Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:1520744 original size:43 final size:43
Alignment explanation
Indices: 1520677--1520779 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
1520667 TTAAGCAATG
* * *
1520677 TCAAGGATATC-ATCTATTATGCTTGGAAACATAGTACCACAGA
1 TCAAGGATATCAAGC-ATTAGGCTTGGAAACATAGCACCACAGA
* * *
1520720 TCAAGGATATCAAGCATTAGGCTTGGAAGCATAGCACTATAGA
1 TCAAGGATATCAAGCATTAGGCTTGGAAACATAGCACCACAGA
1520763 TCAAGGATATCAAGCAT
1 TCAAGGATATCAAGCAT
1520780 AATGATTTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 51 0.96
44 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (43 bp):
TCAAGGATATCAAGCATTAGGCTTGGAAACATAGCACCACAGA
Found at i:1520801 original size:43 final size:43
Alignment explanation
Indices: 1520717--1520866 Score: 201
Period size: 43 Copynumber: 3.5 Consensus size: 43
1520707 ATAGTACCAC
* * * * *** *
1520717 AGATCAAGGATATCAAGCATTAGGCTTGGAAGCATAGCACTAT
1 AGATCAAGGATATCAAGCATAATGATTTGAATTGTATCACTAT
1520760 AGATCAAGGATATCAAGCATAATGATTTGAATTGTATCACTAAT
1 AGATCAAGGATATCAAGCATAATGATTTGAATTGTATCACT-AT
* *
1520804 AGATCAAGGATATTAAGCATAATAATTTGAATTGTATCACTAT
1 AGATCAAGGATATCAAGCATAATGATTTGAATTGTATCACTAT
1520847 AGATCAAGGATATCAAGCAT
1 AGATCAAGGATATCAAGCAT
1520867 TACGTTTGGT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 54 0.57
44 41 0.43
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (43 bp):
AGATCAAGGATATCAAGCATAATGATTTGAATTGTATCACTAT
Found at i:1520822 original size:44 final size:43
Alignment explanation
Indices: 1520754--1520866 Score: 199
Period size: 44 Copynumber: 2.6 Consensus size: 43
1520744 GGAAGCATAG
*
1520754 CACTATAGATCAAGGATATCAAGCATAATGATTTGAATTGTAT
1 CACTATAGATCAAGGATATCAAGCATAATAATTTGAATTGTAT
*
1520797 CACTAATAGATCAAGGATATTAAGCATAATAATTTGAATTGTAT
1 CACT-ATAGATCAAGGATATCAAGCATAATAATTTGAATTGTAT
1520841 CACTATAGATCAAGGATATCAAGCAT
1 CACTATAGATCAAGGATATCAAGCAT
1520867 TACGTTTGGT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 25 0.38
44 41 0.62
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (43 bp):
CACTATAGATCAAGGATATCAAGCATAATAATTTGAATTGTAT
Found at i:1527198 original size:17 final size:17
Alignment explanation
Indices: 1527176--1527209 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1527166 GACAAATCTT
1527176 ATGTCTTAATGAAGATA
1 ATGTCTTAATGAAGATA
**
1527193 ATGTCTTGTTGAAGATA
1 ATGTCTTAATGAAGATA
1527210 GCAGTAGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (17 bp):
ATGTCTTAATGAAGATA
Found at i:1535629 original size:15 final size:16
Alignment explanation
Indices: 1535601--1535630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1535591 AAACAAAAGG
1535601 AAAAGCAAAGTTTTAA
1 AAAAGCAAAGTTTTAA
1535617 AAAAGCAAA-TTTTA
1 AAAAGCAAAGTTTTA
1535631 TTGATACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.27
Consensus pattern (16 bp):
AAAAGCAAAGTTTTAA
Found at i:1541493 original size:12 final size:12
Alignment explanation
Indices: 1541463--1541501 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
1541453 AGAATAGTTT
1541463 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1541475 T-TTGCTGCCTC
1 TCTTGCTGCCTC
1541486 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1541498 TCTT
1 TCTT
1541502 CTCTGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.00, C:0.38, G:0.15, T:0.46
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:1544369 original size:21 final size:22
Alignment explanation
Indices: 1544340--1544383 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1544330 TAAGTGATTA
1544340 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1544361 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1544383 T
1 T
1544384 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1545053 original size:12 final size:13
Alignment explanation
Indices: 1545035--1545070 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1545025 CAGAGATTTT
1545035 GGAGGCAGCAAGA
1 GGAGGCAGCAAGA
1545048 -GAGGCAGCAA-A
1 GGAGGCAGCAAGA
1545059 GGAGGCAGCAAG
1 GGAGGCAGCAAG
1545071 CAACTATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.05
12 20 0.95
ACGTcount: A:0.39, C:0.17, G:0.44, T:0.00
Consensus pattern (13 bp):
GGAGGCAGCAAGA
Found at i:1546920 original size:15 final size:15
Alignment explanation
Indices: 1546895--1546935 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1546885 AAATTAAAAT
1546895 AATAAAA-AAAATAA
1 AATAAAAGAAAATAA
1546909 AATAAAAGAAAATAA
1 AATAAAAGAAAATAA
* *
1546924 AGTAAATGAAAA
1 AATAAAAGAAAA
1546936 ATCCATACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (15 bp):
AATAAAAGAAAATAA
Found at i:1547694 original size:16 final size:16
Alignment explanation
Indices: 1547675--1547705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1547665 AAATTTCTAT
1547675 TATTGTTTATTTTTTA
1 TATTGTTTATTTTTTA
*
1547691 TATTTTTTATTTTTT
1 TATTGTTTATTTTTT
1547706 TCAATTTTTA
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:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TATTGTTTATTTTTTA
Found at i:1547696 original size:9 final size:8
Alignment explanation
Indices: 1547680--1547735 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 8
1547670 TCTATTATTG
1547680 TTTA-TTT
1 TTTATTTT
1547687 TTTATATTT
1 TTTAT-TTT
1547696 TTTATTTT
1 TTTATTTT
*
1547704 TTTCA-ATT
1 TTT-ATTTT
1547712 TTTATTTT
1 TTTATTTT
1547720 ATTTATTTT
1 -TTTATTTT
1547729 TATTATT
1 T-TTATT
1547736 GAGATAACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 22 0.54
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTATTTT
Found at i:1547713 original size:16 final size:15
Alignment explanation
Indices: 1547680--1547732 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
1547670 TCTATTATTG
*
1547680 TTTATTTTTTATATTT
1 TTTATTTTTT-TAATT
1547696 TTTATTTTTTTCAATT
1 TTTATTTTTTT-AATT
1547712 TTTATTTTATTT-ATT
1 TTTATTTT-TTTAATT
1547727 TTTATT
1 TTTATT
1547733 ATTGAGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.29
16 21 0.62
17 3 0.09
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTTAATT
Found at i:1561985 original size:47 final size:46
Alignment explanation
Indices: 1561924--1562018 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 46
1561914 CAAAGTATCA
1561924 TCCATACCAAACCAAGCATTAACAAGTTCTAAACCACTACATTAGG
1 TCCATACCAAACCAAGCATTAACAAGTTCTAAACCACTACATTAGG
* *
1561970 TCCATACACACACCAAGCATTAACAAGTTTTAAACCACTACATTAGG
1 TCCATAC-CAAACCAAGCATTAACAAGTTCTAAACCACTACATTAGG
1562017 TC
1 TC
1562019 AACGACTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 7 0.15
47 39 0.85
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.23
Consensus pattern (46 bp):
TCCATACCAAACCAAGCATTAACAAGTTCTAAACCACTACATTAGG
Found at i:1563352 original size:23 final size:23
Alignment explanation
Indices: 1563322--1563367 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1563312 TCCAAGATTG
1563322 AGTGGGTTGCATCGAACGTAAAT
1 AGTGGGTTGCATCGAACGTAAAT
1563345 AGTGGGTTGCATCGAACGTAAAT
1 AGTGGGTTGCATCGAACGTAAAT
1563368 TCCATTTGCT
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:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (23 bp):
AGTGGGTTGCATCGAACGTAAAT
Found at i:1568695 original size:76 final size:77
Alignment explanation
Indices: 1568553--1568712 Score: 243
Period size: 76 Copynumber: 2.1 Consensus size: 77
1568543 AATACCATCT
* **
1568553 ATTTCAATTTTAGGTAATTCATAAAAAAAAAGAAATTGTTTCCTACTTTAAAAGTTATTCCTAAA
1 ATTTTAATTTTAGGTAATTCATAAAAAAAAAGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
1568618 ATTAAGGATAGA
66 ATTAAGGATAGA
* *
1568630 ATTTTAATTTTAGGTAATTCATAAAAATAGA-AAATTGTTTCCTACTTTAAAAGAAATT-CTCAA
1 ATTTTAATTTTAGGTAATTCATAAAAAAAAAGAAATTGTTTCCTACTTTAAAAGAAATTCCT-AA
*
1568693 AATTAAGGATAGT
65 AATTAAGGATAGA
1568706 ATTTTAA
1 ATTTTAA
1568713 CTTGAGAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 2 0.03
76 46 0.61
77 28 0.37
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (77 bp):
ATTTTAATTTTAGGTAATTCATAAAAAAAAAGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
ATTAAGGATAGA
Found at i:1586761 original size:19 final size:20
Alignment explanation
Indices: 1586737--1586784 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1586727 TGGTCTATGG
1586737 AATTGAATTAG-TTAATTTA
1 AATTGAATTAGATTAATTTA
* *
1586756 AATTGAATAAGATTCATTTA
1 AATTGAATTAGATTAATTTA
1586776 AATT-AATTA
1 AATTGAATTA
1586785 ACTAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (20 bp):
AATTGAATTAGATTAATTTA
Found at i:1586776 original size:20 final size:19
Alignment explanation
Indices: 1586737--1586779 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1586727 TGGTCTATGG
*
1586737 AATTGAATTAGTTAATTTA
1 AATTGAATAAGTTAATTTA
*
1586756 AATTGAATAAGATTCATTTA
1 AATTGAATAAG-TTAATTTA
1586776 AATT
1 AATT
1586780 AATTAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (19 bp):
AATTGAATAAGTTAATTTA
Found at i:1600407 original size:22 final size:22
Alignment explanation
Indices: 1600358--1600407 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1600348 GATCCATTGC
*
1600358 TACCACAAACAAAATCCCACAT
1 TACCATAAACAAAATCCCACAT
1600380 TACCATAAACAAAATCCCACAT
1 TACCATAAACAAAATCCCACAT
1600402 TACCAT
1 TACCAT
1600408 TGATTTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (22 bp):
TACCATAAACAAAATCCCACAT
Found at i:1602230 original size:25 final size:25
Alignment explanation
Indices: 1602167--1602254 Score: 88
Period size: 25 Copynumber: 3.4 Consensus size: 25
1602157 TCGAGGGCTA
*
1602167 TTATACGTGGCTAGGCCAC-AGTCTGTG
1 TTATACGTGGCAAGGCCACGAG--T-TG
* *
1602194 ATTATACATGGCAAGGCCACGGGTTG
1 -TTATACGTGGCAAGGCCACGAGTTG
*
1602220 TTATACGTGGCAAGGCCATGAGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
*
1602245 ATATACGTGG
1 TTATACGTGG
1602255 TTGTAGCCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 31 0.60
26 2 0.04
27 1 0.02
28 17 0.33
29 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (25 bp):
TTATACGTGGCAAGGCCACGAGTTG
Found at i:1604188 original size:86 final size:86
Alignment explanation
Indices: 1604086--1604262 Score: 327
Period size: 86 Copynumber: 2.1 Consensus size: 86
1604076 TGGTATATTT
*
1604086 TCAAAGCTAGAAATTACTCAAAGCAATATCAATGAGCCCTAGAAAAATTCTTAATTTTTCTAGGC
1 TCAAAGCTAGAAATTACTCAAAGCAATATCAATGAGCCCTAGAAAAATTCTTAATTTTTCTAAGC
1604151 ATAATTTATCATCATTCAAGC
66 ATAATTTATCATCATTCAAGC
* *
1604172 TCAAAGCTAGAAATTACTCAAAGTAATATCAATGAGCCCTAGAAAAATTCTTAATTTTTCTAATC
1 TCAAAGCTAGAAATTACTCAAAGCAATATCAATGAGCCCTAGAAAAATTCTTAATTTTTCTAAGC
1604237 ATAATTTATCATCATTCAAGC
66 ATAATTTATCATCATTCAAGC
1604258 TCAAA
1 TCAAA
1604263 CTTGCATGAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (86 bp):
TCAAAGCTAGAAATTACTCAAAGCAATATCAATGAGCCCTAGAAAAATTCTTAATTTTTCTAAGC
ATAATTTATCATCATTCAAGC
Found at i:1606270 original size:202 final size:204
Alignment explanation
Indices: 1605921--1606319 Score: 631
Period size: 202 Copynumber: 2.0 Consensus size: 204
1605911 GTCAATGCCC
1605921 TTATTCTTGACAATACACTAAATAGGAACATATTTTTAAAAAAAAGGCTTTGATGTATAAGAATC
1 TTATTCTTGACAATACACTAAATAGGAACATA-TTTTAAAAAAAAGGCTTTGATGTATAAGAATC
* *
1605986 TCATAATCATAATCTTTATAATTTCTTTAAAAGGACAGTATGTTCCAAAGACATTATCTACATAA
65 TCAAAATCATAACCTTTATAATTTCTTTAAAAGGACAGTATGTTCCAAAGACATTATCTACATAA
*
1606051 GTCTCTCATGACTCTTTATAAATAAACTCATGGATAAAGAAATACCTTGCACATTATATAAAATA
130 GTCTCTCATGACTCTTTATAAATAAACTCATGGATAAAGAAATACCTTACACATTATATAAAATA
1606116 TCCAAGGACT
195 TCCAAGGACT
* ** * *
1606126 TTATTCTTGACAATACACTAACTAGGAACATA-TTTAGGAACAAGGCTTTGATGTATAAGAATTT
1 TTATTCTTGACAATACACTAAATAGGAACATATTTTAAAAAAAAGGCTTTGATGTATAAGAATCT
* * ** * *
1606190 CAAAATTATAACCTTT-TAATTTCTTTGAAAGGTTATTATGTTCCAAAGACTTTATCTACATAAG
66 CAAAATCATAACCTTTATAATTTCTTTAAAAGGACAGTATGTTCCAAAGACATTATCTACATAAG
* *
1606254 TCTCTCATGGCTCTTTATAAATAAACTCGTGGATAAAGAAATACCTTACACATTATATAAAATAT
131 TCTCTCATGACTCTTTATAAATAAACTCATGGATAAAGAAATACCTTACACATTATATAAAATAT
1606319 C
196 C
1606320 TATAATATAT
Statistics
Matches: 178, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
202 106 0.60
203 41 0.23
205 31 0.17
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (204 bp):
TTATTCTTGACAATACACTAAATAGGAACATATTTTAAAAAAAAGGCTTTGATGTATAAGAATCT
CAAAATCATAACCTTTATAATTTCTTTAAAAGGACAGTATGTTCCAAAGACATTATCTACATAAG
TCTCTCATGACTCTTTATAAATAAACTCATGGATAAAGAAATACCTTACACATTATATAAAATAT
CCAAGGACT
Found at i:1610358 original size:37 final size:37
Alignment explanation
Indices: 1610308--1610386 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
1610298 TTGTAAGGCT
*
1610308 AAAAAGAAAGATGCTAAAGATCAGGCTGTTATAGTAG
1 AAAAAGAAAGATGCTAAAGATCAGGCTGTTAAAGTAG
*
1610345 AAAAAGAAAGATGCTAAAGATCAGGCTGTTAAAGTGG
1 AAAAAGAAAGATGCTAAAGATCAGGCTGTTAAAGTAG
1610382 AAAAA
1 AAAAA
1610387 ACTAAGGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.19
Consensus pattern (37 bp):
AAAAAGAAAGATGCTAAAGATCAGGCTGTTAAAGTAG
Found at i:1634231 original size:19 final size:19
Alignment explanation
Indices: 1634204--1634254 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1634194 GGAGAAACAA
*
1634204 AAGGCAGAAAGAAAAAGGT
1 AAGGAAGAAAGAAAAAGGT
1634223 AAGGAAGAAAGAAAAAGGT
1 AAGGAAGAAAGAAAAAGGT
1634242 AAGGAAGAAAGAA
1 AAGGAAGAAAGAA
1634255 TCGATTCTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.63, C:0.02, G:0.31, T:0.04
Consensus pattern (19 bp):
AAGGAAGAAAGAAAAAGGT
Found at i:1635114 original size:36 final size:36
Alignment explanation
Indices: 1635074--1635156 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
1635064 CTTAATTCTA
*
1635074 TAAAAGGCAAATTGTGAAGGTTACGCTTTGATCTTG-
1 TAAAAGGCAAATTGCGAAGGTTACG-TTTGATCTTGT
****
1635110 TAAAAGGTGTGTTGCGAAGGTTACGTTTGATCTTGT
1 TAAAAGGCAAATTGCGAAGGTTACGTTTGATCTTGT
1635146 TGAAAAGGCAA
1 T-AAAAGGCAA
1635157 GCTGATAGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
35 10 0.27
36 21 0.57
37 6 0.16
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (36 bp):
TAAAAGGCAAATTGCGAAGGTTACGTTTGATCTTGT
Found at i:1638950 original size:29 final size:30
Alignment explanation
Indices: 1638903--1638961 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1638893 ATGCTATATA
*
1638903 ATATATTCTAATTGTACATCTCCTGGTTCTC
1 ATATATTCTAA-TCTACATCTCCTGGTTCTC
*
1638934 ATATATTCTAA-CTACATCTCCTTGTTCT
1 ATATATTCTAATCTACATCTCCTGGTTCT
1638962 TCTTGCAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
31 11 0.42
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.46
Consensus pattern (30 bp):
ATATATTCTAATCTACATCTCCTGGTTCTC
Found at i:1642920 original size:15 final size:15
Alignment explanation
Indices: 1642902--1642952 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
1642892 CTCATCATCT
1642902 TCATCTCCTTGCATG
1 TCATCTCCTTGCATG
* *
1642917 TCATCTTC-TGCATCT
1 TCATCTCCTTGCAT-G
*
1642932 TCACCTCCTTGCATG
1 TCATCTCCTTGCATG
1642947 TCATCT
1 TCATCT
1642953 TCTTCATCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 5 0.18
ACGTcount: A:0.14, C:0.35, G:0.10, T:0.41
Consensus pattern (15 bp):
TCATCTCCTTGCATG
Found at i:1642931 original size:30 final size:30
Alignment explanation
Indices: 1642897--1642960 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1642887 TCATCCTCAT
*
1642897 CATCTTCATCTCCTTGCATGTCATCTTCTG
1 CATCTTCACCTCCTTGCATGTCATCTTCTG
*
1642927 CATCTTCACCTCCTTGCATGTCATCTTCTT
1 CATCTTCACCTCCTTGCATGTCATCTTCTG
1642957 CATC
1 CATC
1642961 CTCAATCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.36, G:0.08, T:0.42
Consensus pattern (30 bp):
CATCTTCACCTCCTTGCATGTCATCTTCTG
Found at i:1647440 original size:12 final size:12
Alignment explanation
Indices: 1647423--1647449 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1647413 TATTCAACAG
1647423 TAGTGAAAGATT
1 TAGTGAAAGATT
1647435 TAGTGAAAGATT
1 TAGTGAAAGATT
1647447 TAG
1 TAG
1647450 AGATTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (12 bp):
TAGTGAAAGATT
Found at i:1651508 original size:16 final size:17
Alignment explanation
Indices: 1651480--1651515 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1651470 TTATTAATTA
1651480 ATAAATAAAATTTAAAT
1 ATAAATAAAATTTAAAT
*
1651497 ATAAAT-AAATTTTAAT
1 ATAAATAAAATTTAAAT
1651513 ATA
1 ATA
1651516 TCTATATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATAAAATTTAAAT
Found at i:1651553 original size:3 final size:3
Alignment explanation
Indices: 1651541--1651578 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1651531 TTATGCAATG
1651541 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1651579 TCTTTAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1651790 original size:19 final size:19
Alignment explanation
Indices: 1651763--1651806 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1651753 AAGTAATTTG
*
1651763 TTTTTTGAAAAATATGAAA
1 TTTTATGAAAAATATGAAA
* *
1651782 TTTTATGAAAAGTATGCAA
1 TTTTATGAAAAATATGAAA
1651801 TTTTAT
1 TTTTAT
1651807 TACTTGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTTATGAAAAATATGAAA
Found at i:1657046 original size:73 final size:70
Alignment explanation
Indices: 1656934--1657070 Score: 168
Period size: 73 Copynumber: 1.9 Consensus size: 70
1656924 TAAGAGACAA
* * *
1656934 TATTAGTCAACTAAGAGCTAACTGCCAAAAATTGAGTTCAGAGACAAAAATGACTTAATCGACTA
1 TATTAGTCAACTAAGAGCTAAAT-CCAAAAACTGAGTTCAGAGAC--AAACGACTTAATCGACTA
1656999 AAACGCTT
63 AAACGCTT
* * *
1657007 TATTAGTCGACTAAGAGCCTACAAT-CAAAAACTGGGTTCAGAGACAGACGACTTAATCGACTAA
1 TATTAGTCAACTAAGAG-CTA-AATCCAAAAACTGAGTTCAGAGACAAACGACTTAATCGACTAA
1657071 GGAGCAACGT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
71 17 0.30
73 34 0.61
74 3 0.05
75 2 0.04
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (70 bp):
TATTAGTCAACTAAGAGCTAAATCCAAAAACTGAGTTCAGAGACAAACGACTTAATCGACTAAAA
CGCTT
Found at i:1665477 original size:73 final size:73
Alignment explanation
Indices: 1665379--1665542 Score: 211
Period size: 73 Copynumber: 2.2 Consensus size: 73
1665369 CAAGAGACAG
** * * *
1665379 TGTTAGTCAACTAAGAGCTTATTGCCAAAAATTGGGTTCAAAGATAGAAACGACTTAATCGAGTA
1 TGTTAGTTGACTAAGAGCCTATTGCCAAAAATTGAGTTCAAAGATAGAAACGACTTAATCGACTA
***
1665444 AAAAGTTT
66 AAAAGCAA
* * *
1665452 TGTTAGTTGACTAAGAGCCTATTGCCAGAAATTGAGTTCAGAGATAGAGACGACTTAATCGACTA
1 TGTTAGTTGACTAAGAGCCTATTGCCAAAAATTGAGTTCAAAGATAGAAACGACTTAATCGACTA
**
1665517 AGTAGCAA
66 AAAAGCAA
1665525 TGTTAGTTGACTAAGAGC
1 TGTTAGTTGACTAAGAGC
1665543 ATTCTGTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (73 bp):
TGTTAGTTGACTAAGAGCCTATTGCCAAAAATTGAGTTCAAAGATAGAAACGACTTAATCGACTA
AAAAGCAA
Found at i:1665745 original size:8 final size:9
Alignment explanation
Indices: 1665723--1665747 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1665713 AAAAAGAGCT
1665723 CAAAAATAG
1 CAAAAATAG
1665732 CAAAAATAG
1 CAAAAATAG
1665741 CAAAAAT
1 CAAAAAT
1665748 TCTCTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.08, T:0.12
Consensus pattern (9 bp):
CAAAAATAG
Found at i:1667864 original size:30 final size:30
Alignment explanation
Indices: 1667828--1667886 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1667818 ACTCTTAATT
*
1667828 AAATTTTTATATTTTTATTTTCAATTAAAC
1 AAATTTTTATATTTTTATTTTAAATTAAAC
1667858 AAATTTTTATATTTTTATTTTAAATTAAA
1 AAATTTTTATATTTTTATTTTAAATTAAA
1667887 TAAACTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
AAATTTTTATATTTTTATTTTAAATTAAAC
Found at i:1667898 original size:30 final size:30
Alignment explanation
Indices: 1667834--1667898 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1667824 AATTAAATTT
* * *
1667834 TTATATTTTTATTTTCAATTAAACAAATTT
1 TTATATTTTTATTTTAAATTAAACAAACTC
*
1667864 TTATATTTTTATTTTAAATTAAATAAACTC
1 TTATATTTTTATTTTAAATTAAACAAACTC
1667894 TTATA
1 TTATA
1667899 CTTAATGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (30 bp):
TTATATTTTTATTTTAAATTAAACAAACTC
Found at i:1668189 original size:26 final size:26
Alignment explanation
Indices: 1668134--1668184 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1668124 TATAAACGTG
1668134 ATTTAAAATAAAAATAAAAATATTTA
1 ATTTAAAATAAAAATAAAAATATTTA
* *
1668160 ATTTAACATAATAA-AAAAAT-TTTA
1 ATTTAAAATAAAAATAAAAATATTTA
1668184 A
1 A
1668185 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 6 0.26
26 12 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTTAAAATAAAAATAAAAATATTTA
Found at i:1687559 original size:24 final size:24
Alignment explanation
Indices: 1687528--1687578 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1687518 TATGTATAAT
1687528 AAAAAAATGTCCATGTGCTATGCC
1 AAAAAAATGTCCATGTGCTATGCC
*
1687552 AAAAAAATGTCCATGTGCTCTGCC
1 AAAAAAATGTCCATGTGCTATGCC
1687576 AAA
1 AAA
1687579 TTGCTAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
AAAAAAATGTCCATGTGCTATGCC
Found at i:1695319 original size:16 final size:16
Alignment explanation
Indices: 1695298--1695336 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1695288 TCGAATTCAG
1695298 AATGACTTGAG-ATTAA
1 AATGACTTG-GCATTAA
*
1695314 AATGACTTGGCCTTAA
1 AATGACTTGGCATTAA
1695330 AATGACT
1 AATGACT
1695337 CAAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (16 bp):
AATGACTTGGCATTAA
Found at i:1707000 original size:80 final size:81
Alignment explanation
Indices: 1706836--1707117 Score: 250
Period size: 80 Copynumber: 3.5 Consensus size: 81
1706826 ATCATCATAC
* * * *
1706836 TTAGCCTATAGTGTATATGACTATCTCAACACATACATGTCA-TGACATACATTTCATAATCTCA
1 TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGATATACATTTCATAGTCTCA
**********
1706900 TAAATCNNNNNNNNNN
66 TAAATCACTTACATGA
*
1706916 TTAGCCCATAGTGTATATGACTATTTCAACACATACATCTCATTG-TATACATTTCATAGTCTCA
1 TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGATATACATTTCATAGTCTCA
1706980 TAAATCACTTACATGA
66 TAAATCACTTACATGA
* * * * ** * *
1706996 TTAGCCC-TAGTGTATATGGCTATCTGAACATATATATCTTGTGGCT-TACATTTCATAGTCTCA
1 TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGATATACATTTCATAGTCTCA
* *
1707059 TAAATCTCTTACATGC
66 TAAATCACTTACATGA
* * * * *
1707075 TTAACCCATA-TCGCATATAACTATCTCAACATATACATATCAT
1 TTAGCCCATAGT-GTATATGACTATCTCAACACATACATCTCAT
1707118 GGCAAACATG
Statistics
Matches: 164, Mismatches: 34, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
79 67 0.41
80 95 0.58
81 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.35
Consensus pattern (81 bp):
TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATTGATATACATTTCATAGTCTCA
TAAATCACTTACATGA
Found at i:1712279 original size:4 final size:4
Alignment explanation
Indices: 1712270--1712294 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1712260 TGTTAAAAAC
1712270 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
1712295 AAAGGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1733798 original size:51 final size:52
Alignment explanation
Indices: 1733656--1733801 Score: 145
Period size: 52 Copynumber: 2.8 Consensus size: 52
1733646 ATCTTAAAAT
* *
1733656 AAAAGAT-AAATAACT-CTCCATCCAAGGCTATACAACTTTAAAACTAATTTG
1 AAAAGATAAAACAACTCCT-CATCCAAGGCTATACAACTTTAAAAATAATTTG
* * ** ** *
1733707 AAAAGATAAAATAACTCCTCATTCTTGGCTCCATAACTTTAAAAATAATTTG
1 AAAAGATAAAACAACTCCTCATCCAAGGCTATACAACTTTAAAAATAATTTG
* * * *
1733759 ACAAGAT-AAACAGCTCCTCATCCGAGGCTTTACAACTTTAAAA
1 AAAAGATAAAACAACTCCTCATCCAAGGCTATACAACTTTAAAA
1733802 GCAAACAATT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
51 35 0.45
52 40 0.52
53 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (52 bp):
AAAAGATAAAACAACTCCTCATCCAAGGCTATACAACTTTAAAAATAATTTG
Found at i:1733808 original size:38 final size:36
Alignment explanation
Indices: 1733766--1733873 Score: 105
Period size: 38 Copynumber: 3.0 Consensus size: 36
1733756 TTGACAAGAT
*
1733766 AAACAGCTCCTCATCCGAGGCTTTACAACTTTAAAAG
1 AAACAACTCCTCAT-CGAGGCTTTACAACTTTAAAAG
* * * *
1733803 CAAACAATTCCTTATTCAAGGCTTTATAACTTT-AAAG
1 -AAACAACTCCTCA-TCGAGGCTTTACAACTTTAAAAG
*
1733840 --ACAACTTCTCATCGAAGGCTTTACAACTTTAAAA
1 AAACAACTCCTCATCG-AGGCTTTACAACTTTAAAA
1733874 ACTATTTGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
33 2 0.04
34 22 0.39
35 3 0.05
37 4 0.07
38 25 0.44
39 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (36 bp):
AAACAACTCCTCATCGAGGCTTTACAACTTTAAAAG
Found at i:1739035 original size:74 final size:74
Alignment explanation
Indices: 1738946--1739135 Score: 240
Period size: 74 Copynumber: 2.6 Consensus size: 74
1738936 TAAAAAAAGT
* * *
1738946 GCTCTTAGTTGACTAGCCATACTTCTTAGTCGATCAAGTCTTCTTTGTCTTGTAATTGAATTCTC
1 GCTCTTAGTTGACTAGCCATGCTTCTTAGTCGATCAAGTCTTCTCTGTCTTGTAATTGAAGTCTC
*
1739011 TGGCAATGA
66 TAGCAATGA
* * * *
1739020 GCTCTTGGTTGACTAGCCATGTTTCTTAGTCGATTAAGT-TCCCTCTGTCTTGTAATTGAAGTCT
1 GCTCTTAGTTGACTAGCCATGCTTCTTAGTCGATCAAGTCT-TCTCTGTCTTGTAATTGAAGTCT
* *
1739084 CTAGTAGTGA
65 CTAGCAATGA
* *
1739094 GCTCTTAGTTGATTAACCATGCTTCTTAGTCGA-CTAAGTCTT
1 GCTCTTAGTTGACTAGCCATGCTTCTTAGTCGATC-AAGTCTT
1739136 TTTTATTTCA
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 95 0.98
75 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (74 bp):
GCTCTTAGTTGACTAGCCATGCTTCTTAGTCGATCAAGTCTTCTCTGTCTTGTAATTGAAGTCTC
TAGCAATGA
Found at i:1744814 original size:12 final size:12
Alignment explanation
Indices: 1744797--1744821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1744787 CGTACACCTC
1744797 ATAACCCTTTCA
1 ATAACCCTTTCA
1744809 ATAACCCTTTCA
1 ATAACCCTTTCA
1744821 A
1 A
1744822 ATAAGGCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACCCTTTCA
Found at i:1752504 original size:21 final size:21
Alignment explanation
Indices: 1752465--1752506 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1752455 TTACTAAAAA
*
1752465 TTAAAAAATTAACATTTATTT
1 TTAAAAAATTAACAATTATTT
1752486 TTAAAAAATTCAA-AATTATTT
1 TTAAAAAATT-AACAATTATTT
1752507 CTATTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAAAATTAACAATTATTT
Found at i:1755725 original size:15 final size:16
Alignment explanation
Indices: 1755707--1755740 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1755697 CTTTCTTAGC
1755707 TTCGTCCTTC-TTCCT
1 TTCGTCCTTCTTTCCT
1755722 TTCGTCCTTCTTTCCT
1 TTCGTCCTTCTTTCCT
1755738 TTC
1 TTC
1755741 CCCCTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.38, G:0.06, T:0.56
Consensus pattern (16 bp):
TTCGTCCTTCTTTCCT
Found at i:1756878 original size:15 final size:16
Alignment explanation
Indices: 1756832--1756880 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 16
1756822 TAAATATTAA
1756832 TATTTTAATAATATTT
1 TATTTTAATAATATTT
1756848 TATTTATAAAATAATATTT
1 TATTT-T--AATAATATTT
1756867 TATTTTAA-AATATT
1 TATTTTAATAATATT
1756881 CTTTTTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.20
16 7 0.23
17 1 0.03
18 1 0.03
19 15 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTAATAATATTT
Found at i:1756888 original size:19 final size:19
Alignment explanation
Indices: 1756838--1756878 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1756828 TTAATATTTT
1756838 AATAATATTTTATTTATAA
1 AATAATATTTTATTTATAA
1756857 AATAATATTTTATTT-TAA
1 AATAATATTTTATTTATAA
1756875 AATA
1 AATA
1756879 TTCTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATATTTTATTTATAA
Found at i:1761546 original size:12 final size:12
Alignment explanation
Indices: 1761527--1761559 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1761517 ATCTAGGCAA
1761527 TCATATATATAT
1 TCATATATATAT
1761539 GT-ATATATATAT
1 -TCATATATATAT
1761551 TCATATATA
1 TCATATATA
1761560 CACATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (12 bp):
TCATATATATAT
Found at i:1762737 original size:12 final size:12
Alignment explanation
Indices: 1762720--1762744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1762710 AATTTTATAC
1762720 TTTAAATGAAAT
1 TTTAAATGAAAT
1762732 TTTAAATGAAAT
1 TTTAAATGAAAT
1762744 T
1 T
1762745 ACATATATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTAAATGAAAT
Found at i:1765479 original size:93 final size:93
Alignment explanation
Indices: 1765320--1765509 Score: 380
Period size: 93 Copynumber: 2.0 Consensus size: 93
1765310 CCTACAACTG
1765320 ATCAAACAAATCATCAATCCTTGGGAGTGGATATTTATTCTTCATTATGACCTTATTCAATTGTC
1 ATCAAACAAATCATCAATCCTTGGGAGTGGATATTTATTCTTCATTATGACCTTATTCAATTGTC
1765385 GGTAGTCAATGCATAACCATAGGCTACC
66 GGTAGTCAATGCATAACCATAGGCTACC
1765413 ATCAAACAAATCATCAATCCTTGGGAGTGGATATTTATTCTTCATTATGACCTTATTCAATTGTC
1 ATCAAACAAATCATCAATCCTTGGGAGTGGATATTTATTCTTCATTATGACCTTATTCAATTGTC
1765478 GGTAGTCAATGCATAACCATAGGCTACC
66 GGTAGTCAATGCATAACCATAGGCTACC
1765506 ATCA
1 ATCA
1765510 TTCTTCTTCA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 97 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (93 bp):
ATCAAACAAATCATCAATCCTTGGGAGTGGATATTTATTCTTCATTATGACCTTATTCAATTGTC
GGTAGTCAATGCATAACCATAGGCTACC
Found at i:1798508 original size:25 final size:25
Alignment explanation
Indices: 1798451--1798511 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1798441 GGTTTCTCTG
** * *
1798451 CCTCTCTCATGCTAACCCACATTTG
1 CCTCTCTTGTGCTAACCCACATCTA
*
1798476 CCTCTCTTGTGCTAACCCACCTCTA
1 CCTCTCTTGTGCTAACCCACATCTA
*
1798501 CCTTTCTTGTG
1 CCTCTCTTGTG
1798512 ATGACCACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.15, C:0.39, G:0.10, T:0.36
Consensus pattern (25 bp):
CCTCTCTTGTGCTAACCCACATCTA
Found at i:1811393 original size:9 final size:9
Alignment explanation
Indices: 1811381--1811407 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1811371 GACTTTGATG
1811381 ATATGCCAA
1 ATATGCCAA
1811390 ATATGCCAA
1 ATATGCCAA
1811399 ATATGCCAA
1 ATATGCCAA
1811408 GTGTATGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (9 bp):
ATATGCCAA
Found at i:1823132 original size:2 final size:2
Alignment explanation
Indices: 1823127--1823163 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1823117 TGTGTGTGTG
* *
1823127 TA TA TA TA TG TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1823164 GTGTGTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1823144 original size:12 final size:12
Alignment explanation
Indices: 1823127--1823159 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1823117 TGTGTGTGTG
1823127 TATATATATGTA
1 TATATATATGTA
1823139 TATATATATGTA
1 TATATATATGTA
1823151 TATATATAT
1 TATATATAT
1823160 ATATGTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
TATATATATGTA
Found at i:1825928 original size:20 final size:21
Alignment explanation
Indices: 1825898--1825979 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 21
1825888 TTATATACAT
1825898 ATTATATTAATAATTCTAGTA
1 ATTATATTAATAATTCTAGTA
*
1825919 ATTA-ATTAATAATTCTACTAATATA
1 ATTATATTAATAA-T-T-CT-A-GTA
*
1825944 TATTATATTAATAATTCTAGCA
1 -ATTATATTAATAATTCTAGTA
1825966 ATTA-ATTAATAATT
1 ATTATATTAATAATT
1825980 AATTTTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 18 0.35
21 9 0.18
22 2 0.04
23 3 0.06
24 3 0.06
25 3 0.06
26 5 0.10
27 8 0.16
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTATATTAATAATTCTAGTA
Found at i:1825980 original size:27 final size:28
Alignment explanation
Indices: 1825921--1825982 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
1825911 TTCTAGTAAT
1825921 TAATTAATAATTCTACTAATATATATTA
1 TAATTAATAATTCTACTAATATATATTA
1825949 T-ATTAATAATTCTAGC-AAT-TA-ATTAA
1 TAATTAATAATTCTA-CTAATATATATT-A
1825975 TAATTAAT
1 TAATTAAT
1825983 TTTTTAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 3 0.10
26 4 0.13
27 22 0.71
28 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATTAATAATTCTACTAATATATATTA
Found at i:1828341 original size:38 final size:38
Alignment explanation
Indices: 1828279--1828351 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
1828269 GCATTGAGTG
** *
1828279 TGATTTGATTTCTCTGTTAGTGGCTTCGACACTGAGCA
1 TGATTTGATTTCTCTGCCAATGGCTTCGACACTGAGCA
* *
1828317 TGATTTGATTTCTGTGCCAATGGCTTCGGCACTGA
1 TGATTTGATTTCTCTGCCAATGGCTTCGACACTGA
1828352 ACCAGTGACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (38 bp):
TGATTTGATTTCTCTGCCAATGGCTTCGACACTGAGCA
Found at i:1830154 original size:21 final size:21
Alignment explanation
Indices: 1830115--1830154 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1830105 ACATTCATGC
*
1830115 AAGTATTGATACCTCTGAATA
1 AAGTATTGATACATCTGAATA
*
1830136 AAGTATTGATACATTTGAA
1 AAGTATTGATACATCTGAA
1830155 AGAAAAAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AAGTATTGATACATCTGAATA
Found at i:1840319 original size:21 final size:22
Alignment explanation
Indices: 1840284--1840327 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1840274 CTCTTAAAGT
1840284 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
1840306 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
1840327 A
1 A
1840328 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:1841209 original size:20 final size:20
Alignment explanation
Indices: 1841184--1841233 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1841174 CTAATATATT
1841184 AATACATTTGGCAAAGTATC
1 AATACATTTGGCAAAGTATC
*
1841204 AATACATTTGGCAATGTATC
1 AATACATTTGGCAAAGTATC
1841224 AATACATTTG
1 AATACATTTG
1841234 CCTTAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (20 bp):
AATACATTTGGCAAAGTATC
Found at i:1842054 original size:2 final size:2
Alignment explanation
Indices: 1842047--1842076 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1842037 ATAATTTTCA
*
1842047 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1842077 TACATATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1854387 original size:44 final size:44
Alignment explanation
Indices: 1854324--1854416 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
1854314 TAAGGTCTAC
1854324 TCTAAATCTCCTTCATCAAGGTTTAACTTAGGTTTTCAATTTAA
1 TCTAAATCTCCTTCATCAAGGTTTAACTTAGGTTTTCAATTTAA
1854368 TCTAAATCTCCTTCATCAAGGTTTAACTTAGGTTTTCAATTTAA
1 TCTAAATCTCCTTCATCAAGGTTTAACTTAGGTTTTCAATTTAA
1854412 TCTAA
1 TCTAA
1854417 TTAGTGGCTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (44 bp):
TCTAAATCTCCTTCATCAAGGTTTAACTTAGGTTTTCAATTTAA
Found at i:1856448 original size:10 final size:10
Alignment explanation
Indices: 1856429--1856459 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1856419 TTCTTTCTTC
1856429 TTAATTTGTT
1 TTAATTTGTT
*
1856439 TTAGTTTGTT
1 TTAATTTGTT
1856449 TTAATTTGTT
1 TTAATTTGTT
1856459 T
1 T
1856460 GATGGGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (10 bp):
TTAATTTGTT
Found at i:1862973 original size:28 final size:28
Alignment explanation
Indices: 1862932--1863084 Score: 114
Period size: 29 Copynumber: 5.3 Consensus size: 28
1862922 ATTAAAACAA
*
1862932 AAATAT-TTTATCTTCTCTAAATTGAA-AC
1 AAATATGTTT-TCTTGTCTAAATT-AAGAC
*
1862960 AAATATGTTTTCTTGT-AAAGATTAAGAC
1 AAATATGTTTTCTTGTCTAA-ATTAAGAC
* * *
1862988 AAAAAATACTTTTCTTTTCTTAAATTAAGAC
1 -AAATAT-GTTTTCTTGTC-TAAATTAAGAC
* * * * *
1863019 AAACATATTTTTTTATCTAAATTAAAATC
1 AAATATGTTTTCTTGTCTAAATTAAGA-C
*
1863048 AAATATGTTTTCTTGTCTAAATTAAGAT
1 AAATATGTTTTCTTGTCTAAATTAAGAC
*
1863076 AAACATGTT
1 AAATATGTT
1863085 GAAGCTGTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.04
28 33 0.33
29 39 0.39
30 13 0.13
31 8 0.08
32 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (28 bp):
AAATATGTTTTCTTGTCTAAATTAAGAC
Found at i:1866304 original size:16 final size:16
Alignment explanation
Indices: 1866259--1866314 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1866249 CAAGCATACA
1866259 AATAATATATATATCAT
1 AATAATATATATAT-AT
** *
1866276 TCTTATATATATATAT
1 AATAATATATATATAT
* *
1866292 ATTAATATGTATATAT
1 AATAATATATATATAT
1866308 AATAATA
1 AATAATA
1866315 ATAATAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (16 bp):
AATAATATATATATAT
Found at i:1866319 original size:22 final size:22
Alignment explanation
Indices: 1866279--1866320 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1866269 ATATCATTCT
*
1866279 TATATATATATATATTAATATG
1 TATATATATATATAATAATATG
1866301 TATATATA-ATAATAATAATA
1 TATATATATAT-ATAATAATA
1866321 ATATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATATATATATATAATAATATG
Found at i:1866351 original size:6 final size:6
Alignment explanation
Indices: 1866290--1866351 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
1866280 ATATATATAT
* * * *
1866290 ATATTA ATATGT- ATATATA ATAATA ATAATA ATATTA TTATTA TTATTA
1 ATATTA ATAT-TA ATAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA
*
1866339 TTATTA ATATTA A
1 ATATTA ATATTA A
1866352 GCCACATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 45 0.92
7 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:1866804 original size:20 final size:20
Alignment explanation
Indices: 1866781--1866830 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1866771 TGCGGCAGCT
* * *
1866781 TGTGCTGCTGCCCAGTAGCA
1 TGTGTTGCTGCCCAGCACCA
1866801 TGTGTTGCTGCCCAGCACCA
1 TGTGTTGCTGCCCAGCACCA
1866821 TGTGTTGCTG
1 TGTGTTGCTG
1866831 TGTGCTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.28, G:0.30, T:0.30
Consensus pattern (20 bp):
TGTGTTGCTGCCCAGCACCA
Found at i:1868362 original size:29 final size:28
Alignment explanation
Indices: 1868272--1868396 Score: 112
Period size: 29 Copynumber: 4.3 Consensus size: 28
1868262 NNNNNNNNNC
* *
1868272 AAATATGTTTTCTTGTCTAGATCAAGA-T
1 AAATAT-TTTTCTTGTCTAAATTAAGACT
1868300 AAAAAATATTTTTCTTGTCTTAAATTAAGA-T
1 ---AAATATTTTTCTTGTC-TAAATTAAGACT
*
1868331 AAATATATTTTCATGTCTAAATTAAGACT
1 AAATAT-TTTTCTTGTCTAAATTAAGACT
* *
1868360 AAACATGTTTTCTTATCTAAATTAAGAC-
1 AAATAT-TTTTCTTGTCTAAATTAAGACT
*
1868388 AAACATTTT
1 AAATATTTT
1868397 AAACTAGCCA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.04
28 22 0.26
29 34 0.40
30 10 0.12
31 15 0.18
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (28 bp):
AAATATTTTTCTTGTCTAAATTAAGACT
Found at i:1871432 original size:12 final size:12
Alignment explanation
Indices: 1871413--1871460 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
1871403 CAGAATAGTT
1871413 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1871425 -CTTTGCTGCCTC
1 TC-TTGCTGCCTC
1871437 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1871449 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1871461 AAAAATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:1872144 original size:21 final size:22
Alignment explanation
Indices: 1872109--1872152 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1872099 CTCTTAAAGT
1872109 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1872131 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1872152 A
1 A
1872153 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1874101 original size:21 final size:21
Alignment explanation
Indices: 1874075--1874130 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1874065 TGTTTTATAT
*
1874075 GTATCAATACTTATGCTTAAA
1 GTATCAATACTTACGCTTAAA
1874096 GTATCAATACTTACGCTTAAA
1 GTATCAATACTTACGCTTAAA
1874117 GTATCAATACTTAC
1 GTATCAATACTTAC
1874131 AAACTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (21 bp):
GTATCAATACTTACGCTTAAA
Found at i:1874783 original size:15 final size:15
Alignment explanation
Indices: 1874725--1874774 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1874715 TTTACAATGC
* *
1874725 AATGTGATTGCATGT
1 AATGTGATTACAAGT
* *
1874740 AATGTAATTACAGGT
1 AATGTGATTACAAGT
1874755 AATGTGATTACAAGT
1 AATGTGATTACAAGT
1874770 AATGT
1 AATGT
1874775 CATTGCAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:1875028 original size:34 final size:34
Alignment explanation
Indices: 1874989--1875089 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 34
1874979 AAAATATTTT
1874989 TAATGTCTATATTTTATTTTCATTTATTTTATTA
1 TAATGTCTATATTTTATTTTCATTTATTTTATTA
* *
1875023 TAATGTTCTATA-TTTATTTTCATTT-TCTTAATA
1 TAATG-TCTATATTTTATTTTCATTTATTTTATTA
* * * * *
1875056 TAATTTTTATATATTATTTTATATTTAATTTATT
1 TAATGTCTATATTTTATTTT-CATTTATTTTATT
1875090 TTACCTATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
32 5 0.09
33 17 0.31
34 22 0.41
35 10 0.19
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (34 bp):
TAATGTCTATATTTTATTTTCATTTATTTTATTA
Found at i:1875073 original size:33 final size:34
Alignment explanation
Indices: 1874989--1875075 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
1874979 AAAATATTTT
* *
1874989 TAATG-TCTATATTTTATTTTCATTTATTTTATTA
1 TAATGTTCTATA-TTTATTTTCATTTATCTTAATA
1875023 TAATGTTCTATATTTATTTTCATTT-TCTTAATA
1 TAATGTTCTATATTTATTTTCATTTATCTTAATA
*
1875056 TAAT-TTTTATATATTATTTT
1 TAATGTTCTATAT-TTATTTT
1875076 ATATTTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 7 0.15
33 17 0.35
34 18 0.38
35 6 0.12
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (34 bp):
TAATGTTCTATATTTATTTTCATTTATCTTAATA
Found at i:1875085 original size:25 final size:26
Alignment explanation
Indices: 1875056--1875143 Score: 67
Period size: 30 Copynumber: 3.3 Consensus size: 26
1875046 TTTCTTAATA
1875056 TAAT-TTTTATATATTATTTTATATT
1 TAATATTTTATATATTATTTTATATT
* *
1875081 TAATTTATTTTACCTATATTA-TATAAATTT
1 TAA--TATTTTA--TATATTATTTTATA-TT
* *
1875111 TAATATTTAATATTTTATTTTAT-TT
1 TAATATTTTATATATTATTTTATATT
1875136 TAAT-TTTT
1 TAATATTTT
1875144 GATTCTTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
24 3 0.06
25 9 0.18
26 6 0.12
27 4 0.08
28 11 0.22
29 4 0.08
30 12 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TAATATTTTATATATTATTTTATATT
Found at i:1875451 original size:15 final size:17
Alignment explanation
Indices: 1875431--1875463 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1875421 CAAATGTCAC
1875431 TTAATAT-T-ATATATA
1 TTAATATATAATATATA
1875446 TTAATATATAATATATA
1 TTAATATATAATATATA
1875463 T
1 T
1875464 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATATATAATATATA
Found at i:1875501 original size:25 final size:23
Alignment explanation
Indices: 1875456--1875502 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1875446 TTAATATATA
* *
1875456 ATATATATATTATTTTTAAATTT
1 ATATAAATATTATTTTAAAATTT
1875479 ATATAAATATATATTTTCAAAATT
1 ATATAAATAT-TATTTT-AAAATT
1875503 AATTTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATAAATATTATTTTAAAATTT
Found at i:1880551 original size:146 final size:141
Alignment explanation
Indices: 1880292--1880554 Score: 328
Period size: 146 Copynumber: 1.8 Consensus size: 141
1880282 TTGTGGTTGA
* **
1880292 ATAGGGAATTTATTTTTGGTAGCTGGGAAACAAGATAGTAATCTTGCCATAGTAATTTTTTCTGT
1 ATAGGGAATTAATTTTTGGTAGCTGGGAAACAAGATAGTAATCTCCCCATAGTAATTTTTTCTGT
* * *
1880357 AAGTTCCAGAAATGGATCAAACATGAGGGTCTCTTCATATTGCATTTCTATGCCCTTTATAGATG
66 AAGTTCCAGAAATGGATCAAACATGAAGATCTCTTCATACTGCATTTCTATGCCCTTTATAGATG
1880422 TCTTTTGTTAT
131 TCTTTTGTTAT
* * * *
1880433 ATAGGGAATTAATTTTTTGTAGCTGGGCAACTAGATAGTTATCTACCCCATAGTTTTAATCTTTT
1 ATAGGGAATTAATTTTTGGTAGCTGGGAAACAAGATAGTAATCT-CCCCATAG---TAAT-TTTT
* ** * ** *
1880498 TCTGTTAGTTCTGGAAATGGATGAAGTATGAAGATCTCTTCATGCTGCATTTCTATG
61 TCTGTAAGTTCCAGAAATGGATCAAACATGAAGATCTCTTCATACTGCATTTCTATG
1880555 TCCTACGTAA
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
141 39 0.39
142 6 0.06
145 4 0.04
146 51 0.51
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (141 bp):
ATAGGGAATTAATTTTTGGTAGCTGGGAAACAAGATAGTAATCTCCCCATAGTAATTTTTTCTGT
AAGTTCCAGAAATGGATCAAACATGAAGATCTCTTCATACTGCATTTCTATGCCCTTTATAGATG
TCTTTTGTTAT
Found at i:1882503 original size:11 final size:10
Alignment explanation
Indices: 1882484--1882534 Score: 57
Period size: 11 Copynumber: 4.7 Consensus size: 10
1882474 GGTAATACTA
1882484 TTTTTAAAAT
1 TTTTTAAAAT
1882494 TTTGTTAAAAT
1 TTT-TTAAAAT
*
1882505 ATTTTAAAATT
1 TTTTTAAAA-T
1882516 TTTTTATAAAT
1 TTTTTA-AAAT
1882527 TTTATTAA
1 TTT-TTAA
1882535 TCTTTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 9 0.26
11 20 0.57
12 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:1882511 original size:21 final size:20
Alignment explanation
Indices: 1882485--1882530 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1882475 GTAATACTAT
1882485 TTTTAAAATTTTGTTAAAATA
1 TTTTAAAATTTTGTTAAAA-A
* *
1882506 TTTTAAAATTTTTTTATAAA
1 TTTTAAAATTTTGTTAAAAA
1882526 TTTTA
1 TTTTA
1882531 TTAATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAAAATTTTGTTAAAAA
Found at i:1887143 original size:12 final size:12
Alignment explanation
Indices: 1887126--1887163 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1887116 CTTAGGTAAG
1887126 ATACGTGAGGAA
1 ATACGTGAGGAA
*
1887138 ATACGTGGGGAA
1 ATACGTGAGGAA
*
1887150 ATACGTGAAGAA
1 ATACGTGAGGAA
1887162 AT
1 AT
1887164 TAAGAATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.32, T:0.18
Consensus pattern (12 bp):
ATACGTGAGGAA
Found at i:1887929 original size:24 final size:24
Alignment explanation
Indices: 1887902--1887954 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1887892 TTTAACGAAA
1887902 AATTTTGTT-GAAAATTTTCAACAG
1 AATTTTGTTAG-AAATTTTCAACAG
**
1887926 AATTTTGTTAGAAATTTTCAGTAG
1 AATTTTGTTAGAAATTTTCAACAG
1887950 AATTT
1 AATTT
1887955 CGGTGGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (24 bp):
AATTTTGTTAGAAATTTTCAACAG
Found at i:1887963 original size:24 final size:24
Alignment explanation
Indices: 1887913--1887966 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1887903 ATTTTGTTGA
* *
1887913 AAATTTTCAACAGAATTTTGTTAG
1 AAATTTTCAACAGAATTTCGGTAG
** *
1887937 AAATTTTCAGTAGAATTTCGGTGG
1 AAATTTTCAACAGAATTTCGGTAG
1887961 AAATTT
1 AAATTT
1887967 CTTCCCAACG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (24 bp):
AAATTTTCAACAGAATTTCGGTAG
Found at i:1888089 original size:25 final size:26
Alignment explanation
Indices: 1888020--1888090 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
1888010 TTTTTCCAAC
*
1888020 AAAATATTTCAACGGAATTTTTCATTG
1 AAAAT-TTTCAACAGAATTTTTCATTG
** *
1888047 AAAA-TTTCAATTGAATTTTTCGTTG
1 AAAATTTTCAACAGAATTTTTCATTG
1888072 AAAATTTTCAACAG-ATTTT
1 AAAATTTTCAACAGAATTTT
1888091 CAACGAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 27 0.71
26 7 0.18
27 4 0.11
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (26 bp):
AAAATTTTCAACAGAATTTTTCATTG
Found at i:1898549 original size:64 final size:64
Alignment explanation
Indices: 1898474--1898594 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
1898464 GAGCCAACAA
* ** * *
1898474 TCTTAAGCAACATTAATGGGTGCACCACGTAATTGGAATCTATAACAGTGGCCTTGCCATGTAG
1 TCTTAAGCAACACTAATGGGCACACCACATAATTGCAATCTATAACAGTGGCCTTGCCATGTAG
1898538 TCTTAAGCAACACTAATGGGCACACCACATAATTGCAATCTATAACAGTGGCCTTGC
1 TCTTAAGCAACACTAATGGGCACACCACATAATTGCAATCTATAACAGTGGCCTTGC
1898595 TAAGTGCCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (64 bp):
TCTTAAGCAACACTAATGGGCACACCACATAATTGCAATCTATAACAGTGGCCTTGCCATGTAG
Found at i:1898725 original size:32 final size:32
Alignment explanation
Indices: 1898667--1898733 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1898657 ACCACGTACA
* *
1898667 CATAATCAACATTAGTGGCAATGCCACATCAT
1 CATAATCAACATTAGTGGCAACGCCACATAAT
***
1898699 CATAATCAACATTAGTGGTTGCGCCACATAAT
1 CATAATCAACATTAGTGGCAACGCCACATAAT
1898731 CAT
1 CAT
1898734 CGACCTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (32 bp):
CATAATCAACATTAGTGGCAACGCCACATAAT
Found at i:1899968 original size:17 final size:17
Alignment explanation
Indices: 1899915--1899969 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1899905 CTTCATTTGT
*
1899915 ATTT-CATTTCACTCTC
1 ATTTCCATTTCACTTTC
* * *
1899931 ATTTGCATTCCA-TTTGT
1 ATTTCCATTTCACTTT-C
1899948 ATTTCCATTTCACTTTC
1 ATTTCCATTTCACTTTC
1899965 ATTTC
1 ATTTC
1899970 ACATGCATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 6 0.20
17 21 0.70
18 3 0.10
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTCCATTTCACTTTC
Found at i:1901054 original size:99 final size:100
Alignment explanation
Indices: 1900871--1901070 Score: 305
Period size: 99 Copynumber: 2.0 Consensus size: 100
1900861 GTGCCCTGAA
*
1900871 AAGCAAGTATATTTTCATATTTAATTCAATTTATTTTATTTGTAATGAAAGACATTTTTGAAAAT
1 AAGCAAGTATATTTTCATATTTAATTCAATTTATTTTATTTGTAATGAAAGACATTTTCGAAAAT
*
1900936 AAGACGAAGAGTTTGTTTT-AAGTAAGCATTTATT
66 AAGACGAAGAGTTTGTTTTAAAATAAGCATTTATT
* * ** *
1900970 AAGCAAGTATATTTTCTTGTTTAATTTGATTTATTTTATTTGTAATGAAAGTACATTTTCGACAA
1 AAGCAAGTATATTTTCATATTTAATTCAATTTATTTTATTTGTAATGAAAG-ACATTTTCGAAAA
*
1901035 TAAGATGAAGAGTTT-TTTTAAAATAAGCATTTATT
65 TAAGACGAAGAGTTTGTTTTAAAATAAGCATTTATT
1901070 A
1 A
1901071 TTTAGTTATA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
99 51 0.56
100 40 0.44
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (100 bp):
AAGCAAGTATATTTTCATATTTAATTCAATTTATTTTATTTGTAATGAAAGACATTTTCGAAAAT
AAGACGAAGAGTTTGTTTTAAAATAAGCATTTATT
Found at i:1909111 original size:69 final size:69
Alignment explanation
Indices: 1909018--1909213 Score: 247
Period size: 69 Copynumber: 2.9 Consensus size: 69
1909008 CCTACCCCGT
* **
1909018 GACTTATAAAAAGGGAAAAGTGGTACTATGCCCAACTTAATCC-TGTGGTATTCTTACCGTCACA
1 GACTCATAAAAAGGGAAAAGTGGTACTATGCCCAACTTAATCCATGTGGTATTCTTACCCCCACA
*
1909082 TCGA
66 TAGA
* * * *
1909086 GACTCATAAAGAGGCGAAAAGTGGTA-TAATACCCAACTT-ATCCTTATGGTATTCTTACCCCCA
1 GACTCATAAAAAGG-GAAAAGTGGTACT-ATGCCCAACTTAATCCATGTGGTATTCTTACCCCCA
*
1909149 CATAGG
64 CATAGA
*
1909155 GACTCATAAAAAGGGGAAAAGTGGTACAATGCCCAACTTAA-CCATGTGGTATTCTTACC
1 GACTCATAAAAA-GGGAAAAGTGGTACTATGCCCAACTTAATCCATGTGGTATTCTTACC
1909214 TCGATTAGAG
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
68 17 0.16
69 89 0.82
70 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (69 bp):
GACTCATAAAAAGGGAAAAGTGGTACTATGCCCAACTTAATCCATGTGGTATTCTTACCCCCACA
TAGA
Found at i:1912575 original size:20 final size:20
Alignment explanation
Indices: 1912539--1912577 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1912529 AATAATTTAT
*
1912539 TGTTGAAAATTTATTTTTGA
1 TGTTGAAAATATATTTTTGA
1912559 TGTTAGAAAATAT-TTTTTG
1 TGTT-GAAAATATATTTTTG
1912578 GTGAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (20 bp):
TGTTGAAAATATATTTTTGA
Found at i:1913361 original size:68 final size:68
Alignment explanation
Indices: 1913226--1913372 Score: 174
Period size: 68 Copynumber: 2.1 Consensus size: 68
1913216 GCACTCATAC
* * * * *
1913226 TTTCATCATATGGTGTGTGGAAACAACATCACATACTTTGCATCATAGCATTCATCATATGCCCA
1 TTTC-TCATGTGGTATGTAGAAACAACATCACATACATTGCAACATAGCATTCATCATATGCCCA
1913291 TTCT
65 TTCT
* *
1913295 TTTCTCATGTGGTATGTAGAAACAACATCACATACATTGCAACAT-GTC-TTACATCATGTGCTC
1 TTTCTCATGTGGTATGTAGAAACAACATCACATACATTGCAACATAG-CATT-CATCATATGCCC
1913358 ATTCT
64 ATTCT
1913363 TATT-TCATGT
1 T-TTCTCATGT
1913373 ACATAACATA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
67 3 0.04
68 59 0.87
69 6 0.09
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (68 bp):
TTTCTCATGTGGTATGTAGAAACAACATCACATACATTGCAACATAGCATTCATCATATGCCCAT
TCT
Found at i:1924438 original size:15 final size:15
Alignment explanation
Indices: 1924418--1924451 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1924408 TTCCTCATAT
*
1924418 ATTTCCCTCCAAAAG
1 ATTTCCCTCCAAAAC
1924433 ATTTCCCTCCAAAAC
1 ATTTCCCTCCAAAAC
1924448 ATTT
1 ATTT
1924452 GGGAAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (15 bp):
ATTTCCCTCCAAAAC
Found at i:1938979 original size:28 final size:25
Alignment explanation
Indices: 1938899--1938957 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
1938889 GTGGTCGCAA
* *
1938899 CCACGTATATCAACTCGTGGCCTTG
1 CCACATATACCAACTCGTGGCCTTG
1938924 CCACATATACCAACTCGTGGCCTTG
1 CCACATATACCAACTCGTGGCCTTG
1938949 CCACATATA
1 CCACATATA
1938958 ATCACAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.25
Consensus pattern (25 bp):
CCACATATACCAACTCGTGGCCTTG
Found at i:1942581 original size:14 final size:14
Alignment explanation
Indices: 1942562--1942592 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1942552 AACTAGTGAT
1942562 CAAGTAGTGAAAAG
1 CAAGTAGTGAAAAG
1942576 CAAGTAGTGAAAAG
1 CAAGTAGTGAAAAG
1942590 CAA
1 CAA
1942593 TAAGCATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.10, G:0.26, T:0.13
Consensus pattern (14 bp):
CAAGTAGTGAAAAG
Found at i:1945074 original size:14 final size:14
Alignment explanation
Indices: 1945033--1945066 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1945023 TTGATTTGCT
**
1945033 ATATTTATACTTAG
1 ATATTTATTGTTAG
1945047 ATATTTATTGTTAG
1 ATATTTATTGTTAG
1945061 ATATTT
1 ATATTT
1945067 GTTTTTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (14 bp):
ATATTTATTGTTAG
Found at i:1956634 original size:2 final size:2
Alignment explanation
Indices: 1956627--1956657 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1956617 GGAACTCAAG
1956627 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1956658 CTGATAAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1960073 original size:29 final size:27
Alignment explanation
Indices: 1960034--1960188 Score: 96
Period size: 29 Copynumber: 5.3 Consensus size: 27
1960024 AACATGTTCA
*
1960034 TCTTAATTTAGACAAGAAAACATGTTATG
1 TCTTAA-TTAGACAAGAAAACATATT-TG
*
1960063 TCTTAACTTAGACAAGAAAAGATATTTG
1 TCTTAA-TTAGACAAGAAAACATATTTG
** *
1960091 TCTTAATTCAAGACAAGAAAATTTTTTTTTG
1 TCTTAATT--AGACAAGAAAA--CATATTTG
* * *
1960122 TCTTAATCTAGATAAAAAAAACATATTTA
1 TCTTAAT-TAGA-CAAGAAAACATATTTG
* *
1960151 TCTCAATTTAGACAA-AATAAAATATTTTTG
1 TCTTAA-TTAGACAAGAA-AACATA--TTTG
1960181 TCTTAATT
1 TCTTAATT
1960189 GAAGATAAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
27 4 0.04
28 15 0.15
29 49 0.49
30 12 0.12
31 18 0.18
32 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (27 bp):
TCTTAATTAGACAAGAAAACATATTTG
Found at i:1961177 original size:21 final size:22
Alignment explanation
Indices: 1961152--1961195 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1961142 AAGTGATTAA
1961152 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1961173 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1961195 T
1 T
1961196 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1965403 original size:13 final size:13
Alignment explanation
Indices: 1965382--1965411 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1965372 CCCATGAAGA
1965382 AAAAGACTATTTC
1 AAAAGACTATTTC
*
1965395 AAAATACTATTTC
1 AAAAGACTATTTC
1965408 AAAA
1 AAAA
1965412 ATGTTTCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAAGACTATTTC
Found at i:1971756 original size:28 final size:28
Alignment explanation
Indices: 1971704--1971861 Score: 110
Period size: 28 Copynumber: 5.5 Consensus size: 28
1971694 GTTTGCCTTA
* * *
1971704 TTAGACAAGAAAACATGTTATGTCTTAAT
1 TTAGACAAAAAAATATG-TCTGTCTTAAT
*
1971733 TTAGATAAAAAAACTATG-CTGTCTT-AT
1 TTAGACAAAAAAA-TATGTCTGTCTTAAT
* *
1971760 TTAAGACAAGAAAATATGTTTGTCTTAAT
1 TT-AGACAAAAAAATATGTCTGTCTTAAT
* *
1971789 TTAAAACAAGAAAAATAT-TTTGTCTTAAT
1 TT-AGACAA-AAAAATATGTCTGTCTTAAT
* * *
1971818 CTAGACAAGAAATATAT-T-TGTCTCAAT
1 TTAGACAA-AAAAATATGTCTGTCTTAAT
1971845 TTAGACAAGATAAAATA
1 TTAGACAA-A-AAAATA
1971862 GTTTAATTAA
Statistics
Matches: 108, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
27 25 0.23
28 40 0.37
29 33 0.31
30 10 0.09
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (28 bp):
TTAGACAAAAAAATATGTCTGTCTTAAT
Found at i:1971792 original size:29 final size:28
Alignment explanation
Indices: 1971704--1971854 Score: 157
Period size: 29 Copynumber: 5.4 Consensus size: 28
1971694 GTTTGCCTTA
*
1971704 TTAGACAAGAAAACATGTTATGTCTTAAT
1 TTAGACAAGAAAATATGTT-TGTCTTAAT
* * *
1971733 TTAGATAAAAAAACTATG-CTGTCTT-AT
1 TTAGACAAGAAAA-TATGTTTGTCTTAAT
1971760 TTAAGACAAGAAAATATGTTTGTCTTAAT
1 TT-AGACAAGAAAATATGTTTGTCTTAAT
*
1971789 TTAAAACAAGAAAAATAT-TTTGTCTTAAT
1 TT-AGACAAG-AAAATATGTTTGTCTTAAT
* * *
1971818 CTAGACAAG-AAATATATTTGTCTCAAT
1 TTAGACAAGAAAATATGTTTGTCTTAAT
1971845 TTAGACAAGA
1 TTAGACAAGA
1971855 TAAAATAGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
26 6 0.06
27 26 0.25
28 27 0.26
29 34 0.33
30 10 0.10
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (28 bp):
TTAGACAAGAAAATATGTTTGTCTTAAT
Found at i:1971813 original size:57 final size:56
Alignment explanation
Indices: 1971690--1971861 Score: 165
Period size: 56 Copynumber: 3.1 Consensus size: 56
1971680 TGATAGCTTT
* * * *
1971690 AATAGTTTGCCTTA-TTAGACAAGAAAACATGTTATGTCTTAATTTAGATA-AA-AAA
1 AATATTTTGTCTTATTTAGACAAGAAAATATGTT-TGTCTTAATTTA-AAACAAGAAA
* **
1971745 ACTATGCTGTCTTATTTAAGACAAGAAAATATGTTTGTCTTAATTTAAAACAAGAAA
1 AATATTTTGTCTTATTT-AGACAAGAAAATATGTTTGTCTTAATTTAAAACAAGAAA
* * * *
1971802 AATATTTTGTCTTAATCTAGACAAG-AAATATATTTGTCTCAATTT-AGACAAGATAA
1 AATATTTTGTCTT-ATTTAGACAAGAAAATATGTTTGTCTTAATTTAAAACAAGA-AA
1971858 AATA
1 AATA
1971862 GTTTAATTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
55 18 0.19
56 40 0.41
57 36 0.37
58 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (56 bp):
AATATTTTGTCTTATTTAGACAAGAAAATATGTTTGTCTTAATTTAAAACAAGAAA
Found at i:1971849 original size:27 final size:28
Alignment explanation
Indices: 1971752--1971854 Score: 122
Period size: 28 Copynumber: 3.7 Consensus size: 28
1971742 AAAACTATGC
*
1971752 TGTCTT-ATTTAAGACAAGAAAATATGTT
1 TGTCTTAATTTAAGACAAG-AAATATATT
* *
1971780 TGTCTTAATTTAAAACAAGAAAAATATTT
1 TGTCTTAATTTAAGACAAGAAATATA-TT
*
1971809 TGTCTTAATCT-AGACAAGAAATATATT
1 TGTCTTAATTTAAGACAAGAAATATATT
*
1971836 TGTCTCAATTT-AGACAAGA
1 TGTCTTAATTTAAGACAAGA
1971855 TAAAATAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
27 19 0.29
28 23 0.35
29 23 0.35
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (28 bp):
TGTCTTAATTTAAGACAAGAAATATATT
Found at i:1976438 original size:15 final size:14
Alignment explanation
Indices: 1976395--1976453 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 14
1976385 TATAATGATA
*
1976395 ATTTAAATATTAAT
1 ATTTTAATATTAAT
1976409 ATTTT-AT-TT-AT
1 ATTTTAATATTAAT
1976420 ATTTTAATCATTAAT
1 ATTTTAAT-ATTAAT
1976435 ATTTTAAATATTAAT
1 ATTTT-AATATTAAT
1976450 ATTT
1 ATTT
1976454 ATTTATAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 7 0.18
12 4 0.10
13 2 0.05
14 6 0.15
15 17 0.44
16 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTTAATATTAAT
Found at i:1976831 original size:20 final size:21
Alignment explanation
Indices: 1976793--1976837 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1976783 TTAAAATATC
1976793 AATAATTTAAATCAAA-TTTT
1 AATAATTTAAATCAAATTTTT
*
1976813 AATAA-TTAAATCGATATTTTT
1 AATAATTTAAATC-AAATTTTT
1976834 AATA
1 AATA
1976838 CATAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 7 0.32
21 8 0.36
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAATTTAAATCAAATTTTT
Found at i:1980455 original size:38 final size:37
Alignment explanation
Indices: 1980405--1980493 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 37
1980395 TAATTTACTA
*
1980405 TTTTCTATTATTTAAG-GGT-AATAAACTAGAATTCCTT
1 TTTTCTATTATTTAAGAGGTGAAT-AACTAG-ATGCCTT
*
1980442 TTTTCATATTATTT-AGTAGGTGAATAAGTAGATGCCTT
1 TTTTC-TATTATTTAAG-AGGTGAATAACTAGATGCCTT
1980480 TTTTCTATTATTTA
1 TTTTCTATTATTTA
1980494 GGGGGTAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
37 15 0.33
38 19 0.42
39 8 0.18
40 3 0.07
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (37 bp):
TTTTCTATTATTTAAGAGGTGAATAACTAGATGCCTT
Found at i:1990658 original size:30 final size:29
Alignment explanation
Indices: 1990579--1990705 Score: 111
Period size: 27 Copynumber: 4.4 Consensus size: 29
1990569 TCTTGTCTTT
* * *
1990579 AATTAGGACAAAATATGTTTTC-TGTCTA
1 AATTAAGACAAAACATGTTTTCTTATCTA
* *
1990607 AATTAAGACAACACA--TTTTCTTATCTC
1 AATTAAGACAAAACATGTTTTCTTATCTA
* *
1990634 AATTAAGACATAACATGTTTTTCTTTGTCTA
1 AATTAAGACAAAACATG-TTTTC-TTATCTA
*
1990665 AATT-AGGCAAAACATGTTTTC-TATCTAA
1 AATTAAGACAAAACATGTTTTCTTATCT-A
*
1990693 AATTAAGAAAAAA
1 AATTAAGACAAAA
1990706 ACTGTTAACT
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
26 5 0.06
27 21 0.27
28 17 0.22
29 11 0.14
30 15 0.19
31 9 0.12
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (29 bp):
AATTAAGACAAAACATGTTTTCTTATCTA
Found at i:1998304 original size:3 final size:3
Alignment explanation
Indices: 1998275--1998315 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
1998265 TAATATGAAA
*
1998275 ATT ATT TTT ATT -TT ATTT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
1998316 TACTTTTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
ATT
Found at i:2000729 original size:29 final size:28
Alignment explanation
Indices: 2000688--2000829 Score: 158
Period size: 29 Copynumber: 4.9 Consensus size: 28
2000678 TAGCTTTAAT
*
2000688 ATGTTTGCCTTAATTTAGACAAGAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAC
* *
2000716 ATGTTATGTCTTAATTTAGATAAAAAAAC
1 ATGTT-TGTCTTAATTTAGACAAGAAAAC
* *
2000745 TATGCTTGTCTTAATTTAAGACAAGAAAAT
1 -ATGTTTGTCTTAATTT-AGACAAGAAAAC
* *
2000775 ATGTTTGTCTTAATTTAAAACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAC
* *
2000805 ATTTTTGTCTTAATCTAGACAAGAA
1 ATGTTTGTCTTAATTTAGACAAGAA
2000830 NNNNNNNNNN
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.07
29 59 0.60
30 32 0.33
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAC
Found at i:2000826 original size:58 final size:58
Alignment explanation
Indices: 2000685--2000829 Score: 186
Period size: 58 Copynumber: 2.5 Consensus size: 58
2000675 TGATAGCTTT
* *
2000685 AATATGTTTGCCTTAATTTAGACAAGAAAACATGTTATGTCTTAATTTAGATAAAAAA
1 AATATGTTTGTCTTAATTTAGACAAGAAAACATGTTATGTCTTAATTTAGAAAAAAAA
* * *
2000743 ACTATGCTTGTCTTAATTTAAGACAAGAAAATATGTT-TGTCTTAATTTA-AAACAAGAAA
1 AATATGTTTGTCTTAATTT-AGACAAGAAAACATGTTATGTCTTAATTTAGAAA-AA-AAA
* *
2000802 AATATTTTTGTCTTAATCTAGACAAGAA
1 AATATGTTTGTCTTAATTTAGACAAGAA
2000830 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.03
58 39 0.52
59 34 0.45
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (58 bp):
AATATGTTTGTCTTAATTTAGACAAGAAAACATGTTATGTCTTAATTTAGAAAAAAAA
Found at i:2002798 original size:36 final size:36
Alignment explanation
Indices: 2002750--2002868 Score: 122
Period size: 35 Copynumber: 3.4 Consensus size: 36
2002740 TATATGAATA
* *
2002750 TTGATCAT-AGCCCA-CTATGGGGGTAAGAATATCAC
1 TTGATTATAAGCCCATC-ATGGGGGTAAGAATACCAC
*
2002785 TTGATTATAAGCCCATCATGGGGGTAAAAATACCAC
1 TTGATTATAAGCCCATCATGGGGGTAAGAATACCAC
* * * * *
2002821 TAGACTATAA-CCCATCATGAGGGTAAGAGTACCAT
1 TTGATTATAAGCCCATCATGGGGGTAAGAATACCAC
2002856 TTGA-TA-AAGCCCA
1 TTGATTATAAGCCCA
2002869 CTGTCGAGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
33 2 0.03
34 6 0.08
35 31 0.44
36 31 0.44
37 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (36 bp):
TTGATTATAAGCCCATCATGGGGGTAAGAATACCAC
Found at i:2002845 original size:35 final size:36
Alignment explanation
Indices: 2002770--2002846 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
2002760 CCCACTATGG
* * * * *
2002770 GGGTAAGAATATCACTTGATTATAAGCCCATCATGG
1 GGGTAAAAATACCACTAGACTATAAGCCCATCATGA
2002806 GGGTAAAAATACCACTAGACTATAA-CCCATCATGA
1 GGGTAAAAATACCACTAGACTATAAGCCCATCATGA
2002841 GGGTAA
1 GGGTAA
2002847 GAGTACCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 15 0.42
36 21 0.58
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (36 bp):
GGGTAAAAATACCACTAGACTATAAGCCCATCATGA
Found at i:2005322 original size:27 final size:27
Alignment explanation
Indices: 2005281--2005332 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2005271 GAATAGATAA
2005281 GAATAGAATAAAATAACTATTATGTGG
1 GAATAGAATAAAATAACTATTATGTGG
* *
2005308 GAATAGAATAGAATAATTATTATGT
1 GAATAGAATAAAATAACTATTATGT
2005333 AGTTTGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (27 bp):
GAATAGAATAAAATAACTATTATGTGG
Found at i:2005559 original size:15 final size:15
Alignment explanation
Indices: 2005541--2005601 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
2005531 ATAATGATAA
2005541 TTTAAATATTAATAT
1 TTTAAATATTAATAT
2005556 TTT--AT-TT-ATAT
1 TTTAAATATTAATAT
2005567 TTT-AATCATTAATAT
1 TTTAAAT-ATTAATAT
2005582 TTTAAAATATTAATAT
1 TTT-AAATATTAATAT
2005598 TTTA
1 TTTA
2005602 TTTATAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
11 7 0.17
12 4 0.10
13 2 0.05
14 2 0.05
15 11 0.28
16 11 0.28
17 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAATATTAATAT
Found at i:2005591 original size:25 final size:25
Alignment explanation
Indices: 2005540--2005592 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2005530 AATAATGATA
**
2005540 ATTTAAATATTAATATTTTATTTAT
1 ATTTAAATATTAATATTTTATAAAT
*
2005565 ATTTTAATCATTAATATTTTA-AAAT
1 ATTTAAAT-ATTAATATTTTATAAAT
2005590 ATT
1 ATT
2005593 AATATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTAAATATTAATATTTTATAAAT
Found at i:2005638 original size:26 final size:25
Alignment explanation
Indices: 2005579--2005638 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2005569 TAATCATTAA
* *
2005579 TATTTTAAAATATTAATATTTTATT
1 TATTTTTAAATATTAATATATTATT
* *
2005604 TATAATTTAAATATTATTATGATTATT
1 TAT-TTTTAAATATTAATAT-ATTATT
2005631 TATTTTTA
1 TATTTTTA
2005639 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.11
26 17 0.61
27 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTTTAAATATTAATATATTATT
Found at i:2005671 original size:22 final size:23
Alignment explanation
Indices: 2005637--2005754 Score: 66
Period size: 25 Copynumber: 5.0 Consensus size: 23
2005627 TATTTATTTT
*
2005637 TATTT-TATTTTTAAAATATTAA
1 TATTTATAATTTTAAAATATTAA
* * *
2005659 TTTTTATACTTTATTAAAATATTCA
1 TATTTATA-ATT-TTAAAATATTAA
2005684 TAATTTATAA-TTT-AAATATTAA
1 T-ATTTATAATTTTAAAATATTAA
* *
2005706 TATTTAATGATAATTTAATA-ATTAA
1 TATTT-AT-A-ATTTTAAAATATTAA
* *
2005731 TAATTTAAAATTTTAATAT-TTAA
1 T-ATTTATAATTTTAAAATATTAA
2005754 T
1 T
2005755 TTATAAGTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 21
0.73 0.08 0.20
Matches are distributed among these distances:
21 4 0.05
22 15 0.19
23 18 0.23
24 6 0.08
25 22 0.29
26 12 0.16
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (23 bp):
TATTTATAATTTTAAAATATTAA
Done.