Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 115 of 147
Found at i:20730534 original size:46 final size:46
Alignment explanation
Indices: 20730481--20730573 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
20730471 TACAAGCTAG
20730481 AGTATAAAATGAGAATAGGGTCAAACTAAGGTTTTTCTCGATTGTT
1 AGTATAAAATGAGAATAGGGTCAAACTAAGGTTTTTCTCGATTGTT
20730527 AGTATAAAATGAGAATAGGGTCAAACTAAGGTTTTTCTCGATTGTT
1 AGTATAAAATGAGAATAGGGTCAAACTAAGGTTTTTCTCGATTGTT
20730573 A
1 A
20730574 CTGTATATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (46 bp):
AGTATAAAATGAGAATAGGGTCAAACTAAGGTTTTTCTCGATTGTT
Found at i:20735661 original size:27 final size:26
Alignment explanation
Indices: 20735625--20735690 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
20735615 GGATTTAGGG
* *
20735625 TTTT-GGGTTTGACCTAAGGTTTTGA
1 TTTTAGGGTTTCACCTAAGGTTTTAA
** *
20735650 TTTTAAGGGTTTCATTTAGGGTTTTAA
1 TTTT-AGGGTTTCACCTAAGGTTTTAA
20735677 TTTTAGGGTTTCAC
1 TTTTAGGGTTTCAC
20735691 TTTTAGGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 4 0.12
26 9 0.27
27 20 0.61
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.50
Consensus pattern (26 bp):
TTTTAGGGTTTCACCTAAGGTTTTAA
Found at i:20735666 original size:14 final size:13
Alignment explanation
Indices: 20735649--20735706 Score: 73
Period size: 14 Copynumber: 4.3 Consensus size: 13
20735639 TAAGGTTTTG
20735649 ATTTTAAGGGTTTC
1 ATTTT-AGGGTTTC
*
20735663 A-TTTAGGGTTTTA
1 ATTTTAGGG-TTTC
20735676 ATTTTAGGGTTTC
1 ATTTTAGGGTTTC
20735689 ACTTTTAGGGTTTC
1 A-TTTTAGGGTTTC
20735703 ATTT
1 ATTT
20735707 AAGATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 4 0.10
13 14 0.36
14 21 0.54
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.53
Consensus pattern (13 bp):
ATTTTAGGGTTTC
Found at i:20735667 original size:13 final size:13
Alignment explanation
Indices: 20735651--20735709 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
20735641 AGGTTTTGAT
20735651 TTTAAGGGTTTCA
1 TTTAAGGGTTTCA
*
20735664 TTT-AGGGTTTTAA
1 TTTAAGGG-TTTCA
*
20735677 TTTTAGGGTTTCA
1 TTTAAGGGTTTCA
*
20735690 CTTTTAGGGTTTCA
1 -TTTAAGGGTTTCA
20735704 TTTAAG
1 TTTAAG
20735710 ATTTTAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 4 0.10
13 19 0.47
14 17 0.43
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (13 bp):
TTTAAGGGTTTCA
Found at i:20735704 original size:40 final size:41
Alignment explanation
Indices: 20735650--20735726 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
20735640 AAGGTTTTGA
* * * *
20735650 TTTTAAGGGTTTCATTTAGGGTTTTAATTTTAGGGTTTCAC
1 TTTTAAGGGTTTCATTTAAGATTTTAATCTTAAGGTTTCAC
20735691 TTTT-AGGGTTTCATTTAAGATTTTAATCTTAAGGTT
1 TTTTAAGGGTTTCATTTAAGATTTTAATCTTAAGGTT
20735727 CCATTTCACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.52
Consensus pattern (41 bp):
TTTTAAGGGTTTCATTTAAGATTTTAATCTTAAGGTTTCAC
Found at i:20735707 original size:26 final size:26
Alignment explanation
Indices: 20735642--20735701 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
20735632 TTTGACCTAA
*
20735642 GGTTTTGATTTTAAGGGTTTCATTTAG
1 GGTTTTAATTTT-AGGGTTTCATTTAG
20735669 GGTTTTAATTTTAGGGTTTCACTTTTAG
1 GGTTTTAATTTTAGGGTTTCA--TTTAG
20735697 GGTTT
1 GGTTT
20735702 CATTTAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.30
27 11 0.37
28 10 0.33
ACGTcount: A:0.17, C:0.05, G:0.25, T:0.53
Consensus pattern (26 bp):
GGTTTTAATTTTAGGGTTTCATTTAG
Found at i:20735932 original size:3 final size:3
Alignment explanation
Indices: 20735912--20735962 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
20735902 ATTAAAAATT
* * *
20735912 TTA TTA TGA TTA TGA TTA TTA TTTA TTA TT- TTA TTA TTTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA
20735958 TTA TT
1 TTA TT
20735963 TAATAACTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20735939 original size:7 final size:7
Alignment explanation
Indices: 20735927--20735964 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
20735917 ATGATTATGA
20735927 TTATTAT
1 TTATTAT
20735934 TTATTATT
1 TTATTA-T
20735942 TTATTAT
1 TTATTAT
20735949 TTATT-T
1 TTATTAT
20735955 TTATTAT
1 TTATTAT
20735962 TTA
1 TTA
20735965 ATAACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTAT
Found at i:20735945 original size:15 final size:15
Alignment explanation
Indices: 20735909--20735964 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
20735899 TCCATTAAAA
*
20735909 ATTTTATTA-TGATT
1 ATTTTATTATTTATT
*
20735923 ATGATTATTATTTATT
1 AT-TTTATTATTTATT
20735939 ATTTTATTATTTA-T
1 ATTTTATTATTTATT
20735953 -TTTTATTATTTA
1 ATTTTATTATTTA
20735965 ATAACTCCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 12 0.32
14 3 0.08
15 16 0.43
16 6 0.16
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (15 bp):
ATTTTATTATTTATT
Found at i:20737628 original size:27 final size:28
Alignment explanation
Indices: 20737563--20737634 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
20737553 AAACTTTTCC
*
20737563 TTATTGTTTATTAATTA-ATAATTTTTA
1 TTATTATTTATTAATTATATAATTTTTA
**
20737590 TTATTAACTATTAATTATAT-A-TTTTA
1 TTATTATTTATTAATTATATAATTTTTA
*
20737616 TTATTATTTTATTTATTAT
1 TTATTA-TTTATTAATTAT
20737635 TTTTATCTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 11 0.30
27 24 0.65
28 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
TTATTATTTATTAATTATATAATTTTTA
Found at i:20737631 original size:12 final size:11
Alignment explanation
Indices: 20737603--20737637 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
20737593 TTAACTATTA
20737603 ATTATATATTTT
1 ATTAT-TATTTT
20737615 ATTATTATTTT
1 ATTATTATTTT
20737626 ATTTATTATTTT
1 A-TTATTATTTT
20737638 TATCTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:20738315 original size:35 final size:34
Alignment explanation
Indices: 20738249--20738315 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
20738239 AAATAAATTG
* *
20738249 CAAGTAAAAAATAAACATAATCGAGATTGAATCA
1 CAAGTAAAAAATAAACATAATCGAAACTGAATCA
20738283 CAAGTAAAAAATAAACGATAA-CTGAAACTGAAT
1 CAAGTAAAAAATAAAC-ATAATC-GAAACTGAAT
20738316 TGTAAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (34 bp):
CAAGTAAAAAATAAACATAATCGAAACTGAATCA
Found at i:20738496 original size:33 final size:34
Alignment explanation
Indices: 20738459--20738553 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 34
20738449 ACTAAGTCGA
* *
20738459 AAGTCAGGAATAAAGATGACC-AGACTAAACTGT
1 AAGTCAGAAATAAAGATGACCAAGACTAAACTAT
* *
20738492 AAGTC-GAAAATAATGATGACCAAGATTAAACTAT
1 AAGTCAG-AAATAAAGATGACCAAGACTAAACTAT
* *
20738526 TAGTTAGAAATAAAGAATGACCAAGACT
1 AAGTCAGAAATAAAG-ATGACCAAGACT
20738554 GAATCACAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
32 1 0.02
33 17 0.34
34 20 0.40
35 12 0.24
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (34 bp):
AAGTCAGAAATAAAGATGACCAAGACTAAACTAT
Found at i:20738676 original size:70 final size:71
Alignment explanation
Indices: 20738498--20738704 Score: 238
Period size: 71 Copynumber: 2.9 Consensus size: 71
20738488 CTGTAAGTCG
** * * * * ** * **
20738498 AAAATAATGATGACCAAGATTAAACTATTAGTTAGAAATAAAGAATGACCAAGACTGAATCACAA
1 AAAATAAAAATGACCGAGATTAAACTATAAGTAAAAAATAAAGAACAATCAAGACTGAATTGCAA
20738563 GTCAAA
66 GTCAAA
* * * * *
20738569 AAAATAAAAGTGACCGTGATTGAACTATAAGTAAAAAATAAAGAACAATTAGGACTGAATTGCAA
1 AAAATAAAAATGACCGAGATTAAACTATAAGTAAAAAATAAAGAACAATCAAGACTGAATTGCAA
20738634 GTC-AA
66 GTCAAA
* *
20738639 AAAATAAAAATGACCGAGATTAAATTATAAGTAAAAAATAAAGGACAATCAAGACT-AATTGCAA
1 AAAATAAAAATGACCGAGATTAAACTATAAGTAAAAAATAAAGAACAATCAAGACTGAATTGCAA
20738703 GT
66 GT
20738705 TTGGAAATAA
Statistics
Matches: 113, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
69 10 0.09
70 51 0.45
71 52 0.46
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (71 bp):
AAAATAAAAATGACCGAGATTAAACTATAAGTAAAAAATAAAGAACAATCAAGACTGAATTGCAA
GTCAAA
Found at i:20738745 original size:70 final size:70
Alignment explanation
Indices: 20738547--20738766 Score: 199
Period size: 69 Copynumber: 3.1 Consensus size: 70
20738537 AAAGAATGAC
** * * ***
20738547 CAAGACTGAATCACAAGTCAAAAAAATAAAAGTGACCGTGATTGAACTATAAGTAAAAAATAAAG
1 CAAGACTGAATTGCAAGTC-AAAAAATAAAAATAACCAAAATTGAACTATAAGTAAAAAATAAAG
*
20738612 AACAAT
65 GACAAT
* * * * * * *
20738618 TAGGACTGAATTGCAAGTCAAAAAATAAAAATGACCGAGATTAAATTATAAGTAAAAAATAAAGG
1 CAAGACTGAATTGCAAGTCAAAAAATAAAAATAACCAAAATTGAACTATAAGTAAAAAATAAAGG
20738683 ACAAT
66 ACAAT
**** * * * *
20738688 CAAGACT-AATTGCAAGTTTGGAAATAAAAATAAGCAAAATTGAACTGTAAGTCAAAAATAAAAG
1 CAAGACTGAATTGCAAGTCAAAAAATAAAAATAACCAAAATTGAACTATAAGTAAAAAATAAAGG
**
20738752 ATGAT
66 ACAAT
20738757 CAAGACTGAA
1 CAAGACTGAA
20738767 CCATAGGTTG
Statistics
Matches: 122, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
69 54 0.44
70 53 0.43
71 15 0.12
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.20
Consensus pattern (70 bp):
CAAGACTGAATTGCAAGTCAAAAAATAAAAATAACCAAAATTGAACTATAAGTAAAAAATAAAGG
ACAAT
Found at i:20740980 original size:197 final size:197
Alignment explanation
Indices: 20740643--20741038 Score: 564
Period size: 197 Copynumber: 2.0 Consensus size: 197
20740633 AATCACATCC
* *
20740643 ATCCCCCACATAGAAAATGGCCATGGAGGTGCCAACACATGCAATGGAACTAGAAGAGAATGAAT
1 ATCCCCCACATAGAAAATAGCCATAGAGGTGCCAACACATGCAATGGAACTAGAAGAGAATGAAT
* *
20740708 TTTATCTACATAAAATTGACACTAGTGACATTTTTTTGGCATAATTAATGCAATCATTTTCCAAT
66 TTTATCTACATAAAATTAACACTAGTGACATCTTTTTGGCATAATTAATGCAATCATTTTCCAAT
* * * **
20740773 ATAGACTAGTAATAACCTACCCTCATTATTTTTCTGGCCATCATATATCTTTTGGCATGTGTTCT
131 ATAGACTAGTAATAA-CT-CCCTCATTATCTGTCTAGCCATCATATATCCATTGGCATGTGTTCT
20740838 ACAA
194 ACAA
* * *
20740842 ATCCCCCACATAGAAAATAGCCATAGAGGT-CCAACATATGCAATGGGA-TTGAAGGAGAATGAA
1 ATCCCCCACATAGAAAATAGCCATAGAGGTGCCAACACATGCAATGGAACTAGAA-GAGAATGAA
* * * *
20740905 TTTTATTTATATAAATTTAACACTTGTGACA-CTTTTTGGCATAATTAATGCAATCATTTTCCAA
65 TTTTATCTACATAAAATTAACACTAGTGACATCTTTTTGGCATAATTAATGCAATCATTTTCCAA
* * * *
20740969 TATAGACTAGTAATAACTGCCTTATTATCTGTCTAGCTATCATATGTCCATTGGCATGTGTTCTA
130 TATAGACTAGTAATAACTCCCTCATTATCTGTCTAGCCATCATATATCCATTGGCATGTGTTCTA
20741034 CAA
195 CAA
20741037 AT
1 AT
20741039 ATGCTCATAG
Statistics
Matches: 176, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
195 43 0.24
196 2 0.01
197 52 0.30
198 51 0.29
199 28 0.16
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (197 bp):
ATCCCCCACATAGAAAATAGCCATAGAGGTGCCAACACATGCAATGGAACTAGAAGAGAATGAAT
TTTATCTACATAAAATTAACACTAGTGACATCTTTTTGGCATAATTAATGCAATCATTTTCCAAT
ATAGACTAGTAATAACTCCCTCATTATCTGTCTAGCCATCATATATCCATTGGCATGTGTTCTAC
AA
Found at i:20747418 original size:3 final size:3
Alignment explanation
Indices: 20747412--20747443 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20747402 ATAATAATAA
20747412 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20747444 ATAATTTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20753006 original size:19 final size:19
Alignment explanation
Indices: 20752982--20753020 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20752972 ATGCTCGAAG
20752982 AAAGGTTGCAAGCTATGGA
1 AAAGGTTGCAAGCTATGGA
20753001 AAAGGTTGCAAGCTATGGA
1 AAAGGTTGCAAGCTATGGA
20753020 A
1 A
20753021 GAAATAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (19 bp):
AAAGGTTGCAAGCTATGGA
Found at i:20757767 original size:52 final size:52
Alignment explanation
Indices: 20757707--20757811 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
20757697 TTGCATTTTA
20757707 TTTTAGATAGTATTTGGTTTTGCATTTTAGGCTTAGTTTCATTAAAATTGGT
1 TTTTAGATAGTATTTGGTTTTGCATTTTAGGCTTAGTTTCATTAAAATTGGT
20757759 TTTTAGATAGTATTTGGTTTTGCATTTTAGGCTTAGTTTCATTAAAATTGGT
1 TTTTAGATAGTATTTGGTTTTGCATTTTAGGCTTAGTTTCATTAAAATTGGT
20757811 T
1 T
20757812 ACCATTTAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (52 bp):
TTTTAGATAGTATTTGGTTTTGCATTTTAGGCTTAGTTTCATTAAAATTGGT
Found at i:20759736 original size:45 final size:47
Alignment explanation
Indices: 20759685--20759780 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 47
20759675 TTTTCTAGGC
20759685 TTTTTCATC-ACTTTGTAGCTTT-TTTTT-TTTTTCATTTTTTCA-TCT
1 TTTTTCA-CAACTTTGTAGCTTTATTTTTATTTTT-ATTTTTTCATTCT
* **
20759730 TTTTTCACAACTTTTTCTCTTTATTTTTATTTTTATTTTTTCATTCT
1 TTTTTCACAACTTTGTAGCTTTATTTTTATTTTTATTTTTTCATTCT
20759777 TTTT
1 TTTT
20759781 CAAGCTCCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 1 0.02
45 17 0.39
46 14 0.32
47 12 0.27
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (47 bp):
TTTTTCACAACTTTGTAGCTTTATTTTTATTTTTATTTTTTCATTCT
Found at i:20766848 original size:38 final size:38
Alignment explanation
Indices: 20766795--20766878 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
20766785 TTTTTAACAT
*
20766795 TTTTAAACTTATGTGCC-ACTATTGATGA-AGAGCCCTTA
1 TTTTAAACTTATGTGCCTA-TAATGATGAGA-AGCCCTTA
* *
20766833 TTTTAAATTTGTGTGCCTATAATGATGAGAAGCCCTTA
1 TTTTAAACTTATGTGCCTATAATGATGAGAAGCCCTTA
20766871 TATTTAAA
1 T-TTTAAA
20766879 GTTACATGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
38 32 0.80
39 8 0.20
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (38 bp):
TTTTAAACTTATGTGCCTATAATGATGAGAAGCCCTTA
Found at i:20768235 original size:4 final size:4
Alignment explanation
Indices: 20768226--20768256 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
20768216 TTTTGATAAA
*
20768226 TTAT TTAT TTAT TTAT TTAT GTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
20768257 ATTTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:20770788 original size:12 final size:13
Alignment explanation
Indices: 20770763--20770791 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20770753 CATGAGAAAC
20770763 AATAAACAAAATA
1 AATAAACAAAATA
20770776 AATAAAC-AAATA
1 AATAAACAAAATA
20770788 AATA
1 AATA
20770792 TAAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
AATAAACAAAATA
Found at i:20770796 original size:6 final size:6
Alignment explanation
Indices: 20770785--20770815 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20770775 AAATAAACAA
20770785 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A
20770816 ATGGCCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:20770796 original size:18 final size:17
Alignment explanation
Indices: 20770773--20770816 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
20770763 AATAAACAAA
20770773 ATAAATAAACAAATAAAT
1 ATAAATAAA-AAATAAAT
*
20770791 ATAAATATAAATATAAAT
1 ATAAATA-AAAAATAAAT
20770809 ATAAATAA
1 ATAAATAA
20770817 TGGCCCAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 21 0.88
19 2 0.08
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAATAAAAAATAAAT
Found at i:20772667 original size:3 final size:3
Alignment explanation
Indices: 20772661--20772692 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20772651 GCTATTATTA
20772661 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
20772693 ATCATTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:20777124 original size:17 final size:19
Alignment explanation
Indices: 20777090--20777127 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
20777080 TTTTTTAGGC
*
20777090 TTTTTGGATTTACTAGTTT
1 TTTTTGGATTTACCAGTTT
20777109 TTTTTGG-TTT-CCAGTTT
1 TTTTTGGATTTACCAGTTT
20777126 TT
1 TT
20777128 CCAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.11, C:0.08, G:0.16, T:0.66
Consensus pattern (19 bp):
TTTTTGGATTTACCAGTTT
Found at i:20784332 original size:42 final size:41
Alignment explanation
Indices: 20784229--20784499 Score: 310
Period size: 42 Copynumber: 6.6 Consensus size: 41
20784219 AGGCTCAATG
* * *
20784229 ACTTTTGAAAGCAAATTGCTCCTCTAAATAAAGGCACCACA
1 ACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
* *
20784270 AC-TTTGAAAGTAAATTGCTCCTCCAAACAGAGGCACCGCA
1 ACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
** **
20784310 ACTTTTGCAAAGTAAATTGCTCCTCTAAACAGAGGTGCCTTA
1 ACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
*
20784352 ACTTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACA
1 ACTTTT-GAAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
* * * **
20784394 ACTTTTGAAAGTAAATTACTCCTCTAAATAGAGGTAACCATG
1 ACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGG-CACCACA
* * * *
20784436 ACTTTGGAAAATAAATTGCTCATCTAAACAGAGGCACCACG
1 ACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
** *
20784477 ACTTTAAAAAATAAATTGCTCCT
1 ACTTTTGAAAGTAAATTGCTCCT
20784500 TAACAATCAT
Statistics
Matches: 197, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
40 35 0.18
41 58 0.29
42 103 0.52
43 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (41 bp):
ACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACA
Found at i:20784453 original size:83 final size:82
Alignment explanation
Indices: 20784229--20784499 Score: 346
Period size: 83 Copynumber: 3.3 Consensus size: 82
20784219 AGGCTCAATG
* * * *
20784229 ACTTTTGAAAGCAAATTGCTCCTCTAAATAAAGGCACCACAACTTT-GAAAGTAAATTGCTCCTC
1 ACTTTTGAAAGTAAATTGCTCCTCTAAATAGAGGTACCATAACTTTGGAAAGTAAATTGCTCCTC
* *
20784293 CAAACAGAGGCACCGCA
66 TAAACAGAGGCACCACA
* * *
20784310 ACTTTTGCAAAGTAAATTGCTCCTCTAAACAGAGGTGCCTTAACTTTTGGAAAGTAAATTGCTCC
1 ACTTTTG-AAAGTAAATTGCTCCTCTAAATAGAGGTACCATAAC-TTTGGAAAGTAAATTGCTCC
*
20784375 TCTAAATAGAGGCACCACA
64 TCTAAACAGAGGCACCACA
* * * *
20784394 ACTTTTGAAAGTAAATTACTCCTCTAAATAGAGGTAACCATGACTTTGGAAAATAAATTGCTCAT
1 ACTTTTGAAAGTAAATTGCTCCTCTAAATAGAGGT-ACCATAACTTTGGAAAGTAAATTGCTCCT
*
20784459 CTAAACAGAGGCACCACG
65 CTAAACAGAGGCACCACA
** *
20784477 ACTTTAAAAAATAAATTGCTCCT
1 ACTTTTGAAAGTAAATTGCTCCT
20784500 TAACAATCAT
Statistics
Matches: 163, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
81 7 0.04
82 29 0.18
83 83 0.51
84 44 0.27
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (82 bp):
ACTTTTGAAAGTAAATTGCTCCTCTAAATAGAGGTACCATAACTTTGGAAAGTAAATTGCTCCTC
TAAACAGAGGCACCACA
Found at i:20784462 original size:125 final size:123
Alignment explanation
Indices: 20784229--20784469 Score: 342
Period size: 125 Copynumber: 1.9 Consensus size: 123
20784219 AGGCTCAATG
*
20784229 ACTTTTGAAAGCAAATTGCTCCTCTAAATAAAGGCACCACAACTTTGAAAGTAAATTGCTCCTCC
1 ACTTTTGAAAGCAAATTGCTCCTCTAAATAAAGGCACCACAACTTTGAAAGTAAATTACTCCTCC
* * *
20784294 AAACAGAGGCACCGCAACTTTTGCAAAGTAAATTGCTCCTCTAAACAGAGGTGCCTTA
66 AAACAGAGGCAACGCAACTTTTGCAAAATAAATTGCTCATCTAAACAGAGGTGCCTTA
* *
20784352 ACTTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACAACTTTTGAAAGTAAATTACTCCT
1 ACTTTT-GAAAGCAAATTGCTCCTCTAAATAAAGGCACCACAAC-TTTGAAAGTAAATTACTCCT
* * * *
20784417 CTAAATAGAGGTAAC-CATGAC-TTTGGAAAATAAATTGCTCATCTAAACAGAGG
64 CCAAACAGAGGCAACGCA--ACTTTTGCAAAATAAATTGCTCATCTAAACAGAGG
20784470 CACCACGACT
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
123 6 0.06
124 37 0.36
125 59 0.57
126 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (123 bp):
ACTTTTGAAAGCAAATTGCTCCTCTAAATAAAGGCACCACAACTTTGAAAGTAAATTACTCCTCC
AAACAGAGGCAACGCAACTTTTGCAAAATAAATTGCTCATCTAAACAGAGGTGCCTTA
Found at i:20786257 original size:32 final size:32
Alignment explanation
Indices: 20786221--20786317 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 32
20786211 TCCTTTCATC
* * *
20786221 TTTTTTTTATTTTTTTTTCA-TTTTCCCCCTTT
1 TTTTTTTT-TTTTTTTTTCACCTTTCACCATTT
* *
20786253 TTTTTCTTTTTTTTTTCCACCTTTCACCATTT
1 TTTTTTTTTTTTTTTTTCACCTTTCACCATTT
* *
20786285 TTTTTTCTTTTTTTTTTTTATCTTTCATCCATT
1 TTTTTT-TTTTTTTTTTTCACCTTTCA-CCATT
20786318 GTTGATATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 10 0.19
32 21 0.40
33 17 0.32
34 5 0.09
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (32 bp):
TTTTTTTTTTTTTTTTTCACCTTTCACCATTT
Found at i:20786262 original size:24 final size:23
Alignment explanation
Indices: 20786230--20786276 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
20786220 CTTTTTTTTA
*
20786230 TTTTTTTTTCATTTTCCCCCTTT
1 TTTTTTTTTCATTTTCCACCTTT
**
20786253 TTTTTCTTTTTTTTTTCCACCTTT
1 TTTTT-TTTTCATTTTCCACCTTT
20786277 CACCATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTTTTTCATTTTCCACCTTT
Found at i:20786310 original size:33 final size:34
Alignment explanation
Indices: 20786250--20786317 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
20786240 ATTTTCCCCC
20786250 TTTTTTTTCTTTTTTTTTTCCACCTTTCA-CCAT
1 TTTTTTTTCTTTTTTTTTTCCACCTTTCATCCAT
** *
20786283 TTTTTTTTCTTTTTTTTTTTTATCTTTCATCCAT
1 TTTTTTTTCTTTTTTTTTTCCACCTTTCATCCAT
20786317 T
1 T
20786318 GTTGATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (34 bp):
TTTTTTTTCTTTTTTTTTTCCACCTTTCATCCAT
Found at i:20801386 original size:26 final size:26
Alignment explanation
Indices: 20801350--20801401 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20801340 ACTAAAAAAC
*
20801350 CTAATGGGTCACACACAATAGGATAA
1 CTAATGGGTCACACACAATAAGATAA
20801376 CTAATGGGTCACACACAATAAGATAA
1 CTAATGGGTCACACACAATAAGATAA
20801402 TTGTGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (26 bp):
CTAATGGGTCACACACAATAAGATAA
Found at i:20802430 original size:13 final size:13
Alignment explanation
Indices: 20802406--20802528 Score: 113
Period size: 13 Copynumber: 9.5 Consensus size: 13
20802396 CATAAAATTT
*
20802406 TGAAATCCTAAAA
1 TGAAACCCTAAAA
*
20802419 TGAAACCTTAAAA
1 TGAAACCCTAAAA
20802432 T-AGAACCCTAAAA
1 TGA-AACCCTAAAA
** *
20802445 CAAAACCCTAAAG
1 TGAAACCCTAAAA
*
20802458 TGAAACCCTAACA
1 TGAAACCCTAAAA
*
20802471 CGAAACCCTAAAA
1 TGAAACCCTAAAA
* * *
20802484 GGAAGCCTTAAAA
1 TGAAACCCTAAAA
*
20802497 TGAAACCTTAAAA
1 TGAAACCCTAAAA
* *
20802510 TGGAACCCCAAAA
1 TGAAACCCTAAAA
20802523 TGAAAC
1 TGAAAC
20802529 TTTAAGAGTG
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
12 1 0.01
13 86 0.98
14 1 0.01
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.15
Consensus pattern (13 bp):
TGAAACCCTAAAA
Found at i:20803131 original size:31 final size:31
Alignment explanation
Indices: 20803073--20803131 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
20803063 CATAATATAA
* **
20803073 AAAATAAAAGGATTATTTAAGGTATTTTTAT
1 AAAATAAAAAGATTATTTAAGACATTTTTAT
*
20803104 AAAATAAAAATATTATTTAAGACATTTT
1 AAAATAAAAAGATTATTTAAGACATTTT
20803132 CTGTATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (31 bp):
AAAATAAAAAGATTATTTAAGACATTTTTAT
Found at i:20805780 original size:111 final size:111
Alignment explanation
Indices: 20805661--20805860 Score: 276
Period size: 111 Copynumber: 1.8 Consensus size: 111
20805651 GTCCTTGCCT
* *
20805661 TTTTTATCTTAAAAAAAAATCTTTTCAACAAAAATTACATTTTTATT-TTAAAAACGTTGTCTTT
1 TTTTTATCTTAAAAAAAAATCTTTTCAACAAAAACTACATTTTT-TTCTTAAAAACGTTATCTTT
*
20805725 CTTGAATTCTAAAAAATATATTTTTCATGTTTTCCATAAAAATTGCA
65 ATTGAATTCTAAAAAATATATTTTTCATGTTTTCCATAAAAATTGCA
* * *** * *
20805772 TTTTTATCTTAGAATATCGTCTTTTTAACAAAGACTACATTTTTTTCTTAAAAACGTTATCTTTA
1 TTTTTATCTTAAAAAAAAATCTTTTCAACAAAAACTACATTTTTTTCTTAAAAACGTTATCTTTA
* *
20805837 TTGAATTTTAAAAACTATATTTTT
66 TTGAATTCTAAAAAATATATTTTT
20805861 TTAATGTTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
110 2 0.03
111 74 0.97
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (111 bp):
TTTTTATCTTAAAAAAAAATCTTTTCAACAAAAACTACATTTTTTTCTTAAAAACGTTATCTTTA
TTGAATTCTAAAAAATATATTTTTCATGTTTTCCATAAAAATTGCA
Found at i:20805887 original size:111 final size:111
Alignment explanation
Indices: 20805680--20805894 Score: 272
Period size: 111 Copynumber: 1.9 Consensus size: 111
20805670 TAAAAAAAAA
* * *
20805680 TCTTTTCAACAAAAATTACATTTTTATTTTAAAAACGTTGTCTTTCTTGAATTCTAAAAAATATA
1 TCTTTTCAACAAAAACTACATTTTTATTTTAAAAACGTTATCTTTATTGAATTCTAAAAAATATA
* * * *
20805745 TTTTTCATGTTTTCCATAAAAATTGCATTTTTATCTTAGAATATCG
66 TTTTTAATGTTTTCAACAAAAATTTCATTTTTATCTTAGAATATCG
* * *
20805791 TCTTTTTAACAAAGACTACATTTTT-TTCTTAAAAACGTTATCTTTATTGAATTTTAAAAACTAT
1 TCTTTTCAACAAAAACTACATTTTTATT-TTAAAAACGTTATCTTTATTGAATTCTAAAAA--AT
* * *
20805855 ATTTTTTTAATGTTTTCAACAAAGATTT-TTTTTTATCTTA
63 ATATTTTTAATGTTTTCAACAAAAATTTCATTTTTATCTTA
20805895 AAAACATTAT
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
110 2 0.02
111 51 0.58
112 11 0.12
113 24 0.27
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (111 bp):
TCTTTTCAACAAAAACTACATTTTTATTTTAAAAACGTTATCTTTATTGAATTCTAAAAAATATA
TTTTTAATGTTTTCAACAAAAATTTCATTTTTATCTTAGAATATCG
Found at i:20805908 original size:111 final size:110
Alignment explanation
Indices: 20805659--20805909 Score: 258
Period size: 111 Copynumber: 2.3 Consensus size: 110
20805649 CTGTCCTTGC
* * *
20805659 CTTTTTTATCTTAAAAA-AAAATCTTTTCAACAAAAATTACATTTTTATTTTAAAAACGTTGTCT
1 CTTTTTTATCTTAAAAACAATAT-TTTT-AACAAAAACTACATTTTTATTTTAAAAACGTTATCT
* * * *
20805723 TTCTTGAATTCTAAAAAATATATTTTTCATGTTTTCCATAAAAATTG
64 TTATTGAATTCTAAAAAATATATTTTTAATGTTTTCAACAAAAATTG
* * * * *
20805770 CATTTTTATCTTAGAATATC-GTCTTTTTAACAAAGACTACATTTTT-TTCTTAAAAACGTTATC
1 CTTTTTTATCTTA-AA-AACAATATTTTTAACAAAAACTACATTTTTATT-TTAAAAACGTTATC
* * *
20805833 TTTATTGAATTTTAAAAACTATATTTTTTTAATGTTTTCAACAAAGATT-
63 TTTATTGAATTCTAAAAA--ATATATTTTTAATGTTTTCAACAAAAATTG
* *
20805882 TTTTTTTATCTTAAAAACATTATTTTTA
1 CTTTTTTATCTTAAAAACAATATTTTTA
20805910 TTGAATTTTG
Statistics
Matches: 113, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
110 4 0.04
111 66 0.58
112 17 0.15
113 26 0.23
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (110 bp):
CTTTTTTATCTTAAAAACAATATTTTTAACAAAAACTACATTTTTATTTTAAAAACGTTATCTTT
ATTGAATTCTAAAAAATATATTTTTAATGTTTTCAACAAAAATTG
Found at i:20805959 original size:73 final size:73
Alignment explanation
Indices: 20805793--20805979 Score: 206
Period size: 73 Copynumber: 2.6 Consensus size: 73
20805783 GAATATCGTC
* * * * *
20805793 TTTTTAACAAAGACTACATTTTTT-TCTTAAAAACGTTATCTTTATTGAATTTTAAAAACTATAT
1 TTTTCAACAAAGACGATATTTTTTATCTTAAAAACATTATTTTTATTGAATTTTAAAAACTATA-
*
20805857 TTTTTTAATG
65 -TTTTTAATA
* *
20805867 TTTTCAACAAAGA--TTTTTTTTTATCTTAAAAACATTATTTTTATTGAATTTTGAAAAA-TATA
1 TTTTCAACAAAGACGATATTTTTTATCTTAAAAACATTATTTTTATTGAATTTT-AAAAACTATA
*
20805929 -TTTTCATA
65 TTTTTAATA
* *
20805937 TTTTCAACAAAGACGATA-TTTTTATCTTAGAAACATTGTTTTT
1 TTTTCAACAAAGACGATATTTTTTATCTTAAAAACATTATTTTT
20805980 CAATAAAGAC
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
70 19 0.20
71 23 0.24
72 7 0.07
73 31 0.32
74 17 0.18
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (73 bp):
TTTTCAACAAAGACGATATTTTTTATCTTAAAAACATTATTTTTATTGAATTTTAAAAACTATAT
TTTTAATA
Found at i:20806259 original size:301 final size:301
Alignment explanation
Indices: 20805918--20806499 Score: 1155
Period size: 301 Copynumber: 1.9 Consensus size: 301
20805908 TATTGAATTT
20805918 TGAAAAATATATTTTCATATTTTCAACAAAGACGATATTTTTATCTTAGAAACATTGTTTTTCAA
1 TGAAAAATATATTTTCATATTTTCAACAAAGACGATATTTTTATCTTAGAAACATTGTTTTTCAA
20805983 TAAAGACTGTGTTTTCTATGTTAGAAATGTCATCTTTATTGAATTCTAAAAAATATTTTTTTTCA
66 TAAAGACTGTGTTTTCTATGTTAGAAATGTCATCTTTATTGAATTCTAAAAAATATTTTTTTTCA
*
20806048 TGTTTACAAATATTGCGTTTTTATTTTTAAAATGTTATTTTTTTAATAAAAGCTGCATTTTTATC
131 TGTTTACAAATATTGCGTTTTTAATTTTAAAATGTTATTTTTTTAATAAAAGCTGCATTTTTATC
20806113 TTAAAAATTATCTTTGTTAAATTTTGAAAAAAAAAATTCATATTTTTAACAAAGATCATGTTTTT
196 TTAAAAATTATCTTTGTTAAATTTTGAAAAAAAAAATTCATATTTTTAACAAAGATCATGTTTTT
20806178 TATTTTAAAAAAGTTGTCTTTCATATTTTCATATTTTCATA
261 TATTTTAAAAAAGTTGTCTTTCATATTTTCATATTTTCATA
20806219 TGAAAAATATATTTTCATATTTTCAACAAAGACGATATTTTTATCTTAGAAACATTGTTTTTCAA
1 TGAAAAATATATTTTCATATTTTCAACAAAGACGATATTTTTATCTTAGAAACATTGTTTTTCAA
20806284 TAAAGACTGTGTTTTCTATGTTAGAAATGTCATCTTTATTGAATTCTAAAAAATATTTTTTTTCA
66 TAAAGACTGTGTTTTCTATGTTAGAAATGTCATCTTTATTGAATTCTAAAAAATATTTTTTTTCA
20806349 TGTTTACAAATATTGCGTTTTTAATTTTAAAATGTTATTTTTTTAATAAAAGCTGCATTTTTATC
131 TGTTTACAAATATTGCGTTTTTAATTTTAAAATGTTATTTTTTTAATAAAAGCTGCATTTTTATC
20806414 TTAAAAATTATCTTTGTTAAATTTTGAAAAAAAAAATTCATATTTTTAACAAAGATCATGTTTTT
196 TTAAAAATTATCTTTGTTAAATTTTGAAAAAAAAAATTCATATTTTTAACAAAGATCATGTTTTT
20806479 TATTTTAAAAAAGTTGTCTTT
261 TATTTTAAAAAAGTTGTCTTT
20806500 GTTGAATTAT
Statistics
Matches: 280, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
301 280 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (301 bp):
TGAAAAATATATTTTCATATTTTCAACAAAGACGATATTTTTATCTTAGAAACATTGTTTTTCAA
TAAAGACTGTGTTTTCTATGTTAGAAATGTCATCTTTATTGAATTCTAAAAAATATTTTTTTTCA
TGTTTACAAATATTGCGTTTTTAATTTTAAAATGTTATTTTTTTAATAAAAGCTGCATTTTTATC
TTAAAAATTATCTTTGTTAAATTTTGAAAAAAAAAATTCATATTTTTAACAAAGATCATGTTTTT
TATTTTAAAAAAGTTGTCTTTCATATTTTCATATTTTCATA
Found at i:20809986 original size:58 final size:58
Alignment explanation
Indices: 20809896--20810013 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
20809886 TCACATTCAG
* *
20809896 TGAGGTTTGCTTTTATCAACAGCAGATTATCATCTGTATAGAACAAGTGAGTTATCCT
1 TGAGGTTTGCTTTTATCAACAGCAGATTATCATATGTAAAGAACAAGTGAGTTATCCT
20809954 TGAGGTTTGCTTTTATCAACAGCAGATTATCATATGTAAAGAACAAGTGAGTTATCCT
1 TGAGGTTTGCTTTTATCAACAGCAGATTATCATATGTAAAGAACAAGTGAGTTATCCT
20810012 TG
1 TG
20810014 GGCCATTGGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (58 bp):
TGAGGTTTGCTTTTATCAACAGCAGATTATCATATGTAAAGAACAAGTGAGTTATCCT
Found at i:20814547 original size:18 final size:18
Alignment explanation
Indices: 20814524--20814576 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
20814514 TTTAACTATC
20814524 ATATGAATAATTTTTTAA
1 ATATGAATAATTTTTTAA
20814542 ATATGAAT-A--TTTT-A
1 ATATGAATAATTTTTTAA
* *
20814556 ATATAAATATTTTTTTAA
1 ATATGAATAATTTTTTAA
20814574 ATA
1 ATA
20814577 AACAAAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
17 5 0.17
18 12 0.41
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATATGAATAATTTTTTAA
Found at i:20814564 original size:14 final size:15
Alignment explanation
Indices: 20814536--20814568 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20814526 ATGAATAATT
*
20814536 TTTTAAATATGAATA
1 TTTTAAATATAAATA
20814551 TTTT-AATATAAATA
1 TTTTAAATATAAATA
20814565 TTTT
1 TTTT
20814569 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTAAATATAAATA
Found at i:20815836 original size:17 final size:17
Alignment explanation
Indices: 20815812--20815852 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
20815802 TATGTTATCT
20815812 AATT-ATTTAT-GCTTAA
1 AATTAATTTATAG-TTAA
20815828 AATTAATTTATAGTTAA
1 AATTAATTTATAGTTAA
20815845 AATATAAT
1 AAT-TAAT
20815853 GAAAAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (17 bp):
AATTAATTTATAGTTAA
Found at i:20816274 original size:8 final size:8
Alignment explanation
Indices: 20816261--20816286 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20816251 ATGGATTCAA
20816261 AATATTAT
1 AATATTAT
20816269 AATATTAT
1 AATATTAT
20816277 AATATTAT
1 AATATTAT
20816285 AA
1 AA
20816287 AATTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATATTAT
Found at i:20816443 original size:14 final size:14
Alignment explanation
Indices: 20816426--20816452 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20816416 ATTCATGTTT
20816426 TTTAAAAAATTATG
1 TTTAAAAAATTATG
20816440 TTTAAAAAATTAT
1 TTTAAAAAATTAT
20816453 CAAGTAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TTTAAAAAATTATG
Found at i:20817034 original size:2 final size:2
Alignment explanation
Indices: 20817023--20817081 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
20817013 CTTTATATCT
* * * *
20817023 TA TA -A TA TA TA TA AA TA TA TA TA TA CA TG TA CA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20817063 TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
20817082 AGGTCAAAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:20819503 original size:40 final size:41
Alignment explanation
Indices: 20819459--20819538 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
20819449 GCATAATTTT
* *
20819459 TTTAAGTATAGATTCAAAATAT-TATTATATTAAAAAATTA
1 TTTAAGTATAAATTCAAAATATATATAATATTAAAAAATTA
* * * *
20819499 TTTAATTTTAAATTTAAAATATATATAATATTATAAAATT
1 TTTAAGTATAAATTCAAAATATATATAATATTAAAAAATT
20819539 TTAACATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 18 0.55
41 15 0.45
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (41 bp):
TTTAAGTATAAATTCAAAATATATATAATATTAAAAAATTA
Found at i:20819548 original size:41 final size:40
Alignment explanation
Indices: 20819474--20819550 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
20819464 GTATAGATTC
* *
20819474 AAAATATTATTATATTAAAAAATTATTTAATTTTAAATTT
1 AAAATATTATAATATTAAAAAATTATTAAATTTTAAATTT
*
20819514 AAAATATATATAATATTATAAAATT-TTAACATTTTAA
1 AAAATAT-TATAATATTAAAAAATTATTAA-ATTTTAA
20819551 TAATAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 10 0.31
41 22 0.69
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (40 bp):
AAAATATTATAATATTAAAAAATTATTAAATTTTAAATTT
Found at i:20820278 original size:2 final size:2
Alignment explanation
Indices: 20820267--20820329 Score: 69
Period size: 2 Copynumber: 33.0 Consensus size: 2
20820257 CTTTATATCT
* * * *
20820267 TA TA -A TA TA TA TA AA TA TA TA TA TA TA TA CA TG TA CA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20820307 TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
20820330 AGGTCAAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:20821304 original size:2 final size:2
Alignment explanation
Indices: 20821297--20821322 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20821287 AAATTTTATC
20821297 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20821323 GTTAGATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20825656 original size:3 final size:3
Alignment explanation
Indices: 20825648--20825697 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
20825638 ATACATTAGA
20825648 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20825696 AA
1 AA
20825698 CATTATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20825705 original size:3 final size:3
Alignment explanation
Indices: 20825699--20825729 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20825689 TAATAATAAC
20825699 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20825730 GCAATGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20833801 original size:21 final size:22
Alignment explanation
Indices: 20833761--20833801 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20833751 GAGAGGGGTT
* *
20833761 GAAACAACGGTGGGTGAAACAG
1 GAAACAACGGTGGATAAAACAG
20833783 GAAACAA-GGTGGATAAAAC
1 GAAACAACGGTGGATAAAAC
20833802 GGAGGCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.12, G:0.32, T:0.10
Consensus pattern (22 bp):
GAAACAACGGTGGATAAAACAG
Found at i:20835140 original size:19 final size:19
Alignment explanation
Indices: 20835113--20835363 Score: 150
Period size: 19 Copynumber: 13.8 Consensus size: 19
20835103 AGGTTTCAAG
20835113 TTCACAAGAAATTCAAAGA
1 TTCACAAGAAATTCAAAGA
*
20835132 TTCATAAGAAATTCAAAGA
1 TTCACAAGAAATTCAAAGA
* ** *
20835151 CTCACAAGAGCTTC--AGT
1 TTCACAAGAAATTCAAAGA
** * *
20835168 TTCGTAGGAAATT--AAGG
1 TTCACAAGAAATTCAAAGA
*
20835185 TTCACAAAAAATTCAAAGA
1 TTCACAAGAAATTCAAAGA
***
20835204 TTTGTAAGAAATTCAAAGA
1 TTCACAAGAAATTCAAAGA
20835223 TT-ATCAAGAAATTCAAAGA
1 TTCA-CAAGAAATTCAAAGA
*
20835242 TTTACAAGAAATTCAAAGA
1 TTCACAAGAAATTCAAAGA
** ** *
20835261 TTTGCAAGAGCTTTC---GT
1 TTCACAAGA-AATTCAAAGA
* * *
20835278 TTTATAAGAAATTC--AGG
1 TTCACAAGAAATTCAAAGA
*
20835295 TTCACAAGAAATTCAAAGG
1 TTCACAAGAAATTCAAAGA
*
20835314 TT-GCAAGAAATTC--AGA
1 TTCACAAGAAATTCAAAGA
*
20835330 TTCACAAGAACTTCAAAGA
1 TTCACAAGAAATTCAAAGA
* *
20835349 TTCATAAGAGATTCA
1 TTCACAAGAAATTCA
20835364 GGTTTGCAAA
Statistics
Matches: 178, Mismatches: 42, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
16 7 0.04
17 50 0.28
18 10 0.06
19 107 0.60
20 4 0.02
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.27
Consensus pattern (19 bp):
TTCACAAGAAATTCAAAGA
Found at i:20835310 original size:110 final size:107
Alignment explanation
Indices: 20835113--20835363 Score: 308
Period size: 110 Copynumber: 2.3 Consensus size: 107
20835103 AGGTTTCAAG
* * *
20835113 TTCACAAGAAATTCAAAGATTCATAAGAAATTCAAAGACTCACAAGAGCTTCAGTTTCGTAGGAA
1 TTCACAAGAAATTCAAAGATTCACAAGAAATTCAAAGACTCACAAGAGCTTCAGTTTCATAAGAA
* *
20835178 ATTAAGGTTCACAAAAAATTCAAAGATTTGTAAGAAATTCAAAGA
66 ATTAAGGTTCACAAAAAATTCAAAG-GTTGCAAGAAATTC--AGA
* * ** *
20835223 TT-ATCAAGAAATTCAAAGATTTACAAGAAATTCAAAGATTTGCAAGAGCTTTC-GTTTTATAAG
1 TTCA-CAAGAAATTCAAAGATTCACAAGAAATTCAAAGACTCACAAGAGC-TTCAGTTTCATAAG
* *
20835286 AAATTCAGGTTCACAAGAAATTCAAAGGTTGCAAGAAATTCAGA
64 AAATTAAGGTTCACAAAAAATTCAAAGGTTGCAAGAAATTCAGA
* * *
20835330 TTCACAAGAACTTCAAAGATTCATAAGAGATTCA
1 TTCACAAGAAATTCAAAGATTCACAAGAAATTCA
20835364 GGTTTGCAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
107 31 0.25
108 1 0.01
109 13 0.11
110 74 0.61
111 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.27
Consensus pattern (107 bp):
TTCACAAGAAATTCAAAGATTCACAAGAAATTCAAAGACTCACAAGAGCTTCAGTTTCATAAGAA
ATTAAGGTTCACAAAAAATTCAAAGGTTGCAAGAAATTCAGA
Found at i:20835575 original size:22 final size:21
Alignment explanation
Indices: 20835550--20835611 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
20835540 AAACTTTTGG
*
20835550 GATTTACATCCGAAATTTTGAA
1 GATTTACATCAGAAATTTT-AA
* *
20835572 GATTCACATTCAAAAATTTTAA
1 GATTTACA-TCAGAAATTTTAA
**
20835594 GATTTACATTTGAAATTT
1 GATTTACATCAGAAATTT
20835612 CAAAAATTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 7 0.22
22 16 0.50
23 9 0.28
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (21 bp):
GATTTACATCAGAAATTTTAA
Found at i:20835598 original size:44 final size:44
Alignment explanation
Indices: 20835534--20835707 Score: 125
Period size: 44 Copynumber: 3.9 Consensus size: 44
20835524 TAAAGATTTT
* ** ** *
20835534 CATTCAAAACTTTTGGGATTTACATCCGAAATTTTGAAGATTCA
1 CATTCAAAAATTTTAAGATTTACATCCGAAATTTCAAAAATTCA
** *
20835578 CATTCAAAAATTTTAAGATTTACATTTGAAATTTCAAAAATTCT
1 CATTCAAAAATTTTAAGATTTACATCCGAAATTTCAAAAATTCA
* * ** * * **
20835622 CATTTGAAAAATTTTAAGATTCACATCTAAAAGTT-AAAGATTTT
1 CA-TTCAAAAATTTTAAGATTTACATCCGAAATTTCAAAAATTCA
* * * * *
20835666 CATTGAAAAATTTTAGGATTTCGCATCCAAAATTTAAAAAAT
1 CATTCAAAAATTTTAAGATTT-ACATCCGAAATTTCAAAAAT
20835708 CTCATTTGAA
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
43 17 0.16
44 56 0.53
45 32 0.30
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.37
Consensus pattern (44 bp):
CATTCAAAAATTTTAAGATTTACATCCGAAATTTCAAAAATTCA
Found at i:20838051 original size:30 final size:30
Alignment explanation
Indices: 20838017--20838111 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
20838007 TTTTTTAGAA
20838017 AACTTATTTTCAAAGAAAATTGATACTTTC
1 AACTTATTTTCAAAGAAAATTGATACTTTC
* * * * *****
20838047 AACTTTTTTCTCAAA-AATATTTAAAAAAAA
1 AACTTATTT-TCAAAGAAAATTGATACTTTC
20838077 AACTTATTTTCAAAGAAAATTGATACTTTC
1 AACTTATTTTCAAAGAAAATTGATACTTTC
20838107 AACTT
1 AACTT
20838112 GATACTTTCA
Statistics
Matches: 45, Mismatches: 18, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
29 5 0.11
30 35 0.78
31 5 0.11
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (30 bp):
AACTTATTTTCAAAGAAAATTGATACTTTC
Found at i:20838097 original size:60 final size:59
Alignment explanation
Indices: 20837974--20838111 Score: 215
Period size: 60 Copynumber: 2.3 Consensus size: 59
20837964 TTGTACAAGA
* *** *
20837974 AAAATTGATACTTTCAAC-TTTTTCTCGAAAATATTTTTTAGAAAACTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTTTCTCAAAAATATTTAAAAAAAAACTTATTTTCAAAG
20838032 AAAATTGATACTTTCAACTTTTTTCTCAAAAATATTTAAAAAAAAAACTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTTTCTCAAAAATATTT-AAAAAAAAACTTATTTTCAAAG
20838092 AAAATTGATACTTTCAACTT
1 AAAATTGATACTTTCAACTT
20838112 GATACTTTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 18 0.25
59 17 0.23
60 38 0.52
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTTTCTCAAAAATATTTAAAAAAAAACTTATTTTCAAAG
Found at i:20838115 original size:14 final size:14
Alignment explanation
Indices: 20838096--20838125 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20838086 TCAAAGAAAA
20838096 TTGATACTTTCAAC
1 TTGATACTTTCAAC
20838110 TTGATACTTTCAAC
1 TTGATACTTTCAAC
20838124 TT
1 TT
20838126 CTCCTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (14 bp):
TTGATACTTTCAAC
Found at i:20838167 original size:72 final size:74
Alignment explanation
Indices: 20838036--20838183 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 74
20838026 TCAAAGAAAA
* *
20838036 TTGATACTTTCAACTTTTTTCTCAAAAATATTTAAAAAAAAAACTTATTTTCAAAGAAAATTGAT
1 TTGATACTTTCAACTTTCTCCTCAAAAATATTTAAAAAAAAAACTTATTTTCAAAGAAAATTGAT
20838101 ACTTTCAAC
66 ACTTTCAAC
*** * *
20838110 TTGATACTTTCAAC-TTCTCCTCAAAAATATTT-TTTAGAAAACTTATTTTCAAGGAAAATTGAT
1 TTGATACTTTCAACTTTCTCCTCAAAAATATTTAAAAAAAAAACTTATTTTCAAAGAAAATTGAT
20838173 ACTTTCAAC
66 ACTTTCAAC
20838182 TT
1 TT
20838184 TTCCTCAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 37 0.55
73 16 0.24
74 14 0.21
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (74 bp):
TTGATACTTTCAACTTTCTCCTCAAAAATATTTAAAAAAAAAACTTATTTTCAAAGAAAATTGAT
ACTTTCAAC
Found at i:20838238 original size:5 final size:5
Alignment explanation
Indices: 20838228--20838285 Score: 71
Period size: 5 Copynumber: 10.8 Consensus size: 5
20838218 AGAAAATCAA
*
20838228 AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAGAT AAAAAT AGAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAA-AT -AAAAT AAAAT AAAAT
20838277 AAAAT AAAA
1 AAAAT AAAA
20838286 AATACTAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
5 30 0.62
6 15 0.31
7 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20838323 original size:3 final size:3
Alignment explanation
Indices: 20838315--20838349 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
20838305 TTAATCAATA
* *
20838315 AAT AAT AAT AAC AAT AAT AAT AAG AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20838350 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:20838332 original size:12 final size:12
Alignment explanation
Indices: 20838315--20838349 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
20838305 TTAATCAATA
20838315 AATAATAATAAC
1 AATAATAATAAC
*
20838327 AATAATAATAAG
1 AATAATAATAAC
20838339 AATAATAATAA
1 AATAATAATAA
20838350 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:20839091 original size:3 final size:3
Alignment explanation
Indices: 20839085--20839191 Score: 85
Period size: 3 Copynumber: 34.7 Consensus size: 3
20839075 AATAAGAAGA
* * *
20839085 AAT AAT AAT AAT AAT AAC AAA AAT AAT -AT ATT AAT AGAT AACT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT
* *
20839130 AAG AA- AAT AAT AAT AAT AAT AAT AAT AGAT AAAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT
*
20839176 AGAT AAAT TAT AAT AA
1 A-AT -AAT AAT AAT AA
20839192 AAAAACATAT
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.07
3 64 0.74
4 14 0.16
5 2 0.02
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20839164 original size:20 final size:20
Alignment explanation
Indices: 20839084--20839301 Score: 116
Period size: 20 Copynumber: 10.8 Consensus size: 20
20839074 GAATAAGAAG
*
20839084 AAATAATAATAATAATA-AC
1 AAATAATAATAATAATAGAT
20839103 AAA-AATAATATATTAATAGAT
1 AAATAATAATA-A-TAATAGAT
* *
20839124 AACTAA-AAGAA-AATA-AT
1 AAATAATAATAATAATAGAT
20839141 -AATAATAATAATAATAGAT
1 AAATAATAATAATAATAGAT
*
20839160 AAATAATACTAATAATAGAT
1 AAATAATAATAATAATAGAT
* * * *
20839180 AAATTATAATAAAAAAACAT
1 AAATAATAATAATAATAGAT
* *
20839200 ATATATTAATAGATAAATA-A-
1 AAATAATAATA-AT-AATAGAT
**
20839220 AAA-AAT-ATGTTAATAGAT
1 AAATAATAATAATAATAGAT
*
20839238 AAA-AATAAATATATTAGTAGAT
1 AAATAAT-AATA-A-TAATAGAT
* *
20839260 AAATAATAAATATATTTAAAAAAT
1 AAATAAT-AATA-A--TAATAGAT
20839284 AAAATAATAATAATAATA
1 -AAATAATAATAATAATA
20839302 AAAGAAAAAA
Statistics
Matches: 153, Mismatches: 27, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.05
17 8 0.05
18 23 0.15
19 8 0.05
20 51 0.33
21 12 0.08
22 15 0.10
23 11 0.07
24 10 0.07
25 7 0.05
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATAATAATAATAATAGAT
Found at i:20839216 original size:24 final size:23
Alignment explanation
Indices: 20839188--20839287 Score: 96
Period size: 24 Copynumber: 4.3 Consensus size: 23
20839178 ATAAATTATA
20839188 ATAAAAAAACATATATATTAATAG
1 ATAAAAAAA-ATATATATTAATAG
* *
20839212 ATAAATAAAAAAATATGTTAATAG
1 ATAAA-AAAAATATATATTAATAG
* *
20839236 ATAAAAATAA-ATATATTAGTAG
1 ATAAAAAAAATATATATTAATAG
* *
20839258 ATAAATAATAAATATAT-TTAAAAA
1 ATAAA-AA-AAATATATATTAATAG
20839282 ATAAAA
1 ATAAAA
20839288 TAATAATAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.24
23 7 0.11
24 33 0.52
25 8 0.13
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (23 bp):
ATAAAAAAAATATATATTAATAG
Found at i:20839227 original size:22 final size:22
Alignment explanation
Indices: 20839202--20839312 Score: 81
Period size: 24 Copynumber: 5.1 Consensus size: 22
20839192 AAAAACATAT
20839202 ATATTAATAGATAAATAAAAAA
1 ATATTAATAGATAAATAAAAAA
*
20839224 ATATGTTAATAGATAAA-AATAAAT
1 ATA--TTAATAGATAAATAA-AAAA
* *
20839248 ATATTAGTAGATAAATAATAAAT
1 ATATTAATAGATAAATAA-AAAA
* *
20839271 ATATT--TA-AAAAATAAAATA
1 ATATTAATAGATAAATAAAAAA
*
20839290 ATAATAATA-ATAAA-AGAAAAA
1 ATATTAATAGATAAATA-AAAAA
20839311 AT
1 AT
20839313 GGACCTATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
19 6 0.08
20 8 0.11
21 14 0.19
22 14 0.19
23 14 0.19
24 18 0.24
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
ATATTAATAGATAAATAAAAAA
Found at i:20839250 original size:46 final size:46
Alignment explanation
Indices: 20839200--20839287 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
20839190 AAAAAAACAT
* *
20839200 ATATATTAATAGATAAATAA-AAAAATATGTTAATAGATAAAAATAA
1 ATATATTAATAGATAAATAATAAAAATAT-TTAAAAAATAAAAATAA
* *
20839246 ATATATTAGTAGATAAATAATAAATATATTTAAAAAATAAAA
1 ATATATTAATAGATAAATAATAAAAATATTTAAAAAATAAAA
20839288 TAATAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 30 0.81
47 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (46 bp):
ATATATTAATAGATAAATAATAAAAATATTTAAAAAATAAAAATAA
Found at i:20841190 original size:268 final size:267
Alignment explanation
Indices: 20840713--20841249 Score: 889
Period size: 268 Copynumber: 2.0 Consensus size: 267
20840703 TTATAGCTCA
* *
20840713 ATTTAGGTTCCAAGATGGTGAGAAAGTCTTCAAAGCTCCTATATTTGATAAATTTGAATTTTATG
1 ATTTAGGTTCCAAGATGGTGAGAAAGTCTTCAAAGCTCCTATATTTGATAAATTTAAATTGTATG
20840778 AACGGAGAAAGAGGATGAAGATATTCATAATGGCCTAAGATTTAAAGCTTGGAATGTGATAAAGA
66 AACGGAGAAAGAGGATGAAGATATTCATAATGGCCTAAGATTTAAAGCTTGGAATGTGATAAAGA
*
20840843 AAGGGCTTGAAATTCCTTCAAATGATGTAAATTATATAAAGCAAATGATGAATAATGCCAAGGTA
131 AAGGGCTTGAAATTCCTTCAAATGATGTAAATTATATAAAGCAAATGATGAATAATGCCAAGGCA
*
20840908 AAGTGCTTACTATATGGAGCTCTTTAACTCCCACAACTGCAATTTAATCTCAAATTGCTCCACTT
196 AAGTGCTTACTATATGGAGCTC-TTAACTCCCACAACTGCAACTTAATCTCAAATTGCTCCACTT
20840973 CAAATGAG
260 CAAATGAG
* *
20840981 ATTTAGGTTCCAAGATGGTGAGAAAGTCTTCAAAGCTCTTATGTTTGATAAATTTAAATTGTATG
1 ATTTAGGTTCCAAGATGGTGAGAAAGTCTTCAAAGCTCCTATATTTGATAAATTTAAATTGTATG
* *
20841046 AACGGAGAAAGAGGATGCAGATATTCATAATGG-CTCAAGATTTAAAGCTTGGAATGTGATAGAG
66 AACGGAGAAAGAGGATGAAGATATTCATAATGGCCT-AAGATTTAAAGCTTGGAATGTGATAAAG
* * * * *
20841110 AAAGTGCTT-AGAATTTCTTCAAATGATGTAAATTATATGAAGCCAATGATGAATAATGCTAAGG
130 AAAGGGCTTGA-AATTCCTTCAAATGATGTAAATTATATAAAGCAAATGATGAATAATGCCAAGG
* * *
20841174 CAAAGTGCTTACTATATGGAGCTCTTGACTCCCACAACTGTAACTTAGTCTCAAATTGCTCCACT
194 CAAAGTGCTTACTATATGGAGCTCTTAACTCCCACAACTGCAACTTAATCTCAAATTGCTCCACT
20841239 TCAAATGAG
259 TCAAATGAG
20841248 AT
1 AT
20841250 ATAGAGAAAG
Statistics
Matches: 251, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
267 51 0.20
268 200 0.80
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (267 bp):
ATTTAGGTTCCAAGATGGTGAGAAAGTCTTCAAAGCTCCTATATTTGATAAATTTAAATTGTATG
AACGGAGAAAGAGGATGAAGATATTCATAATGGCCTAAGATTTAAAGCTTGGAATGTGATAAAGA
AAGGGCTTGAAATTCCTTCAAATGATGTAAATTATATAAAGCAAATGATGAATAATGCCAAGGCA
AAGTGCTTACTATATGGAGCTCTTAACTCCCACAACTGCAACTTAATCTCAAATTGCTCCACTTC
AAATGAG
Found at i:20849906 original size:189 final size:189
Alignment explanation
Indices: 20849586--20849965 Score: 724
Period size: 189 Copynumber: 2.0 Consensus size: 189
20849576 GTAACCTCTT
*
20849586 ATCAAGTATTTTCATCTTGTCATTAGCTTTCGAATCTTAATTTTTAGAATCCCTTAAAATTTCTC
1 ATCAAGTATTTTCATCTTGTAATTAGCTTTCGAATCTTAATTTTTAGAATCCCTTAAAATTTCTC
*
20849651 CAAATTAAATTTAACTTTAATTCCTTGATTTGGTTTCTTTTCAACCTTTCTTTAATATCTGAAGA
66 CAAATTAAATTTAACTTTAATTCCTTGATTTGGTTTCTTTTCAACCTTTCTTTAATATATGAAGA
20849716 GATCATGTTGAAGTCTTAATTGCCAATATCATCTTTGATTAATGCTCAAATTACTCCAC
131 GATCATGTTGAAGTCTTAATTGCCAATATCATCTTTGATTAATGCTCAAATTACTCCAC
20849775 ATCAAGTATTTTCATCTTGTAATTAGCTTTCGAATCTTAATTTTTAGAATCCCTTAAAATTTCTC
1 ATCAAGTATTTTCATCTTGTAATTAGCTTTCGAATCTTAATTTTTAGAATCCCTTAAAATTTCTC
20849840 CAAATTAAATTTAACTTTAATTCCTTGATTTGGTTTCTTTTCAACCTTTCTTTAATATATGAAGA
66 CAAATTAAATTTAACTTTAATTCCTTGATTTGGTTTCTTTTCAACCTTTCTTTAATATATGAAGA
* *
20849905 GATCATGTTTAAGTCTTAATTGTCAATATCATCTTTGATTAATGCTCAAATTACTCCAC
131 GATCATGTTGAAGTCTTAATTGCCAATATCATCTTTGATTAATGCTCAAATTACTCCAC
20849964 AT
1 AT
20849966 GATTTATGAT
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 187 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (189 bp):
ATCAAGTATTTTCATCTTGTAATTAGCTTTCGAATCTTAATTTTTAGAATCCCTTAAAATTTCTC
CAAATTAAATTTAACTTTAATTCCTTGATTTGGTTTCTTTTCAACCTTTCTTTAATATATGAAGA
GATCATGTTGAAGTCTTAATTGCCAATATCATCTTTGATTAATGCTCAAATTACTCCAC
Found at i:20856075 original size:2 final size:2
Alignment explanation
Indices: 20856068--20856093 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20856058 CTTCTTCCCG
20856068 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
20856094 AATAGATGAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20857391 original size:14 final size:15
Alignment explanation
Indices: 20857372--20857405 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20857362 AGTTTCTTTA
20857372 TTTTTTAT-TTTAAT
1 TTTTTTATATTTAAT
*
20857386 TTTTTTATATTTTAT
1 TTTTTTATATTTAAT
20857401 TTTTT
1 TTTTT
20857406 CAAATCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTATATTTAAT
Found at i:20858258 original size:3 final size:3
Alignment explanation
Indices: 20858250--20858348 Score: 85
Period size: 3 Copynumber: 32.0 Consensus size: 3
20858240 TCGATACATG
* ** *
20858250 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT TCT CCAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
20858296 CCA- AAT CCA- AAT CCAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 -AAT AAT -AAT AAT --AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20858343 AAT AAT
1 AAT AAT
20858349 TATTCCAAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
2 2 0.02
3 73 0.88
4 5 0.06
5 3 0.04
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20862032 original size:19 final size:19
Alignment explanation
Indices: 20862001--20862195 Score: 71
Period size: 17 Copynumber: 10.9 Consensus size: 19
20861991 TAAGGTTCAC
*
20862001 AAGAAATTC--AGATTTGT
1 AAGAAATTCAAAGATTCGT
20862018 ACA-AAATTCAAAGATTCGT
1 A-AGAAATTCAAAGATTCGT
**
20862037 AAGAAATTCAAAGATTCAC
1 AAGAAATTCAAAGATTCGT
** *
20862056 AAGAGCTT--TAGTATT-GT
1 AAGAAATTCAAAG-ATTCGT
* **
20862073 AAGAAATTC-AAG-GTCAC
1 AAGAAATTCAAAGATTCGT
* *
20862090 AAAAAATTC-AAG-TTCGC
1 AAGAAATTCAAAGATTCGT
* *
20862107 AAGAAATTCAAAGGTT-AT
1 AAGAAATTCAAAGATTCGT
*
20862125 AAGAAATTC--AGATTCGC
1 AAGAAATTCAAAGATTCGT
* *
20862142 AA-AAACTTTAAAGATTCGC
1 AAGAAA-TTCAAAGATTCGT
* * *
20862161 AAGAGATTC--AGGTTCGC
1 AAGAAATTCAAAGATTCGT
*
20862178 AAGAAATTCAATGATTCG
1 AAGAAATTCAAAGATTCG
20862196 CATTCAAAAG
Statistics
Matches: 132, Mismatches: 30, Indels: 30
0.69 0.16 0.16
Matches are distributed among these distances:
16 8 0.06
17 56 0.42
18 19 0.14
19 47 0.36
20 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (19 bp):
AAGAAATTCAAAGATTCGT
Found at i:20862132 original size:35 final size:35
Alignment explanation
Indices: 20862073--20862188 Score: 112
Period size: 35 Copynumber: 3.3 Consensus size: 35
20862063 TTAGTATTGT
* *
20862073 AAGAAATTC-AAGGTCACAAAAAATTCAAGTTCGC
1 AAGAAATTCAAAGGTTACAAGAAATTCAAGTTCGC
*
20862107 AAGAAATTCAAAGGTTATAAGAAATTC-AGATTCGC
1 AAGAAATTCAAAGGTTACAAGAAATTCAAG-TTCGC
* * * * *
20862142 AA-AAACTTTAAAGATTCGCAAGAGATTCAGGTTCGC
1 AAGAAA-TTCAAAGGTT-ACAAGAAATTCAAGTTCGC
20862178 AAGAAATTCAA
1 AAGAAATTCAA
20862189 TGATTCGCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
34 14 0.21
35 29 0.44
36 19 0.29
37 4 0.06
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (35 bp):
AAGAAATTCAAAGGTTACAAGAAATTCAAGTTCGC
Found at i:20862177 original size:36 final size:36
Alignment explanation
Indices: 20862029--20862197 Score: 125
Period size: 36 Copynumber: 4.8 Consensus size: 36
20862019 CAAAATTCAA
* * ** *
20862029 AGATTCGTAAGAAATTCAAAGATTCACAAGAGCTTT
1 AGATTCGCAAGAAATTCAAAGATTCGCAAGAAATTC
* * * *
20862065 AGTATT-GTAAGAAATTC-AAG-GTCACAAAAAATTC
1 AG-ATTCGCAAGAAATTCAAAGATTCGCAAGAAATTC
* **
20862099 A-AGTTCGCAAGAAATTCAAAGGTT-ATAAGAAATTC
1 AGA-TTCGCAAGAAATTCAAAGATTCGCAAGAAATTC
* *
20862134 AGATTCGCAA-AAACTTTAAAGATTCGCAAGAGATTC
1 AGATTCGCAAGAAA-TTCAAAGATTCGCAAGAAATTC
* *
20862170 AGGTTCGCAAGAAATTCAATGATTCGCA
1 AGATTCGCAAGAAATTCAAAGATTCGCA
20862198 TTCAAAAGAT
Statistics
Matches: 107, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
32 1 0.01
33 2 0.02
34 23 0.21
35 31 0.29
36 44 0.41
37 6 0.06
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (36 bp):
AGATTCGCAAGAAATTCAAAGATTCGCAAGAAATTC
Found at i:20862386 original size:27 final size:27
Alignment explanation
Indices: 20862318--20862490 Score: 238
Period size: 27 Copynumber: 6.0 Consensus size: 27
20862308 AAAGTTAAAT
20862318 ATTTTCATTGAAAATTTTACGATTCACATCCAA
1 ATTTTCATTGAAAATTTTACGA-T----T-CAA
20862351 ATTTTCATTGAAAATTTTACGATTCAA
1 ATTTTCATTGAAAATTTTACGATTCAA
20862378 ATTTTCATTGAAAATTTTACGATTCACATCCAA
1 ATTTTCATTGAAAATTTTACGA-T----T-CAA
20862411 ATTTTCATTGAAAATTTTACGATTCAA
1 ATTTTCATTGAAAATTTTACGATTCAA
20862438 ATTTTCATTGAAAATTTTACGATTCAA
1 ATTTTCATTGAAAATTTTACGATTCAA
20862465 ATTTTCATTGAAAATTTTACGATTCA
1 ATTTTCATTGAAAATTTTACGATTCA
20862491 CATCCAAATT
Statistics
Matches: 134, Mismatches: 0, Indels: 18
0.88 0.00 0.12
Matches are distributed among these distances:
27 81 0.60
28 3 0.02
32 3 0.02
33 47 0.35
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (27 bp):
ATTTTCATTGAAAATTTTACGATTCAA
Found at i:20862387 original size:60 final size:60
Alignment explanation
Indices: 20862318--20862490 Score: 304
Period size: 60 Copynumber: 3.0 Consensus size: 60
20862308 AAAGTTAAAT
20862318 ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCAA
1 ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCAA
20862378 ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCAA
1 ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCAA
20862438 ATTTTCATTGAAAATTTTACGA-T----T-CAAATTTTCATTGAAAATTTTACGATTCA
1 ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCA
20862491 CATCCAAATT
Statistics
Matches: 113, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
54 29 0.26
55 1 0.01
59 1 0.01
60 82 0.73
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (60 bp):
ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCAA
Found at i:20862460 original size:87 final size:90
Alignment explanation
Indices: 20862318--20862504 Score: 326
Period size: 87 Copynumber: 2.1 Consensus size: 90
20862308 AAAGTTAAAT
20862318 ATTTTCATTGAAAATTTTACGATTCACATCCAAATTTTCATTGAAAATTTTACGATTCAAATTTT
1 ATTTTCATTGAAAATTTTACGATT---ATCCAAATTTTCATTGAAAATTTTACGATTCAAATTTT
20862383 CATTGAAAATTTTACGATTCACATCCAA
63 CATTGAAAATTTTACGATTCACATCCAA
20862411 ATTTTCATTGAAAATTTTACGA-T-T-CAAATTTTCATTGAAAATTTTACGATTCAAATTTTCAT
1 ATTTTCATTGAAAATTTTACGATTATCCAAATTTTCATTGAAAATTTTACGATTCAAATTTTCAT
20862473 TGAAAATTTTACGATTCACATCCAA
66 TGAAAATTTTACGATTCACATCCAA
20862498 ATTTTCA
1 ATTTTCA
20862505 AAGATTCACA
Statistics
Matches: 94, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
87 70 0.74
88 1 0.01
92 1 0.01
93 22 0.23
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (90 bp):
ATTTTCATTGAAAATTTTACGATTATCCAAATTTTCATTGAAAATTTTACGATTCAAATTTTCAT
TGAAAATTTTACGATTCACATCCAA
Found at i:20862576 original size:43 final size:44
Alignment explanation
Indices: 20862465--20862598 Score: 139
Period size: 43 Copynumber: 3.1 Consensus size: 44
20862455 TACGATTCAA
* * * *
20862465 ATTTTCATTG-AAAATTTTACGATTCACATC-CAAATTTTCAAAG
1 ATTTTCATCGAAAAATTTTAGGATTCACATCTGAAA-GTTCAAAG
**
20862508 ATTCACATTCGAAAAATTTTAGGATTCACATCTGAAAGTT-AAAG
1 ATTTTCA-TCGAAAAATTTTAGGATTCACATCTGAAAGTTCAAAG
* ** *
20862552 ATTTTCATCGAAAAATTTTGGGATTCGTATCTGAAATTTCAAAG
1 ATTTTCATCGAAAAATTTTAGGATTCACATCTGAAAGTTCAAAG
20862596 ATT
1 ATT
20862599 CACATTCAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
43 33 0.44
44 18 0.24
45 21 0.28
46 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (44 bp):
ATTTTCATCGAAAAATTTTAGGATTCACATCTGAAAGTTCAAAG
Found at i:20862990 original size:23 final size:23
Alignment explanation
Indices: 20862943--20862990 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20862933 CCATACCCCA
*
20862943 ACAATGATGTAAATGCAATTATC
1 ACAATGATGTAAATGCAAATATC
*
20862966 ACAATGTATGT-AATGCAAATGTC
1 ACAATG-ATGTAAATGCAAATATC
20862989 AC
1 AC
20862991 TAAATCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (23 bp):
ACAATGATGTAAATGCAAATATC
Found at i:20863644 original size:18 final size:16
Alignment explanation
Indices: 20863613--20863655 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
20863603 TAAATCTTCC
20863613 TTTTTTTTATTTTTTG
1 TTTTTTTTATTTTTTG
*
20863629 TTTTTGTTTCATTTTTTCA
1 TTTTT-TTT-ATTTTTT-G
20863648 TTTTTTTT
1 TTTTTTTT
20863656 GCACACCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 3 0.13
18 10 0.43
19 5 0.22
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.84
Consensus pattern (16 bp):
TTTTTTTTATTTTTTG
Found at i:20866488 original size:16 final size:16
Alignment explanation
Indices: 20866469--20866509 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
20866459 GGGCTAGTAC
*
20866469 AAAAAAAATTATATAT
1 AAAAAAAATAATATAT
*
20866485 AAAAAGAATAATATAT
1 AAAAAAAATAATATAT
20866501 ACAAAAAAA
1 A-AAAAAAA
20866510 ACAATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAAAAATAATATAT
Found at i:20871464 original size:16 final size:17
Alignment explanation
Indices: 20871445--20871476 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20871435 TAAATCGAAT
20871445 ATAATAT-TAAAATTAA
1 ATAATATCTAAAATTAA
20871461 ATAATATCTAAAATTA
1 ATAATATCTAAAATTA
20871477 CGAAACGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATCTAAAATTAA
Found at i:20871977 original size:15 final size:16
Alignment explanation
Indices: 20871948--20871979 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20871938 TTTTTATATA
20871948 TTTAATTGTTGAAAAT
1 TTTAATTGTTGAAAAT
*
20871964 TTTAATTGTTAAAAAT
1 TTTAATTGTTGAAAAT
20871980 AGTCATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TTTAATTGTTGAAAAT
Found at i:20874922 original size:21 final size:21
Alignment explanation
Indices: 20874898--20874938 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20874888 TAAGATGTAT
20874898 TTGGATATGTGAAAGGAGTTA
1 TTGGATATGTGAAAGGAGTTA
20874919 TTGGATATGTGAAAGGAGTT
1 TTGGATATGTGAAAGGAGTT
20874939 GACTACTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (21 bp):
TTGGATATGTGAAAGGAGTTA
Found at i:20876287 original size:20 final size:20
Alignment explanation
Indices: 20876262--20876302 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20876252 TTATCAAACA
20876262 TAGTCAAAATTAATATTCTT
1 TAGTCAAAATTAATATTCTT
20876282 TAGTCAAAATTAATATTCTT
1 TAGTCAAAATTAATATTCTT
20876302 T
1 T
20876303 TCACTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
TAGTCAAAATTAATATTCTT
Found at i:20876416 original size:13 final size:12
Alignment explanation
Indices: 20876394--20876426 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
20876384 AAAATGTTAG
20876394 ATTTAATTTTGA
1 ATTTAATTTTGA
20876406 ATTTCAATTTTGA
1 ATTT-AATTTTGA
20876419 ATTTAATT
1 ATTTAATT
20876427 CGCATATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (12 bp):
ATTTAATTTTGA
Found at i:20877757 original size:20 final size:20
Alignment explanation
Indices: 20877715--20877763 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
20877705 ATTAAGCAAA
*
20877715 AAACAAAAAAAAAGAAGAAG
1 AAACAAAAAAAAACAAGAAG
*
20877735 AAACAAACAAAAACAA-AAGG
1 AAACAAAAAAAAACAAGAA-G
20877755 AAACTAAAA
1 AAAC-AAAA
20877764 TCAGAGGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (20 bp):
AAACAAAAAAAAACAAGAAG
Found at i:20885556 original size:21 final size:21
Alignment explanation
Indices: 20885530--20885584 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
20885520 CCTTTTTTTA
20885530 GGTGATCGATCCCCTAGTCTG
1 GGTGATCGATCCCCTAGTCTG
20885551 GGTGATCGATCCCCTAGTCTG
1 GGTGATCGATCCCCTAGTCTG
20885572 GGTGATCGATCCC
1 GGTGATCGATCCC
20885585 TTCTTAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTGATCGATCCCCTAGTCTG
Found at i:20890485 original size:26 final size:25
Alignment explanation
Indices: 20890430--20890485 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
20890420 TCTCACTTAA
*
20890430 AAATTTTATAAAAATTTACCATTTG
1 AAATTTTATAAAAATTTACCATTGG
* *
20890455 AAATTTT-TATAAATTTCATCATTGG
1 AAATTTTATAAAAATTT-ACCATTGG
20890480 ATAATT
1 A-AATT
20890486 AATACTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 8 0.31
25 14 0.54
26 4 0.15
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (25 bp):
AAATTTTATAAAAATTTACCATTGG
Found at i:20891314 original size:8 final size:8
Alignment explanation
Indices: 20891302--20891343 Score: 66
Period size: 8 Copynumber: 5.1 Consensus size: 8
20891292 TTTTTAAAAT
20891302 TTTTTTTA
1 TTTTTTTA
*
20891310 GTTTTTCTA
1 -TTTTTTTA
20891319 TTTTTTTA
1 TTTTTTTA
20891327 TTTTTTTA
1 TTTTTTTA
20891335 TTTTTTTA
1 TTTTTTTA
20891343 T
1 T
20891344 GAATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 24 0.77
9 7 0.23
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:20891555 original size:42 final size:42
Alignment explanation
Indices: 20891456--20891598 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
20891446 TCAAACATCT
* * * *
20891456 TCTAAATAAAGGCTCAATAAC-TTTAAAAAATAAAATTAGGCTCC
1 TCTAAACAGAGGCTCAATGACTTTTGAAAAAT--AA-TAGGCTCC
* **
20891500 TCTAAGCAGAGGCTTGATGACTTTTGAAAAATAATAGGCTCC
1 TCTAAACAGAGGCTCAATGACTTTTGAAAAATAATAGGCTCC
* * *
20891542 TCTAAACAAAGGCTCAATGACTTTTGAAAAATAAAAGGCTCT
1 TCTAAACAGAGGCTCAATGACTTTTGAAAAATAATAGGCTCC
20891584 TCTAAACAGAGGCTC
1 TCTAAACAGAGGCTC
20891599 TTCTAAACAA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 58 0.69
43 2 0.02
44 15 0.18
45 9 0.11
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (42 bp):
TCTAAACAGAGGCTCAATGACTTTTGAAAAATAATAGGCTCC
Found at i:20891598 original size:16 final size:16
Alignment explanation
Indices: 20891575--20891614 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20891565 TTGAAAAATA
20891575 AAAGGCTCTTCTAAAC
1 AAAGGCTCTTCTAAAC
*
20891591 AGAGGCTCTTCTAAAC
1 AAAGGCTCTTCTAAAC
20891607 AAAGGCTC
1 AAAGGCTC
20891615 AACAACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (16 bp):
AAAGGCTCTTCTAAAC
Found at i:20891605 original size:58 final size:58
Alignment explanation
Indices: 20891535--20891656 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 58
20891525 GAAAAATAAT
** *
20891535 AGGCTCCTCTAAACAAAGGCTCAATGACTTTTGAAAAATAAAAGGCTCTTCTAAACAG
1 AGGCTCCTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAAAGGCTCCTCTAAACAG
* *
20891593 AGGCTCTTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAAAGGCTCCTCTAAATAG
1 AGGCTCCTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAAAGGCTCCTCTAAACAG
20891651 AGGCTC
1 AGGCTC
20891657 AACGACTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (58 bp):
AGGCTCCTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAAAGGCTCCTCTAAACAG
Found at i:20891639 original size:42 final size:41
Alignment explanation
Indices: 20891593--20891925 Score: 323
Period size: 41 Copynumber: 8.0 Consensus size: 41
20891583 TTCTAAACAG
*
20891593 AGGCTCTTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAA
1 AGGCTCTTCTAAACAGAGGCTCAACAAC-TTTGAAAAATAAA
* * *
20891635 AGGCTCCTCTAAATAGAGGCTCAACGACTTTTGAAAAATAAA
1 AGGCTCTTCTAAACAGAGGCTCAACAAC-TTTGAAAAATAAA
* * * *
20891677 AAGCT-TCTCTAAATAGAGACTCAACAACTTAAGAAAACA-AATA
1 AGGCTCT-TCTAAACAGAGGCTCAACAACTT-TGAAAA-ATAA-A
* * * * **
20891720 ATGTTCTTCGAAACAGAGGCTTAATGACTTTGAAAAATAAA
1 AGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* *
20891761 AAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
1 AGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* ** *
20891802 AGGCTCCTT-TAAACAAAGGCTCAATGACTTTGAAGAATAAA
1 AGGCT-CTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* * * * * *
20891843 AGGCTCCTCTAAGCAGAGACACAATAACTTTAAAAAATAAA
1 AGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* *
20891884 A-GCTCTTCTAAATAGAGGCACAACAACTTTGAAAAATAAA
1 AGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
20891924 AG
1 AG
20891926 CTTCTTGACA
Statistics
Matches: 237, Mismatches: 45, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
40 36 0.15
41 101 0.43
42 77 0.32
43 22 0.09
44 1 0.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (41 bp):
AGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
Found at i:20891849 original size:82 final size:83
Alignment explanation
Indices: 20891593--20891925 Score: 354
Period size: 84 Copynumber: 4.0 Consensus size: 83
20891583 TTCTAAACAG
* * * *
20891593 AGGCTCTTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAAAGGCTCC-TCTAAATAGAGGCTC
1 AGGCTCCTCTAAACAGAGACTCAACAAC-TTTGAAAAATAAAAGGCTCCTTCTAAACAGAGGCTC
20891657 AACGACTTTTGAAAAATAAA
65 AACGAC-TTTGAAAAATAAA
* * * * * * *
20891677 AAGCTTCTCTAAATAGAGACTCAACAACTTAAGAAAACA-AATAATG-TTCTTCGAAACAGAGGC
1 AGGCTCCTCTAAACAGAGACTCAACAACTT-TGAAAA-ATAA-AAGGCTCCTTCTAAACAGAGGC
* *
20891740 TTAATGACTTTGAAAAATAAA
63 TCAACGACTTTGAAAAATAAA
* * *
20891761 AAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAAAGGCTCCTT-TAAACAAAGGCTCA
1 AGGCTCCTCTAAACAGAGACTCAACAACTTTGAAAAATAAAAGGCTCCTTCTAAACAGAGGCTCA
* *
20891825 ATGACTTTGAAGAATAAA
66 ACGACTTTGAAAAATAAA
* * * * * *
20891843 AGGCTCCTCTAAGCAGAGACACAATAACTTTAAAAAATAAAA-GCT-CTTCTAAATAGAGGCACA
1 AGGCTCCTCTAAACAGAGACTCAACAACTTTGAAAAATAAAAGGCTCCTTCTAAACAGAGGCTCA
*
20891906 ACAACTTTGAAAAATAAA
66 ACGACTTTGAAAAATAAA
20891924 AG
1 AG
20891926 CTTCTTGACA
Statistics
Matches: 207, Mismatches: 35, Indels: 17
0.80 0.14 0.07
Matches are distributed among these distances:
80 3 0.01
81 31 0.15
82 68 0.33
83 13 0.06
84 71 0.34
85 21 0.10
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (83 bp):
AGGCTCCTCTAAACAGAGACTCAACAACTTTGAAAAATAAAAGGCTCCTTCTAAACAGAGGCTCA
ACGACTTTGAAAAATAAA
Found at i:20892360 original size:21 final size:21
Alignment explanation
Indices: 20892335--20892381 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20892325 ACATCTCAAT
* *
20892335 AATTCTCATTTGAAATTCAAA
1 AATTCTCAATTGAAATTAAAA
*
20892356 GATTCTCAATTGAAATTAAAA
1 AATTCTCAATTGAAATTAAAA
20892377 AATTC
1 AATTC
20892382 ACAAATTCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (21 bp):
AATTCTCAATTGAAATTAAAA
Found at i:20893529 original size:17 final size:17
Alignment explanation
Indices: 20893507--20893613 Score: 74
Period size: 16 Copynumber: 6.9 Consensus size: 17
20893497 TTAAGTATTC
20893507 TTTTTCTCTCA-TTTTCA
1 TTTTT-TCTCATTTTTCA
20893524 -TTTTTCTCATTTTTCA
1 TTTTTTCTCATTTTTCA
**
20893540 TTTTTT-T--TCCTT--
1 TTTTTTCTCATTTTTCA
* *
20893552 TTTTTCCT-TTTTTTCA
1 TTTTTTCTCATTTTTCA
*
20893568 TTTTTTTTCATTTTTCA
1 TTTTTTCTCATTTTTCA
*
20893585 TTTTTT-T-ATTTTTTA
1 TTTTTTCTCATTTTTCA
20893600 TTTTTT-TCATTTTT
1 TTTTTTCTCATTTTT
20893614 TTACCCATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.07
13 1 0.01
14 6 0.08
15 19 0.26
16 24 0.33
17 18 0.25
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTCTCATTTTTCA
Found at i:20893535 original size:9 final size:9
Alignment explanation
Indices: 20893518--20893615 Score: 102
Period size: 9 Copynumber: 11.4 Consensus size: 9
20893508 TTTTCTCTCA
20893518 TTTTCATTT
1 TTTTCATTT
*
20893527 TTCTCA--T
1 TTTTCATTT
20893534 TTTTCATTTT
1 TTTTCA-TTT
*
20893544 TTTTCCTTT
1 TTTTCATTT
*
20893553 TTTTCCTTT
1 TTTTCATTT
20893562 TTTTCATTTT
1 TTTTCA-TTT
20893572 TTTTCA--T
1 TTTTCATTT
20893579 TTTTCATTT
1 TTTTCATTT
20893588 TTTT-A-TT
1 TTTTCATTT
20893595 TTTT-ATTT
1 TTTTCATTT
20893603 TTTTCATTT
1 TTTTCATTT
20893612 TTTT
1 TTTT
20893616 ACCCATTATT
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
7 20 0.26
8 7 0.09
9 35 0.45
10 15 0.19
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:20893614 original size:17 final size:17
Alignment explanation
Indices: 20893533--20893616 Score: 84
Period size: 15 Copynumber: 4.9 Consensus size: 17
20893523 ATTTTTCTCA
*
20893533 TTTTTCATTTTTTTTCCTT
1 TTTTTCA-TTTTTTT-ATT
*
20893552 TTTTTCCTTTTTTTCATTT
1 TTTTTCATTTTTTT-A-TT
*
20893571 TTTTTCA-TTTTTCATT
1 TTTTTCATTTTTTTATT
20893587 TTTTT-A-TTTTTTATT
1 TTTTTCATTTTTTTATT
20893602 TTTTTCATTTTTTTA
1 TTTTTCATTTTTTTA
20893617 CCCATTATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
15 14 0.25
16 8 0.14
17 8 0.14
18 13 0.23
19 14 0.25
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCATTTTTTTATT
Found at i:20893615 original size:10 final size:10
Alignment explanation
Indices: 20893533--20893615 Score: 75
Period size: 10 Copynumber: 8.4 Consensus size: 10
20893523 ATTTTTCTCA
20893533 TTTTTCATTT
1 TTTTTCATTT
*
20893543 TTTTTC-CTT
1 TTTTTCATTT
*
20893552 TTTTTC-CTT
1 TTTTTCATTT
20893561 TTTTTCATTT
1 TTTTTCATTT
20893571 TTTTTCATTT
1 TTTTTCATTT
*
20893581 TTCATTT-TTTT
1 TT--TTTCATTT
*
20893592 ATTTTTTA-TT
1 -TTTTTCATTT
20893602 TTTTTCATTT
1 TTTTTCATTT
20893612 TTTT
1 TTTT
20893616 ACCCATTATT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
9 23 0.37
10 31 0.50
11 3 0.05
12 5 0.08
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:20893624 original size:24 final size:24
Alignment explanation
Indices: 20893578--20893625 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20893568 TTTTTTTTCA
****
20893578 TTTTTCATTTTTTTATTTTTTATT
1 TTTTTCATTTTTTTACCCATTATT
20893602 TTTTTCATTTTTTTACCCATTATT
1 TTTTTCATTTTTTTACCCATTATT
20893626 GATATCTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCATTTTTTTACCCATTATT
Found at i:20901093 original size:28 final size:28
Alignment explanation
Indices: 20901052--20901108 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
20901042 AAATGTTTTC
** * *
20901052 AAAAAAAATGAAAGGAA-AAAAATAAAA
1 AAAAAAAAAAAAAAGAAGAAAAAGAAAA
20901079 AAAAAAAAAAAAAAGAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAGAAGAAAAAGAAAA
20901107 AA
1 AA
20901109 GAGCAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.04
Consensus pattern (28 bp):
AAAAAAAAAAAAAAGAAGAAAAAGAAAA
Found at i:20906810 original size:10 final size:10
Alignment explanation
Indices: 20906795--20906842 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
20906785 AAAATTATCT
20906795 TTTTAATAAA
1 TTTTAATAAA
*
20906805 TTTTAATTAA
1 TTTTAATAAA
*
20906815 TTTTAATTAA
1 TTTTAATAAA
20906825 TTTT-A-AAA
1 TTTTAATAAA
*
20906833 TTTTATTAAA
1 TTTTAATAAA
20906843 AATGTAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 6 0.18
9 1 0.03
10 26 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:20906825 original size:133 final size:133
Alignment explanation
Indices: 20906672--20906916 Score: 463
Period size: 133 Copynumber: 1.8 Consensus size: 133
20906662 AAAATTATCT
20906672 TTTTAATAAATTTTAATTAATTTTAAAAATTTATTAAAAATGTAAGTTATAATAAATGATCAATC
1 TTTTAATAAATTTTAATTAATTTTAAAAATTTATTAAAAATGTAAGTTATAATAAATGATCAATC
20906737 ATATCTAATAAAAAATGATTGATAGTAACTTTATCTTCTATTTTTAATAAAATTATCTTTTTAAT
66 ATATCTAATAAAAAATGATTGATAGTAACTTTATCTTCTATTTTTAATAAAATTATCTTTTTAAT
20906802 AAA
131 AAA
* *
20906805 TTTTAATTAATTTTAATTAATTTTAAAATTTTATTAAAAATGTAAGTTATAATAAATGATCAATC
1 TTTTAATAAATTTTAATTAATTTTAAAAATTTATTAAAAATGTAAGTTATAATAAATGATCAATC
*
20906870 ATATCTAATAAAAAATGATTGATAGTAACTTTATCTTTTATTTTTAA
66 ATATCTAATAAAAAATGATTGATAGTAACTTTATCTTCTATTTTTAA
20906917 ATTTATCTAA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 109 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (133 bp):
TTTTAATAAATTTTAATTAATTTTAAAAATTTATTAAAAATGTAAGTTATAATAAATGATCAATC
ATATCTAATAAAAAATGATTGATAGTAACTTTATCTTCTATTTTTAATAAAATTATCTTTTTAAT
AAA
Found at i:20909767 original size:19 final size:19
Alignment explanation
Indices: 20909745--20909791 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
20909735 TAATAATTAA
20909745 AAAAAATTT-TAAAAGAATT
1 AAAAAATTTATAAAA-AATT
*
20909764 -AAAAATTTATGAAAAATT
1 AAAAAATTTATAAAAAATT
20909782 AAAAAATTTA
1 AAAAAATTTA
20909792 ACTTAGCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
AAAAAATTTATAAAAAATT
Found at i:20909769 original size:18 final size:17
Alignment explanation
Indices: 20909746--20909792 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
20909736 AATAATTAAA
20909746 AAAAATTTTAAAAGAATT
1 AAAAATTTTAAAA-AATT
*
20909764 AAAAATTTATGAAAAATT
1 AAAAATTT-TAAAAAATT
*
20909782 AAAAAATTTAA
1 AAAAATTTTAA
20909793 CTTAGCGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 19 0.76
19 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAAATTTTAAAAAATT
Found at i:20909866 original size:20 final size:21
Alignment explanation
Indices: 20909843--20909903 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 21
20909833 ATTTTAAATT
20909843 TATAAAATTATTA-ATAAAAA
1 TATAAAATTATTACATAAAAA
*
20909863 TAT---ATTATTACAAAAAAA
1 TATAAAATTATTACATAAAAA
* * *
20909881 T-TAAAAATATTATATTAAAA
1 TATAAAATTATTACATAAAAA
20909901 TAT
1 TAT
20909904 TTACCAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
17 8 0.26
18 7 0.23
20 15 0.48
21 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAAAATTATTACATAAAAA
Found at i:20913810 original size:3 final size:3
Alignment explanation
Indices: 20913804--20913839 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20913794 TTTTTGTGAA
20913804 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20913840 TTCGTATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20914586 original size:17 final size:17
Alignment explanation
Indices: 20914553--20914596 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
20914543 ATTCTAACAA
* *
20914553 AAAATAAAAATTAAATT
1 AAAATAGAAACTAAATT
*
20914570 AAATTAGAAACTAAATT
1 AAAATAGAAACTAAATT
20914587 AAAATAGAAA
1 AAAATAGAAA
20914597 AAAAAAACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (17 bp):
AAAATAGAAACTAAATT
Found at i:20914733 original size:8 final size:8
Alignment explanation
Indices: 20914720--20914745 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20914710 CACTTTCTTC
20914720 TTTTATTT
1 TTTTATTT
20914728 TTTTATTT
1 TTTTATTT
20914736 TTTTATTT
1 TTTTATTT
20914744 TT
1 TT
20914746 CCTTTCTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:20917640 original size:14 final size:13
Alignment explanation
Indices: 20917621--20917650 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
20917611 AAATTGAGCC
20917621 GAATAAGGAAAGAA
1 GAATAAGGAAA-AA
20917635 GAATAAGGAAAAA
1 GAATAAGGAAAAA
20917648 GAA
1 GAA
20917651 AGAAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (13 bp):
GAATAAGGAAAAA
Found at i:20917672 original size:8 final size:8
Alignment explanation
Indices: 20917644--20917684 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
20917634 AGAATAAGGA
20917644 AAAAGAAAG
1 AAAA-AAAG
*
20917653 AAAGAAAG
1 AAAAAAAG
20917661 AAAAAAAG
1 AAAAAAAG
20917669 AAAAAAAAG
1 -AAAAAAAG
20917678 AAAAAAA
1 AAAAAAA
20917685 TATAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 18 0.62
9 11 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:20917684 original size:12 final size:13
Alignment explanation
Indices: 20917642--20917684 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
20917632 GAAGAATAAG
20917642 GAAAAAGAAAGAAA
1 GAAAAA-AAAGAAA
*
20917656 GAAAGAAAA-AAA
1 GAAAAAAAAGAAA
20917668 GAAAAAAAAGAAA
1 GAAAAAAAAGAAA
20917681 -AAAA
1 GAAAA
20917685 TATAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 15 0.58
13 6 0.23
14 5 0.19
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAGAAA
Found at i:20917692 original size:3 final size:3
Alignment explanation
Indices: 20917686--20917734 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
20917676 AGAAAAAAAT
20917686 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20917734 A
1 A
20917735 CTACAAAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20918013 original size:44 final size:44
Alignment explanation
Indices: 20917892--20918023 Score: 158
Period size: 44 Copynumber: 3.0 Consensus size: 44
20917882 TCAATGACAT
* **
20917892 TTTTGAAAATTTAAAAA-GCTTATCTAAACAGAGACTCAATGAC
1 TTTTGAAAATTTAAAAAGGCTTATCTAAACAGAGGCTCAACAAC
* * ** * ** *
20917935 TTTTAAAAATTTAAATAGGCTCCTTTAAGTAGAGGCTTAACAAC
1 TTTTGAAAATTTAAAAAGGCTTATCTAAACAGAGGCTCAACAAC
20917979 TTTTGAAAATTTAAAAAGGCTTATCTAAACAGAGGCTCAACAAC
1 TTTTGAAAATTTAAAAAGGCTTATCTAAACAGAGGCTCAACAAC
20918023 T
1 T
20918024 CTAAAATCCA
Statistics
Matches: 69, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
43 15 0.22
44 54 0.78
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (44 bp):
TTTTGAAAATTTAAAAAGGCTTATCTAAACAGAGGCTCAACAAC
Done.