Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167832.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_104, 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: 85611
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Found at i:1564 original size:22 final size:23
Alignment explanation
Indices: 1538--1582 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1528 GAATAATCGA
1538 AAATA-AAATTTTTAAAAATTCT
1 AAATAGAAATTTTTAAAAATTCT
*
1560 AAATAGAGATTTTTAAAAATTCT
1 AAATAGAAATTTTTAAAAATTCT
1583 TTAAGTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
AAATAGAAATTTTTAAAAATTCT
Found at i:1806 original size:26 final size:26
Alignment explanation
Indices: 1767--1893 Score: 83
Period size: 26 Copynumber: 4.9 Consensus size: 26
1757 TTCGGGATCT
** *
1767 ATTAGGCTTATTGATGTTTGGGTCCA
1 ATTAGGCCCATTGATGTTTGGGTCCG
* ** *
1793 ATTAGGCCCGTTGATGTCCGGATCCG
1 ATTAGGCCCATTGATGTTTGGGTCCG
* * * * *
1819 ATTAGGTCCATTTATATTCGGGTCCT
1 ATTAGGCCCATTGATGTTTGGGTCCG
* * **
1845 ATTAGACCCATTGATGTCTAAGTCCG
1 ATTAGGCCCATTGATGTTTGGGTCCG
* * *
1871 ATTAGGCCCGTTTACGTTTGGGT
1 ATTAGGCCCATTGATGTTTGGGT
1894 TTAATTAAAC
Statistics
Matches: 71, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (26 bp):
ATTAGGCCCATTGATGTTTGGGTCCG
Found at i:2034 original size:3 final size:3
Alignment explanation
Indices: 2026--2055 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2016 TTCTTTTTAT
2026 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2056 CATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2063 original size:3 final size:3
Alignment explanation
Indices: 2057--2083 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2047 TAATAATAAC
2057 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2084 TCTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2119 original size:22 final size:22
Alignment explanation
Indices: 2088--2137 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2078 ATTATTTCTA
*
2088 TTTTTATTTTCGTTCTTT-TTTC
1 TTTTTCTTTTC-TTCTTTGTTTC
2110 TTTTTCTTTTCTTCTTTGTTTC
1 TTTTTCTTTTCTTCTTTGTTTC
*
2132 CTTTTC
1 TTTTTC
2138 CATTCAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTTTCTTTTCTTCTTTGTTTC
Found at i:2699 original size:20 final size:19
Alignment explanation
Indices: 2651--2697 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2641 TCTGACAAAA
*
2651 TTTTCAAAATTTGGCATGT
1 TTTTCAAAATTTGGCATAT
2670 TTTTCAAAATTTGGCATAT
1 TTTTCAAAATTTGGCATAT
2689 TTTTCAAAA
1 TTTTCAAAA
2698 ATCGATGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
TTTTCAAAATTTGGCATAT
Found at i:3004 original size:19 final size:19
Alignment explanation
Indices: 2976--3019 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2966 CGATTGCAGG
* *
2976 TTTTTCTTTTTTCATTTTA
1 TTTTTATTTTTTCATTTGA
*
2995 TTTTTATTTTTTGATTTGA
1 TTTTTATTTTTTCATTTGA
3014 TTTTTA
1 TTTTTA
3020 ACTTATTTTT
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:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTTTCATTTGA
Found at i:3212 original size:21 final size:20
Alignment explanation
Indices: 3155--3212 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
3145 GAATAATAAC
3155 AAAAAAAAAT-ATCATTTCAAT
1 AAAAAAAAATAAT--TTTCAAT
**
3176 AAAAAAAAATGGTTTTCAAAT
1 AAAAAAAAATAATTTTC-AAT
*
3197 AAACAAAAATAATTTT
1 AAAAAAAAATAATTTT
3213 TATCCTCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 26 0.84
22 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAAAAAATAATTTTCAAT
Found at i:14651 original size:117 final size:117
Alignment explanation
Indices: 14471--14834 Score: 355
Period size: 117 Copynumber: 3.1 Consensus size: 117
14461 TATCCTAATT
** * ** * * * *
14471 ATTTATTTTTAACCTCGACTCGATCCT-AGTTGCTTTATTTTAACTCATGATATTGTCCTAGTCA
1 ATTTATTTTCGACCTCAACTCGATCCTGA-TCACTTTATTTTGACTCGTGATATCGTCCCAGTCA
*
14535 TTTGATCTCGACTCAGGTCAGATCATTTTTAGACTCGCGACATCAATCCAGTC
65 TTTGATCTCGACTCAGGTCAGATCATTTTTAGACTCGCGACATCAGTCCAGTC
*** * * *
14588 ATTTATTTTCGA-CTGTGGCTCGGTCCTGATCACTTTATTTTGACTCGTGGTATCATCCCAGTCA
1 ATTTATTTTCGACCT-CAACTCGATCCTGATCACTTTATTTTGACTCGTGATATCGTCCCAGTCA
* * * * *
14652 TTTGATCTCGACTCAAGTTAGATCACTTTTAGATTCGTGACATCAGTCC-GATC
65 TTTGATCTCGACTCAGGTCAGATCATTTTTAGACTCGCGACATCAGTCCAG-TC
* * * * * *
14705 ATTTATTTTTGACCTCAACTTGATCTTGGTCAC---CTTTTGACTCGTGACATCGTCCCAGTCAT
1 ATTTATTTTCGACCTCAACTCGATCCTGATCACTTTATTTTGACTCGTGATATCGTCCCAGTCAT
* * * * *
14767 TTGATCTCGACTCAGGTCACATCATCTTCAGACTCGCGACATTAGTCCAATC
66 TTGATCTCGACTCAGGTCAGATCATTTTTAGACTCGCGACATCAGTCCAGTC
14819 ATTTATTTAT-GACCTC
1 ATTTATTT-TCGACCTC
14835 GACTTGGTTT
Statistics
Matches: 200, Mismatches: 41, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
114 80 0.40
115 1 0.00
116 3 0.01
117 113 0.56
118 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (117 bp):
ATTTATTTTCGACCTCAACTCGATCCTGATCACTTTATTTTGACTCGTGATATCGTCCCAGTCAT
TTGATCTCGACTCAGGTCAGATCATTTTTAGACTCGCGACATCAGTCCAGTC
Found at i:14808 original size:114 final size:113
Alignment explanation
Indices: 14530--14915 Score: 384
Period size: 114 Copynumber: 3.4 Consensus size: 113
14520 ATATTGTCCT
* * *
14530 AGTCATTTGATCTCGACTCAGGTCAGATCATTTTTAGACTCGCGACATCAATCCAGTCATTTATT
1 AGTCATTTGATCTCGACTCAGGTCAGATCATCTTCAGACTCGCGACATCAGTCCA-TCATTTATT
* * * * * * *
14595 TTCGA-CTGTGGCTCGGTCCTGATCACTTTATTTTGACTCGTGGTATCATCCC
65 TTTGACCT-CGACTTGGTCTTGGTCAC---CTTTTGACTCGTGGTATCATCCC
* * * * *
14647 AGTCATTTGATCTCGACTCAAGTTAGATCA-CTTTTAGATTCGTGACATCAGTCCGATCATTTAT
1 AGTCATTTGATCTCGACTCAGGTCAGATCATC-TTCAGACTCGCGACATCAGTCC-ATCATTTAT
* * ** *
14711 TTTTGACCTCAACTTGATCTTGGTCACCTTTTGACTCGTGACATCGTCCC
64 TTTTGACCTCGACTTGGTCTTGGTCACCTTTTGACTCGTGGTATCATCCC
* *
14761 AGTCATTTGATCTCGACTCAGGTCACATCATCTTCAGACTCGCGACATTAGTCCAATCATTTATT
1 AGTCATTTGATCTCGACTCAGGTCAGATCATCTTCAGACTCGCGACATCAGTCC-ATCATTTATT
* * * * * *
14826 TATGACCTCGACTTGGTTTTAGTCTCCTTTAGACTCGTGGTATCATCCT
65 TTTGACCTCGACTTGGTCTTGGTCACCTTTTGACTCGTGGTATCATCCC
* *
14875 AGTTATTTGATCTC-AGCTTC-GGTCAGATCATCTTCTGACTC
1 AGTCATTTGATCTCGA-C-TCAGGTCAGATCATCTTCAGACTC
14916 ACGGCATTGT
Statistics
Matches: 223, Mismatches: 40, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
113 1 0.00
114 145 0.65
115 3 0.01
117 71 0.32
118 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (113 bp):
AGTCATTTGATCTCGACTCAGGTCAGATCATCTTCAGACTCGCGACATCAGTCCATCATTTATTT
TTGACCTCGACTTGGTCTTGGTCACCTTTTGACTCGTGGTATCATCCC
Found at i:15469 original size:16 final size:17
Alignment explanation
Indices: 15450--15484 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15440 CTATTTTTAT
*
15450 TTTTTTTTC-TTTTCTA
1 TTTTGTTTCTTTTTCTA
15466 TTTTGTTTCTTTTTCTA
1 TTTTGTTTCTTTTTCTA
15483 TT
1 TT
15485 CAAATCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTGTTTCTTTTTCTA
Found at i:15469 original size:17 final size:18
Alignment explanation
Indices: 15443--15484 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
15433 ACTATTACTA
*
15443 TTTT-TATTTTTTTTTC-
1 TTTTCTATTTTTGTTTCT
15459 TTTTCTA-TTTTGTTTCT
1 TTTTCTATTTTTGTTTCT
15476 TTTTCTATT
1 TTTTCTATT
15485 CAAATCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 12 0.55
17 9 0.41
18 1 0.05
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTCTATTTTTGTTTCT
Found at i:17288 original size:3 final size:3
Alignment explanation
Indices: 17280--17319 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
17270 AATGATGGTA
17280 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
17320 AACATGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:21795 original size:15 final size:15
Alignment explanation
Indices: 21777--21840 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
21767 TCAATGAAAC
21777 ATTTATTG-TCAAAAT
1 ATTTATTGAT-AAAAT
*
21792 ATTTATGGATAAAAT
1 ATTTATTGATAAAAT
*
21807 -TTT-TTGTCTATAAAT
1 ATTTATTG-ATA-AAAT
21822 -TTTATTGATAAAAT
1 ATTTATTGATAAAAT
21836 ATTTA
1 ATTTA
21841 CCTATGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
13 2 0.05
14 9 0.22
15 25 0.62
16 4 0.10
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (15 bp):
ATTTATTGATAAAAT
Found at i:22579 original size:23 final size:23
Alignment explanation
Indices: 22547--22595 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
22537 AATACAAAAT
22547 TTTAAAAATAAAATATGA-TTTTA
1 TTTAAAAATAAAATAT-ATTTTTA
* *
22570 TTTAACAATAATATATATTTTTA
1 TTTAAAAATAAAATATATTTTTA
22593 TTT
1 TTT
22596 TTATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTAAAAATAAAATATATTTTTA
Found at i:25052 original size:4 final size:4
Alignment explanation
Indices: 25043--25086 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
25033 AAATATTTAA
*
25043 AAAT AAAT AAAT AAAT AGAT AAAT AAAAT AAAT ATAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A-AAT AAAT AAA
25087 AATACTAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 2 0.06
4 27 0.77
5 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:25073 original size:17 final size:17
Alignment explanation
Indices: 25045--25087 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
25035 ATATTTAAAA
25045 ATAAAT-AAATAAATAG
1 ATAAATAAAATAAATAG
*
25061 ATAAATAAAATAAATAT
1 ATAAATAAAATAAATAG
*
25078 AAAAATAAAA
1 ATAAATAAAA
25088 ATACTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAATAAAATAAATAG
Found at i:27331 original size:27 final size:26
Alignment explanation
Indices: 27278--27331 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
27268 TCACATAAGG
* * *
27278 TTATAATAAGATAGGATAATATGATA
1 TTATAATAAGATAAGATAAAATAATA
*
27304 TTATGAATAAGATCAGATAAAATAATA
1 TTAT-AATAAGATAAGATAAAATAATA
27331 T
1 T
27332 AATTTTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (26 bp):
TTATAATAAGATAAGATAAAATAATA
Found at i:29277 original size:2 final size:2
Alignment explanation
Indices: 29270--29302 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29260 ACAGGATCAA
29270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29303 GTCAAGGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29525 original size:128 final size:129
Alignment explanation
Indices: 29362--29622 Score: 506
Period size: 128 Copynumber: 2.0 Consensus size: 129
29352 GATCGGACTA
29362 TGGTAAAGGGTTCTGAATTAGTTGCATACTTGCATAGCAATCAAACTAACCAGTCCTGGAGTGAG
1 TGGTAAAGGGTTCTGAATTAGTTGCATACTTGCATAGCAATCAAACTAACCAGTCCTGGAGTGAG
29427 AAGATCTGTTTATAAATTTAAATAAGAGACATAGAGAAAGAATTGCAAGTGAATTCT-GTTTAG
66 AAGATCTGTTTATAAATTTAAATAAGAGACATAGAGAAAGAATTGCAAGTGAATTCTGGTTTAG
29490 TGGTAAAGGGTTCTGAATTAGTTGCATACTTGCATAGCAATCAAACTAACCAGTCCTGGAGTGAG
1 TGGTAAAGGGTTCTGAATTAGTTGCATACTTGCATAGCAATCAAACTAACCAGTCCTGGAGTGAG
*
29555 AAGATCTGTTTATAAATTTAAATAAGAGACATAGAGAAAGAGTTGCAAGTGAATTCTGGTTTAG
66 AAGATCTGTTTATAAATTTAAATAAGAGACATAGAGAAAGAATTGCAAGTGAATTCTGGTTTAG
29619 TGGT
1 TGGT
29623 GGGTTCTCAC
Statistics
Matches: 131, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
128 121 0.92
129 10 0.08
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (129 bp):
TGGTAAAGGGTTCTGAATTAGTTGCATACTTGCATAGCAATCAAACTAACCAGTCCTGGAGTGAG
AAGATCTGTTTATAAATTTAAATAAGAGACATAGAGAAAGAATTGCAAGTGAATTCTGGTTTAG
Found at i:38153 original size:21 final size:21
Alignment explanation
Indices: 38129--38172 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
38119 CCTCATTACT
38129 TTAAACATCAAGATCACCAAC
1 TTAAACATCAAGATCACCAAC
** **
38150 TTAAGTATCATTATCACCAAC
1 TTAAACATCAAGATCACCAAC
38171 TT
1 TT
38173 GAGTAATAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (21 bp):
TTAAACATCAAGATCACCAAC
Found at i:40835 original size:62 final size:61
Alignment explanation
Indices: 40769--40981 Score: 182
Period size: 63 Copynumber: 3.4 Consensus size: 61
40759 TCCCTGAAAA
* ** *
40769 ATTTTA-AAAAAATTATTGAAGGTATTTTTTTATAGAAAACACCTTCAATAATCTCTTCCAAT
1 ATTTTACAAAAAATTATTGAAGGCA-TTTTTTATAGAAAATGCCTTCAATAATCCCTT-CAAT
*** * * * *
40831 ATTTTATCAGGGAATTATTGAAGGCA-TTTTTAGTCA-TAAATGCCTTTAATAATCCCTTGAAA
1 ATTTTA-CAAAAAATTATTGAAGGCATTTTTTA-T-AGAAAATGCCTTCAATAATCCCTTCAAT
*
40893 ATTTTTGA-AAAAAATTATTGAAGGCATTTTTTACAGAAAATTGCCTTCAATAATCCCCTTCAAT
1 A-TTTT-ACAAAAAATTATTGAAGGCATTTTTTATAGAAAA-TGCCTTCAATAAT-CCCTTCAA-
40957 T
61 T
*
40958 TTTTTATCAAAAAATTATTGAAGG
1 ATTTTA-CAAAAAATTATTGAAGG
40982 TGATTTTGAC
Statistics
Matches: 118, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
61 1 0.01
62 33 0.28
63 41 0.35
64 27 0.23
65 16 0.14
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (61 bp):
ATTTTACAAAAAATTATTGAAGGCATTTTTTATAGAAAATGCCTTCAATAATCCCTTCAAT
Found at i:40836 original size:125 final size:124
Alignment explanation
Indices: 40685--41305 Score: 540
Period size: 125 Copynumber: 4.9 Consensus size: 124
40675 AGGCAAAATG
* * * * *
40685 CCTTCAATAATCAAC-TCTAATTTTTTATCAGGGGATTATTGAAGGCATTTTCAGTTACAAACAC
1 CCTTCAATAATC-CCTTC-AATTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTTAAAAATAC
40749 CTTTAATAATTCCCTGAAAAATTTTAAAAAAATTATTGAAGGTATTTTTTTATAGAAAACA
64 CTTTAATAATTCCCTGAAAAATTTTAAAAAAATTATTGAAGGTATTTTTTTATAGAAAACA
* * * * *
40810 CCTTCAATAATCTCTTCCAATATTTTATCAGGGAATTATTGAAGGCATTTTTAGTCATAAATGCC
1 CCTTCAATAATCCCTT-CAATTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTTAAAAATACC
* * * **
40875 TTTAATAA-TCCCTTGAAAATTTTTGAAAAAAATTATTGAAGGCA-TTTTTTACAGAAAATTG
65 TTTAATAATTCCC-TGAAAAATTTT-AAAAAAATTATTGAAGGTATTTTTTTATAGAAAA-CA
*** * * *
40936 CCTTCAATAATCCCCTTCAATTTTTTTATCAAAAAATTATTGAAGGTGATTTTGA-CTAAAAATA
1 CCTTCAATAAT-CCCTTCAA-TTTTTTATCAGGGAATTATTGAAGG-CATTTTTAGTTAAAAATA
* * * * * * * * * *
41000 TCTTCAACAATTCCTTAAAAAAAATTTT-TAAAAATTATTGAATGCATTTTTTTTGTAGCAAACA
63 CCTTTAATAATTCCCT--GAAAAATTTTAAAAAAATTATTGAAGGTA-TTTTTTTATAGAAAACA
* * * * * * *
41064 CCTTCAATAATCCTCTTCAATTTTTTTATCAAGGCATTATTAAAAGCGTTTTTAGTTACAAATGC
1 CCTTCAATAATCC-CTTCAA-TTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTTAAAAATAC
* * * * **
41129 CTTCAATAA-TCCCTTGAAAATTTTTAAAGAAATTTATTAAAGGTA-TTTTTGCT-GAAAACA
64 CTTTAATAATTCCC-TGAAAAATTTTAAA-AAAATTATTGAAGGTATTTTTTTATAGAAAACA
* * * *
41189 TCTTCAATAATCCCTTTTAATTTTTTATCAGGGGATTATTGAAGGCATTTTTAGTTAAAAAAAAC
1 CCTTCAATAATCCC-TTCAATTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTT-AAAAATAC
* * *
41254 CTTTAATAATCCCCT-AAAAATTTTTAAAAAAAATTATTGAATGTGTTTTTTT
64 CTTTAATAATTCCCTGAAAAA-TTTT-AAAAAAATTATTGAAGGTATTTTTTT
41306 TTTTTTTGTA
Statistics
Matches: 393, Mismatches: 79, Indels: 47
0.76 0.15 0.09
Matches are distributed among these distances:
124 41 0.10
125 136 0.35
126 58 0.15
127 65 0.17
128 74 0.19
129 19 0.05
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (124 bp):
CCTTCAATAATCCCTTCAATTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTTAAAAATACCT
TTAATAATTCCCTGAAAAATTTTAAAAAAATTATTGAAGGTATTTTTTTATAGAAAACA
Found at i:40945 original size:63 final size:61
Alignment explanation
Indices: 40719--41294 Score: 190
Period size: 64 Copynumber: 9.1 Consensus size: 61
40709 TTATCAGGGG
* * *
40719 ATTATTGAAGGCATTTTCAGTTACA-AACA--CCTTTAATAATTCCC-TGAAAAATTTTAAAAAA
1 ATTATTGAAGGCATTTT---TTACAGAAAATGCCTTCAATAA-TCCCTTGAAAATTTTTAAAAAA
* * ** * * * * ***
40780 ATTATTGAAGGTATTTTTTTATAGAAAACACCTTCAATAATCTCTTCCAATATTTTATCAGGGA
1 ATTATTGAAGGCA-TTTTTTACAGAAAATGCCTTCAATAATCCCTT-GAAAATTTT-TAAAAAA
* *
40844 ATTATTGAAGGCA-TTTTTAGTCA-TAAATGCCTTTAATAATCCCTTGAAAATTTTTGAAAAAA
1 ATTATTGAAGGCATTTTTTA--CAGAAAATGCCTTCAATAATCCCTTGAAAATTTTT-AAAAAA
* **
40906 ATTATTGAAGGCATTTTTTACAGAAAATTGCCTTCAATAATCCCCTTCAATTTTTTTATCAAAAA
1 ATTATTGAAGGCATTTTTTACAGAAAA-TGCCTTCAATAAT-CCCTTGAAAATTTTTA--AAAAA
* * ** * * *
40971 ATTATTGAAGGTGA-TTTTGACTA-AAAATATCTTCAACAATTCCTTAAAAAAAATTTTT--AAA
1 ATTATTGAAGG-CATTTTTTAC-AGAAAATGCCTTCAATAATCCCTT---GAAAATTTTTAAAAA
41032 A
61 A
* ** * ** * ** **
41033 ATTATTGAATGCATTTTTTTTGTAGCAAACACCTTCAATAATCCTCTTCAATTTTTTTATCAAGG
1 ATTATTGAAGGCA--TTTTTTACAGAAAATGCCTTCAATAATCC-CTTGAAAATTTTTA--AAAA
*
41098 C
61 A
* * * ***
41099 ATTATTAAAAGC-GTTTTTAGTTACAAATGCCTTCAATAATCCCTTGAAAATTTTTAAAGAAA
1 ATTATTGAAGGCATTTTTTACAGA-AAATGCCTTCAATAATCCCTTGAAAATTTTTAAA-AAA
* * * * * *** ** * ****
41161 TTTATTAAAGGTA-TTTTTGCTGAAAACATCTTCAATAATCCCTTTTAATTTTTTATCAGGGG
1 ATTATTGAAGGCATTTTTTACAGAAAATGCCTTCAATAATCCCTTGAAAATTTTTA--AAAAA
** * * *
41223 ATTATTGAAGGCATTTTTAGTTA-A-AAAAAACCTTTAATAATCCCCTAAAAATTTTTAAAAAAA
1 ATTATTGAAGGCA-TTTT--TTACAGAAAATGCCTTCAATAATCCCTTGAAAATTTTT-AAAAAA
41286 ATTATTGAA
1 ATTATTGAA
41295 TGTGTTTTTT
Statistics
Matches: 372, Mismatches: 103, Indels: 78
0.67 0.19 0.14
Matches are distributed among these distances:
59 4 0.01
60 3 0.01
61 47 0.13
62 92 0.25
63 74 0.20
64 100 0.27
65 30 0.08
66 22 0.06
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (61 bp):
ATTATTGAAGGCATTTTTTACAGAAAATGCCTTCAATAATCCCTTGAAAATTTTTAAAAAA
Found at i:43414 original size:21 final size:22
Alignment explanation
Indices: 43381--43422 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
43371 TAAAGACTTG
*
43381 ATGAGCAAAAGCAATG-CCTGA
1 ATGACCAAAAGCAATGACCTGA
*
43402 ATGACCAATAGCAATGACCTG
1 ATGACCAAAAGCAATGACCTG
43423 TAGCTTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (22 bp):
ATGACCAAAAGCAATGACCTGA
Found at i:45164 original size:35 final size:35
Alignment explanation
Indices: 45118--45190 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
45108 CATATATAAA
* *
45118 TCAAATGTTTTCTAGGCATAAACTTACAACTGATT
1 TCAAATGTTTTCTAGGCATAAACCTACAACTGACT
*
45153 TCAAATGTTTTCTAGGCATAAACCTACAATTGACT
1 TCAAATGTTTTCTAGGCATAAACCTACAACTGACT
45188 TCA
1 TCA
45191 CATATATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (35 bp):
TCAAATGTTTTCTAGGCATAAACCTACAACTGACT
Found at i:45846 original size:61 final size:60
Alignment explanation
Indices: 45766--45929 Score: 170
Period size: 61 Copynumber: 2.7 Consensus size: 60
45756 ATAGGATATT
* * *
45766 TATTGAAGGTATTTTTGACAAAAAATGCCTTTAATAATCCTCTCTAATTTTT-TAAGGGAAA
1 TATTAAAGGT-TTTCTGACAAAAAATGCCTTCAATAATCC-CTCTAATTTTTATAAGGGAAA
* * * *
45827 TATTAAAGGTGTTTCTGACAAAAAATGCCTTCAACAATTGCCTCTATTTTTTATAAGGGAAT
1 TATTAAAGGT-TTTCTGACAAAAAATGCCTTCAATAA-TCCCTCTAATTTTTATAAGGGAAA
* * *
45889 TATTCAAGGCATTTTCAG-CCAAAAATGCCTTCAATAATCCC
1 TATTAAAGG--TTTTCTGACAAAAAATGCCTTCAATAATCCC
45930 CTATCCATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
61 45 0.52
62 35 0.41
63 5 0.06
64 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (60 bp):
TATTAAAGGTTTTCTGACAAAAAATGCCTTCAATAATCCCTCTAATTTTTATAAGGGAAA
Found at i:45954 original size:63 final size:63
Alignment explanation
Indices: 45847--46021 Score: 185
Period size: 63 Copynumber: 2.8 Consensus size: 63
45837 GTTTCTGACA
* ** *
45847 AAAAATGCCTTCAACAATTGCC--TCTATTTTTTAT-AAGGGAATTATTCAAGGCATTTTCAGCC
1 AAAAATGCCTTCAATAATCCCCTATCCATTTTTT-TGAAGGG-ATTATTCAAGGCATTTTCAGCC
** *
45909 AAAAATGCCTTCAATAATCCCCTATCCATTTTTTTGAAGGGATTATTCAAGGTGTTTTCTGCC
1 AAAAATGCCTTCAATAATCCCCTATCCATTTTTTTGAAGGGATTATTCAAGGCATTTTCAGCC
** * * * * *
45972 AAAAACACTTTCAATAATCTCTTATTCATTTTTATGAAGGGATTATTCAA
1 AAAAATGCCTTCAATAATCCCCTATCCATTTTTTTGAAGGGATTATTCAA
46022 TGTGTTTTCT
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
62 19 0.20
63 63 0.66
64 14 0.15
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (63 bp):
AAAAATGCCTTCAATAATCCCCTATCCATTTTTTTGAAGGGATTATTCAAGGCATTTTCAGCC
Found at i:46027 original size:63 final size:63
Alignment explanation
Indices: 45874--46090 Score: 228
Period size: 63 Copynumber: 3.5 Consensus size: 63
45864 TTGCCTCTAT
** * * *
45874 TTTTTAT-AAGGGAATTATTCAAGGCATTTTCAGCCAAAAATGCCTTCAATAATCCCCTATCCA
1 TTTTTATGAAGGG-ATTATTCAAGGTGTTTTCTGCCAAAAATACTTTCAATAATCCCCTATCCA
* * * * *
45937 TTTTTTTGAAGGGATTATTCAAGGTGTTTTCTGCCAAAAACACTTTCAATAATCTCTTATTCA
1 TTTTTATGAAGGGATTATTCAAGGTGTTTTCTGCCAAAAATACTTTCAATAATCCCCTATCCA
* * * * *
46000 TTTTTATGAAGGGATTATTCAATGTGTTTTCTACCAAAAATACTTTTAATAAT-CACTAT-AA
1 TTTTTATGAAGGGATTATTCAAGGTGTTTTCTGCCAAAAATACTTTCAATAATCCCCTATCCA
*
46061 TTTTT-T-AGAGAGGATTAATCAAGGTGTTTT
1 TTTTTATGA-AG-GGATTATTCAAGGTGTTTT
46091 AGTCAATAAA
Statistics
Matches: 130, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 3 0.02
61 23 0.18
62 3 0.02
63 95 0.73
64 5 0.04
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (63 bp):
TTTTTATGAAGGGATTATTCAAGGTGTTTTCTGCCAAAAATACTTTCAATAATCCCCTATCCA
Found at i:50796 original size:27 final size:27
Alignment explanation
Indices: 50727--50796 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
50717 TTTAGAAGCA
*
50727 AAATAAGT-TCTATTTCCTATAGAATCT
1 AAATAA-TCTCTATTTTCTATAGAATCT
50754 AAATAATCTCTATTTTCTATAGAATCT
1 AAATAATCTCTATTTTCTATAGAATCT
*
50781 AAATAATCTTTATTTT
1 AAATAATCTCTATTTT
50797 TTGTTGCAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (27 bp):
AAATAATCTCTATTTTCTATAGAATCT
Found at i:54754 original size:20 final size:20
Alignment explanation
Indices: 54731--54781 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
54721 TTTTTTAAAA
54731 TCTAAAA-ATTTTAAAAAAGT
1 TCTAAAAGATTTT-AAAAAGT
* *
54751 TCTAAAAGATTTTCAAAATT
1 TCTAAAAGATTTTAAAAAGT
54771 TCTAAAAGATT
1 TCTAAAAGATT
54782 ACTAAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (20 bp):
TCTAAAAGATTTTAAAAAGT
Found at i:54864 original size:19 final size:19
Alignment explanation
Indices: 54842--54881 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
54832 AAAAAAATCT
*
54842 AAAAGTTTTAAAATTAAAA
1 AAAAATTTTAAAATTAAAA
54861 AAAAATTTTAAAATTAAAA
1 AAAAATTTTAAAATTAAAA
54880 AA
1 AA
54882 TTCTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATTTTAAAATTAAAA
Found at i:54873 original size:9 final size:9
Alignment explanation
Indices: 54861--55017 Score: 61
Period size: 9 Copynumber: 16.4 Consensus size: 9
54851 AAAATTAAAA
54861 AAAAATTTT
1 AAAAATTTT
*
54870 -AAAA-TTA
1 AAAAATTTT
*
54877 AAAAATTCTA
1 AAAAATT-TT
*
54887 AAAAATTCT
1 AAAAATTTT
54896 AAAAATTTT
1 AAAAATTTT
*
54905 CCAAAATTTT
1 -AAAAATTTT
* *
54915 TAAAATTAT
1 AAAAATTTT
54924 AAAAA-TTT
1 AAAAATTTT
* *
54932 AAAAGTTATAAA
1 AAAAATT-T--T
**
54944 AAAAATACT
1 AAAAATTTT
54953 AAAAAGTTATT
1 AAAAA-TT-TT
*
54964 AAAAATGTCT
1 AAAAAT-TTT
54974 ACAAAATTTTT
1 A-AAAA-TTTT
54985 AAAATATTTT
1 AAAA-ATTTT
*
54995 -AAAATTCT
1 AAAAATTTT
55003 AAAATATTGTT
1 AAAA-ATT-TT
55014 AAAA
1 AAAA
55018 CATCTAAACA
Statistics
Matches: 110, Mismatches: 21, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
7 2 0.02
8 18 0.16
9 32 0.29
10 32 0.29
11 20 0.18
12 6 0.05
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAAATTTT
Found at i:54940 original size:17 final size:16
Alignment explanation
Indices: 54913--54945 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
54903 TTCCAAAATT
54913 TTTAAAATTATAAAAA
1 TTTAAAATTATAAAAA
54929 TTTAAAAGTTATAAAAA
1 TTTAAAA-TTATAAAAA
54946 AAATACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTTAAAATTATAAAAA
Found at i:55025 original size:20 final size:18
Alignment explanation
Indices: 54984--55039 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
54974 ACAAAATTTT
*
54984 TAAAATATTTTAAAATTC
1 TAAAATATTTTAAAAATC
55002 TAAAATATTGTTAAAACATC
1 TAAAATATT-TTAAAA-ATC
*
55022 TAAACAATTTTTTAAAAA
1 T-AA-AATATTTTAAAAA
55040 AATTATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 4 0.12
21 8 0.25
22 5 0.16
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAATATTTTAAAAATC
Found at i:55059 original size:9 final size:10
Alignment explanation
Indices: 55036--55064 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
55026 CAATTTTTTA
55036 AAAAAATTAT
1 AAAAAATTAT
55046 AAAAAATTAT
1 AAAAAATTAT
55056 -AAAAATTAT
1 AAAAAATTAT
55065 TGAAATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:55144 original size:24 final size:24
Alignment explanation
Indices: 55097--55144 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55087 AAATTTTGAA
*
55097 AAAATAAAAAATAAAAATATTTTT
1 AAAATAAAAAATAAAAATAATTTT
* * *
55121 AAAATATAAAATTAAGATAATTTT
1 AAAATAAAAAATAAAAATAATTTT
55145 TGTAATTAAA
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:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATAAAAAATAAAAATAATTTT
Found at i:55437 original size:17 final size:17
Alignment explanation
Indices: 55403--55437 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55393 ATTCTGAAAT
* *
55403 ATTCTTAAAAATTAAAA
1 ATTCTGAAAAATAAAAA
55420 ATTCTGAAAAATAAAAA
1 ATTCTGAAAAATAAAAA
55437 A
1 A
55438 GAAAGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
ATTCTGAAAAATAAAAA
Found at i:55722 original size:19 final size:19
Alignment explanation
Indices: 55700--55769 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
55690 TTTATGAATT
55700 TTTTGAAAATTTTTGAAAA
1 TTTTGAAAATTTTTGAAAA
** *
55719 TTTTGAGATTTTTTTGAAGA
1 TTTTGA-AAATTTTTGAAAA
* *
55739 TTTT-AAATTTATTTGAATA
1 TTTTGAAAATT-TTTGAAAA
55758 -TTTGAAGAATTT
1 TTTTGAA-AATTT
55770 AGAAAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
18 7 0.17
19 17 0.41
20 17 0.41
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TTTTGAAAATTTTTGAAAA
Found at i:55732 original size:20 final size:19
Alignment explanation
Indices: 55709--55760 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
55699 TTTTTGAAAA
*
55709 TTTTTGAAAATTTTGAGATT
1 TTTTTGAAAATTTT-AAATT
*
55729 TTTTTGAAGATTTTAAATT
1 TTTTTGAAAATTTTAAATT
* *
55748 TATTTGAATATTT
1 TTTTTGAAAATTT
55761 GAAGAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (19 bp):
TTTTTGAAAATTTTAAATT
Found at i:55795 original size:10 final size:10
Alignment explanation
Indices: 55776--55830 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
55766 ATTTAGAAAA
55776 ATTTTAAGAAT
1 ATTTT-AGAAT
55787 ATTTTAGAAT
1 ATTTTAGAAT
* *
55797 ATTTTAAAAC
1 ATTTTAGAAT
55807 ATTTTAGAAT
1 ATTTTAGAAT
*
55817 TTTTTA-AA-
1 ATTTTAGAAT
55825 ATTTTA
1 ATTTTA
55831 AAAAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
10 26 0.68
11 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (10 bp):
ATTTTAGAAT
Found at i:55812 original size:20 final size:20
Alignment explanation
Indices: 55776--55825 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
55766 ATTTAGAAAA
*
55776 ATTTTAAGAATATTTTAGAAT
1 ATTTTAA-AACATTTTAGAAT
55797 ATTTTAAAACATTTTAGAAT
1 ATTTTAAAACATTTTAGAAT
*
55817 TTTTTAAAA
1 ATTTTAAAA
55826 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (20 bp):
ATTTTAAAACATTTTAGAAT
Found at i:55956 original size:11 final size:11
Alignment explanation
Indices: 55940--55973 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
55930 TTCAAAAAAA
55940 TTTTGAAATTT
1 TTTTGAAATTT
*
55951 TTTTGAAATCT
1 TTTTGAAATTT
55962 TTTTG-AATTT
1 TTTTGAAATTT
55972 TT
1 TT
55974 AAAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (11 bp):
TTTTGAAATTT
Found at i:58250 original size:27 final size:29
Alignment explanation
Indices: 58192--58263 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
58182 TTGAGATTTT
*
58192 TTTTAA-AAAAAGTT-AAATTAATAAAAA
1 TTTTAATAAAAAATTAAAATTAATAAAAA
*
58219 TTTTAATAAAAAATTAAAATTGAT-AAAA
1 TTTTAATAAAAAATTAAAATTAATAAAAA
*
58247 -TTTAATATGAAAATTAA
1 TTTTAATA-AAAAATTAA
58264 TACTATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.33
28 19 0.49
29 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTTAATAAAAAATTAAAATTAATAAAAA
Found at i:58349 original size:15 final size:14
Alignment explanation
Indices: 58329--58378 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
58319 AAAGTTTATT
*
58329 AATATTTTTATTAAA
1 AATATTTAT-TTAAA
58344 AATATTTATTTAAA
1 AATATTTATTTAAA
*
58358 AA-ATATA-TTAAA
1 AATATTTATTTAAA
58370 ATATATTTA
1 A-ATATTTA
58379 AATTTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.20
13 5 0.17
14 11 0.37
15 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTATTTAAA
Found at i:58353 original size:13 final size:13
Alignment explanation
Indices: 58335--58378 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
58325 TATTAATATT
58335 TTTATTAAAAATA
1 TTTATTAAAAATA
58348 TTTATTTAAAAA-A
1 TTTA-TTAAAAATA
*
58361 TATATTAAAATATA
1 TTTATTAAAA-ATA
58375 TTTA
1 TTTA
58379 AATTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTATTAAAAATA
Found at i:58458 original size:21 final size:21
Alignment explanation
Indices: 58418--58459 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58408 ATGTGATGAG
*
58418 ATTTTTAATTAATTAATTTTA
1 ATTTTTAATTAATCAATTTTA
* *
58439 ATTTTTATTTAATCATTTTTA
1 ATTTTTAATTAATCAATTTTA
58460 GTAAAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAATTAATCAATTTTA
Found at i:58734 original size:28 final size:28
Alignment explanation
Indices: 58694--58747 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
58684 AGTTAAAGAC
* *
58694 AATTCAATTTAATTATATAGAAAATTTT
1 AATTAAATTTAATTATATAAAAAATTTT
58722 AATTAAATTTAATTATATAAAAAATT
1 AATTAAATTTAATTATATAAAAAATT
58748 ATATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTAAATTTAATTATATAAAAAATTTT
Found at i:60231 original size:40 final size:39
Alignment explanation
Indices: 60186--60264 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
60176 TTTTTTTTAG
60186 ATATTTAGATTTAAAATATAAGAACATGAAATTTTATGTT
1 ATATTTAGATTTAAAATATAAGAACATGAAA-TTTATGTT
*
60226 ATATTTAGATTTAAAATGTAAGAACATGAAATTTATGTT
1 ATATTTAGATTTAAAATATAAGAACATGAAATTTATGTT
60265 CTGATGAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (39 bp):
ATATTTAGATTTAAAATATAAGAACATGAAATTTATGTT
Found at i:62301 original size:17 final size:16
Alignment explanation
Indices: 62279--62324 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
62269 AATATTTTGC
*
62279 AATTTTAAAAATTTCTA
1 AATTTTAAAAATTT-AA
* *
62296 ATTTTTTAAAATTTAA
1 AATTTTAAAAATTTAA
62312 AATTTTAAAAATT
1 AATTTTAAAAATT
62325 ACCACAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTAAAAATTTAA
Found at i:62601 original size:22 final size:22
Alignment explanation
Indices: 62562--62607 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
62552 TCATATGAAA
*
62562 AAAAATCTTATACCAATTTATT
1 AAAAATCTTATACAAATTTATT
*
62584 AAAAATC-TATTACAAATTTTTT
1 AAAAATCTTA-TACAAATTTATT
62606 AA
1 AA
62608 TATATGATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATCTTATACAAATTTATT
Found at i:63765 original size:15 final size:15
Alignment explanation
Indices: 63747--63778 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
63737 TAAATTAATA
63747 ATCATGCAATTAGAC
1 ATCATGCAATTAGAC
63762 ATCATGCAATTAGAC
1 ATCATGCAATTAGAC
63777 AT
1 AT
63779 GCAATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
ATCATGCAATTAGAC
Found at i:63781 original size:12 final size:14
Alignment explanation
Indices: 63746--63785 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
63736 ATAAATTAAT
63746 AATCATGCAATTAG
1 AATCATGCAATTAG
63760 ACATCATGCAATTAG
1 A-ATCATGCAATTAG
63775 -A-CATGCAATTA
1 AATCATGCAATTA
63786 AATATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 1 0.04
14 1 0.04
15 13 0.52
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (14 bp):
AATCATGCAATTAG
Found at i:63826 original size:41 final size:41
Alignment explanation
Indices: 63775--64086 Score: 182
Period size: 41 Copynumber: 7.5 Consensus size: 41
63765 ATGCAATTAG
*
63775 ACATGCAATTAAATATATAATCACATAATTAACAATGTCAA
1 ACATGCAATTAAATATATAATCACACAATTAACAATGTCAA
* * ** *
63816 ACATGTAATTAAATATTTAATCATGCAATTAACAATGTAAA
1 ACATGCAATTAAATATATAATCACACAATTAACAATGTCAA
* ** *
63857 ACATGCGACATGTAATTAAATATTTAATCATGCAATTAACAATGTAAA
1 ACAT--G-C----AATTAAATATATAATCACACAATTAACAATGTCAA
* * ** *
63905 ACATGCAAATAAATATATAAACATGCAATTAACAATAT-AA
1 ACATGCAATTAAATATATAATCACACAATTAACAATGTCAA
* * * ** * *
63945 ATTATCCAAATAAATATATAATCATGCAATTAACAATATAAA
1 A-CATGCAATTAAATATATAATCACACAATTAACAATGTCAA
* * * ** * *
63987 ACATGCAAATAAATAAATTATCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCACACAATTAACAATGTCAA
* * * ** * *
64028 ACATGCAA--AAAAAAAT-ATTATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCACACAATTAACAATGTCAA
* *
64066 ATATGCAAATAAATATATAAT
1 ACATGCAATTAAATATATAAT
64087 AATAATCATG
Statistics
Matches: 236, Mismatches: 23, Indels: 24
0.83 0.08 0.08
Matches are distributed among these distances:
38 28 0.12
39 7 0.03
40 9 0.04
41 147 0.62
42 3 0.01
43 1 0.00
45 1 0.00
46 1 0.00
48 39 0.17
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.29
Consensus pattern (41 bp):
ACATGCAATTAAATATATAATCACACAATTAACAATGTCAA
Found at i:63872 original size:48 final size:44
Alignment explanation
Indices: 63869--64100 Score: 190
Period size: 41 Copynumber: 5.5 Consensus size: 44
63859 ATGCGACATG
*
63869 TAATTAAATATTTAATCATGCAATTAACAATGTAAAACATG--CA
1 TAAT-AAATATTTAATCATGCAATTAACAATATAAAACATGCACA
* * **
63912 -AATAAATATATAAACATGCAATTAACAATATAAATTAT-C-CA
1 TAATAAATATTTAATCATGCAATTAACAATATAAAACATGCACA
*
63953 -AATAAATATATAATCATGCAATTAACAATATAAAACATG--CA
1 TAATAAATATTTAATCATGCAATTAACAATATAAAACATGCACA
*
63994 -AATAAATAAATT-ATCATGCAATTAACAATATAAAACATGCA-A
1 TAATAAAT-ATTTAATCATGCAATTAACAATATAAAACATGCACA
* * * *
64036 -AA-AAA-A-AT-ATTATGCAATTAACAATATAAAATATGCAAA
1 TAATAAATATTTAATCATGCAATTAACAATATAAAACATGCACA
* *
64075 TAAATATATAATAATAATCATGCAAT
1 T-AATAAAT-AT-TTAATCATGCAAT
64101 CACACAAATA
Statistics
Matches: 160, Mismatches: 15, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
38 28 0.17
39 2 0.01
41 108 0.68
42 10 0.06
44 1 0.01
46 2 0.01
47 9 0.06
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.29
Consensus pattern (44 bp):
TAATAAATATTTAATCATGCAATTAACAATATAAAACATGCACA
Found at i:63885 original size:89 final size:88
Alignment explanation
Indices: 63774--64086 Score: 325
Period size: 89 Copynumber: 3.7 Consensus size: 88
63764 CATGCAATTA
*** * * *
63774 GACATGCAATTAAATATATAATCACATAATTAACAATGTCAAACATGTAATTAAATATTTAATCA
1 GACATG-AATTAAATATATAATCATGCAATTAACAATGTAAAACATGCAAATAAATATTTAATCA
*
63839 TGCAATTAACAATGTAAAACATGC
65 TGCAATTAACAATATAAAACATGC
* * *
63863 GACATGTAATTAAATATTTAATCATGCAATTAACAATGTAAAACATGCAAATAAATATATAAACA
1 GACATG-AATTAAATATATAATCATGCAATTAACAATGTAAAACATGCAAATAAATATTTAATCA
**
63928 TGCAATTAACAATATAAATTAT-C
65 TGCAATTAACAATATAAAACATGC
* *
63951 --CA--AA-TAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATAAATT-ATCA
1 GACATGAATTAAATATATAATCATGCAATTAACAATGTAAAACATGCAAATAAAT-ATTTAATCA
64010 TGCAATTAACAATATAAAACATGC
65 TGCAATTAACAATATAAAACATGC
* * * *
64034 -A-A--AA--AAA-A-AT-ATTATGCAATTAACAATATAAAATATGCAAATAAATATATAAT
1 GACATGAATTAAATATATAATCATGCAATTAACAATGTAAAACATGCAAATAAATATTTAAT
64087 AATAATCATG
Statistics
Matches: 196, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.01
79 36 0.18
80 2 0.01
81 1 0.01
82 70 0.36
83 8 0.04
86 2 0.01
88 1 0.01
89 74 0.38
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (88 bp):
GACATGAATTAAATATATAATCATGCAATTAACAATGTAAAACATGCAAATAAATATTTAATCAT
GCAATTAACAATATAAAACATGC
Found at i:63974 original size:82 final size:82
Alignment explanation
Indices: 63873--64085 Score: 306
Period size: 82 Copynumber: 2.6 Consensus size: 82
63863 GACATGTAAT
* *
63873 TAAATATTTAATCATGCAATTAACAATGTAAAACATGCAAATAAATATATAAACATGCAATTAAC
1 TAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATATATAAACATGCAATTAAC
**
63938 AATATAAATTATCCAAA
66 AATATAAAACATCCAAA
* * *
63955 TAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATAAATTATCATGCAATTAAC
1 TAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATATATAAACATGCAATTAAC
*
64020 AATATAAAACATGCAAA
66 AATATAAAACATCCAAA
* * *
64037 -AAA-AAAT-ATTATGCAATTAACAATATAAAATATGCAAATAAATATATAA
1 TAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATATATAA
64086 TAATAATCAT
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 38 0.32
80 3 0.03
81 3 0.03
82 74 0.63
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (82 bp):
TAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATATATAAACATGCAATTAAC
AATATAAAACATCCAAA
Found at i:64089 original size:123 final size:130
Alignment explanation
Indices: 63825--64086 Score: 364
Period size: 120 Copynumber: 2.1 Consensus size: 130
63815 AACATGTAAT
* * * *
63825 TAAATATTTAATCATGCAATTAACAATGTAAAACATGCGACATGTAATTAAATATTTAATCATGC
1 TAAATATATAATCATGCAATTAACAATATAAAACATGCGACATATAAATAAATATTTAATCATGC
* * *
63890 AATTAACAATGTAAAACATGCAAATAAATATATAAACATGCAATTAACAATATAAATTATCCAAA
66 AATTAACAATATAAAACATGCAAATAAATAAATAAACATGCAATTAACAATATAAAATATCCAAA
63955 TAAATATATAATCATGCAATTAACAATATAAAACATGC-A-A-ATAAAT-AA-A-TT-ATCATGC
1 TAAATATATAATCATGCAATTAACAATATAAAACATGCGACATATAAATAAATATTTAATCATGC
** *
64013 AATTAACAATATAAAACATGCAAA-AAA-AAAT-ATTATGCAATTAACAATATAAAATATGCAAA
66 AATTAACAATATAAAACATGCAAATAAATAAATAAACATGCAATTAACAATATAAAATATCCAAA
64075 TAAATATATAAT
1 TAAATATATAAT
64087 AATAATCATG
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
120 39 0.32
121 3 0.02
122 3 0.02
123 30 0.25
124 2 0.02
125 1 0.01
126 2 0.02
127 4 0.03
128 1 0.01
129 1 0.01
130 36 0.30
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (130 bp):
TAAATATATAATCATGCAATTAACAATATAAAACATGCGACATATAAATAAATATTTAATCATGC
AATTAACAATATAAAACATGCAAATAAATAAATAAACATGCAATTAACAATATAAAATATCCAAA
Found at i:64139 original size:20 final size:20
Alignment explanation
Indices: 64114--64217 Score: 97
Period size: 20 Copynumber: 5.3 Consensus size: 20
64104 ACAAATAAAT
64114 AAATTAATAATCATGCAAAC
1 AAATTAATAATCATGCAAAC
*
64134 AAATTAATAGTCATGCAAAC
1 AAATTAATAATCATGCAAAC
* * *
64154 ATATTAATAGTCATGCAAAT
1 AAATTAATAATCATGCAAAC
* *
64174 ATATTAATAA--AT-CACAC
1 AAATTAATAATCATGCAAAC
* * *
64191 AAATATATTAATCATGTAAAT
1 AAAT-TAATAATCATGCAAAC
64212 AAATTA
1 AAATTA
64218 TCATGCAACT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.09
18 7 0.10
20 50 0.72
21 6 0.09
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATTAATAATCATGCAAAC
Found at i:64906 original size:20 final size:20
Alignment explanation
Indices: 64865--64907 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
64855 TTTTTTTACT
*
64865 AAAAAATTAAAATTAAACTA
1 AAAAAATTAAAATTAAAATA
64885 AAAAAATTAAAA-TACAAATA
1 AAAAAATTAAAATTA-AAATA
64905 AAA
1 AAA
64908 TTTAGGACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATTAAAATTAAAATA
Found at i:65237 original size:43 final size:43
Alignment explanation
Indices: 65190--65388 Score: 183
Period size: 43 Copynumber: 4.6 Consensus size: 43
65180 CCAACTAAGG
* * *
65190 CTTTGAAATTTTTGAAAAATAAAATGCTCCTCCATAGTTGAAA
1 CTTTGAAACTTTTGAAAAATAAAATGCTCCTCCACAGTTGAGA
* * * * *
65233 CTTTGGAACTTTTG-AAAATACAATGTTGTTCC-CCAACAATTGAGG
1 CTTTGAAACTTTTGAAAAATA-AA--ATGCTCCTCC-ACAGTTGAGA
* * *
65278 CTTT-AGAACTTTTGAAAAATAAAATACTCCTCCACAGCTGAGG
1 CTTTGA-AACTTTTGAAAAATAAAATGCTCCTCCACAGTTGAGA
* * *
65321 CTTTAAAAC-TTTGAAAAATAAAATG-TTCTCTCACAATTGAGA
1 CTTTGAAACTTTTGAAAAATAAAATGCTCCTC-CACAGTTGAGA
65363 CTTTGAAACTTTTGAAAAATAAAATG
1 CTTTGAAACTTTTGAAAAATAAAATG
65389 AGATCATTTT
Statistics
Matches: 126, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
41 4 0.03
42 37 0.29
43 49 0.39
44 5 0.04
45 25 0.20
46 6 0.05
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (43 bp):
CTTTGAAACTTTTGAAAAATAAAATGCTCCTCCACAGTTGAGA
Found at i:65291 original size:88 final size:85
Alignment explanation
Indices: 65190--65388 Score: 231
Period size: 88 Copynumber: 2.3 Consensus size: 85
65180 CCAACTAAGG
* * * ** *
65190 CTTTGAAATTTTTGAAAAATAAAATGCTCCTCCATAGTTGAAACTTTGGAACTTTTG-AAAATAC
1 CTTTGAAACTTTTGAAAAATAAAATGCTCCTCCACAGCTGAAACTTTAAAAC-TTTGAAAAATAA
* *
65254 AATGTTGTTCCCCAACAATTGAGG
65 AATGTT-CT-CCC-ACAATTGAGA
* **
65278 CTTT-AGAACTTTTGAAAAATAAAATACTCCTCCACAGCTGAGGCTTTAAAACTTTGAAAAATAA
1 CTTTGA-AACTTTTGAAAAATAAAATGCTCCTCCACAGCTGAAACTTTAAAACTTTGAAAAATAA
*
65342 AATGTTCTCTCACAATTGAGA
65 AATGTTCTCCCACAATTGAGA
65363 CTTTGAAACTTTTGAAAAATAAAATG
1 CTTTGAAACTTTTGAAAAATAAAATG
65389 AGATCATTTT
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
85 32 0.34
86 3 0.03
87 6 0.06
88 54 0.57
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (85 bp):
CTTTGAAACTTTTGAAAAATAAAATGCTCCTCCACAGCTGAAACTTTAAAACTTTGAAAAATAAA
ATGTTCTCCCACAATTGAGA
Found at i:65577 original size:13 final size:13
Alignment explanation
Indices: 65559--65583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65549 TTTCAAACAT
65559 ATGCAATGAATGC
1 ATGCAATGAATGC
65572 ATGCAATGAATG
1 ATGCAATGAATG
65584 AAAAGATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATGCAATGAATGC
Found at i:67210 original size:15 final size:14
Alignment explanation
Indices: 67190--67235 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
67180 TTTTCATCAA
*
67190 TTTTCTTTGTTTCTT
1 TTTTCTTTCTTT-TT
67205 TTTTCTTTC-TTTT
1 TTTTCTTTCTTTTT
67218 TTTT-TTTCATTTTT
1 TTTTCTTTC-TTTTT
67232 TTTT
1 TTTT
67236 GGTATGCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 10 0.36
15 8 0.29
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:67219 original size:13 final size:13
Alignment explanation
Indices: 67203--67235 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
67193 TCTTTGTTTC
*
67203 TTTTTTCTTTC-T
1 TTTTTTTTTTCAT
67215 TTTTTTTTTTCAT
1 TTTTTTTTTTCAT
67228 TTTTTTTT
1 TTTTTTTT
67236 GGTATGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTCAT
Found at i:69700 original size:24 final size:24
Alignment explanation
Indices: 69673--69721 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
69663 CATACCAAAT
69673 ATCATG-TAATAATA-TCATGCTTAG
1 ATCATGCTAA-AATATTCATG-TTAG
69697 ATCATGCTAAAATATTCATGTTAG
1 ATCATGCTAAAATATTCATGTTAG
69721 A
1 A
69722 ATGTCGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (24 bp):
ATCATGCTAAAATATTCATGTTAG
Found at i:70004 original size:22 final size:21
Alignment explanation
Indices: 69963--70010 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
69953 TTAATCATAC
*
69963 AATCACACAAATGAATATATA
1 AATCACACAAATGAAAATATA
69984 TAATCACACAAAT-AACAATATA
1 -AATCACACAAATGAA-AATATA
70006 AATCA
1 AATCA
70011 TGCAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.58, C:0.17, G:0.02, T:0.23
Consensus pattern (21 bp):
AATCACACAAATGAAAATATA
Found at i:70041 original size:41 final size:41
Alignment explanation
Indices: 69970--70284 Score: 309
Period size: 41 Copynumber: 7.7 Consensus size: 41
69960 TACAATCACA
** * *
69970 CAAATGAATATATATAATCACACAAATAACAATATAAATCATG
1 CAAAT-AA-ATATATAATCATGCAATTAACAATATAAAACATG
* *
70013 CAATTAAATATATAATCATGCAATTAACAACATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* *
70054 CAAATAAATATTTAATCATGCAATTAACAACATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * *
70095 CAATTAAATATATAATTATACAATTAACAATATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * * * * *
70136 TAATTAAATATATTATCATACAGTTAACAATATAAAACATA
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* ** *
70177 CAAATAAACATAT--T-ATGCAATTAATGATACAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * *
70215 CAAATAAATATATTATCATGCAATTAA-ATATATAATA-ATA
1 CAAATAAATATATAATCATGCAATTAACA-ATATAAAACATG
* *
70255 CAAAT-AATAATATAAATCATCCAATAAACA
1 CAAATAAAT-ATAT-AATCATGCAATTAACA
70285 TGCAATTAAA
Statistics
Matches: 230, Mismatches: 35, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
38 30 0.13
39 4 0.02
40 12 0.05
41 177 0.77
42 3 0.01
43 4 0.02
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (41 bp):
CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
Found at i:70351 original size:20 final size:20
Alignment explanation
Indices: 70326--70430 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
70316 TCACACAAAT
*
70326 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
*
70346 AAATAAATTAATAATCATGT
1 AAATAAATTAATAATCATGC
* * * *
70366 AAACATATTAATAGTCATGT
1 AAATAAATTAATAATCATGC
* *
70386 AAACATATTAATAA--AT-C
1 AAATAAATTAATAATCATGC
* * *
70403 ACATAAATATATTAATCATGT
1 AAATAAAT-TAATAATCATGC
70424 AAATAAA
1 AAATAAA
70431 ATATTAGACA
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
17 5 0.07
18 7 0.10
20 50 0.74
21 6 0.09
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:70454 original size:32 final size:33
Alignment explanation
Indices: 70407--70469 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
70397 TAAATCACAT
* *
70407 AAATATATTAATCATGTAAATAAAATATTAGAC
1 AAATAAATTAATCATGCAAATAAAATATTAGAC
*
70440 AAATAAATT-ATCATGCAAATATAATATTAG
1 AAATAAATTAATCATGCAAATAAAATATTAG
70470 TCATGCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (33 bp):
AAATAAATTAATCATGCAAATAAAATATTAGAC
Found at i:70475 original size:20 final size:18
Alignment explanation
Indices: 70442--70479 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
70432 TATTAGACAA
70442 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
70460 ATAATATTAGTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
70480 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Found at i:70480 original size:32 final size:31
Alignment explanation
Indices: 70417--70493 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 31
70407 AAATATATTA
* * *
70417 ATCATGTAAATAAAATATTAGACAAATAAATT
1 ATCATGCAAATATAATATTAGACAAACAAA-T
* **
70449 ATCATGCAAATATAATATTAGTCATGCAAAT
1 ATCATGCAAATATAATATTAGACAAACAAAT
*
70480 -TCATGCAAAAATAA
1 ATCATGCAAATATAA
70494 ATACCATGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 13 0.34
31 1 0.03
32 24 0.63
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATCATGCAAATATAATATTAGACAAACAAAT
Found at i:74342 original size:11 final size:10
Alignment explanation
Indices: 74325--74481 Score: 101
Period size: 10 Copynumber: 16.0 Consensus size: 10
74315 TTAAAAAAAC
74325 TTTTTAGAAA
1 TTTTTAGAAA
74335 TCTTTTAGAAA
1 T-TTTTAGAAA
74346 TTTTTA-AAA
1 TTTTTAGAAA
*
74355 TTTTTTGAAA
1 TTTTTAGAAA
*
74365 TTTTTA-CAA
1 TTTTTAGAAA
*
74374 TTTTTTGAAA
1 TTTTTAGAAA
* *
74384 TTTTTACAATT
1 TTTTTAGAA-A
*
74395 TTTTTTGAAA
1 TTTTTAGAAA
*
74405 -TTTTAAAAA
1 TTTTTAGAAA
* *
74414 TTTTT-TAAT
1 TTTTTAGAAA
*
74423 TTTTTA-TAA
1 TTTTTAGAAA
* *
74432 CTTTTAAAAA
1 TTTTTAGAAA
74442 TTTTTAGAAA
1 TTTTTAGAAA
* * *
74452 ATTTCAAAAA
1 TTTTTAGAAA
*
74462 ATTTTA-AAA
1 TTTTTAGAAA
74471 TCTTTTAGAAA
1 T-TTTTAGAAA
74482 CCTTTTTTTC
Statistics
Matches: 112, Mismatches: 26, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
9 38 0.34
10 54 0.48
11 20 0.18
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (10 bp):
TTTTTAGAAA
Found at i:74364 original size:19 final size:19
Alignment explanation
Indices: 74325--74447 Score: 122
Period size: 19 Copynumber: 6.3 Consensus size: 19
74315 TTAAAAAAAC
*
74325 TTTTTAGAAATCTTTTAGAAA
1 TTTTTA-AAAT-TTTTTGAAA
74346 TTTTTAAAATTTTTTGAAA
1 TTTTTAAAATTTTTTGAAA
*
74365 TTTTTACAATTTTTTGAAA
1 TTTTTAAAATTTTTTGAAA
*
74384 TTTTTACAATTTTTTTTGAAA
1 TTTTTA-AA-ATTTTTTGAAA
* *
74405 TTTTAAAAATTTTTT-AAT
1 TTTTTAAAATTTTTTGAAA
* * **
74423 TTTTTATAACTTTTAAAAA
1 TTTTTAAAATTTTTTGAAA
74442 TTTTTA
1 TTTTTA
74448 GAAAATTTCA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
18 13 0.15
19 46 0.53
20 7 0.08
21 21 0.24
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATTTTTTGAAA
Found at i:76559 original size:17 final size:15
Alignment explanation
Indices: 76529--76588 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
76519 TTTGAGATTT
76529 TTTAAAAAAATTTAA
1 TTTAAAAAAATTTAA
76544 TTTAATAAAAATTTTAA
1 TTTAA-AAAAA-TTTAA
76561 --T-AAAAAATTTAA
1 TTTAAAAAAATTTAA
* * *
76573 ATTGATAAAATTTAA
1 TTTAAAAAAATTTAA
76588 T
1 T
76589 ATGAAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 5 0.13
13 5 0.13
14 2 0.05
15 16 0.42
16 5 0.13
17 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TTTAAAAAAATTTAA
Found at i:76561 original size:12 final size:12
Alignment explanation
Indices: 76542--76572 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
76532 AAAAAAATTT
76542 AATTTAATAAAA
1 AATTTAATAAAA
*
76554 ATTTTAATAAAA
1 AATTTAATAAAA
76566 AATTTAA
1 AATTTAA
76573 ATTGATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTTAATAAAA
Found at i:76595 original size:29 final size:29
Alignment explanation
Indices: 76533--76589 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
76523 AGATTTTTTA
*
76533 AAAAAATTTAATTTAATAAAAATTTTAAT
1 AAAAAATTTAAATTAATAAAAATTTTAAT
*
76562 AAAAAATTTAAATTGAT-AAAA-TTTAAT
1 AAAAAATTTAAATTAATAAAAATTTTAAT
76589 A
1 A
76590 TGAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAAAATTTAAATTAATAAAAATTTTAAT
Found at i:76689 original size:13 final size:12
Alignment explanation
Indices: 76652--76716 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
76642 TTTTCAATGA
76652 TAAAAATTTTAT
1 TAAAAATTTTAT
* *
76664 TAATAGTTTTAT
1 TAAAAATTTTAT
76676 TAAAAATATTTATT
1 TAAAAAT-TTTA-T
* *
76690 TAAAAAATATAT
1 TAAAAATTTTAT
*
76702 T-AAAATTTTTT
1 TAAAAATTTTAT
76713 TAAA
1 TAAA
76717 TTTAATAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
11 8 0.20
12 19 0.46
13 7 0.17
14 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
TAAAAATTTTAT
Found at i:80127 original size:34 final size:34
Alignment explanation
Indices: 80089--80156 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
80079 TTTTTAGAAC
* * * * *
80089 AAAATATAATTTTTGAAAATCTTTTTCTCAAAAT
1 AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
80123 AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
1 AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
80157 TATAATGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
Done.