Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 32 of 121
Found at i:5669580 original size:1 final size:1
Alignment explanation
Indices: 5669574--5669599 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5669564 ATTGTATGGG
5669574 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5669600 CTGGTCGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5679443 original size:8 final size:8
Alignment explanation
Indices: 5679430--5679466 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
5679420 TTTTTATTTA
5679430 TATATATT
1 TATATATT
*
5679438 TATATAAT
1 TATATATT
5679446 TATATATT
1 TATATATT
*
5679454 TAAATATT
1 TATATATT
5679462 TATAT
1 TATAT
5679467 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:5679470 original size:14 final size:16
Alignment explanation
Indices: 5679430--5679484 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
5679420 TTTTTATTTA
*
5679430 TATATATTTATATAAT
1 TATATATTTAAATAAT
5679446 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
5679461 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
*
5679476 AATAT-TTTA
1 TATATATTTA
5679485 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:5679486 original size:21 final size:22
Alignment explanation
Indices: 5679456--5679507 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5679446 TATATATTTA
5679456 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
5679476 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
5679498 AATATTTTAT
1 AATATTTTAT
5679508 TAATTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:5682842 original size:35 final size:35
Alignment explanation
Indices: 5682799--5682886 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
5682789 TCTAGGTTGT
* **
5682799 TTTTATTTTTGGACTTACAG-GTTGGTCTTGATCA
1 TTTTATTTTTGGACTTACAGAGTTGATCCCGATCA
* * *
5682833 TTTTAATTTTTTGACTTAC-GATTTTATCCCGATCA
1 TTTT-ATTTTTGGACTTACAGAGTTGATCCCGATCA
5682868 TTTTATTTTTGGACTTACA
1 TTTTATTTTTGGACTTACA
5682887 ATACAGTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 18 0.41
35 26 0.59
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (35 bp):
TTTTATTTTTGGACTTACAGAGTTGATCCCGATCA
Found at i:5685751 original size:13 final size:13
Alignment explanation
Indices: 5685735--5685765 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5685725 ACCCCAAAAC
*
5685735 CAAACCCTAAAGT
1 CAAACCATAAAGT
5685748 CAAACCATAAAGT
1 CAAACCATAAAGT
5685761 CAAAC
1 CAAAC
5685766 TCGAAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.29, G:0.06, T:0.13
Consensus pattern (13 bp):
CAAACCATAAAGT
Found at i:5685798 original size:21 final size:20
Alignment explanation
Indices: 5685772--5685825 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
5685762 AAACTCGAAA
5685772 CCCAAAGTCAAATGC-TTAAAC
1 CCCAAAGTCAAA--CATTAAAC
*
5685793 CCCAAAGTCTAACATTAAAC
1 CCCAAAGTCAAACATTAAAC
*
5685813 CCCAATGTCAAAC
1 CCCAAAGTCAAAC
5685826 CCCTAAACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 17 0.59
21 11 0.38
ACGTcount: A:0.43, C:0.31, G:0.07, T:0.19
Consensus pattern (20 bp):
CCCAAAGTCAAACATTAAAC
Found at i:5687291 original size:177 final size:178
Alignment explanation
Indices: 5686950--5687305 Score: 642
Period size: 177 Copynumber: 2.0 Consensus size: 178
5686940 GGATTTATTA
* * *
5686950 AAAATATAAACTTTTTGAGTAATTAATCACACCTAATAAAAAATATTTGTGACGACTTCATATTT
1 AAAATATAAACTTTTTAAATAATCAATCACACCTAATAAAAAATATTTGTGACGACTTCATATTT
5687015 TTTAATTTATAAAATTTTGCATCATGCGGTCGGACTCATGAACCCATACATTACAATAGCTAGAG
66 TTTAATTTATAAAATTTTGCATCATGCGGTCGGACTCATGAACCCATACATTACAATAGCTAGAG
*
5687080 ATCAATTTTTTAAGTTAGCCATGGTCTATGGTACACACTTCTTCTACT
131 ATCAATTTTTTAAGTTAGCCATGGTCTATGGTACACACTTCTTCCACT
* *
5687128 AAAATATAAATTTTTTAAATGATCAATCACACCTAATAAAAAATATTTGTGACGACTTCATATTT
1 AAAATATAAACTTTTTAAATAATCAATCACACCTAATAAAAAATATTTGTGACGACTTCATATTT
*
5687193 TTTAATTTATAAAATTTTGCAT-ATGGGGTCGGACTCATGAACCCATACATTACAATAGCTAGAG
66 TTTAATTTATAAAATTTTGCATCATGCGGTCGGACTCATGAACCCATACATTACAATAGCTAGAG
5687257 ATCAATTTTTTAAGTTAGCCATGGTCTATGGTACACACTTCTTCCACT
131 ATCAATTTTTTAAGTTAGCCATGGTCTATGGTACACACTTCTTCCACT
5687305 A
1 A
5687306 TGATATATAT
Statistics
Matches: 171, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
177 89 0.52
178 82 0.48
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (178 bp):
AAAATATAAACTTTTTAAATAATCAATCACACCTAATAAAAAATATTTGTGACGACTTCATATTT
TTTAATTTATAAAATTTTGCATCATGCGGTCGGACTCATGAACCCATACATTACAATAGCTAGAG
ATCAATTTTTTAAGTTAGCCATGGTCTATGGTACACACTTCTTCCACT
Found at i:5687477 original size:2 final size:2
Alignment explanation
Indices: 5687470--5687496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5687460 ATACCTAGTC
5687470 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 A
5687497 CACATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5689367 original size:16 final size:18
Alignment explanation
Indices: 5689336--5689368 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5689326 TTTTAAAAAA
5689336 ATTTTCTTCAAATTTTTT
1 ATTTTCTTCAAATTTTTT
5689354 ATTTT-TTC-AATTTTT
1 ATTTTCTTCAAATTTTT
5689369 GAGAGTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTCTTCAAATTTTTT
Found at i:5690088 original size:3 final size:3
Alignment explanation
Indices: 5690080--5690114 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5690070 ATTTATCCTC
5690080 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5690115 ACTTGTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5695288 original size:22 final size:22
Alignment explanation
Indices: 5695241--5695290 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5695231 TATTTAAAGG
* *
5695241 AAAATTTTCTCATAAATATTTT
1 AAAATTTTCTCATAAACATTTA
*
5695263 AAAATTTTCTC-TGAACATTATA
1 AAAATTTTCTCATAAACATT-TA
5695285 AAAATT
1 AAAATT
5695291 GAAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTTTCTCATAAACATTTA
Found at i:5695857 original size:8 final size:8
Alignment explanation
Indices: 5695838--5695890 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
5695828 ACATCTCCTG
5695838 TTAATAAAT
1 TTAAT-AAT
5695847 TTAATAAT
1 TTAATAAT
5695855 TTAATAAT
1 TTAATAAT
*
5695863 TTATATCAT
1 TTA-ATAAT
*
5695872 ATAA-AAT
1 TTAATAAT
5695879 ATTAATAAT
1 -TTAATAAT
5695888 TTA
1 TTA
5695891 TATATGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
7 2 0.05
8 21 0.57
9 14 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (8 bp):
TTAATAAT
Found at i:5695901 original size:33 final size:32
Alignment explanation
Indices: 5695843--5695906 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
5695833 TCCTGTTAAT
*
5695843 AAATTTAATAATTTAATAATTTATATCATATA
1 AAATTTAATAATTTAATAATGTATATCATATA
*
5695875 AAATATTAATAATTT-ATATATGTATATTATAT
1 AAAT-TTAATAATTTAATA-ATGTATATCATAT
5695907 TTTATACGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
AAATTTAATAATTTAATAATGTATATCATATA
Found at i:5696037 original size:26 final size:26
Alignment explanation
Indices: 5696002--5696054 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5695992 TTTAATAAAA
5696002 TTTTAAATCA-TGTTATATTCATATTT
1 TTTTAAATCATTGTTATATT-ATATTT
* *
5696028 TTTTATATCATTTTTATATTATATTT
1 TTTTAAATCATTGTTATATTATATTT
5696054 T
1 T
5696055 AAATTTTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTAAATCATTGTTATATTATATTT
Found at i:5696968 original size:13 final size:13
Alignment explanation
Indices: 5696950--5696982 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5696940 AATTATAATA
*
5696950 AATAAAAGTTTAT
1 AATAAAAATTTAT
5696963 AATAAAAATTTAT
1 AATAAAAATTTAT
5696976 AA-AAAAA
1 AATAAAAA
5696983 AATAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AATAAAAATTTAT
Found at i:5698913 original size:12 final size:11
Alignment explanation
Indices: 5698896--5698944 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
5698886 TTTCTCAAAA
5698896 AAATAAATGAAT
1 AAATAAAT-AAT
5698908 AAATAAATAAT
1 AAATAAATAAT
*
5698919 -AATAATATCAT
1 AAATAA-ATAAT
5698930 ATAATAAATAAT
1 A-AATAAATAAT
5698942 AAA
1 AAA
5698945 ATGAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 5 0.16
11 9 0.28
12 13 0.41
13 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:5698976 original size:16 final size:17
Alignment explanation
Indices: 5698957--5698994 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5698947 GAAATATGAT
* *
5698957 GAAAATAAGAA-AATAA
1 GAAAATAAAAAGAAAAA
5698973 GAAAATAAAAAGAAAAA
1 GAAAATAAAAAGAAAAA
5698990 GAAAA
1 GAAAA
5698995 ACTCTCCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (17 bp):
GAAAATAAAAAGAAAAA
Found at i:5699120 original size:12 final size:12
Alignment explanation
Indices: 5699103--5699131 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5699093 ATACAAGGCC
5699103 TTTTTTTT-ATT
1 TTTTTTTTAATT
5699114 TTTTTTTTAATT
1 TTTTTTTTAATT
5699126 TTTTTT
1 TTTTTT
5699132 CCTTTCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTAATT
Found at i:5699879 original size:14 final size:14
Alignment explanation
Indices: 5699860--5699888 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5699850 AAAAAATCAC
5699860 TCTAGTAGCTTAAT
1 TCTAGTAGCTTAAT
5699874 TCTAGTAGCTTAAT
1 TCTAGTAGCTTAAT
5699888 T
1 T
5699889 TCAGTTGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (14 bp):
TCTAGTAGCTTAAT
Found at i:5700307 original size:40 final size:40
Alignment explanation
Indices: 5700152--5700430 Score: 198
Period size: 40 Copynumber: 7.0 Consensus size: 40
5700142 TAAATCTTGA
* * *
5700152 AAATTTAAACATGCTCCTCTGACTAAAGGCTATGAAACTTT
1 AAATTTAAA-AGGCTCATCTGACCAAAGGCTATGAAACTTT
* * * * *
5700193 AATTTTAAAA-GTTTATCTG-CCAAAGG-TAATAAAATTTT
1 AAATTTAAAAGGCTCATCTGACCAAAGGCT-ATGAAACTTT
* * * *
5700231 AAATTTAAAAGGCTTC-TTTAACCAAA-GTTAAAGAAACTTT
1 AAATTTAAAAGGC-TCATCTGACCAAAGGCT-ATGAAACTTT
* *
5700271 AAATTTAAAAGGCTCATCTGTCCAGAGGCTATGAAACTTT
1 AAATTTAAAAGGCTCATCTGACCAAAGGCTATGAAACTTT
* *
5700311 AAATTTAAAA--CTCCT-TAGACCAAAAGG-TATGAAACTTC
1 AAATTTAAAAGGCTCATCT-GACC-AAAGGCTATGAAACTTT
* * ** * * * *
5700349 AAATTGAAAATGCTTTTTTAACTAAAGGCTATGAAACTTG
1 AAATTTAAAAGGCTCATCTGACCAAAGGCTATGAAACTTT
* * *
5700389 AAATTCAAAAGGTTCATTTGACCAAAGGCTATGAAACTTT
1 AAATTTAAAAGGCTCATCTGACCAAAGGCTATGAAACTTT
5700429 AA
1 AA
5700431 GATAAAGCTT
Statistics
Matches: 186, Mismatches: 39, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
37 2 0.01
38 49 0.26
39 21 0.11
40 103 0.55
41 11 0.06
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (40 bp):
AAATTTAAAAGGCTCATCTGACCAAAGGCTATGAAACTTT
Found at i:5700334 original size:118 final size:115
Alignment explanation
Indices: 5700110--5700430 Score: 306
Period size: 118 Copynumber: 2.7 Consensus size: 115
5700100 CAACTTTTGA
* * * *
5700110 AAATTTAAAAGCTTCTTTAAGCAAAGGCTCAATAAATCTTGAAAATTTAAACATGCTCCTCTGAC
1 AAATTTAAAAGCTTCTTTAACCAAAGGCT-AAGAAA-CTT-AAAATTTAAA-AGGCTCATCTGAC
* * * * *
5700175 TAAAGGCTATGAAACTTTAATTTTAAAAGTTTATCTGCC-AAAGGTAATAAAATTTT
62 CAAAGGCTATGAAACTTTAAATTTAAAACTTTA--TGCCAAAAGGT-ATAAAACTTC
* * *
5700231 AAATTTAAAAGGCTTCTTTAACCAAA-GTTAAAGAAACTTTAAATTTAAAAGGCTCATCTGTCCA
1 AAATTTAAAA-GCTTCTTTAACCAAAGGCT-AAGAAACTTAAAATTTAAAAGGCTCATCTGACCA
* *
5700295 GAGGCTATGAAACTTTAAATTTAAAACTCCTTA-GACCAAAAGGTATGAAACTTC
64 AAGGCTATGAAACTTTAAATTTAAAACT--TTATG-CCAAAAGGTATAAAACTTC
* * * * * * * *
5700349 AAATTGAAAATGCTTTTTTAACTAAAGGCTATGAAACTTGAAATTCAAAAGGTTCATTTGACCAA
1 AAATTTAAAA-GCTTCTTTAACCAAAGGCTAAGAAACTTAAAATTTAAAAGGCTCATCTGACCAA
5700414 AGGCTATGAAACTTTAA
65 AGGCTATGAAACTTTAA
5700431 GATAAAGCTT
Statistics
Matches: 167, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
117 1 0.01
118 112 0.67
119 17 0.10
120 6 0.04
121 17 0.10
122 14 0.08
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (115 bp):
AAATTTAAAAGCTTCTTTAACCAAAGGCTAAGAAACTTAAAATTTAAAAGGCTCATCTGACCAAA
GGCTATGAAACTTTAAATTTAAAACTTTATGCCAAAAGGTATAAAACTTC
Found at i:5700345 original size:78 final size:76
Alignment explanation
Indices: 5700176--5700358 Score: 174
Period size: 78 Copynumber: 2.3 Consensus size: 76
5700166 TCCTCTGACT
* * * *
5700176 AAAGGCTATGAAACTTTAATTTTAAAAGTTTATCTGCCAAAGGTAATAAAATTTTAAATTTAAAA
1 AAAGG-TATGAAACTTTAAATTTAAAAGCTCATCTGCCAAAGGTAATAAAACTTTAAATTTAAAA
*
5700241 GGCTTCTTTAACC
65 -GCTTCCTTAACC
* * * *
5700254 AAAGTTAAAGAAACTTTAAATTTAAAAGGCTCATCTGTCCAGAGGCT-ATGAAACTTTAAATTTA
1 AAAGGT-ATGAAACTTTAAATTTAAAA-GCTCATCTG-CCAAAGG-TAATAAAACTTTAAATTTA
5700318 AAA-C-TCCTTAGACC
62 AAAGCTTCCTTA-ACC
* *
5700332 AAAAGGTATGAAACTTCAAATTGAAAA
1 -AAAGGTATGAAACTTTAAATTTAAAA
5700359 TGCTTTTTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
77 6 0.07
78 43 0.50
79 12 0.14
80 24 0.28
81 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (76 bp):
AAAGGTATGAAACTTTAAATTTAAAAGCTCATCTGCCAAAGGTAATAAAACTTTAAATTTAAAAG
CTTCCTTAACC
Found at i:5706990 original size:13 final size:13
Alignment explanation
Indices: 5706972--5706996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5706962 TTCATTGAAC
5706972 TTTTTTCATGTTT
1 TTTTTTCATGTTT
5706985 TTTTTTCATGTT
1 TTTTTTCATGTT
5706997 CGTCATAAAA
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:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTCATGTTT
Found at i:5707533 original size:43 final size:43
Alignment explanation
Indices: 5707471--5707554 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
5707461 GGTTTGAAAG
* * *
5707471 GCTCTATGGGTTGTTGGGCCACCAAGTGTTTCTAGAATAAAAA
1 GCTCTATGGGTTATCGGGCCACCAAGTGTTTCTAAAATAAAAA
*
5707514 GCTCTATGGGTTATCGGGCCACCAAGTGTTTTTAAAATAAA
1 GCTCTATGGGTTATCGGGCCACCAAGTGTTTCTAAAATAAA
5707555 TGAAGAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
GCTCTATGGGTTATCGGGCCACCAAGTGTTTCTAAAATAAAAA
Found at i:5717790 original size:22 final size:21
Alignment explanation
Indices: 5717750--5717794 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5717740 AAACACAAAG
*
5717750 TATATATTTTTTGTCAAATCTT
1 TATATAATTTTTGTCAAAT-TT
5717772 TATATAATTTTT-TCAAAATTT
1 TATATAATTTTTGTC-AAATTT
5717793 TA
1 TA
5717795 AATTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (21 bp):
TATATAATTTTTGTCAAATTT
Found at i:5721330 original size:22 final size:22
Alignment explanation
Indices: 5721275--5721339 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
5721265 GTATTATAAA
*
5721275 AATATTATTTTTTAAATAAAT-T
1 AATATT-TTTATTAAATAAATAT
* * *
5721297 -ATATCTTAATTATATAAATAT
1 AATATTTTTATTAAATAAATAT
*
5721318 AATATTTTTATTAAATTAATAT
1 AATATTTTTATTAAATAAATAT
5721340 TTTACATTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 11 0.33
21 5 0.15
22 17 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTTATTAAATAAATAT
Found at i:5721339 original size:17 final size:19
Alignment explanation
Indices: 5721268--5721342 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 19
5721258 TATTATTGTA
* *
5721268 TTATAAAAATATTAT-TTT
1 TTATATAAATATAATATTT
*
5721286 TTAAATAAAT-T-ATATCTT
1 TTATATAAATATAATAT-TT
5721304 AATTATATAAATATAATATTT
1 --TTATATAAATATAATATTT
5721325 TTAT-TAAAT-TAATATTT
1 TTATATAAATATAATATTT
5721342 T
1 T
5721343 ACATTAAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.04
17 11 0.23
18 15 0.31
19 4 0.08
20 9 0.19
21 3 0.06
22 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATAAATATAATATTT
Found at i:5721348 original size:18 final size:18
Alignment explanation
Indices: 5721311--5721354 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5721301 CTTAATTATA
*
5721311 TAAATATAATATTTTTAT
1 TAAATATAATATTTTCAT
5721329 TAAAT-TAATATTTTACAT
1 TAAATATAATATTTT-CAT
5721347 TAAGATAT
1 TAA-ATAT
5721355 TAAATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 10 0.45
19 2 0.09
20 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TAAATATAATATTTTCAT
Found at i:5723487 original size:318 final size:314
Alignment explanation
Indices: 5722914--5723548 Score: 1200
Period size: 318 Copynumber: 2.0 Consensus size: 314
5722904 AATCCCTAAC
5722914 ATTAGGTGAGGTTTTCTATCTTCAAAAGGGAGTAACACCCCCACTTCATGAAATTTTAGCACCAG
1 ATTAGGTGAGGTTTTCTATCTTCAAAAGGGAGTAACACCCCCACTTCATGAAATTTTAGCACCAG
*
5722979 AAGAATCAACGAGCTCAGATTTTTTTTTTTTTGGGGGGGGGGGTTGGTGGCGGGAAAGCAAAGCT
66 AAGAATCAACGAGCTCAGATTTTTTTTTTTTTGGGGGGGGGGGGTGGTGGCGGGAAAGCAAAGCT
5723044 GATTTTCATTTAATGAAATAGCAGTACAAAAGGTAGCCGATACAAGGACTGCAAAGCAGCAAAAA
131 GATTTTCATTTAATGAAATAGCAGTACAAAAGGTAGCCGATACAAGGACTGCAAAGCAGCAAAAA
5723109 AGAGAATGAGCACCAGAGACAACCTGTAATAGCCACCAACATGCAACTCAGATTAACTAAACATC
196 AGAGAATGAGCACCAGAGACAACCTGTAATAGCCACCAACATGCAACTCAGATTAACTAAACATC
5723174 AACATTAAACTGTTAATCTATTGATGCCAGACTTAGCAAGACCAACAGCTTAAA
261 AACATTAAACTGTTAATCTATTGATGCCAGACTTAGCAAGACCAACAGCTTAAA
5723228 ATTAGGTGAGGTTTTCTATCTTCAAAAGGGAGTAACACCCCCACTTCATGAAATTTTAGCACCAG
1 ATTAGGTGAGGTTTTCTATCTTCAAAAGGGAGTAACACCCCCACTTCATGAAATTTTAGCACCAG
5723293 AAGAATCAACGAGCTCAGATTTTTTTATTTTTTTTTTGGGGGGGGGGGGT-GTGGCGGGAAAGCA
66 AAGAATCAACGAGCTCAGA----TTT-TTTTTTTTTTGGGGGGGGGGGGTGGTGGCGGGAAAGCA
5723357 AAGCTGATTTTCATTTAATGAAATAGCAGTACAAAAGGTAGCCGATACAAGGACTGCAAAGCAGC
126 AAGCTGATTTTCATTTAATGAAATAGCAGTACAAAAGGTAGCCGATACAAGGACTGCAAAGCAGC
*
5723422 AAAAAAGAGAATGAGCAGCAGAGACAACCTGTAATAGCCACCAACATGCAACTCAGATTAACTAA
191 AAAAAAGAGAATGAGCACCAGAGACAACCTGTAATAGCCACCAACATGCAACTCAGATTAACTAA
5723487 ACATCAACATTAAACTGTTAATCTATTGATGCCAGACTTAGCAAGACCAACAGCTTAAA
256 ACATCAACATTAAACTGTTAATCTATTGATGCCAGACTTAGCAAGACCAACAGCTTAAA
5723546 ATT
1 ATT
5723549 TTGTTCTATC
Statistics
Matches: 314, Mismatches: 2, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
314 84 0.27
318 208 0.66
319 22 0.07
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (314 bp):
ATTAGGTGAGGTTTTCTATCTTCAAAAGGGAGTAACACCCCCACTTCATGAAATTTTAGCACCAG
AAGAATCAACGAGCTCAGATTTTTTTTTTTTTGGGGGGGGGGGGTGGTGGCGGGAAAGCAAAGCT
GATTTTCATTTAATGAAATAGCAGTACAAAAGGTAGCCGATACAAGGACTGCAAAGCAGCAAAAA
AGAGAATGAGCACCAGAGACAACCTGTAATAGCCACCAACATGCAACTCAGATTAACTAAACATC
AACATTAAACTGTTAATCTATTGATGCCAGACTTAGCAAGACCAACAGCTTAAA
Found at i:5725941 original size:59 final size:59
Alignment explanation
Indices: 5725848--5725967 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
5725838 CCAAGAGTTT
*
5725848 CCACAAGTTATCAACGCTGCTTTCATGTCATAGTTGTATTTTGTCCACAGATTGAACCA
1 CCACAAGTTATCAACACTGCTTTCATGTCATAGTTGTATTTTGTCCACAGATTGAACCA
*
5725907 CCACAAGTTATCAACACTGCTTTCATGTCGTAGTTGTATTTTGTCCACAGATTGAACCA
1 CCACAAGTTATCAACACTGCTTTCATGTCATAGTTGTATTTTGTCCACAGATTGAACCA
5725966 CC
1 CC
5725968 CTTCCATGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (59 bp):
CCACAAGTTATCAACACTGCTTTCATGTCATAGTTGTATTTTGTCCACAGATTGAACCA
Found at i:5728388 original size:30 final size:30
Alignment explanation
Indices: 5728325--5728389 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
5728315 AGGTGGAGCA
* * * *
5728325 GGAGGAGGTGGTGGTTGTGTTGGCAGAGGT
1 GGAGGAGGTGGAGGTGGTGATGGCAGAGAT
5728355 GGAGGAGGTGGAGGTGGTGATGG-AGATGAT
1 GGAGGAGGTGGAGGTGGTGATGGCAGA-GAT
5728385 GGAGG
1 GGAGG
5728390 TGGGGGTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.18, C:0.02, G:0.58, T:0.22
Consensus pattern (30 bp):
GGAGGAGGTGGAGGTGGTGATGGCAGAGAT
Found at i:5735510 original size:12 final size:13
Alignment explanation
Indices: 5735482--5735511 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5735472 TAGCTCAAAT
5735482 ATTAAAAAATTAC
1 ATTAAAAAATTAC
5735495 ATTAAAAAATTA-
1 ATTAAAAAATTAC
5735507 ATTAA
1 ATTAA
5735512 GGCAACATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAAAAAATTAC
Found at i:5739246 original size:15 final size:16
Alignment explanation
Indices: 5739226--5739256 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5739216 TTTGTGAATA
5739226 TATTTA-ATTTTTATT
1 TATTTATATTTTTATT
5739241 TATTTATATTTTTATT
1 TATTTATATTTTTATT
5739257 AAATTTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTATATTTTTATT
Found at i:5747999 original size:18 final size:18
Alignment explanation
Indices: 5747972--5748019 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5747962 CAGGGCTTAA
* *
5747972 TTTTCATCTTTCTTCTCT
1 TTTTCTTCTTTCTCCTCT
*
5747990 TTTTCTTCTTTGTCCTCT
1 TTTTCTTCTTTCTCCTCT
*
5748008 TTCTCATTCTTT
1 TTTTC-TTCTTT
5748020 TCAGATTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.04, C:0.27, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTCTTCTTTCTCCTCT
Found at i:5749748 original size:19 final size:19
Alignment explanation
Indices: 5749724--5749764 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5749714 AGCTCGAACG
*
5749724 TGATGAGTTGAGCACATGT
1 TGATGAGTTGAACACATGT
*
5749743 TGATGAGTTGAATACATGT
1 TGATGAGTTGAACACATGT
5749762 TGA
1 TGA
5749765 GATAGTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (19 bp):
TGATGAGTTGAACACATGT
Found at i:5752237 original size:20 final size:19
Alignment explanation
Indices: 5752212--5752269 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
5752202 TTATTTGATA
5752212 TTAAATAATTTAATAATTTT
1 TTAAAT-ATTTAATAATTTT
5752232 TTAAATTATTTAATAATTTT
1 TTAAA-TATTTAATAATTTT
*
5752252 ATAAAT-TTTAAATAATTT
1 TTAAATATTT-AATAATTT
5752270 AAAATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 3 0.09
19 9 0.26
20 22 0.63
21 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAATATTTAATAATTTT
Found at i:5752621 original size:22 final size:23
Alignment explanation
Indices: 5752596--5752639 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5752586 GAAGGGAAAG
*
5752596 AAAGGAAAGGAAA-ATAAAAAAA
1 AAAGGAAAGGAAACAGAAAAAAA
* *
5752618 AAAGTAATGGAAACAGAAAAAA
1 AAAGGAAAGGAAACAGAAAAAA
5752640 CATTTCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (23 bp):
AAAGGAAAGGAAACAGAAAAAAA
Found at i:5753455 original size:32 final size:32
Alignment explanation
Indices: 5753414--5753476 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
5753404 CATTTCTAGC
5753414 CTTAAATAATCCAAAAAAAAAAAAGTAATCCT
1 CTTAAATAATCCAAAAAAAAAAAAGTAATCCT
* *
5753446 CTTAAATAATCCAAAAAGAATAAAGTAATCC
1 CTTAAATAATCCAAAAAAAAAAAAGTAATCC
5753477 CCAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (32 bp):
CTTAAATAATCCAAAAAAAAAAAAGTAATCCT
Found at i:5753919 original size:100 final size:96
Alignment explanation
Indices: 5753771--5753988 Score: 219
Period size: 100 Copynumber: 2.2 Consensus size: 96
5753761 ACCTTAAATA
* *
5753771 ATTTTTTTTTAAAAAAATAAAAATTATGTAAGATATTTTTGATAAAAAA-GCCTTAAATAATA-C
1 ATTTTTTTTTAAAAAAATAAAAATTATGTAAGATATTTTTGATAAAAAATGCATTAAATAACATC
*
5753834 TCTTCAAAAAATTAAAAAGGTATTATTTAAGGT
66 -CTTCAAAAAATTAAAAA-GTATTATTTAAGGC
* * *
5753867 ATTTTTCTTTTAAAAAAATATTAGATATTATTTAA-AGTATTTTT-AGTCAAAAATGCATTAAAT
1 ATTTTT-TTTTAAAAAAATA--A-AAATTATGTAAGA-TATTTTTGA-TAAAAAATGCATTAAAT
* ** *
5753930 AACATCCTTTAAAAAATTGGAGAGTATTATTTAAGGC
60 AACATCCTTCAAAAAATTAAAAAGTATTATTTAAGGC
*
5753967 GTTTATTTTTTACAAAAAATAA
1 ATTT-TTTTTTA-AAAAAATAA
5753989 TCCTCTCATA
Statistics
Matches: 101, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
96 6 0.06
97 13 0.13
99 4 0.04
100 43 0.43
101 34 0.34
102 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (96 bp):
ATTTTTTTTTAAAAAAATAAAAATTATGTAAGATATTTTTGATAAAAAATGCATTAAATAACATC
CTTCAAAAAATTAAAAAGTATTATTTAAGGC
Found at i:5755129 original size:12 final size:12
Alignment explanation
Indices: 5755112--5755153 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
5755102 TAAAAGATTG
5755112 AATTAAACACAA
1 AATTAAACACAA
5755124 AATTAAA-A-ATA
1 AATTAAACACA-A
5755135 AATTAAACACAA
1 AATTAAACACAA
5755147 AATTAAA
1 AATTAAA
5755154 AATAAATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 9 0.33
12 16 0.59
13 1 0.04
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (12 bp):
AATTAAACACAA
Found at i:5755139 original size:11 final size:11
Alignment explanation
Indices: 5755123--5755160 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
5755113 ATTAAACACA
5755123 AAATTAAAAAT
1 AAATTAAAAAT
5755134 AAATTAAACACA-
1 AAATTAAA-A-AT
5755146 AAATTAAAAAT
1 AAATTAAAAAT
5755157 AAAT
1 AAAT
5755161 CAATAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 13 0.54
12 9 0.38
13 1 0.04
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:5755139 original size:23 final size:23
Alignment explanation
Indices: 5755112--5755160 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5755102 TAAAAGATTG
5755112 AATTAAACACAAAATTAAAAATA
1 AATTAAACACAAAATTAAAAATA
5755135 AATTAAACACAAAATTAAAAATA
1 AATTAAACACAAAATTAAAAATA
5755158 AAT
1 AAT
5755161 CAATAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (23 bp):
AATTAAACACAAAATTAAAAATA
Found at i:5755302 original size:16 final size:17
Alignment explanation
Indices: 5755272--5755305 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5755262 TATGTTATTT
*
5755272 TTAAAAAAATGTTATAA
1 TTAAAAAAATATTATAA
5755289 TTAAAAAAA-ATTATAA
1 TTAAAAAAATATTATAA
5755305 T
1 T
5755306 AAATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATATTATAA
Found at i:5756083 original size:2 final size:2
Alignment explanation
Indices: 5756072--5756101 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5756062 CCGTAACCTG
5756072 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5756102 GCATTGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5761116 original size:44 final size:45
Alignment explanation
Indices: 5761051--5761136 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
5761041 GATCAGTTTT
* * *
5761051 CCTAAAATCTTCGACT-AAAAAACATGAGTATCAACCCTTCCATA
1 CCTAAAATCTTCAACTAAAAAAAAATGAGTATCAACACTTCCATA
*
5761095 CCTAACAATC-TCAACTTAAAAAAAATGAGTATCAACACTTCC
1 CCTAA-AATCTTCAACTAAAAAAAAATGAGTATCAACACTTCC
5761137 CTGCCCACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 10 0.27
45 27 0.73
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (45 bp):
CCTAAAATCTTCAACTAAAAAAAAATGAGTATCAACACTTCCATA
Found at i:5761563 original size:21 final size:21
Alignment explanation
Indices: 5761514--5761575 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5761504 AAGTTACGAT
*
5761514 AAAAA-ATA-AAATTTTTTAA
1 AAAAATATATAAATTTTATAA
*
5761533 AAAATTATATATAAATTATATAA
1 AAAA--ATATATAAATTTTATAA
*
5761556 AAAAATATATATATTTTATA
1 AAAAATATATAAATTTTATA
5761576 TTTAAAGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.11
21 15 0.43
22 3 0.09
23 13 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATATATAAATTTTATAA
Found at i:5762616 original size:21 final size:21
Alignment explanation
Indices: 5762590--5762632 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5762580 CGCAAACACC
5762590 ATCTCATGATCCTTTTGGCTT
1 ATCTCATGATCCTTTTGGCTT
5762611 ATCTCATGATCCTTTTGGCTT
1 ATCTCATGATCCTTTTGGCTT
5762632 A
1 A
5762633 AAGAGGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (21 bp):
ATCTCATGATCCTTTTGGCTT
Found at i:5764519 original size:24 final size:23
Alignment explanation
Indices: 5764492--5764557 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
5764482 GTGATCCTCT
*
5764492 AACCATGAGAACTCATGGTCCATC
1 AACCAT-AGAACTCATGGTCCACC
5764516 AACCA-ACGTAACTCATGGTCCACC
1 AACCATA-G-AACTCATGGTCCACC
* *
5764540 GACCATTACAACTCATGG
1 AACCA-TAGAACTCATGG
5764558 CTTTCATCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 32 0.91
26 1 0.03
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (23 bp):
AACCATAGAACTCATGGTCCACC
Found at i:5767064 original size:792 final size:796
Alignment explanation
Indices: 5765507--5767064 Score: 1985
Period size: 792 Copynumber: 2.0 Consensus size: 796
5765497 TGCAAGCACA
* * *
5765507 ACACTTATGCTGATCAACAGCCAGCTCGAAGCCTCTAGGCTCATCTCATCCCATGGGACTCAGTT
1 ACACTTATGCTGATCAACAGCCAACTCGAAGCCTCTAAGCTCATCTCATCCCACGGGACTCAGTT
* * * * *
5765572 CTTAGGGCTTAGGCCCTTAGCTTTTATGTAGACTGTCTGCACGTATGATTGACACCCAACATCAT
66 CTTAGAGCTTAGGCCCTTAGCTTCTATGTAGACTGTCCGCACGCATGATTGACACCCAACATCAG
* ** * * * * *
5765637 GCTAGTCTCGCAAGGGGGACTTGGGTAGACTACCCTAGCTGCAGCACACCTCTATCGATTGGCCA
131 GCTAGTCTCACAAGGAAGACTTAGGTAGACTACCCCAACTACAGCACACCTCTACCGATTGGCCA
* * * * * * *
5765702 TAAGGGTCTAGCAGCGTGCTTGCTTGCTAGTCCGCACATCTCTCAGGCTTGATGGCGTCCCTCTT
196 CAAGGGTCTAGCA-CGTACTAGC-T-CTAGT---CACATCTCTCAAGCTCGATGGCATCCCTCCT
* * *
5765767 ACGTAAACACCATCTCATGATCCTTTTGGCTTAAAAAAGAGAAACAGAAGGGTATACCAAACTCT
255 ACGCAAACACCATCTCATGATCCTTTTGGCTTAAAAAAGAGAAACAGAAGGGCATAACAAACTCT
* * * *
5765832 ACCGCATAACCCCATGGCTTAACGTAAAAGTGCGATACGAGGCCCGCCTGCCCCAACTGTCCTCG
320 ACCGCATAACCCCATGGCTTAACGCAAAAGCGCGATACAAGGCCCGCCTGCCCCAACCGTCCTCG
* *
5765897 GGTTTATCATGACCCAAGAAAACATCGTGCCACGCTCGTGACCCTACAATGCCCGCCCACTTAGA
385 GGTTTACCATGACCCAAGAAAACATCGTGCCACGCTCGTGACCCTACAATGCCCGCCCACCTAGA
** * * * * *
5765962 CATTACTAGTACCTAGGAGTAGCTCACTTCAGACTAGCTAGGCCGTTGCTTGCCTGCTAGCTAAG
450 CACCACTAGTACCTAGGAATAGCTCACTTCAGACTAACCAGGCC---GCCTGCCTACTAGCTAAG
* * * *
5766027 GGGTGGTGGAGAGTTGACACCAGTCATCCCCTTATAAAGAGCGTAAGAGATTTTCTCAGTTTCCT
512 GGGTGGTGGAGAGCTAACACCAGTCATCCCCTTATAAAAAGCGTAAGAGATTTTCTCAGTCTCCT
* * *** *
5766092 ACCAGTAACCATAAGATTGTCTGAAATGGAGACACTTTTCTTTTCAGTCATCTTAGGACCTTTCT
577 ACCAGTAACCATAAGATTATCTGAAATGGAGACAATTTTCTCCCCAGTCATCTCAGGACCTTTCT
*
5766157 CCGACTAACTCAGGGCCCCATAACCTTCCTCTTGGTCATCATTATTCATTGATTCTACTCATTGC
642 CCAACTAACTCAGGGCCCCATAACCTTCCTCTTGGTCATCATTATTCATTGATTCTACTCATTGC
*** ** *
5766222 TCCACCAACCTACTCAAAGGTACTTGCACATGGCTTCGACTGACAGCACCTGATTGGCTAGCTGA
707 TCCACCAACCTACTCAAAGGTACCCACACATAACTTCGACCGACAGCACCTGATTGGCTAGCTGA
5766287 TCCTAGGGCACCGGTGCATTGCCTC
772 TCCTAGGGCACCGGTGCATTGCCTC
* *
5766312 ACACTTATGCTGGTCAAACAGCCAACTCGGAGCCTCTAAGCTCATCTCATCCCACGGGACTCAGT
1 ACACTTATGCTGATC-AACAGCCAACTCGAAGCCTCTAAGCTCATCTCATCCCACGGGACTCAGT
**
5766377 TCTTAGAGCTTAGGCCCTTAGCTTCTATGTAGACTGTCCGCACGCATGATTGACACCCAATTTCA
65 TCTTAGAGCTTAGGCCCTTAGCTTCTATGTAGACTGTCCGCACGCATGATTGACACCCAACATCA
* *
5766442 GGCTAGTCTCACAAGGAAGACTTAGGTGGACTGCCCCAACTACAGCACACCTCTACCGATTGGCC
130 GGCTAGTCTCACAAGGAAGACTTAGGTAGACTACCCCAACTACAGCACACCTCTACCGATTGGCC
** *
5766507 ACAAGTGTGTCT-GC-C-TACTAGC-CT-GT-ACATAC-CTCAAGCTCGATGGCATCTTTCCTAT
195 ACAAG-G-GTCTAGCACGTACTAGCTCTAGTCACAT-CTCTCAAGCTCGATGGCATCCCTCCTAC
** * *
5766565 GCAAACACCATCTCATGAT-CTTTCTGGCTT-AAGGAGGGAAAACTG-AGGGACATAACAAACTC
257 GCAAACACCATCTCATGATCCTTT-TGGCTTAAAAAAGAG-AAACAGAAGGG-CATAACAAACTC
* ** * * *
5766627 TATCGCATAACCTTATTGCTTAACGCAAAGGCGCGATACAAGGCCCG-CTGACCCCAACCGTCTT
319 TACCGCATAACCCCATGGCTTAACGCAAAAGCGCGATACAAGGCCCGCCTG-CCCCAACCGTCCT
* * *
5766691 CGGGTTTACCATGA-CCAGAGGAAACATCGTGCCACGCTTGTGACCCTACGATGCCCGCCCACCT
383 CGGGTTTACCATGACCCA-AGAAAACATCGTGCCACGCTCGTGACCCTACAATGCCCGCCCACCT
* * *
5766755 AGACACCACTAGTGCCTAGGAATATCTCACTTCAGACTAACCATGCC-CCTGCCTACTAGCTAAG
447 AGACACCACTAGTACCTAGGAATAGCTCACTTCAGACTAACCAGGCCGCCTGCCTACTAGCTAAG
* *
5766819 GGGTGGTGGAGAGCTAACACTAGTCATCTCCC-TATAAAAAGCGTAAGAGATTTTTTCAGTCTCC
512 GGGTGGTGGAGAGCTAACACCAGTCATC-CCCTTATAAAAAGCGTAAGAGATTTTCTCAGTCTCC
* *
5766883 TACGAGTAACCATAAGATTATCTGAAATGGAGATAATTTTCTCCCCAGTCATCTCAGGACCTTTC
576 TACCAGTAACCATAAGATTATCTGAAATGGAGACAATTTTCTCCCCAGTCATCTCAGGACCTTTC
* * *
5766948 TCCAACTAACTCAGGGCTCCATAACCTTCCTTTTGGTCATCATTATTCATTGATTCTACTCGTTG
641 TCCAACTAACTCAGGGCCCCATAACCTTCCTCTTGGTCATCATTATTCATTGATTCTACTCATTG
* ** * * *
5767013 CTCCATCAATCC-ACTTGAAGGTGCCCACACATAACTTTGACCGATAGCACCT
706 CTCCACCAA-CCTACTCAAAGGTACCCACACATAACTTCGACCGACAGCACCT
5767065 AACTGACTAG
Statistics
Matches: 648, Mismatches: 94, Indels: 35
0.83 0.12 0.05
Matches are distributed among these distances:
792 224 0.35
793 5 0.01
795 19 0.03
796 206 0.32
797 1 0.00
800 2 0.00
801 2 0.00
804 5 0.01
805 15 0.02
806 162 0.25
807 3 0.00
808 4 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (796 bp):
ACACTTATGCTGATCAACAGCCAACTCGAAGCCTCTAAGCTCATCTCATCCCACGGGACTCAGTT
CTTAGAGCTTAGGCCCTTAGCTTCTATGTAGACTGTCCGCACGCATGATTGACACCCAACATCAG
GCTAGTCTCACAAGGAAGACTTAGGTAGACTACCCCAACTACAGCACACCTCTACCGATTGGCCA
CAAGGGTCTAGCACGTACTAGCTCTAGTCACATCTCTCAAGCTCGATGGCATCCCTCCTACGCAA
ACACCATCTCATGATCCTTTTGGCTTAAAAAAGAGAAACAGAAGGGCATAACAAACTCTACCGCA
TAACCCCATGGCTTAACGCAAAAGCGCGATACAAGGCCCGCCTGCCCCAACCGTCCTCGGGTTTA
CCATGACCCAAGAAAACATCGTGCCACGCTCGTGACCCTACAATGCCCGCCCACCTAGACACCAC
TAGTACCTAGGAATAGCTCACTTCAGACTAACCAGGCCGCCTGCCTACTAGCTAAGGGGTGGTGG
AGAGCTAACACCAGTCATCCCCTTATAAAAAGCGTAAGAGATTTTCTCAGTCTCCTACCAGTAAC
CATAAGATTATCTGAAATGGAGACAATTTTCTCCCCAGTCATCTCAGGACCTTTCTCCAACTAAC
TCAGGGCCCCATAACCTTCCTCTTGGTCATCATTATTCATTGATTCTACTCATTGCTCCACCAAC
CTACTCAAAGGTACCCACACATAACTTCGACCGACAGCACCTGATTGGCTAGCTGATCCTAGGGC
ACCGGTGCATTGCCTC
Found at i:5777339 original size:16 final size:16
Alignment explanation
Indices: 5777313--5777353 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
5777303 TGAAATAGAA
5777313 AAACGTTTTCACATCTT
1 AAAC-TTTTCACATCTT
5777330 AAACTTTTCACATCTT
1 AAACTTTTCACATCTT
5777346 AAACTTTT
1 AAACTTTT
5777354 ATAATAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (16 bp):
AAACTTTTCACATCTT
Found at i:5781384 original size:6 final size:6
Alignment explanation
Indices: 5781375--5781408 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5781365 GGGGAGACAG
*
5781375 AGAGCA AGAGAA AGAGAA AGAGAA AGAGAGA AGA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGA-A AGA
5781409 AACATACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:5784997 original size:2 final size:2
Alignment explanation
Indices: 5784986--5785020 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5784976 TCTTGAGCTT
5784986 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5785021 GATGTAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5786160 original size:3 final size:3
Alignment explanation
Indices: 5786152--5786189 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
5786142 TGTATCTTAC
5786152 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5786190 GCTGATAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5788474 original size:44 final size:45
Alignment explanation
Indices: 5788412--5788502 Score: 175
Period size: 44 Copynumber: 2.0 Consensus size: 45
5788402 TACAGGTCTC
5788412 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTG-ATTT
1 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTT
5788456 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTT
1 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTT
5788501 CT
1 CT
5788503 TTGCTTCCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 40 0.87
45 6 0.13
ACGTcount: A:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (45 bp):
CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTT
Found at i:5788582 original size:154 final size:154
Alignment explanation
Indices: 5788302--5788609 Score: 589
Period size: 154 Copynumber: 2.0 Consensus size: 154
5788292 TACAGGTCTC
5788302 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGT
1 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGT
* * *
5788367 TTGACAAGACTTGTTAATGAATGCCTTGGCTGGGTTACAGGTCTCCTCTCTCTAGCTCTTTACCA
66 TTGACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCACTCTCTAGCTCTTTACCA
5788432 TCTCTTCAGCTTTTCATTTGATTT
131 TCTCTTCAGCTTTTCATTTGATTT
5788456 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGT
1 CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGT
5788521 TTGACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCACTCTCTAGCTCTTTACCA
66 TTGACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCACTCTCTAGCTCTTTACCA
5788586 TCTCTTCAGCTTTTCATTTGATTT
131 TCTCTTCAGCTTTTCATTTGATTT
5788610 TCTTTGCTTC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 151 1.00
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.43
Consensus pattern (154 bp):
CTCTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGT
TTGACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCACTCTCTAGCTCTTTACCA
TCTCTTCAGCTTTTCATTTGATTT
Found at i:5788595 original size:110 final size:110
Alignment explanation
Indices: 5788458--5788657 Score: 382
Period size: 110 Copynumber: 1.8 Consensus size: 110
5788448 TTTGATTTCT
5788458 CTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGTTT
1 CTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGTTT
5788523 GACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCA
66 GACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCA
*
5788568 CTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGATTTTCTTTGCTTCCACGCATGAGTTT
1 CTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGTTT
*
5788633 GACAAGACTTGTTAATGAATGCCTT
66 GACAAGACTTGTTAATAAATGCCTT
5788658 GGCTAGGGCT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 88 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (110 bp):
CTCTCTAGCTCTTTACCATCTCTTCAGCTTTTCATTTGAATTTCTTTGCTTCCACGCATGAGTTT
GACAAGACTTGTTAATAAATGCCTTAGCTGGGTTACAGGTCTCCA
Found at i:5791690 original size:6 final size:6
Alignment explanation
Indices: 5791681--5791714 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5791671 GGGGAGACAG
*
5791681 AGAGCA AGAGAA AGAGAA AGAGAA AGAGAGA AGA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGA-A AGA
5791715 AACATACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:5795295 original size:2 final size:2
Alignment explanation
Indices: 5795288--5795337 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
5795278 GAGCTTTATC
5795288 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
*
5795330 AT AG AT AT
1 AT AT AT AT
5795338 GGATATCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5798667 original size:21 final size:21
Alignment explanation
Indices: 5798619--5798661 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5798609 TACCATCTCT
5798619 TCAGCTTTTCATTTGATTTTC
1 TCAGCTTTTCATTTGATTTTC
5798640 TCAGCTTTTCATTTGATTTTC
1 TCAGCTTTTCATTTGATTTTC
5798661 T
1 T
5798662 TTGCTTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.09, T:0.58
Consensus pattern (21 bp):
TCAGCTTTTCATTTGATTTTC
Found at i:5799015 original size:21 final size:21
Alignment explanation
Indices: 5798983--5799036 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
5798973 GTGAATTTTT
*
5798983 TTTTATATTAAA-AAGATAAAA
1 TTTTATATTAAATAA-AAAAAA
5799004 TTTTAGTA-TAAATAAAAAAAA
1 TTTTA-TATTAAATAAAAAAAA
5799025 TTTTGAT-TTAAA
1 TTTT-ATATTAAA
5799037 ATTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (21 bp):
TTTTATATTAAATAAAAAAAA
Found at i:5804314 original size:36 final size:36
Alignment explanation
Indices: 5804258--5804341 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
5804248 ATTTAGATAT
* ** *
5804258 AAATTAAAGATTAAGTACTTACTT-GATACAAATTAA
1 AAATTAAAAATTAAAAACTTACTTAGACACAAATT-A
* * *
5804294 AAATTAAAAATTAAAAACTTATTTAGACATAAATTC
1 AAATTAAAAATTAAAAACTTACTTAGACACAAATTA
5804330 AAATTAAAAATT
1 AAATTAAAAATT
5804342 TATTTGAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 32 0.80
37 8 0.20
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (36 bp):
AAATTAAAAATTAAAAACTTACTTAGACACAAATTA
Found at i:5808193 original size:2 final size:2
Alignment explanation
Indices: 5808186--5808215 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5808176 GAGGTACAAT
5808186 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5808216 AAACTCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5821653 original size:2 final size:2
Alignment explanation
Indices: 5821646--5821688 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5821636 ACATCCTTTC
5821646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5821688 T
1 T
5821689 GAACAGATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5822116 original size:36 final size:36
Alignment explanation
Indices: 5822060--5822143 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
5822050 ATTTAGATAT
* ** *
5822060 AAATTAAAGATTAAGTACTTACTT-GATACAAATTAA
1 AAATTAAAAATTAAAAACTTACTTAGACACAAATT-A
* * *
5822096 AAATTAAAAATTAAAAACTTATTTAGACATAAATTC
1 AAATTAAAAATTAAAAACTTACTTAGACACAAATTA
5822132 AAATTAAAAATT
1 AAATTAAAAATT
5822144 TATTGAAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 32 0.80
37 8 0.20
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (36 bp):
AAATTAAAAATTAAAAACTTACTTAGACACAAATTA
Found at i:5825989 original size:2 final size:2
Alignment explanation
Indices: 5825982--5826011 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5825972 GAGGTACAAT
5825982 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5826012 AAACTCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5830840 original size:22 final size:22
Alignment explanation
Indices: 5830800--5830841 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5830790 CTCCAAGAAG
* *
5830800 TTGTTAAGAAGTATTGTCTAAT
1 TTGTTAAGAACTATCGTCTAAT
*
5830822 TTGTTAAGGACTATCGTCTA
1 TTGTTAAGAACTATCGTCTA
5830842 TTGTGATCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (22 bp):
TTGTTAAGAACTATCGTCTAAT
Found at i:5838049 original size:66 final size:66
Alignment explanation
Indices: 5837929--5838059 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
5837919 TCCTTGTTCA
* * **
5837929 AGGTAATCCATCCAAGTATAATCATCTGCCCCAGCAGCATCTTCCTGGGGTGTA-TCTGCCATTA
1 AGGTAATCCATCCAAGCAAAATCATCTGCCCCAGCAGCATCTTCCTGCAGTGTATTCT-CCATTA
5837993 CG
65 CG
* * *
5837995 AGGTAATCCATCCAAGCAAAATCATCTGCCCCAGCTGCATTTTCCTGCATTGTATTCTCCATTAC
1 AGGTAATCCATCCAAGCAAAATCATCTGCCCCAGCAGCATCTTCCTGCAGTGTATTCTCCATTAC
5838060 TTGCTCATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 54 0.95
67 3 0.05
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (66 bp):
AGGTAATCCATCCAAGCAAAATCATCTGCCCCAGCAGCATCTTCCTGCAGTGTATTCTCCATTAC
G
Found at i:5840955 original size:39 final size:39
Alignment explanation
Indices: 5840901--5840982 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
5840891 ATCGTATTTT
**
5840901 TCATAACAACTAAGAAAAATGGTCATATGGAATGTAATA
1 TCATAACAACTAAGAAAAATGGTCATATAAAATGTAATA
5840940 TCATAACAACTAAGAAAAATGGTCATATAAAATGTAATA
1 TCATAACAACTAAGAAAAATGGTCATATAAAATGTAATA
5840979 TCAT
1 TCAT
5840983 GTATGATGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (39 bp):
TCATAACAACTAAGAAAAATGGTCATATAAAATGTAATA
Found at i:5842690 original size:42 final size:41
Alignment explanation
Indices: 5842629--5842727 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 41
5842619 GGAGTTTTTA
*
5842629 TTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATC
1 TTTT-AGAAAAATTTATACTTTCAACTTTTTC-CAAAAATATC
* *
5842672 TTTTAGAAAAATTTATACTTTCAACTTTTTCCTAAAATATT
1 TTTTAGAAAAATTTATACTTTCAACTTTTTCCAAAAATATC
*
5842713 TTTTA-AAAATTTTAT
1 TTTTAGAAAAATTTAT
5842728 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 9 0.17
41 13 0.25
42 26 0.50
43 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.47
Consensus pattern (41 bp):
TTTTAGAAAAATTTATACTTTCAACTTTTTCCAAAAATATC
Found at i:5842747 original size:57 final size:57
Alignment explanation
Indices: 5842678--5842853 Score: 212
Period size: 61 Copynumber: 3.0 Consensus size: 57
5842668 TATCTTTTAG
*
5842678 AAAAATTTATACTTTCAACTTTTTCCTAAAATATTTTTTAAAAATTTTATTTTTAAA
1 AAAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTTAAAAATTTTATTTTTAAA
* * *
5842735 AAAAATTGATACTTTCAACTTTTTCCTAAAAACATTTTTTAGAAATCTTTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCT-AAAATATTTTTTA-AAA--ATTTTATTTTTAAA
* * * **
5842796 AGAAATTGATACTTTCAACTTTCTCCCAAAAT-GCTTTTAAAAATTTT-TATTTTAAA
1 AAAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTTAAAAATTTTAT-TTTTAAA
5842852 AA
1 AA
5842854 TTTTATTTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.01
56 11 0.11
57 26 0.26
58 15 0.15
59 8 0.08
60 4 0.04
61 36 0.36
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTTAAAAATTTTATTTTTAAA
Found at i:5842865 original size:15 final size:15
Alignment explanation
Indices: 5842830--5842862 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
5842820 CCCAAAATGC
5842830 TTTTAAAAATTTTTA
1 TTTTAAAAATTTTTA
5842845 TTTTAAAAA-TTTTA
1 TTTTAAAAATTTTTA
5842859 TTTT
1 TTTT
5842863 TAAGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAAAATTTTTA
Found at i:5843998 original size:45 final size:45
Alignment explanation
Indices: 5843889--5844271 Score: 470
Period size: 45 Copynumber: 8.6 Consensus size: 45
5843879 TTCTTGGAAA
*
5843889 ATAAACAAAACTCCTCTAAACAGAGGCTCAACGACTTTTGAAAA-
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
* * *
5843933 ATAAACAAAGCTCCTTTAAGCAGAGGCTCAATGACTTTTGAAAAC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
* * * *
5843978 ATAAATAGAGCTCCTCTAAGCAGAGGCTCAACAACTTTTGAAAA-
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
** * *
5844022 ATAAAC-AAGCTTTTCTGAACAGAGGCTCAACGACTTTAGAAAAC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
** * *
5844066 ATAAACAAAGCTCCTCTAATTAGAGGCTCAATGACTTTGGAAAAC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
* * * *
5844111 ATAAACAAAGCTCCTCTAATCAGAAGCTCAATGACTTTGGAAAAC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
* * *
5844156 ATAAACAAAGCTCCTCTAAACAAAGGCTCAACAACTTTT-AAAAA
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
** * *
5844200 ATAAACAAAGCTCCTCTAAGTAAAGGTTCAACGAC-TTTGAAAAAC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTG-AAAAC
*
5844245 ATAAACAAAGCTCTTCTAAACAGAGGC
1 ATAAACAAAGCTCCTCTAAACAGAGGC
5844272 CACAGAACTT
Statistics
Matches: 291, Mismatches: 43, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
43 33 0.11
44 86 0.30
45 172 0.59
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (45 bp):
ATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAC
Found at i:5844251 original size:89 final size:88
Alignment explanation
Indices: 5843889--5844293 Score: 442
Period size: 89 Copynumber: 4.6 Consensus size: 88
5843879 TTCTTGGAAA
* * * *
5843889 ATAAACAAAACTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAACAAAGCTCCTTTAAGC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTCTAA-C
* *
5843954 AGAGGCTCAATGACTTTTG-AAAAC
65 AAAGGCTCAACGAC-TTTGAAAAAC
* * * * **
5843978 ATAAATAGAGCTCCTCTAAGCAGAGGCTCAACAACTTTTGAAAAATAAAC-AAGCTTTTCTGAAC
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTCT-AAC
*
5844042 AGAGGCTCAACGACTTT-AGAAAAC
65 AAAGGCTCAACGACTTTGA-AAAAC
** ** * *
5844066 ATAAACAAAGCTCCTCTAATTAGAGGCTCAATGACTTTGGAAAACATAAACAAAGCTCCTCTAAT
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTT-TAAAAAATAAACAAAGCTCCTCTAA-
* *
5844131 CAGAA-GCTCAATGACTTTGGAAAAC
64 CA-AAGGCTCAACGACTTTGAAAAAC
* *
5844156 ATAAACAAAGCTCCTCTAAACAAAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTCTAAGT
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTCTAA-C
*
5844221 AAAGGTTCAACGACTTTGAAAAAC
65 AAAGGCTCAACGACTTTGAAAAAC
* * * *
5844245 ATAAACAAAGCTCTTCTAAACAGAGGC-CACAGAACTTTGAGAAAATAAA
1 ATAAACAAAGCTCCTCTAAACAGAGGCTCA-ACAACTTTTAAAAAATAAA
5844294 TGGCTCCTCT
Statistics
Matches: 266, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
87 3 0.01
88 62 0.23
89 140 0.53
90 60 0.23
91 1 0.00
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.22
Consensus pattern (88 bp):
ATAAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTCTAACA
AAGGCTCAACGACTTTGAAAAAC
Found at i:5844610 original size:16 final size:16
Alignment explanation
Indices: 5844584--5844624 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
5844574 AATGCGGTAT
5844584 ATGCTATGCGAAATGCA
1 ATGC-ATGCGAAATGCA
*
5844601 ATGCATGCGAAATTCA
1 ATGCATGCGAAATGCA
5844617 ATGCATGC
1 ATGCATGC
5844625 TAATTAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (16 bp):
ATGCATGCGAAATGCA
Found at i:5845341 original size:15 final size:14
Alignment explanation
Indices: 5845315--5845369 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
5845305 TGAGTTCTCA
5845315 TTTTTCATTTTTTTC
1 TTTTT-ATTTTTTTC
5845330 TTCTTTATTTTTTT-
1 TT-TTTATTTTTTTC
*
5845344 TTTTCA-TTTTTTC
1 TTTTTATTTTTTTC
5845357 ATTTTTTATTTTT
1 --TTTTTATTTTT
5845370 CATTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 6 0.18
13 3 0.09
14 2 0.06
15 15 0.45
16 7 0.21
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTTTTTC
Found at i:5845346 original size:28 final size:28
Alignment explanation
Indices: 5845315--5845369 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5845305 TGAGTTCTCA
5845315 TTTTTCATTTTTTTC-TTCTTTATTTTTT
1 TTTTTCA-TTTTTTCATTCTTTATTTTTT
*
5845343 TTTTTCATTTTTTCATTTTTTATTTTT
1 TTTTTCATTTTTTCATTCTTTATTTTT
5845370 CATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTTCATTTTTTCATTCTTTATTTTTT
Found at i:5845353 original size:6 final size:7
Alignment explanation
Indices: 5845312--5845376 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
5845302 CCTTGAGTTC
5845312 TCATTTT
1 TCATTTT
5845319 TCATTTTTT
1 TCA--TTTT
5845328 TC-TTCTT
1 TCATT-TT
5845335 T-ATTTT
1 TCATTTT
*
5845341 T-TTTTT
1 TCATTTT
5845347 TCATTTTT
1 TCA-TTTT
5845355 TCATTTT
1 TCATTTT
*
5845362 TTATTTT
1 TCATTTT
5845369 TCATTTT
1 TCATTTT
5845376 T
1 T
5845377 TTTCAAGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
6 10 0.21
7 25 0.52
8 7 0.15
9 6 0.12
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (7 bp):
TCATTTT
Found at i:5845355 original size:8 final size:8
Alignment explanation
Indices: 5845315--5845377 Score: 59
Period size: 8 Copynumber: 8.6 Consensus size: 8
5845305 TGAGTTCTCA
5845315 TTTTTCATT
1 TTTTTCA-T
5845324 TTTTTC-T
1 TTTTTCAT
*
5845331 TCTTT-A-
1 TTTTTCAT
5845337 TTTTT--T
1 TTTTTCAT
5845343 TTTTTCAT
1 TTTTTCAT
5845351 TTTTTCAT
1 TTTTTCAT
5845359 TTTTT-A-
1 TTTTTCAT
5845365 TTTTTCAT
1 TTTTTCAT
5845373 TTTTT
1 TTTTT
5845378 TTCAAGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
6 14 0.30
7 7 0.15
8 19 0.41
9 6 0.13
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCAT
Found at i:5852673 original size:14 final size:15
Alignment explanation
Indices: 5852643--5852675 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5852633 CTTTCGTTTA
*
5852643 CATAGAGTTTATCAT
1 CATAGAGTTTATAAT
5852658 CATAGAG-TTATAAT
1 CATAGAGTTTATAAT
5852672 CATA
1 CATA
5852676 AAATCGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (15 bp):
CATAGAGTTTATAAT
Found at i:5855758 original size:60 final size:58
Alignment explanation
Indices: 5855680--5855811 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 58
5855670 CATTTGGGAG
* * *
5855680 TTTTTA-TTTTAAAAAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTGATAA
1 TTTTTATTTTTAAAAAAAATTGATACTTCCAACTTTTCATCAAAATA--TTTTTTGATAA
** *
5855739 TTTTTATTTTTAAGGAAAATTGGTACTTCCAACTTTTCATCAAAATATTTTTTGATAA
1 TTTTTATTTTTAAAAAAAATTGATACTTCCAACTTTTCATCAAAATATTTTTTGATAA
5855797 TTTTTA-TTTTAAAAA
1 TTTTTATTTTTAAAAA
5855812 TTTTACTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 7 0.11
58 17 0.27
59 6 0.09
60 34 0.53
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (58 bp):
TTTTTATTTTTAAAAAAAATTGATACTTCCAACTTTTCATCAAAATATTTTTTGATAA
Found at i:5855816 original size:131 final size:129
Alignment explanation
Indices: 5855681--5855935 Score: 327
Period size: 131 Copynumber: 2.0 Consensus size: 129
5855671 ATTTGGGAGT
* * * * **
5855681 TTTTATTTTAAAAAAAATTGATACT-TTCAACTTTTCCT-TAAAATATTTTTTTTGATAATTTTT
1 TTTTACTTTAAAAAAAATTAATA-TGTTCAACTTTTCCTCAAAAATA-TTTTTTAGA-AAAATTT
* * * *
5855744 ATTTTTAAGGAAAATTGGTACTTCCAAC-TTTTCATCAAAATATTTTTTGATAATTTTTATTTTA
63 ATTTTCAAGGAAAATTGATACTTCCAACTTTTTCATAAAAATATTTTTT-A-AAATTTTATTTTA
5855808 AAAA
126 AAAA
*
5855812 TTTTACTTTAAGAAAAATTAATATGTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAATTTATT
1 TTTTACTTTAAAAAAAATTAATATGTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAATTTATT
* *
5855877 TTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTAAAATTTTATTTT
66 TTCAAGGAAAATTGATACTTCCAACTTTTTCATAAAAATATTTTTTAAAATTTTATTTT
5855936 CAAGAAAAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
129 11 0.10
130 32 0.30
131 59 0.55
132 6 0.06
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (129 bp):
TTTTACTTTAAAAAAAATTAATATGTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAATTTATT
TTCAAGGAAAATTGATACTTCCAACTTTTTCATAAAAATATTTTTTAAAATTTTATTTTAAAAA
Found at i:5855889 original size:59 final size:58
Alignment explanation
Indices: 5855803--5856139 Score: 382
Period size: 59 Copynumber: 5.8 Consensus size: 58
5855793 ATAATTTTTA
* * *
5855803 TTTTAAAAATTTTACTTT-AAGAAAAATTAATA-TGTTCAACTTTTCCTCAAAAATATT
1 TTTTAAAAATTTTATTTTCAAGGAAAATTGATACT-TTCAACTTTTCCTCAAAAATATT
* * *
5855860 TTTTAGAAAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATT
1 TTTTA-AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
* ** *
5855919 TTTT-AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATC
1 TTTTAAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
* * ** *
5855976 TTTTAGAAAAATTTATTTTCAAAGAAGTTTGATACTTTCAA-TTTTACCTTAAAAATATT
1 TTTTA-AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTT-CCTCAAAAATATT
* *
5856035 TTTTAAAAATTTTATTTTCAAGGAAAAATTGATATTTTCAACTTTTCC-C-TAAATATAT
1 TTTTAAAAATTTTATTTTCAAGG-AAAATTGATACTTTCAACTTTTCCTCAAAAATAT-T
*
5856093 TTTTAAAATTTTTTTTATTTTCAAGG-AAATTGATACTTTCAACTTTT
1 TTTTAAAA---ATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTT
5856140 TCCAAAATGC
Statistics
Matches: 239, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
57 63 0.26
58 40 0.17
59 117 0.49
60 5 0.02
61 14 0.06
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.47
Consensus pattern (58 bp):
TTTTAAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
Found at i:5855944 original size:116 final size:115
Alignment explanation
Indices: 5855803--5856231 Score: 438
Period size: 116 Copynumber: 3.6 Consensus size: 115
5855793 ATAATTTTTA
* * *
5855803 TTTTAAAAATTTTACTTT-AAGAAAAATTAATATGTTCAACTTTTCCTCAAAAATATTTTTTAGA
1 TTTTTAAAATTTTATTTTCAAGAAAAATTGATAT-TTCAACTTTTCCTCAAAAATATTTTTTAGA
5855867 AAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATAT
65 AAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATAT
** *
5855918 TTTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATCTTTTAGA
1 TTTTTAAAATTTTATTTTCAAGAAAAATTGATA-TTTCAACTTTTCCTCAAAAATATTTTTTAGA
* ** *
5855983 AAAATTTATTTTCAAAGAAGTTTGATACTTTCAA-TTTTACCTTAAAAATAT
65 AAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTT-TCTTAAAAATAT
*
5856034 TTTTTAAAAATTTTATTTTCAAGGAAAAATTGATATTTTCAACTTTTCC-C-TAAATATATTTTT
1 TTTTT-AAAATTTTATTTTCAA-GAAAAATTGATA-TTTCAACTTTTCCTCAAAAATAT-TTTTT
** *
5856097 A-AAATTTTTTTTATTTTCAAGG-AAATTGATACTTTCAACTTTTTCCAAAATGCTTTTAGAAAT
62 AGAAA---AATTTATTTTCAAGGAAAATTGATACTTTCAAC-TTTT------T-C--TTA-AAAA
*
5856160 TTT
113 TAT
* *
5856163 TATTTTATAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG
1 T-TTTTA-AAATTTTATTTTCAAGAAAAATTGATA-TTTCAACTTTTCCTCAAAAATATTTTTT-
5856228 AGAA
62 AGAA
5856232 TTTTTATTTT
Statistics
Matches: 261, Mismatches: 27, Indels: 35
0.81 0.08 0.11
Matches are distributed among these distances:
115 20 0.08
116 96 0.37
117 23 0.09
118 37 0.14
119 12 0.05
120 4 0.02
125 1 0.00
126 1 0.00
128 3 0.01
129 31 0.12
130 24 0.09
131 7 0.03
132 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.47
Consensus pattern (115 bp):
TTTTTAAAATTTTATTTTCAAGAAAAATTGATATTTCAACTTTTCCTCAAAAATATTTTTTAGAA
AAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATAT
Found at i:5855966 original size:30 final size:30
Alignment explanation
Indices: 5855875--5855968 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
5855865 GAAAAATTTA
*
5855875 TTTTCAAGGAAAATTGATACTTTCAACTTT
1 TTTTCAAGAAAAATTGATACTTTCAACTTT
* * *
5855905 TTCTT-AA-AAATATT--T--TTTAAAATTTT
1 TT-TTCAAGAAAAATTGATACTTT-CAACTTT
5855931 ATTTTCAAGAAAAATTGATACTTTCAACTTT
1 -TTTTCAAGAAAAATTGATACTTTCAACTTT
5855962 TTTTCAA
1 TTTTCAA
5855969 AAATATCTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
25 3 0.06
26 7 0.15
27 5 0.10
28 6 0.12
29 5 0.10
30 12 0.25
31 7 0.15
32 3 0.06
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (30 bp):
TTTTCAAGAAAAATTGATACTTTCAACTTT
Found at i:5856184 original size:15 final size:15
Alignment explanation
Indices: 5856150--5856182 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5856140 TCCAAAATGC
5856150 TTTTAGAAATTTTTA
1 TTTTAGAAATTTTTA
*
5856165 TTTTATAAA-TTTTA
1 TTTTAGAAATTTTTA
5856179 TTTT
1 TTTT
5856183 TAAGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTAGAAATTTTTA
Found at i:5856206 original size:70 final size:71
Alignment explanation
Indices: 5856105--5856242 Score: 199
Period size: 70 Copynumber: 1.9 Consensus size: 71
5856095 TTAAAATTTT
* *
5856105 TTTTATTTTCAAGGAAATTGATACTTTCAACTTTT-TCCAAAATGCTTTTAGA-AATTTTTATTT
1 TTTTATTTTCAAGGAAATTGATACTTTCAACTTTTCTCAAAAATACTTTTAGAGAATTTTTATTT
5856168 TATAAA
66 TATAAA
* * *
5856174 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAGAATTTTTAT
1 TTTTATTTTCAAGG-AAATTGATACTTTCAACTTTT-CTCAAAAATACTTTTAGAGAATTTTTAT
5856239 TTTA
64 TTTA
5856243 GGAAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
69 13 0.22
70 21 0.35
72 13 0.22
73 13 0.22
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (71 bp):
TTTTATTTTCAAGGAAATTGATACTTTCAACTTTTCTCAAAAATACTTTTAGAGAATTTTTATTT
TATAAA
Found at i:5857884 original size:3 final size:3
Alignment explanation
Indices: 5857876--5857908 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
5857866 AAGTTTATGC
5857876 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
5857909 ATGCTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5860598 original size:17 final size:17
Alignment explanation
Indices: 5860578--5860630 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5860568 AAAATTATTT
5860578 TTTAAAAATTTATATAA
1 TTTAAAAATTTATATAA
* *
5860595 TTTAAATTATTGATATAA
1 TTTAAA-AATTTATATAA
** *
5860613 TTTTTAAATGTATATAA
1 TTTAAAAATTTATATAA
5860630 T
1 T
5860631 ACATGTAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTAAAAATTTATATAA
Found at i:5861016 original size:18 final size:18
Alignment explanation
Indices: 5860993--5861049 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
5860983 TATTAATAAT
5860993 TTTTATATTAATGTTATA
1 TTTTATATTAATGTTATA
* **
5861011 TTTTATACTAAAATTATA
1 TTTTATATTAATGTTATA
* *
5861029 TATTATAATTTATGTTTATA
1 TTTTAT-ATTAATG-TTATA
5861049 T
1 T
5861050 AAAATTATAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 20 0.69
19 3 0.10
20 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTTATATTAATGTTATA
Found at i:5861079 original size:22 final size:22
Alignment explanation
Indices: 5861049--5861090 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5861039 TATGTTTATA
5861049 TAAAATTATAAAATATATATTT
1 TAAAATTATAAAATATATATTT
* *
5861071 TAAATTTATTAAATATATAT
1 TAAAATTATAAAATATATAT
5861091 AATTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATTATAAAATATATATTT
Found at i:5861601 original size:19 final size:19
Alignment explanation
Indices: 5861560--5861602 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5861550 TAAGTTCAGC
*
5861560 TAAATTTTTTTTTTCAAGC
1 TAAATTTTTTTTTTCAAGA
*
5861579 TAAAGTTTTTTTTTT-AATA
1 TAAA-TTTTTTTTTTCAAGA
5861598 TAAAT
1 TAAAT
5861603 ATATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 10 0.48
20 10 0.48
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (19 bp):
TAAATTTTTTTTTTCAAGA
Found at i:5862231 original size:20 final size:20
Alignment explanation
Indices: 5862171--5862231 Score: 52
Period size: 24 Copynumber: 2.9 Consensus size: 20
5862161 CTATTAGAAT
* *
5862171 AATAATATTTTTATAT-TAA
1 AATATTATTTATATATATAA
*
5862190 AATATTTATTATTAAATCATATAA
1 AATA-TTA-T-TTATAT-ATATAA
5862214 AATATTATTTATATATAT
1 AATATTATTTATATATAT
5862232 TTATTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 6 0.18
22 5 0.15
23 5 0.15
24 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTATTTATATATATAA
Found at i:5862429 original size:14 final size:14
Alignment explanation
Indices: 5862410--5862443 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5862400 TTAATGATAC
5862410 TTAAAA-TAAAATA
1 TTAAAATTAAAATA
5862423 TTTAAAATTAAAATA
1 -TTAAAATTAAAATA
5862438 TTAAAA
1 TTAAAA
5862444 GACTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATTAAAATA
Found at i:5867736 original size:23 final size:23
Alignment explanation
Indices: 5867704--5867752 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
5867694 TTTATAGAGC
* *
5867704 TTTTTGGGATTCAAATCTCATAT
1 TTTTTAGGATTCAAATCTCAAAT
5867727 TTTTTAGGATTCAAATCTCAAAT
1 TTTTTAGGATTCAAATCTCAAAT
5867750 TTT
1 TTT
5867753 CAATCGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (23 bp):
TTTTTAGGATTCAAATCTCAAAT
Found at i:5867952 original size:3 final size:3
Alignment explanation
Indices: 5867944--5867968 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5867934 AAAAGAAAAG
5867944 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5867969 ATGGTGTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5868712 original size:17 final size:18
Alignment explanation
Indices: 5868692--5868726 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5868682 TAAAATTGAT
5868692 TTAATTAAAT-TTAAAAA
1 TTAATTAAATATTAAAAA
*
5868709 TTAATTAATTATTAAAAA
1 TTAATTAAATATTAAAAA
5868727 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAATTAAATATTAAAAA
Found at i:5869060 original size:12 final size:12
Alignment explanation
Indices: 5869045--5869072 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5869035 AAAAAATACT
5869045 ACAAAAAAAAAA
1 ACAAAAAAAAAA
5869057 ACAAAAAAAAAA
1 ACAAAAAAAAAA
5869069 ACAA
1 ACAA
5869073 CACAGTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAAAAAAAAAA
Found at i:5869068 original size:15 final size:15
Alignment explanation
Indices: 5869031--5869074 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5869021 GTGATGCTGC
* *
5869031 AAAAAAAAAATACTA
1 AAAAAAAAAAAACAA
*
5869046 CAAAAAAAAAAACAA
1 AAAAAAAAAAAACAA
*
5869061 AAAAAAAAACAACA
1 AAAAAAAAAAAACA
5869075 CAGTCTTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (15 bp):
AAAAAAAAAAAACAA
Found at i:5869653 original size:20 final size:20
Alignment explanation
Indices: 5869628--5869676 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5869618 CTGCGCGTCG
5869628 AACCGAACCTTTTTCGATCC
1 AACCGAACCTTTTTCGATCC
*
5869648 AACCGAACCTTTTTCGGTCC
1 AACCGAACCTTTTTCGATCC
5869668 AACCGAACC
1 AACCGAACC
5869677 ACCGTTGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (20 bp):
AACCGAACCTTTTTCGATCC
Found at i:5869884 original size:3 final size:3
Alignment explanation
Indices: 5869876--5869909 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5869866 TAAAAATGCT
5869876 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5869910 TTGAGAGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5881485 original size:109 final size:109
Alignment explanation
Indices: 5881372--5881840 Score: 598
Period size: 109 Copynumber: 4.4 Consensus size: 109
5881362 CCGGTCGTTG
*
5881372 TTAATCTTTGACTCGTGGTTTAATCTCGATCATTCTTATAGCTTCTCGACTTACGGTTTAATCCT
1 TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCGACTTACGGTTTAATCCT
* * *
5881437 AGTCACTTTTATTTCTTTAACTTGCGGTTCAGTCTCAGTTATCT
66 AGTCACTTTTATTTCTTTGACTTACAGTTCAGTCTCAGTTATCT
5881481 TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTC-A---AC---TTAATCCT
1 TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCGACTTACGGTTTAATCCT
* ** *
5881539 AGTCACTTTTATTTCTTTGACTTATAGTTCAGTCTCAGTCGTCG
66 AGTCACTTTTATTTCTTTGACTTACAGTTCAGTCTCAGTTATCT
** * * * *
5881583 TTAATCTTTGACTCGTGGTTTAATTTCGAACATTCTTATAGCTTCTTGACTTATGGTTTAATCTT
1 TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCGACTTACGGTTTAATCCT
* * * *
5881648 AGTCACTTTTATTTCTTTGACTTGCAGTTCAGTTTTAATTATCT
66 AGTCACTTTTATTTCTTTGACTTACAGTTCAGTCTCAGTTATCT
* * *
5881692 TTAATTTTTGACTCGTGGTTTAATCCCGATCATTTTTATAGCTTCTTGACTTACGGTTTAATCCT
1 TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCGACTTACGGTTTAATCCT
** *
5881757 AGTCGTTTTTATTT-TTCTGACTTAC-GATTCAATC-CTAGTTATCT
66 AGTCACTTTTATTTCTT-TGACTTACAG-TTCAGTCTC-AGTTATCT
** *
5881801 TTAATCTTTGACTCGTGGTTTAATCCTAATCATTTTTATA
1 TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATA
5881841 ATTTTTGAAT
Statistics
Matches: 311, Mismatches: 39, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
102 88 0.28
103 1 0.00
105 2 0.01
106 1 0.00
108 4 0.01
109 215 0.69
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.48
Consensus pattern (109 bp):
TTAATCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCGACTTACGGTTTAATCCT
AGTCACTTTTATTTCTTTGACTTACAGTTCAGTCTCAGTTATCT
Found at i:5881696 original size:211 final size:211
Alignment explanation
Indices: 5881355--5881825 Score: 631
Period size: 211 Copynumber: 2.2 Consensus size: 211
5881345 TGACTTGCGA
* * *
5881355 TTCAGTCCCGGTCGTTGTTAATCTTTGACTCGTGGTTTAATCTCGATCATTCTTATAGCTTCTCG
1 TTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGAACATTCTTATAGCTTCTCG
* *
5881420 ACTTACGGTTTAATCCTAGTCACTTTTATTTCTTTAACTTGCGGTTCAGTCTCAGTTATCTTTAA
66 ACTTACGGTTTAATCCTAGTCACTTTTATTTCTTTAACTTGCAGTTCAGTCTCAATTATCTTTAA
5881485 TCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCAACTTAATCCTAGTCACTTTTA
131 TCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCAACTTAATCCTAGTCACTTTTA
5881550 TTTCTTTGACTTATAG
196 TTTCTTTGACTTATAG
* * *
5881566 TTCAGTCTCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATTTCGAACATTCTTATAGCTTCTTG
1 TTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGAACATTCTTATAGCTTCTCG
* * * * *
5881631 ACTTATGGTTTAATCTTAGTCACTTTTATTTCTTTGACTTGCAGTTCAGTTTTAATTATCTTTAA
66 ACTTACGGTTTAATCCTAGTCACTTTTATTTCTTTAACTTGCAGTTCAGTCTCAATTATCTTTAA
* * *
5881696 TTTTTGACTCGTGGTTTAATCCCGATCATTTTTATAGCTTCTTGACTTACGGTTTAATCCTAGTC
131 TCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTC-T--C-AAC---TTAATCCTAGTC
** *
5881761 GTTTTTATTT-TTCTGACTTA-CG
189 ACTTTTATTTCTT-TGACTTATAG
* * ** *
5881783 ATTCAATCCTAGTTATCTTTAATCTTTGACTCGTGGTTTAATC
1 -TTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATC
5881826 CTAATCATTT
Statistics
Matches: 225, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
211 156 0.69
212 1 0.00
214 1 0.00
215 2 0.01
217 3 0.01
218 62 0.28
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (211 bp):
TTCAGTCCCAGTCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGAACATTCTTATAGCTTCTCG
ACTTACGGTTTAATCCTAGTCACTTTTATTTCTTTAACTTGCAGTTCAGTCTCAATTATCTTTAA
TCTTTGACTCGTGGTTTAATCCCGATCATTCTTATAGCTTCTCAACTTAATCCTAGTCACTTTTA
TTTCTTTGACTTATAG
Found at i:5881860 original size:37 final size:37
Alignment explanation
Indices: 5881710--5881868 Score: 110
Period size: 36 Copynumber: 4.4 Consensus size: 37
5881700 TGACTCGTGG
** * * *
5881710 TTTAATCCCGATCATTTTTATAGCTTCTTGACTTACGG
1 TTTAATCCTAATCATTTTTATA-ATTTTTGACTTACGA
* *
5881748 TTTAATCCTAGTCGTTTTTAT--TTTTCTGACTTACGA
1 TTTAATCCTAATCATTTTTATAATTTT-TGACTTACGA
* * * * * *** *
5881784 TTCAATCCTAGTTA-TCTT-TAATCTTTGACTCGTGG
1 TTTAATCCTAATCATTTTTATAATTTTTGACTTACGA
*
5881819 TTTAATCCTAATCATTTTTATAATTTTTGAATTACGA
1 TTTAATCCTAATCATTTTTATAATTTTTGACTTACGA
*
5881856 TTTAATCCCAATC
1 TTTAATCCTAATC
5881869 TCCTTATTTC
Statistics
Matches: 90, Mismatches: 26, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
34 1 0.01
35 23 0.26
36 26 0.29
37 23 0.26
38 17 0.19
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (37 bp):
TTTAATCCTAATCATTTTTATAATTTTTGACTTACGA
Found at i:5881994 original size:68 final size:67
Alignment explanation
Indices: 5881908--5882077 Score: 155
Period size: 68 Copynumber: 2.5 Consensus size: 67
5881898 AATCTCTTTA
* * * * **
5881908 TATTCTGACTCACTGTTCAATCTCAATCTCTTTAAATCCAAAAATCACAGTTTAATCTTGATTAA
1 TATTTTGACTCGCGGTTCAATCTCAATCTCTTTAAATCC-AAAATCACAGGTTAATCTCAATTAA
5881973 CGT
65 CGT
* * * **
5881976 TATTTTGACTCGCGGTTCAATC-CTGATTTCTTT-AATCCAAAATCGCAGGTTAATCTCAATTGT
1 TATTTTGACTCGCGGTTCAATCTC-AATCTCTTTAAATCCAAAATCACAGGTTAATCTCAATTAA
*
5882039 TGT
65 CGT
* * *
5882042 TATTTTCTGACTCGTGGTTTAATCTCAGTCTCTTTA
1 TA-TTT-TGACTCGCGGTTCAATCTCAATCTCTTTA
5882078 TTTTCTGACT
Statistics
Matches: 80, Mismatches: 17, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
66 23 0.29
67 9 0.11
68 47 0.59
69 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (67 bp):
TATTTTGACTCGCGGTTCAATCTCAATCTCTTTAAATCCAAAATCACAGGTTAATCTCAATTAAC
GT
Found at i:5882328 original size:180 final size:179
Alignment explanation
Indices: 5882023--5882382 Score: 522
Period size: 180 Copynumber: 2.0 Consensus size: 179
5882013 CAAAATCGCA
* *
5882023 GGTTAATCTCAATTGTTGTTATTTTCTGACTCGTGGTTTAATCTCAGTCTCTTTATTTTCTGACT
1 GGTTAATCTCAATTGTTGTTATTTTCTGACTCGTGATTTAATCCCAGTCTCTTTATTTTCTGACT
**
5882088 TGTGATTCAATCCAAGTTGACGTTATTCTAACTCGCGGTTCAATCCCGATTTTTTTAATCCAAAA
66 TGTGATTCAATCCAAGTTGACGTTATTCTAACTCGCGGTTCAATCCCGATTTCGTTAATCCAAAA
* * * *
5882153 TCGTAGTTTACTCTCAATTATTGTTATTTTTTGACTCATGGTTTAATCCC
131 TCGCAGTTTAATCTCAATTATTATT-TTTTTTGACTCATGATTTAATCCC
* * * * * * *
5882203 GGTTAATCTCGATTGTTGTTATTTTTTTATTTGTGATTTAATCCCGGTCTCTTTATTTTTTGACT
1 GGTTAATCTCAATTGTTGTTATTTTCTGACTCGTGATTTAATCCCAGTCTCTTTATTTTCTGACT
* *
5882268 TGTGATTCAATCCAAGTTGACGTTATTCTGACTCGCGGTTCAATCTCGATTTCGTTAATCCAAAA
66 TGTGATTCAATCCAAGTTGACGTTATTCTAACTCGCGGTTCAATCCCGATTTCGTTAATCCAAAA
* * * *
5882333 TCGCAGTTTAATCTCGATTGTTATTTTTTTTTACTCGTGATTTAATCCC
131 TCGCAGTTTAATCTCAATTATTATTTTTTTTGACTCATGATTTAATCCC
5882382 G
1 G
5882383 ATCTCTTTAT
Statistics
Matches: 159, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
179 22 0.14
180 137 0.86
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (179 bp):
GGTTAATCTCAATTGTTGTTATTTTCTGACTCGTGATTTAATCCCAGTCTCTTTATTTTCTGACT
TGTGATTCAATCCAAGTTGACGTTATTCTAACTCGCGGTTCAATCCCGATTTCGTTAATCCAAAA
TCGCAGTTTAATCTCAATTATTATTTTTTTTGACTCATGATTTAATCCC
Found at i:5883870 original size:19 final size:18
Alignment explanation
Indices: 5883822--5883871 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5883812 AAATTTTTAA
* *
5883822 ATTTTTTTATATATTATT
1 ATTTTTTTATATTTTAGT
*
5883840 ATTTTTGTTAT-TTTAAGT
1 ATTTTT-TTATATTTTAGT
5883858 ATTTTTTTATATTT
1 ATTTTTTTATATTT
5883872 ATGCATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
ATTTTTTTATATTTTAGT
Found at i:5884273 original size:31 final size:32
Alignment explanation
Indices: 5884238--5884317 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 32
5884228 CTTAAACACT
* * * *
5884238 AACCCTA-AAAATTCAAAATCCTTTAAATCCA
1 AACCCTATAAAATCCAAAACCCCTAAAATCCA
*
5884269 AACCC-ATAAAATCCGAAACCCCTAAAATCCA
1 AACCCTATAAAATCCAAAACCCCTAAAATCCA
5884300 AACCCT-T-AAAT-CAAAACC
1 AACCCTATAAAATCCAAAACC
5884318 TTAAACCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
29 6 0.15
30 5 0.12
31 30 0.73
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.19
Consensus pattern (32 bp):
AACCCTATAAAATCCAAAACCCCTAAAATCCA
Found at i:5884287 original size:16 final size:15
Alignment explanation
Indices: 5884262--5884309 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
5884252 AAAATCCTTT
5884262 AAATCCAAACCCATA
1 AAATCCAAACCCATA
*
5884277 AAATCCGAAACCCCTA
1 AAATCC-AAACCCATA
*
5884293 AAATCCAAACCCTTA
1 AAATCCAAACCCATA
5884308 AA
1 AA
5884310 TCAAAACCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.15
Consensus pattern (15 bp):
AAATCCAAACCCATA
Found at i:5884310 original size:14 final size:14
Alignment explanation
Indices: 5884260--5884322 Score: 65
Period size: 13 Copynumber: 4.4 Consensus size: 14
5884250 TCAAAATCCT
5884260 TTAAATCCAAACCC
1 TTAAATCCAAACCC
*
5884274 ATAAAATCCGAAACCCC
1 -TTAAATCC-AAA-CCC
*
5884291 TAAAATCCAAACCC
1 TTAAATCCAAACCC
*
5884305 TTAAAT-CAAAACC
1 TTAAATCCAAACCC
5884318 TTAAA
1 TTAAA
5884323 CCTTCTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
13 11 0.26
14 8 0.19
15 10 0.23
16 11 0.26
17 3 0.07
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (14 bp):
TTAAATCCAAACCC
Found at i:5885677 original size:2 final size:2
Alignment explanation
Indices: 5885672--5885698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5885662 TTTTTTTCTT
5885672 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5885699 GCTAAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5887054 original size:1 final size:1
Alignment explanation
Indices: 5887048--5887072 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5887038 TTAAAGAGGC
5887048 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5887073 GAAACCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5889226 original size:20 final size:20
Alignment explanation
Indices: 5889197--5889253 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
5889187 ATTTGATTTT
5889197 AGAGAGAAGATGAATTGTAG
1 AGAGAGAAGATGAATTGTAG
* *
5889217 AGATAGAAGATGAATAGTAG
1 AGAGAGAAGATGAATTGTAG
*
5889237 AGAGAAAAGATGAATTG
1 AGAGAGAAGATGAATTG
5889254 AAGATGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.19
Consensus pattern (20 bp):
AGAGAGAAGATGAATTGTAG
Found at i:5892370 original size:11 final size:11
Alignment explanation
Indices: 5892356--5892387 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5892346 ACACAATACG
5892356 AAAATAATATA
1 AAAATAATATA
*
5892367 AAAATTATATA
1 AAAATAATATA
5892378 AAAATAATAT
1 AAAATAATAT
5892388 GATTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATAATATA
Found at i:5894976 original size:24 final size:22
Alignment explanation
Indices: 5894923--5894985 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
5894913 AGAAATAAAA
5894923 AAAAAAGAAAAGAAAAGAAGAT
1 AAAAAAGAAAAGAAAAGAAGAT
**
5894945 AATGAAGAGAAAGAAGTAA-AAGAT
1 AAAAAAGA-AAAGAA--AAGAAGAT
*
5894969 AAAAAAGAATA-AAAAGA
1 AAAAAAGAAAAGAAAAGA
5894986 GAGGATGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
20 2 0.06
21 1 0.03
22 8 0.25
23 8 0.25
24 11 0.34
25 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (22 bp):
AAAAAAGAAAAGAAAAGAAGAT
Found at i:5895117 original size:14 final size:14
Alignment explanation
Indices: 5895098--5895130 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5895088 TTTTTCAAAA
5895098 ATCATTATATAT-AT
1 ATCATTATAT-TCAT
5895112 ATCATTATATTCAT
1 ATCATTATATTCAT
5895126 ATCAT
1 ATCAT
5895131 ATTATATCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (14 bp):
ATCATTATATTCAT
Found at i:5897973 original size:2 final size:2
Alignment explanation
Indices: 5897966--5897990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5897956 TTGACTGTAT
5897966 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5897991 CAGGGTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5898670 original size:35 final size:34
Alignment explanation
Indices: 5898617--5898729 Score: 137
Period size: 32 Copynumber: 3.4 Consensus size: 34
5898607 TTAAGGAAAA
5898617 TAGTGACGTTT-TAT--AAAAAATAACGTTAATT
1 TAGTGACGTTTGTATAAAAAAAATAACGTTAATT
*
5898648 TAGTGACGTTTGTATAAAAAAAATCAC--TAATT
1 TAGTGACGTTTGTATAAAAAAAATAACGTTAATT
* *
5898680 TAGTGACGTTTGTATAAAAAAAAATATCGTTAATA
1 TAGTGACGTTTGTAT-AAAAAAAATAACGTTAATT
* *
5898715 TAATAACGTTTGTAT
1 TAGTGACGTTTGTAT
5898730 CATAAAACGC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.16
32 23 0.33
33 10 0.14
34 9 0.13
35 17 0.24
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (34 bp):
TAGTGACGTTTGTATAAAAAAAATAACGTTAATT
Found at i:5900348 original size:161 final size:160
Alignment explanation
Indices: 5900141--5900608 Score: 582
Period size: 161 Copynumber: 2.9 Consensus size: 160
5900131 TTAATCATGG
* ** * *
5900141 AAACCAAATTCAATCATTTGGACAAATTTAATATCATGTATTGAAGCCATCCAAATTGTTAAAAT
1 AAACCAAGTTCAATCATTTCAAAAAATTTAATATCATGTATTGAAGCCATCCAAACTGTTAAAAT
* * * * *
5900206 AAAACAATAACAACAACTTTGTATTTTTGCCTTTTAACGATAAAAATAGTCCTATACAGAGGTAA
66 AAAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGAT-AAAATAGTCCTAAACAAAGGTAA
*
5900271 ACAACAACTTTTTCACATATATCAACTGTGA
130 ACAATAACTTTTTCACATATATCAACTGTGA
* * * * *
5900302 AAACTAAGTTCAATCA-TTCAAAAAAGTTTAATATCATGTTTTGAAGCTATCCAAACTATAAAAA
1 AAACCAAGTTCAATCATTTCAAAAAA-TTTAATATCATGTATTGAAGCCATCCAAACTGTTAAAA
* * *
5900366 CAAAACAATAATAGTAAAATTGTATTTTTGCCTTTTAACAGCATGAAAA-A-TCCTAAACAAAGG
65 TAAAACAATAATAGCAAATTTGTATTTTTGCCTTTTAAC-G-AT-AAAATAGTCCTAAACAAAGG
5900429 TAAACAATAACTTTTTCACATATATCAACTGTGA
127 TAAACAATAACTTTTTCACATATATCAACTGTGA
* * * *
5900463 AAACCAAGTTTAATCATTTGAAAAAATTTAATATCATATATTGAAGCCATGCAAACTGTTAAAAT
1 AAACCAAGTTCAATCATTTCAAAAAATTTAATATCATGTATTGAAGCCATCCAAACTGTTAAAAT
* * * * * * * *
5900528 AGAATAAGAATAGCAAGTTTGTATTTTTGCCTTTAAATGATAAAATAGTCCTAAATAAACGTAAA
66 AAAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGATAAAATAGTCCTAAACAAAGGTAAA
*
5900593 CGATAACTTTTTCACA
131 CAATAACTTTTTCACA
5900609 CACATATCAA
Statistics
Matches: 260, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
158 4 0.02
159 3 0.01
160 37 0.14
161 200 0.77
162 10 0.04
163 6 0.02
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (160 bp):
AAACCAAGTTCAATCATTTCAAAAAATTTAATATCATGTATTGAAGCCATCCAAACTGTTAAAAT
AAAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGATAAAATAGTCCTAAACAAAGGTAAA
CAATAACTTTTTCACATATATCAACTGTGA
Found at i:5900866 original size:264 final size:264
Alignment explanation
Indices: 5900391--5900870 Score: 642
Period size: 264 Copynumber: 1.8 Consensus size: 264
5900381 AAAATTGTAT
* *
5900391 TTTTGCCTTTTAACAGCATGAAAAATCCTAAACAAAGGTAAACAATAACTTTTTCACATATATCA
1 TTTTACCTTTTAACAGCATGAAAAATCCTAAACAAAGGTAAACAATAACTTTTTCACACATATCA
* **
5900456 ACTGTGAAAACCAAGTTTAATCATTTGAAAAAATTTAATATCATATATTGAAGCCATGCAAACTG
66 ACTGTGAAAACCAAGTTCAATCATTCCAAAAAATTTAATATCATATATTGAAGCCATGCAAACTG
* * * ** * *
5900521 TTAAAATAGAATAAGAATAGCAAGTTTGTATTTTTGCCTTTAAATGATAAAATAGTCCTAAATAA
131 TTAAAATAAAATAAGAACAACAAAATTGTATTTTTACCTTTAAAGGATAAAATAGTCCTAAATAA
* *
5900586 ACGTAAACGATAACTTTTTCACACACATATCAATCATAGAATCATTCAGATAAGTTTATCAAATT
196 ACATAAACAATAACTTTTTCACACACATATCAATCATAGAATCATTCAGATAAGTTTATCAAATT
5900651 TGCA
261 TGCA
* * * * * *
5900655 TTTTACCTTTTAACGGCAT-AAAAAGTCCTAAACATATGTAAACATTAGCTTTTTCATACATATC
1 TTTTACCTTTTAACAGCATGAAAAA-TCCTAAACAAAGGTAAACAATAACTTTTTCACACATATC
* * * * * * *
5900719 AACTGTGGATACCAAGTTCAATTATTCCAACAAGTTTAATATCATGTATTGAAGCTATGCAAACT
65 AACTGTGAAAACCAAGTTCAATCATTCCAAAAAATTTAATATCATATATTGAAGCCATGCAAACT
* *
5900784 GTTAAAATAAAATAATAACAACAAAATTGTATTTTTACCTATTAACGG-TATAAA-AGTCCTAAA
130 GTTAAAATAAAATAAGAACAACAAAATTGTATTTTTACCT-TTAAAGGATA-AAATAGTCCTAAA
*
5900847 TAGACATAAACAATAACTTTTTCA
193 TAAACATAAACAATAACTTTTTCA
5900871 TACATATCAA
Statistics
Matches: 183, Mismatches: 30, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
263 5 0.03
264 170 0.93
265 8 0.04
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (264 bp):
TTTTACCTTTTAACAGCATGAAAAATCCTAAACAAAGGTAAACAATAACTTTTTCACACATATCA
ACTGTGAAAACCAAGTTCAATCATTCCAAAAAATTTAATATCATATATTGAAGCCATGCAAACTG
TTAAAATAAAATAAGAACAACAAAATTGTATTTTTACCTTTAAAGGATAAAATAGTCCTAAATAA
ACATAAACAATAACTTTTTCACACACATATCAATCATAGAATCATTCAGATAAGTTTATCAAATT
TGCA
Done.