATTTTTTTTAAA
* *
19979273 -AATATC-
65 GAAAAACT
* * * * * *
19979279 TTCATTACTTATTCTACTATTTTT-AGGAAAACATCTTCATT-ACT-TATTGTACTCTTTTTAAA
1 TTCATTACTTATTCTACTATTTTTAAGGGAAACATCTT-ATTAATTGTTTTTTATTTTTTTTAAA
19979341 GAAAAACT
65 GAAAAACT
* * *
19979349 TTCATTACTTATTCTCCTATTTTTTAA-GGAAACACTCTCATTATTTGTTTTTCTATTTTTT
1 TTCATTACTTATTCTACTA-TTTTTAAGGGAAACA-TCTTATTAATTGTTTTT-TATTTTTT
19979410 AAGGAAACAC
Statistics
Matches: 102, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
68 13 0.13
69 10 0.10
70 29 0.28
71 36 0.35
72 5 0.05
73 3 0.03
74 6 0.06
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.52
Consensus pattern (72 bp):
TTCATTACTTATTCTACTATTTTTAAGGGAAACATCTTATTAATTGTTTTTTATTTTTTTTAAAG
AAAAACT
Found at i:19979309 original size:35 final size:35
Alignment explanation
Indices: 19979168--19979372 Score: 138
Period size: 35 Copynumber: 5.9 Consensus size: 35
19979158 TTTTTTTTAT
* * *
19979168 AAATATTTTCATT-CTTGTTTTACTATTTTTTAAGA
1 AAATATCTTCATTACTTATTCTACTA-TTTTTAAGA
* * *
19979203 AAGTA--TTCATCACTTATTCTTCTATTTTTAAGGGA
1 AAATATCTTCATTACTTATTCTACTATTTTTAA--GA
* * ** **
19979238 AACAT-TCTT-ATTAATTGTT-TTTTATTTTTTTTGA
1 AA-ATATCTTCATTACTTATTCTACTA-TTTTTAAGA
*
19979272 AAATATCTTCATTACTTATTCTACTATTTTTAGGA
1 AAATATCTTCATTACTTATTCTACTATTTTTAAGA
* * *
19979307 AAACATCTTCATTACTTATTGTACTCTTTTTAAAGA
1 AAATATCTTCATTACTTATTCTACTATTTTT-AAGA
*
19979343 AAA-A-CTTTCATTACTTATTCTCCTATTTTT
1 AAATATC-TTCATTACTTATTCTACTATTTTT
19979373 TAAGGAAACA
Statistics
Matches: 133, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
33 14 0.11
34 18 0.14
35 77 0.58
36 22 0.17
37 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (35 bp):
AAATATCTTCATTACTTATTCTACTATTTTTAAGA
Done.