Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 10 of 126
Found at i:3331486 original size:18 final size:20
Alignment explanation
Indices: 3331458--3331498 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3331448 GAAATATGGC
*
3331458 AAAGATATTTT-TTTAATAA
1 AAAGATATTTTAATTAATAA
3331477 AAAG-TATTTTAATTAATAA
1 AAAGATATTTTAATTAATAA
3331496 AAA
1 AAA
3331499 CCATAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAGATATTTTAATTAATAA
Found at i:3342253 original size:31 final size:31
Alignment explanation
Indices: 3342217--3342280 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3342207 CTTGCATTTT
3342217 GCCATATTCGCTGCATCAGAAGGCAGCTCTG
1 GCCATATTCGCTGCATCAGAAGGCAGCTCTG
3342248 GCCATATTCGCTGCATCAGAAGGCAGCTCTG
1 GCCATATTCGCTGCATCAGAAGGCAGCTCTG
3342279 GC
1 GC
3342281 TCAAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (31 bp):
GCCATATTCGCTGCATCAGAAGGCAGCTCTG
Found at i:3359825 original size:2 final size:2
Alignment explanation
Indices: 3359818--3359844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3359808 TTTGGCGGGG
3359818 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
3359845 TAAGAGTAAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3360038 original size:17 final size:18
Alignment explanation
Indices: 3360018--3360052 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3360008 AATAAATTTT
3360018 AAAAATATAT-AAATAAA
1 AAAAATATATGAAATAAA
*
3360035 AAAAATTTATGAAATAAA
1 AAAAATATATGAAATAAA
3360053 TAATTAATTT
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATATGAAATAAA
Found at i:3361125 original size:229 final size:229
Alignment explanation
Indices: 3360724--3361187 Score: 910
Period size: 229 Copynumber: 2.0 Consensus size: 229
3360714 ATGAACCATG
3360724 TTCGCTAACTGATCTCTACATACTTATTTTCCTCGCAAAAAATATATCTAATTTCCAGAATCCAA
1 TTCGCTAACTGATCTCTACATACTTATTTTCCTCGCAAAAAATATATCTAATTTCCAGAATCCAA
3360789 TTGCCCTTTATGAAATAATCTTTAATCAAGGTGTAATAAGAATGAGAATCAATCATCGTGGACTA
66 TTGCCCTTTATGAAATAATCTTTAATCAAGGTGTAATAAGAATGAGAATCAATCATCGTGGACTA
3360854 AAGAAAATAAACAACCACACCGCTGCATCTATCTCTACTATCAACGGTGAAAATCCTCTCTCCTT
131 AAGAAAATAAACAACCACACCGCTGCATCTATCTCTACTATCAACGGTGAAAATCCTCTCTCCTT
3360919 TGTTAATAATAACCATTCTCCTATGTCCCATAGC
196 TGTTAATAATAACCATTCTCCTATGTCCCATAGC
3360953 TTCGCTAACTGATCTCTACATACTTATTTTCCTCGCAAAAAATATATCTAATTTCCAGAATCCAA
1 TTCGCTAACTGATCTCTACATACTTATTTTCCTCGCAAAAAATATATCTAATTTCCAGAATCCAA
3361018 TTGCCCTTTATGAAATAATCTTTAATCAAGGTGTAATAAGAATGAGAATCAATCATCGTGGACTA
66 TTGCCCTTTATGAAATAATCTTTAATCAAGGTGTAATAAGAATGAGAATCAATCATCGTGGACTA
*
3361083 AAGAAAATAAACAACCACACCGCTGCATCTATCTCTACTATCAATGGTGAAAATCCTCTCTCCTT
131 AAGAAAATAAACAACCACACCGCTGCATCTATCTCTACTATCAACGGTGAAAATCCTCTCTCCTT
*
3361148 TGTTAATAATAACCATTCTCCTATGTCCCATTGC
196 TGTTAATAATAACCATTCTCCTATGTCCCATAGC
3361182 TTCGCT
1 TTCGCT
3361188 TCAAGGCTGT
Statistics
Matches: 233, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 233 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (229 bp):
TTCGCTAACTGATCTCTACATACTTATTTTCCTCGCAAAAAATATATCTAATTTCCAGAATCCAA
TTGCCCTTTATGAAATAATCTTTAATCAAGGTGTAATAAGAATGAGAATCAATCATCGTGGACTA
AAGAAAATAAACAACCACACCGCTGCATCTATCTCTACTATCAACGGTGAAAATCCTCTCTCCTT
TGTTAATAATAACCATTCTCCTATGTCCCATAGC
Found at i:3362527 original size:3 final size:3
Alignment explanation
Indices: 3362519--3362562 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
3362509 TACCAAACAA
* * *
3362519 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT ATT GTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3362563 ATGATTATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3368940 original size:13 final size:13
Alignment explanation
Indices: 3368907--3368945 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3368897 CTATTACAAG
3368907 TTGAATAATTAAC
1 TTGAATAATTAAC
3368920 TT-AATAATTGAA-
1 TTGAATAATT-AAC
3368932 TTGAATAATTAAC
1 TTGAATAATTAAC
3368945 T
1 T
3368946 ACTAAACAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (13 bp):
TTGAATAATTAAC
Found at i:3369308 original size:2 final size:2
Alignment explanation
Indices: 3369301--3369369 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
3369291 GAATATTATT
3369301 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
3369343 TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3369370 GAGTTTAATT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3383413 original size:19 final size:18
Alignment explanation
Indices: 3383389--3383427 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3383379 AAAATAGAAA
3383389 AATTTTCATTTAAACTTTT
1 AATTTTCATTTAAA-TTTT
**
3383408 AATTTTTTTTTAAATTTT
1 AATTTTCATTTAAATTTT
3383426 AA
1 AA
3383428 ATTAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTCATTTAAATTTT
Found at i:3384280 original size:22 final size:23
Alignment explanation
Indices: 3384250--3384306 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
3384240 ACAGATTGAC
*
3384250 ATAAAAATTACCAC-CAGAATAT
1 ATAAAAATTACCACACAGAAAAT
* *
3384272 ATAATAATTA-TACACAGAAAAT
1 ATAAAAATTACCACACAGAAAAT
*
3384294 ATAACAATTACCA
1 ATAAAAATTACCA
3384307 TTTTTAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 25 0.89
23 1 0.04
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.25
Consensus pattern (23 bp):
ATAAAAATTACCACACAGAAAAT
Found at i:3387941 original size:97 final size:96
Alignment explanation
Indices: 3387768--3387960 Score: 248
Period size: 97 Copynumber: 2.0 Consensus size: 96
3387758 AATATTTTCA
* * *
3387768 TTCATGCGAGCTTTGTCTCCAATAAAATTCATCCACCTAACTCTATTCTTTGCTCACTCTATATT
1 TTCATGCAAGCGTTGCCTCCAATAAAATTCATCCACCTAACTCTATTCTTTGCTCACTCTATATT
*
3387833 TGACATCCTTTGACCAATATGTGTCACTTTTT
66 TGACATCCTTTGACCAATATGAGTCA-TTTTT
* * *
3387865 TTCATGCAAGCGTTGCCTCCAATAAAATTCATCCACCTAA-TCCTATTCTTT-C-CACTTTGTGT
1 TTCATGCAAGCGTTGCCTCCAATAAAATTCATCCACCTAACT-CTATTCTTTGCTCACTCTATAT
* *
3387927 TTGGCATATTCTTTGACCAATATGAGTCATTTTT
65 TT-G-ACATCCTTTGACCAATATGAGTCATTTTT
3387961 ATGTGAGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
95 9 0.11
96 8 0.10
97 67 0.80
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.41
Consensus pattern (96 bp):
TTCATGCAAGCGTTGCCTCCAATAAAATTCATCCACCTAACTCTATTCTTTGCTCACTCTATATT
TGACATCCTTTGACCAATATGAGTCATTTTT
Found at i:3388870 original size:91 final size:91
Alignment explanation
Indices: 3388715--3389440 Score: 1184
Period size: 91 Copynumber: 8.0 Consensus size: 91
3388705 AGATCAAAAT
* *
3388715 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTAGGATAGCAAGTTTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
*
3388780 TTGTAGTAAGAGCAAGATGAAGCATT
66 TTGTAGTAAGAGCAAGATGAAGCATC
* * * *
3388806 AACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTAGATAGCAAGTCTTTAACTCTTTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
3388871 TTGTAATAAGAGCAAGATGAAGCACC
66 TTGTAGTAAGAGCAAGATGAAGCATC
* *
3388897 AACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
*
3388962 TTGTAGTAAGAGCAAGATGAAGCACC
66 TTGTAGTAAGAGCAAGATGAAGCATC
* * *
3388988 AACATCATTTCCTATCCTCTTGAAGATGTAGTAAAGCTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
3389053 TTATAGTAAGAGCAAGATGAAGCACC
66 TTGTAGTAAGAGCAAGATGAAGCATC
* * * *
3389079 AACATCATTTCCTATCCTCTTGAAGTTTTAGTAAAGCTGGATAACAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* *
3389144 TTTTAGTAAGAGTAAGATGAAGCATC
66 TTGTAGTAAGAGCAAGATGAAGCATC
3389170 AAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATA-CAAGTCTTTATCTCTCTGAA
1 -AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAA
* *
3389234 CTTGTAGTAATAGCAAGATGAAGCATC
65 GTTGTAGTAAGAGCAAGATGAAGCATC
* *
3389261 AAACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGCATAGCAAGTCTTTATCTCTCTGAA
1 -AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAA
3389326 GTTGTAGTAAGAGCAAGATGAAGCATC
65 GTTGTAGTAAGAGCAAGATGAAGCATC
3389353 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
3389418 TTGTAGTAAGAGCAAGATGAAGC
66 TTGTAGTAAGAGCAAGATGAAGC
3389441 CCTGACATCA
Statistics
Matches: 597, Mismatches: 36, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
91 512 0.86
92 85 0.14
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (91 bp):
AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
TTGTAGTAAGAGCAAGATGAAGCATC
Found at i:3389723 original size:11 final size:12
Alignment explanation
Indices: 3389703--3389795 Score: 90
Period size: 11 Copynumber: 7.9 Consensus size: 12
3389693 TGGTTTTTAA
3389703 TTAAAGTTTAAA-
1 TTAAA-TTTAAAT
*
3389715 TTAATTTTAAAT
1 TTAAATTTAAAT
3389727 TTAAATTT--AT
1 TTAAATTTAAAT
3389737 CTTAAATTTAAAT
1 -TTAAATTTAAAT
*
3389750 TTACTTATTTAAAT
1 TTA--AATTTAAAT
3389764 TT-AATTTAAAT
1 TTAAATTTAAAT
3389775 TTAAATTT-AA-
1 TTAAATTTAAAT
3389785 TTAAATTTAAA
1 TTAAATTTAAA
3389796 ATAATATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
10 10 0.14
11 28 0.41
12 19 0.28
13 2 0.03
14 10 0.14
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:3389729 original size:6 final size:6
Alignment explanation
Indices: 3389703--3389795 Score: 90
Period size: 6 Copynumber: 15.8 Consensus size: 6
3389693 TGGTTTTTAA
*
3389703 TTAAAGT TTAAA- TTAATT TTAAAT TTAAAT TT--AT CTTAAAT TTAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT
*
3389750 TTACTTAT TTAAAT TT-AAT TTAAAT TTAAAT TT-AA- TTAAAT TTAAA
1 TTA--AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
3389796 ATAATATTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.05
5 15 0.21
6 42 0.58
7 7 0.10
8 5 0.07
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:3389763 original size:31 final size:31
Alignment explanation
Indices: 3389725--3389783 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3389715 TTAATTTTAA
3389725 ATTTAAATTT-ATCTTAAATTTAAATTTACTT
1 ATTTAAATTTAAT-TTAAATTTAAATTTACTT
3389756 ATTTAAATTTAATTTAAATTTAAATTTA
1 ATTTAAATTTAATTTAAATTTAAATTTA
3389784 ATTAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTAAATTTAATTTAAATTTAAATTTACTT
Found at i:3389797 original size:17 final size:16
Alignment explanation
Indices: 3389698--3389795 Score: 112
Period size: 17 Copynumber: 6.0 Consensus size: 16
3389688 GCTTTTGGTT
3389698 TTTAATTAAAGTTTAAA
1 TTTAATTAAA-TTTAAA
3389715 -TTAATTTTAAATTTAAA
1 TTTAA--TTAAATTTAAA
*
3389732 TTTATCTTAAATTTAAA
1 TTTA-ATTAAATTTAAA
*
3389749 TTTACTT--ATTTAAA
1 TTTAATTAAATTTAAA
3389763 TTTAATTTAAATTTAAA
1 TTTAA-TTAAATTTAAA
3389780 TTTAATTAAATTTAAA
1 TTTAATTAAATTTAAA
3389796 ATAATATTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 15
0.81 0.02 0.17
Matches are distributed among these distances:
14 11 0.15
15 2 0.03
16 18 0.25
17 33 0.46
18 8 0.11
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (16 bp):
TTTAATTAAATTTAAA
Found at i:3389804 original size:17 final size:17
Alignment explanation
Indices: 3389702--3389811 Score: 97
Period size: 17 Copynumber: 6.6 Consensus size: 17
3389692 TTGGTTTTTA
3389702 ATTAAAGTTTAAATTAAT
1 ATTAAA-TTTAAATTAAT
* *
3389720 TTTAAATTTAAATTTAT
1 ATTAAATTTAAATTAAT
*
3389737 CTTAAATTTAAATT--T
1 ATTAAATTTAAATTAAT
3389752 ACTT--ATTTAAATTTAAT
1 A-TTAAATTTAAA-TTAAT
*
3389769 -TTAAATTTAAATTTA-
1 ATTAAATTTAAATTAAT
*
3389784 ATTAAATTTAAAATAAT
1 ATTAAATTTAAATTAAT
*
3389801 ATTAAACTTAA
1 ATTAAATTTAA
3389812 TATAAAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
14 7 0.09
15 5 0.07
16 18 0.24
17 41 0.54
18 5 0.07
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (17 bp):
ATTAAATTTAAATTAAT
Found at i:3390709 original size:41 final size:45
Alignment explanation
Indices: 3390636--3390718 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 45
3390626 GGGACAATAT
* *
3390636 TAATGGCATTAAATAATATTAGTAATTATTTTT-TTAATAATTAA
1 TAATGGCAATAAATAATATTAATAATTATTTTTATTAATAATTAA
* *
3390680 TAATGGTAATAAATAATATTAAT-ATT-TTTTAATTAATAA
1 TAATGGCAATAAATAATATTAATAATTATTTTTATTAATAA
3390719 ATAAGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 4 0.12
43 10 0.29
44 20 0.59
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (45 bp):
TAATGGCAATAAATAATATTAATAATTATTTTTATTAATAATTAA
Found at i:3391834 original size:30 final size:30
Alignment explanation
Indices: 3391794--3392058 Score: 185
Period size: 29 Copynumber: 8.9 Consensus size: 30
3391784 AGAGGTCCCT
* ** *
3391794 AAACTGTCCAAAAATTGTATTTTGACC-CC
1 AAACTTTCCAAAAATTACATTTTGACCTCA
* *
3391823 AAACTTATCC-AAAATTACATTTTTACCTCG
1 AAACTT-TCCAAAAATTACATTTTGACCTCA
3391853 AAACTTCTCC-AAAATTACATTTTTGACC-CA
1 AAACTT-TCCAAAAATTACA-TTTTGACCTCA
** *
3391883 AAACTTT-TGAAAATTACATTTTAACCTCA
1 AAACTTTCCAAAAATTACATTTTGACCTCA
* * *
3391912 AAAC-TTCTAAAAATTACATTTTAACCTCG
1 AAACTTTCCAAAAATTACATTTTGACCTCA
* *
3391941 AAAC-TTCCAAAAATTATATTTTGACCCCA
1 AAACTTTCCAAAAATTACATTTTGACCTCA
* * *
3391970 AATCTTTCC-AAAATTACATTTTTACC-CTT
1 AAACTTTCCAAAAATTACATTTTGACCTC-A
*
3391999 AAAC-TTCCAAAAATTAATTACATTTTTG-CCTCC
1 AAACTTTCC--AAA--AATTACA-TTTTGACCTCA
*
3392032 AAAC-TTCCAAAAATTTCATTTTTGACC
1 AAACTTTCCAAAAATTACA-TTTTGACC
3392059 CCGAACCTCC
Statistics
Matches: 195, Mismatches: 25, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
28 14 0.07
29 112 0.57
30 35 0.18
31 12 0.06
33 17 0.09
34 5 0.03
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTGACCTCA
Found at i:3391986 original size:87 final size:90
Alignment explanation
Indices: 3391833--3392060 Score: 270
Period size: 87 Copynumber: 2.5 Consensus size: 90
3391823 AAACTTATCC
* * **
3391833 AAAATTACATTTTTACCTCGAAACTTCTCCAAAATTACATTTTTGA-CCCAAAACTTTTGAAAAT
1 AAAATTACATTTTTACCTCGAAACTTC-CAAAAATTATATTTTTGACCCCAAAACTTTCCAAAAT
*
3391897 TACATTTTAA-CCTCAAAACTT-C-TA
65 TACATTTTAACCCT-AAAACTTCCAAA
* *
3391921 AAAATTACATTTTAACCTCGAAACTTCCAAAAATTATA-TTTTGACCCCAAATCTTTCCAAAATT
1 AAAATTACATTTTTACCTCGAAACTTCCAAAAATTATATTTTTGACCCCAAAACTTTCCAAAATT
* *
3391985 ACATTTTTACCCTTAAACTTCCAAA
66 ACATTTTAACCCTAAAACTTCCAAA
* *
3392010 AATTAATTACATTTTTGCCTCCAAACTTCCAAAAATT-TCATTTTTGACCCC
1 AA--AATTACATTTTTACCTCGAAACTTCCAAAAATTAT-ATTTTTGACCCC
3392061 GAACCTCCAA
Statistics
Matches: 120, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
86 6 0.05
87 39 0.32
88 30 0.25
89 3 0.03
90 1 0.01
91 31 0.26
92 10 0.08
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.36
Consensus pattern (90 bp):
AAAATTACATTTTTACCTCGAAACTTCCAAAAATTATATTTTTGACCCCAAAACTTTCCAAAATT
ACATTTTAACCCTAAAACTTCCAAA
Found at i:3392023 original size:33 final size:33
Alignment explanation
Indices: 3391981--3392046 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3391971 ATCTTTCCAA
*
3391981 AATTACATTTTTACCCT-TAAACTTCCAAAAATT
1 AATTACATTTTT-CCCTCCAAACTTCCAAAAATT
*
3392014 AATTACATTTTTGCCTCCAAACTTCCAAAAATT
1 AATTACATTTTTCCCTCCAAACTTCCAAAAATT
3392047 TCATTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (33 bp):
AATTACATTTTTCCCTCCAAACTTCCAAAAATT
Found at i:3409045 original size:18 final size:17
Alignment explanation
Indices: 3409012--3409055 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
3409002 TTTTAAAAAA
3409012 TATTT-AATATATAAAT
1 TATTTAAATATATAAAT
3409028 TATTTAAATATATCAAAT
1 TATTTAAATATAT-AAAT
* *
3409046 GAATTAAATA
1 TATTTAAATA
3409056 AAATAATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.21
17 7 0.29
18 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TATTTAAATATATAAAT
Found at i:3410307 original size:15 final size:15
Alignment explanation
Indices: 3410262--3410307 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
3410252 CGGGGAGAAT
*
3410262 ATATTATTTTAGTAT
1 ATATTATTTTAGTAA
**
3410277 ATATTATTTTTTTAA
1 ATATTATTTTAGTAA
3410292 ATATTATTTTAGTAA
1 ATATTATTTTAGTAA
3410307 A
1 A
3410308 AAACCCATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
ATATTATTTTAGTAA
Found at i:3424275 original size:30 final size:31
Alignment explanation
Indices: 3424208--3424275 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
3424198 AAGATTAAGT
* * *
3424208 ACCAAATTAAGAAAAAATGTTAAGTTTAAAT
1 ACCAAATTAAGAAAAAATGTCAAGTTCAAAA
*
3424239 GCCAAATTAA-AAAAAATGTCAAGTTCAAAA
1 ACCAAATTAAGAAAAAATGTCAAGTTCAAAA
*
3424269 ATCAAAT
1 ACCAAAT
3424276 GGACGAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (31 bp):
ACCAAATTAAGAAAAAATGTCAAGTTCAAAA
Found at i:3431885 original size:30 final size:30
Alignment explanation
Indices: 3431849--3431913 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
3431839 CAACTTAACA
* *
3431849 AACAAATGCCTCTAAAATAGTAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
3431879 AACAAATACCTCTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
3431909 AACAA
1 AACAA
3431914 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.58, C:0.17, G:0.03, T:0.22
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:3440503 original size:19 final size:19
Alignment explanation
Indices: 3440468--3440511 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3440458 CCGTCCAATT
*
3440468 TTATATTTTTAATATTATA
1 TTATATTTTTAACATTATA
3440487 TTAT-TTTTTATACATTATA
1 TTATATTTTTA-ACATTATA
*
3440506 TAATAT
1 TTATAT
3440512 AAATAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATTTTTAACATTATA
Found at i:3441402 original size:124 final size:123
Alignment explanation
Indices: 3441266--3441506 Score: 365
Period size: 124 Copynumber: 2.0 Consensus size: 123
3441256 AAATGAATTT
*
3441266 AATAAAATATTTTATAATTATTATTTATATTAAAATATATTGAAATAATGTTTAAATAAGCATTA
1 AATAAAATATTTTATAATTATTATTTATATTAAAATATATTGAAATAATATTTAAATAAGCATTA
3441331 ATATTTTATGTAATTGGGAAATAAAATTTACATTATTCGATTTTACTTAAATTCAATGC
66 ATATTTTATGTAATTGGGAAATAAAATTTACATTATTCGATTTTAC-TAAATTCAATGC
* * * * * *
3441390 AATAAACTATTTTGTACTTTTTATTTATATTAAAATGTGTTGAAATAATATTTAAATAAGCATTA
1 AATAAAATATTTTATAATTATTATTTATATTAAAATATATTGAAATAATATTTAAATAAGCATTA
* * * **
3441455 CTATTTTATGTAATTGGGAAATTAATTTTACATTATTTTATTTTACTAAATT
66 ATATTTTATGTAATTGGGAAATAAAATTTACATTATTCGATTTTACTAAATT
3441507 AAAATGATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
123 6 0.06
124 99 0.94
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (123 bp):
AATAAAATATTTTATAATTATTATTTATATTAAAATATATTGAAATAATATTTAAATAAGCATTA
ATATTTTATGTAATTGGGAAATAAAATTTACATTATTCGATTTTACTAAATTCAATGC
Found at i:3450041 original size:21 final size:21
Alignment explanation
Indices: 3450016--3450059 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3450006 TTTCATTCTC
3450016 ATTTCCACTTTCCTTCATCAT
1 ATTTCCACTTTCCTTCATCAT
3450037 ATTTCCACTTTCCTTCATCAT
1 ATTTCCACTTTCCTTCATCAT
3450058 AT
1 AT
3450060 CAAGGGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTCCACTTTCCTTCATCAT
Found at i:3455934 original size:15 final size:16
Alignment explanation
Indices: 3455914--3455943 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3455904 CTTCCCTATT
3455914 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
3455929 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
3455944 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:3455948 original size:22 final size:22
Alignment explanation
Indices: 3455909--3455969 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
3455899 TTCGACTTCC
* *
3455909 CTATTTTCTATTT-CTTTTAGTT
1 CTATTTTCT-TTTATTTTTAATT
3455931 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
3455953 C-AGTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
3455970 TCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.15, C:0.11, G:0.03, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:3457396 original size:21 final size:21
Alignment explanation
Indices: 3457366--3457405 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3457356 GCAATCTATA
3457366 GATTTCCAAAA-ACAAACTGTG
1 GATTTCCAAAAGA-AAACTGTG
*
3457387 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
3457406 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:3458484 original size:23 final size:22
Alignment explanation
Indices: 3458453--3458577 Score: 92
Period size: 23 Copynumber: 5.5 Consensus size: 22
3458443 CTAGGGAAAT
*
3458453 AGTAAGCACTCACAGTGCAATCC
1 AGTAAGCACACACAGTGCAAT-C
*
3458476 AGTAGGCACACACAGTGCAATC
1 AGTAAGCACACACAGTGCAATC
* * *
3458498 AGTAAGCGCACATAGCGCAAATC
1 AGTAAGCACACACAGTGC-AATC
* * * *
3458521 AATAGGCACACGA-AGGGCGAAAC
1 AGTAAGCACAC-ACAGTGC-AATC
*
3458544 AGTAAGCACACAAAGTGCTAATC
1 AGTAAGCACACACAGTGC-AATC
3458567 AG-AGAGCACAC
1 AGTA-AGCACAC
3458578 GAAGTGCTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
22 17 0.21
23 63 0.78
24 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.12
Consensus pattern (22 bp):
AGTAAGCACACACAGTGCAATC
Found at i:3458567 original size:46 final size:45
Alignment explanation
Indices: 3458448--3458581 Score: 112
Period size: 46 Copynumber: 2.9 Consensus size: 45
3458438 AAGTGCTAGG
* * * * *
3458448 GAAATAGTAAGCACTCACAGTGCAATCCAGTAGGCACAC-ACAGTGC
1 GAAACAGTAAGCACACAAAGTGCAAT-CAATAGGCACACGA-AGGGC
* * * *
3458494 -AATCAGTAAGCGCACATAGCGCAAATCAATAGGCACACGAAGGGC
1 GAAACAGTAAGCACACAAAGTGC-AATCAATAGGCACACGAAGGGC
*
3458539 GAAACAGTAAGCACACAAAGTGCTAATC-AGAGAGCACACGAAG
1 GAAACAGTAAGCACACAAAGTGC-AATCAATAG-GCACACGAAG
3458582 TGCTAATAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
45 34 0.49
46 36 0.51
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (45 bp):
GAAACAGTAAGCACACAAAGTGCAATCAATAGGCACACGAAGGGC
Found at i:3458582 original size:23 final size:23
Alignment explanation
Indices: 3458526--3458639 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 23
3458516 AAATCAATAG
* *
3458526 GCACACGAAGGGCGAAACAGTA-A
1 GCACACGAAGTGCTAAACAG-AGA
* *
3458549 GCACACAAAGTGCTAATCAGAGA
1 GCACACGAAGTGCTAAACAGAGA
3458572 GCACACGAAGTGCTAATAACAGAGA
1 GCACACGAAGTGCT-A-AACAGAGA
3458597 G--CACGAAACGTGCTAAACAGAGA
1 GCACACG-AA-GTGCTAAACAGAGA
*
3458620 GCACAC-ACAGTGCTGAACAG
1 GCACACGA-AGTGCTAAACAG
3458640 TAAGCGCGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.01
23 54 0.71
24 5 0.07
25 16 0.21
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (23 bp):
GCACACGAAGTGCTAAACAGAGA
Found at i:3464344 original size:4 final size:4
Alignment explanation
Indices: 3464300--3464355 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
3464290 CCCAATTTTT
*
3464300 TTTA TTT- TTTA TTTT TTTA TTT- TTCTA TCTTA TTATA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA TT-TA TTTA TTTA TTTA
3464349 TTTA TTT
1 TTTA TTT
3464356 TTGTCAAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 5 0.11
4 31 0.69
5 8 0.18
6 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3465819 original size:19 final size:19
Alignment explanation
Indices: 3465797--3465841 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3465787 TTATATTAGG
3465797 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
3465816 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
3465835 ATTTAAT
1 ATTTAAT
3465842 TTATGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:3465845 original size:24 final size:25
Alignment explanation
Indices: 3465816--3465864 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3465806 TTAAGATATT
*
3465816 ATTTATTATT-TAAATTTGTATTTA
1 ATTTATGATTATAAATTTGTATTTA
* *
3465840 ATTTATGATTATCATTTTGTATTTA
1 ATTTATGATTATAAATTTGTATTTA
3465865 TGTTTTAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
ATTTATGATTATAAATTTGTATTTA
Found at i:3466665 original size:15 final size:16
Alignment explanation
Indices: 3466645--3466674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3466635 CTTCCCTATT
3466645 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
3466660 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
3466675 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:3466679 original size:22 final size:22
Alignment explanation
Indices: 3466640--3466700 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
3466630 TTCGACTTCC
* *
3466640 CTATTTTCTATTT-CTTTTAGTT
1 CTATTTTCT-TTTATTTTTAATT
3466662 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
3466684 C-AGTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
3466701 CCTTATCACG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.15, C:0.11, G:0.03, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:3470115 original size:16 final size:16
Alignment explanation
Indices: 3470096--3470140 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 16
3470086 TATTAAATTA
3470096 ATATAATAACATATTG
1 ATATAATAACATATTG
*
3470112 ATATCATAA-ATA-T-
1 ATATAATAACATATTG
*
3470125 ATATAATAACAAATTG
1 ATATAATAACATATTG
3470141 GCATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
13 8 0.35
14 3 0.13
15 4 0.17
16 8 0.35
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (16 bp):
ATATAATAACATATTG
Found at i:3474024 original size:25 final size:27
Alignment explanation
Indices: 3473960--3474060 Score: 75
Period size: 31 Copynumber: 3.7 Consensus size: 27
3473950 AAAAAGATTG
* *
3473960 AGTATCAAATTAAGAAAAAATGTTAACTCCA
1 AGTACCAAATTAAGAAAAAA---TAA-TCTA
**
3473991 AGTGTCAAATTAAGAAAAAAT-ATC-A
1 AGTACCAAATTAAGAAAAAATAATCTA
*
3474016 AGTACCAAATT-AGACAAAATAATCTTA
1 AGTACCAAATTAAGAAAAAATAATC-TA
3474043 AGTACCAAAATTAA-AAAA
1 AGTACC-AAATTAAGAAAA
3474061 TATCAAATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
24 8 0.13
25 13 0.22
26 2 0.03
27 8 0.13
28 9 0.15
29 1 0.02
31 19 0.32
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (27 bp):
AGTACCAAATTAAGAAAAAATAATCTA
Found at i:3479809 original size:17 final size:18
Alignment explanation
Indices: 3479782--3479815 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3479772 CTGCTACTTC
3479782 AAACTTGGAAATATGATT
1 AAACTTGGAAATATGATT
3479800 AAAC-TGGAAATATGAT
1 AAACTTGGAAATATGAT
3479816 CCAACAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (18 bp):
AAACTTGGAAATATGATT
Found at i:3483393 original size:13 final size:14
Alignment explanation
Indices: 3483372--3483400 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3483362 AAAAATTAAA
3483372 ATTTAAAAAATATT
1 ATTTAAAAAATATT
3483386 ATTT-AAAAATATT
1 ATTTAAAAAATATT
3483399 AT
1 AT
3483401 AAATTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTAAAAAATATT
Found at i:3483664 original size:19 final size:18
Alignment explanation
Indices: 3483625--3483666 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3483615 CTTTACAAGT
*
3483625 ATTAAATTAAATAATATA
1 ATTAAATTAAATAATACA
3483643 ATTAAATCTAAATCAAT-CA
1 ATTAAAT-TAAAT-AATACA
3483662 ATTAA
1 ATTAA
3483667 TTCACACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 11 0.52
20 3 0.14
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAATTAAATAATACA
Found at i:3484744 original size:48 final size:48
Alignment explanation
Indices: 3484654--3484745 Score: 116
Period size: 50 Copynumber: 1.9 Consensus size: 48
3484644 TTTTATTATA
* * *
3484654 TAAAACAAATTTAAAAATATATAATATATCAAATACACTTAAAAAGAT
1 TAAAACAAATTAAAAAATAAATAATATATAAAATACACTTAAAAAGAT
*
3484702 TAAAACAAACATTAAAAAATAAATAA-ATTTAAAATACA-TTAAAA
1 TAAAAC-AA-ATTAAAAAATAAATAATATATAAAATACACTTAAAA
3484746 TTCTTTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 12 0.32
49 12 0.32
50 14 0.37
ACGTcount: A:0.64, C:0.08, G:0.01, T:0.27
Consensus pattern (48 bp):
TAAAACAAATTAAAAAATAAATAATATATAAAATACACTTAAAAAGAT
Found at i:3484935 original size:35 final size:34
Alignment explanation
Indices: 3484896--3485018 Score: 99
Period size: 37 Copynumber: 3.5 Consensus size: 34
3484886 AAATAACAAC
* *
3484896 AAAAATAGCAGTAAAAATACAACATCAAAAAAGTAAA
1 AAAAATAGCACTAAAAATACAA-ATCAAAACAGT--A
*
3484933 AAAAATAGCACCAAAACAT-C-AATCAAAACAGTA
1 AAAAATAGCACTAAAA-ATACAAATCAAAACAGTA
* *
3484966 AAAAA-AGCATTGAAACAATAAAAAAATCAAAACAGTA
1 AAAAATAGCACT-AAA-AAT--ACAAATCAAAACAGTA
*
3485003 AAAAATAGCACCAAAA
1 AAAAATAGCACTAAAA
3485019 CAATAATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
32 4 0.06
33 11 0.16
34 1 0.01
35 10 0.14
36 2 0.03
37 36 0.51
38 6 0.09
ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12
Consensus pattern (34 bp):
AAAAATAGCACTAAAAATACAAATCAAAACAGTA
Found at i:3484981 original size:20 final size:17
Alignment explanation
Indices: 3484956--3485012 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 17
3484946 AAACATCAAT
3484956 CAAAACAGTAAAAAAAG
1 CAAAACAGTAAAAAAAG
* *
3484973 CATTGAAACAATAAAAAAAT
1 CA---AAACAGTAAAAAAAG
3484993 CAAAACAGTAAAAAATAG
1 CAAAACAGTAAAAAA-AG
3485011 CA
1 CA
3485013 CCAAAACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 14 0.44
18 3 0.09
20 15 0.47
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (17 bp):
CAAAACAGTAAAAAAAG
Found at i:3484998 original size:17 final size:17
Alignment explanation
Indices: 3484953--3485007 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
3484943 CCAAAACATC
3484953 AATCAAAACAGTAAAAA
1 AATCAAAACAGTAAAAA
* *
3484970 AAGCATTGAAACAATAAAAA
1 AATCA---AAACAGTAAAAA
3484990 AATCAAAACAGTAAAAA
1 AATCAAAACAGTAAAAA
3485007 A
1 A
3485008 TAGCACCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 16 0.52
20 15 0.48
ACGTcount: A:0.69, C:0.11, G:0.07, T:0.13
Consensus pattern (17 bp):
AATCAAAACAGTAAAAA
Found at i:3485020 original size:38 final size:37
Alignment explanation
Indices: 3484953--3485024 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
3484943 CCAAAACATC
***
3484953 AATCAAAACAGTAAAAAAAGCATTGAAACAATAAAAA
1 AATCAAAACAGTAAAAAAAGCACCAAAACAATAAAAA
3484990 AATCAAAACAGTAAAAAATAGCACCAAAACAATAA
1 AATCAAAACAGTAAAAAA-AGCACCAAAACAATAA
3485025 TATAACTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 18 0.58
38 13 0.42
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (37 bp):
AATCAAAACAGTAAAAAAAGCACCAAAACAATAAAAA
Found at i:3490799 original size:3 final size:3
Alignment explanation
Indices: 3490793--3490830 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3490783 GTCGTCGTCG
3490793 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3490831 TTCTTCTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:3494656 original size:14 final size:14
Alignment explanation
Indices: 3494637--3494663 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3494627 TTTGAAAAAT
3494637 AATTTAGAATTGAA
1 AATTTAGAATTGAA
3494651 AATTTAGAATTGA
1 AATTTAGAATTGA
3494664 GTTTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
AATTTAGAATTGAA
Found at i:3515556 original size:9 final size:9
Alignment explanation
Indices: 3515542--3515571 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3515532 ACCTTCACTT
3515542 CTATTACTA
1 CTATTACTA
3515551 CTATTACTA
1 CTATTACTA
*
3515560 CTACTACTA
1 CTATTACTA
3515569 CTA
1 CTA
3515572 CTACCAGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (9 bp):
CTATTACTA
Found at i:3515561 original size:3 final size:3
Alignment explanation
Indices: 3515546--3515575 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3515536 TCACTTCTAT
*
3515546 TAC TAC TAT TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
3515576 CAGTGCTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (3 bp):
TAC
Found at i:3517551 original size:22 final size:22
Alignment explanation
Indices: 3517512--3517555 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3517502 GTTGTTGTAC
3517512 TCTTTATAAATTTAGAATTTAA
1 TCTTTATAAATTTAGAATTTAA
* * *
3517534 TCTTTTTAATTTTTGAATTTAA
1 TCTTTATAAATTTAGAATTTAA
3517556 AAATTTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
TCTTTATAAATTTAGAATTTAA
Found at i:3519085 original size:15 final size:15
Alignment explanation
Indices: 3519065--3519097 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3519055 ATGTTCATTA
3519065 TATCTCTTTCTATAT
1 TATCTCTTTCTATAT
3519080 TATCTCTTTCTATAT
1 TATCTCTTTCTATAT
3519095 TAT
1 TAT
3519098 TATGAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (15 bp):
TATCTCTTTCTATAT
Found at i:3523451 original size:3 final size:3
Alignment explanation
Indices: 3523445--3523472 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3523435 ATACATGATG
3523445 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3523473 GTTTAATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3524018 original size:15 final size:15
Alignment explanation
Indices: 3523998--3524040 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3523988 GTAGGACATT
3523998 ATATGATATGATCCG
1 ATATGATATGATCCG
3524013 ATATG--ATG-T--G
1 ATATGATATGATCCG
3524023 ATATGATATGATCCG
1 ATATGATATGATCCG
3524038 ATA
1 ATA
3524041 CGTTATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 6 0.26
12 4 0.17
13 4 0.17
15 9 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (15 bp):
ATATGATATGATCCG
Found at i:3524049 original size:25 final size:25
Alignment explanation
Indices: 3523998--3524053 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3523988 GTAGGACATT
* *
3523998 ATATGATATGATCCGATATGATGTG
1 ATATGATATGATCCGATACGATATG
*
3524023 ATATGATATGATCCGATACGTTATG
1 ATATGATATGATCCGATACGATATG
3524048 ATATGA
1 ATATGA
3524054 ATAGTTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (25 bp):
ATATGATATGATCCGATACGATATG
Found at i:3526940 original size:18 final size:18
Alignment explanation
Indices: 3526919--3526964 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3526909 CCTTTCCCCC
*
3526919 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
3526937 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
3526955 TTCTTT-ATTT
1 TTCTTTCATTT
3526965 TTATGCGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:3541290 original size:29 final size:28
Alignment explanation
Indices: 3541260--3541595 Score: 124
Period size: 29 Copynumber: 11.5 Consensus size: 28
3541250 ATCGGGATTA
*
3541260 AAAATGG-AATTTTAAAAGATTCAGGGGT
1 AAAATGGCAATTTTAGAAGATTC-GGGGT
* * *
3541288 AAAATGGCAATTTTCGATGAAATCGGGGTT
1 AAAATGGCAATTTTAGAAG-ATTCGGGG-T
* *
3541318 AAAAACGG-AATTTTAGAAGCTTCGGGGGT
1 -AAAATGGCAATTTTAGAAGATTC-GGGGT
* * ** *
3541347 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGCAATTTTAGAAG-ATTCGGGG-T
* *
3541377 AAAAATGG-AACTTTAGAAGCTTCGGGGGT
1 -AAAATGGCAATTTTAGAAGATTC-GGGGT
* * ** *
3541406 AAAATGGTAATTTTCGGTGAAATCGGGGTT
1 AAAATGGCAATTTTAGAAG-ATTCGGGG-T
** * * *
3541436 AAAAACGAAACTTTAGAAGCTTCGGGGT
1 AAAATGGCAATTTTAGAAGATTCGGGGT
* * ** *
3541464 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGCAATTTTAGAAG-ATTCGGGG-T
* * *
3541494 AAAAAT-GAAACTTTAGAAGCTTCGGGGGT
1 -AAAATGGCAATTTTAGAAGATTC-GGGGT
* * ** *
3541523 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGCAATTTTAGAAG-ATTCGGGG-T
*
3541553 AAAAATGG-AATTTTAAAAGATTCAGGGGT
1 -AAAATGGCAATTTTAGAAGATTC-GGGGT
*
3541582 AAAATGGTAATTTT
1 AAAATGGCAATTTT
3541596 TGAAAGTTTT
Statistics
Matches: 221, Mismatches: 64, Indels: 45
0.67 0.19 0.14
Matches are distributed among these distances:
28 45 0.20
29 78 0.35
30 73 0.33
31 25 0.11
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (28 bp):
AAAATGGCAATTTTAGAAGATTCGGGGT
Found at i:3541321 original size:59 final size:59
Alignment explanation
Indices: 3541223--3541597 Score: 556
Period size: 59 Copynumber: 6.4 Consensus size: 59
3541213 TATGGATATC
* * * * * *
3541223 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGATTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
* * * * * *
3541281 CAGGGGTAAAATGGCAATTTTCGATGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
3541340 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
* * *
3541399 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGAAACTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
*
3541458 C-GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAACTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
* * *
3541516 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
*
3541575 CAGGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
3541598 AAAGTTTTGG
Statistics
Matches: 289, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
58 70 0.24
59 219 0.76
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
Found at i:3541487 original size:176 final size:176
Alignment explanation
Indices: 3541223--3541595 Score: 568
Period size: 176 Copynumber: 2.1 Consensus size: 176
3541213 TATGGATATC
* * * * *
3541223 CGGGGGCAAAATGGTAATTTTGGTGTAATCGGGATTAAAAATGGAATTTTAAAAGATTCAGGGGT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGATTAAAAACGAAACTTTAAAAGATTCAGGGGT
* *
3541288 AAAATGGCAATTTTCGATGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGTAAAATG
66 AAAATGGCAATTTTCGATGAAATCGGGGTTAAAAACGAAACTTTAGAAGCTTCGGGGGTAAAATG
* *
3541353 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTT
131 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAAAAGATT
* * *
3541399 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGAAACTTTAGAAGCTTC-GGGG
1 CGGGGGTAAAATGGTAATTTT-GGTGAAATCGGGATTAAAAACGAAACTTTAAAAGATTCAGGGG
* * * *
3541463 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAACTTTAGAAGCTTCGGGGGTAAAAT
65 TAAAATGGCAATTTTCGATGAAATCGGGGTTAAAAACGAAACTTTAGAAGCTTCGGGGGTAAAAT
*
3541528 GGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
130 GGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAAAAGATT
*
3541575 CAGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
3541596 TGAAAGTTTT
Statistics
Matches: 178, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
176 147 0.83
177 31 0.17
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (176 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGATTAAAAACGAAACTTTAAAAGATTCAGGGGT
AAAATGGCAATTTTCGATGAAATCGGGGTTAAAAACGAAACTTTAGAAGCTTCGGGGGTAAAATG
GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAAAAGATT
Found at i:3541515 original size:117 final size:118
Alignment explanation
Indices: 3541225--3541597 Score: 579
Period size: 117 Copynumber: 3.2 Consensus size: 118
3541215 TGGATATCCG
* * * * * * *
3541225 GGGGCAAAATGGTAA-TTTTGGTGTAATCGGGATTAAAAATGGAATTTTAAAAGATTCAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTTCGGGGGTA
* * *
3541289 AAATGGCAATTTTCGATGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCG
66 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCA
3541342 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTTCGGGGGTA
* *
3541407 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGAAACTTTAGAAGCTTC-
66 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCA
*
3541459 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAACTTTAGAAGCTTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTTCGGGGGTA
* * * *
3541524 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
66 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCA
3541577 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
3541598 AAAGTTTTGG
Statistics
Matches: 236, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
117 124 0.53
118 112 0.47
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (118 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAACTTTAGAAGCTTCGGGGGTA
AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCA
Found at i:3541632 original size:30 final size:30
Alignment explanation
Indices: 3541577--3541658 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
3541567 AAAAGATTCA
* *
3541577 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTATT
3541606 GGGGTCAAAATGTAATTTTGGAAAAGTATT
1 GGGGTCAAAATGTAATTTTGGAAAAGTATT
* *
3541636 AGGGTCAAAATATAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
3541659 CAATTTAGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 14 0.30
30 28 0.61
31 4 0.09
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTATT
Found at i:3542527 original size:18 final size:15
Alignment explanation
Indices: 3542467--3542522 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
3542457 GCAGGTTTAA
*
3542467 TGGTGGTGGCAGGGC
1 TGGTGGTGGCAGAGC
3542482 ATGGTGGAT-G--GAGC
1 -TGGTGG-TGGCAGAGC
3542496 TGGTGGTGGCAGAGC
1 TGGTGGTGGCAGAGC
3542511 TGGTGGTGGCAG
1 TGGTGGTGGCAG
3542523 CAGAGGCACG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 7 0.20
14 3 0.09
15 16 0.46
16 7 0.20
17 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.55, T:0.21
Consensus pattern (15 bp):
TGGTGGTGGCAGAGC
Found at i:3542681 original size:6 final size:6
Alignment explanation
Indices: 3542672--3542762 Score: 54
Period size: 6 Copynumber: 15.8 Consensus size: 6
3542662 CTTTTCTTTT
*
3542672 TTTAAA TTTATAA --TAATA TT-AAA TTTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
* * *
3542719 TTTAAA -TTGAA TTTAAA -GTAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
3542763 TTTTCAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
4 1 0.02
5 23 0.35
6 36 0.55
7 6 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:3542716 original size:17 final size:16
Alignment explanation
Indices: 3542673--3542765 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 16
3542663 TTTTCTTTTT
3542673 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
3542690 TTAAATTTTAAATTAAA
1 TTAAA-TTTAAATTAAA
3542707 TTCAAATTTAAATTTAAA
1 TT-AAATTTAAA-TTAAA
* *
3542725 TTGAATTTAAAGTAAA
1 TTAAATTTAAATTAAA
*
3542741 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
3542758 TTTAATTT
1 TTAAATTT
3542766 TCAAATGGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 9 0.14
17 36 0.56
18 18 0.28
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:3542731 original size:11 final size:11
Alignment explanation
Indices: 3542689--3542765 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
3542679 TTATAATAAT
3542689 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
3542701 ATTAAATTCAA
1 ATTAAATTTAA
3542712 ATTTAAATTTAA
1 A-TTAAATTTAA
*
3542724 ATTGAATTTAA
1 ATTAAATTTAA
*
3542735 AGTAAATTTAA
1 ATTAAATTTAA
*
3542746 GATTAAA-ATAA
1 -ATTAAATTTAA
*
3542757 ATTTAATTT
1 ATTAAATTT
3542766 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:3557501 original size:20 final size:20
Alignment explanation
Indices: 3557476--3557518 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3557466 TGTTAGATAT
*
3557476 TTGATAAATCT-ATATAAATA
1 TTGATAAAT-TGATAGAAATA
3557496 TTGATAAATTGATAGAAATA
1 TTGATAAATTGATAGAAATA
3557516 TTG
1 TTG
3557519 GTAAGTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
TTGATAAATTGATAGAAATA
Found at i:3557880 original size:16 final size:17
Alignment explanation
Indices: 3557851--3557883 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3557841 TGATTATGAT
*
3557851 TGATATAATTTATTATA
1 TGATATAATATATTATA
3557868 TGATA-AATATATTATA
1 TGATATAATATATTATA
3557884 AAATTTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TGATATAATATATTATA
Found at i:3572073 original size:29 final size:30
Alignment explanation
Indices: 3572026--3572098 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
3572016 ATCAAATCAA
** *
3572026 AAATTTCATACATAAAATTACACA-AAATC
1 AAATTTCATGTATAAAATTACACATAAACC
* *
3572055 AAATTTCATGTATACAATTGCACATTAAACC
1 AAATTTCATGTATAAAATTACACA-TAAACC
*
3572086 ATATTTCATGTAT
1 AAATTTCATGTAT
3572099 CTATGATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 20 0.56
31 16 0.44
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.34
Consensus pattern (30 bp):
AAATTTCATGTATAAAATTACACATAAACC
Found at i:3572970 original size:4 final size:4
Alignment explanation
Indices: 3572963--3572994 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
3572953 GGACTGTTTG
3572963 TTAA TTAA TTAA TTAA TTAA TT-A -TAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
3572995 CATTCATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.04
3 2 0.08
4 23 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:3586000 original size:17 final size:16
Alignment explanation
Indices: 3585978--3586019 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3585968 TAGTAAAAAT
3585978 ATAATTTTATCATTTTA
1 ATAATTTTAT-ATTTTA
*
3585995 ATAA-TTTATATTTTT
1 ATAATTTTATATTTTA
3586010 ATAAATTTTA
1 AT-AATTTTA
3586020 AAAGATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAATTTTATATTTTA
Found at i:3586016 original size:16 final size:17
Alignment explanation
Indices: 3585977--3586017 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3585967 ATAGTAAAAA
*
3585977 TATAATTTTATCATTTT
1 TATAAATTTATCATTTT
*
3585994 AAT-AATTTAT-ATTTT
1 TATAAATTTATCATTTT
3586009 TATAAATTT
1 TATAAATTT
3586018 TAAAAGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 11 0.55
17 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATAAATTTATCATTTT
Found at i:3600246 original size:8 final size:8
Alignment explanation
Indices: 3600218--3600251 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
3600208 AAGCTTGTCT
3600218 ATTTTAAA
1 ATTTTAAA
3600226 CATTTTAAAA
1 -ATTTT-AAA
3600236 ATTTTAAA
1 ATTTTAAA
3600244 ATTTTAAA
1 ATTTTAAA
3600252 TTAGTAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.46
9 10 0.42
10 3 0.12
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTTTAAA
Found at i:3631431 original size:19 final size:19
Alignment explanation
Indices: 3631389--3631445 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
3631379 AATTACAAAA
*
3631389 AAAAATTCAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
3631408 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
3631427 AAAAATTTCAAAT-TTTAT
1 AAAAATTTAAAATATTTAT
3631445 A
1 A
3631446 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:3631502 original size:21 final size:18
Alignment explanation
Indices: 3631449--3631520 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
3631439 TTTTATATTT
*
3631449 TTAAAAAAGTTATAAATA
1 TTAAAAAAGTTAAAAATA
*
3631467 TTAAAAAAATCTAAAGAATA
1 TTAAAAAAGT-TAAA-AATA
*
3631487 TATAAAGAAAGTT-AAAATT
1 T-TAAA-AAAGTTAAAAATA
*
3631506 TTAAAAAAATTAAAA
1 TTAAAAAAGTTAAAA
3631521 TAATAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.11
18 16 0.36
19 7 0.16
20 7 0.16
21 5 0.11
22 4 0.09
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (18 bp):
TTAAAAAAGTTAAAAATA
Found at i:3631687 original size:22 final size:22
Alignment explanation
Indices: 3631644--3631688 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3631634 TGTAATAAGA
* ***
3631644 TTTTAATTTAACTTATTTAATT
1 TTTTAATTTAACTAAAACAATT
3631666 TTTTAATTTAACTAAAACAATT
1 TTTTAATTTAACTAAAACAATT
3631688 T
1 T
3631689 CACTTAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACTAAAACAATT
Found at i:3632657 original size:20 final size:20
Alignment explanation
Indices: 3632634--3632681 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3632624 TTTTCTTTTA
* *
3632634 ATTTTAATATTTTTTATAAT
1 ATTTTAATATTTCTAATAAT
3632654 ATTTTACA-ATTTCTAATAAT
1 ATTTTA-ATATTTCTAATAAT
*
3632674 TTTTTAAT
1 ATTTTAAT
3632682 CCTATTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTAATATTTCTAATAAT
Found at i:3633499 original size:328 final size:328
Alignment explanation
Indices: 3632902--3633890 Score: 1969
Period size: 328 Copynumber: 3.0 Consensus size: 328
3632892 CTCAATTTAG
3632902 TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
1 TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
*
3632967 TAATTGGTATTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
66 TAATTGGTACTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
3633032 TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
131 TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
3633097 GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
196 GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
3633162 TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
261 TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
3633227 GAA
326 GAA
3633230 TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
1 TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
3633295 TAATTGGTACTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
66 TAATTGGTACTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
3633360 TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
131 TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
3633425 GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
196 GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
3633490 TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
261 TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
3633555 GAA
326 GAA
3633558 TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
1 TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
3633623 TAATTGGTACTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
66 TAATTGGTACTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
3633688 TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
131 TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
3633753 GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
196 GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
3633818 TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
261 TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
3633883 GAA
326 GAA
3633886 TAATA
1 TAATA
3633891 GCAACTTTAA
Statistics
Matches: 660, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
328 660 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (328 bp):
TAATATAGCGTTAATTTTTTAAGAGTTAACATGTAATTTGTCCATTAAATTTGTTAAAAAATATC
TAATTGGTACTTGAACTTATCCAAAAAATTACATTTTCTAAGTTAATTTATAATATGTTTTACAT
TTTTTGAGTTTTCTTTTTTTTTTTAATGATATAATAATGTTGATCAAATAGGGTAAATTACTCTA
GTAGTCATCCAACTATTACTAATTTTCTTTTCTGGCTACTCAATTATGAAAATTTACAAAATGAT
TTGTCAACTATTCAATTTTTTCTTTTTTGATCTCGATTGATTAACGATAGCAACATTTAAGATTG
GAA
Found at i:3634562 original size:26 final size:27
Alignment explanation
Indices: 3634532--3634587 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
3634522 TTTGAACCCT
*
3634532 GAACTCCGAATCTCAAACTCGAA-CTC
1 GAACTCCGAATCCCAAACTCGAATCTC
*
3634558 GAACTCTGAATCCCAAACTCGAATCTC
1 GAACTCCGAATCCCAAACTCGAATCTC
3634585 GAA
1 GAA
3634588 TAAAACCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (27 bp):
GAACTCCGAATCCCAAACTCGAATCTC
Found at i:3635299 original size:17 final size:18
Alignment explanation
Indices: 3635272--3635307 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3635262 TTTTTAAAAA
3635272 AAAAGTTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
*
3635290 AAAA-TTATAAAATTTTT
1 AAAAGTTATAAAAATTTT
3635307 A
1 A
3635308 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAAGTTATAAAAATTTT
Found at i:3636882 original size:29 final size:30
Alignment explanation
Indices: 3636822--3636893 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
3636812 AAATTTTAAA
* * *
3636822 TTAATAATGAT-AAAATTGTATTTAGGTGT
1 TTAAAAATGATAAAAATTGTATTTAAGTCT
*
3636851 TTAAAAATGATAAAAATTG-ATTTAATTCT
1 TTAAAAATGATAAAAATTGTATTTAAGTCT
*
3636880 TTAAAAATTATAAA
1 TTAAAAATGATAAA
3636894 GATATAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.42
Consensus pattern (30 bp):
TTAAAAATGATAAAAATTGTATTTAAGTCT
Found at i:3638042 original size:21 final size:21
Alignment explanation
Indices: 3638016--3638063 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3638006 TATCAACCAT
3638016 TCAAAACAAAATTAAATAATA
1 TCAAAACAAAATTAAATAATA
* *
3638037 TCAAAACATAATTATATAATA
1 TCAAAACAAAATTAAATAATA
*
3638058 TTAAAA
1 TCAAAA
3638064 AGTTAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (21 bp):
TCAAAACAAAATTAAATAATA
Found at i:3643482 original size:63 final size:64
Alignment explanation
Indices: 3643404--3643530 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 64
3643394 GGTTCATTAC
3643404 TTCAATTCTCTGTTCGATCCTTCATTAGACTTTAGTTCA-TATATGTGATTAGAAAGAACTTAG
1 TTCAATTCTCTGTTCGATCCTTCATTAGACTTTAGTTCATTATATGTGATTAGAAAGAACTTAG
*
3643467 TTCAATTCTCTGTTCGATCTTTCATTAGACTTTAGTTCATTATATGTGATTAGAAAGAACTTAG
1 TTCAATTCTCTGTTCGATCCTTCATTAGACTTTAGTTCATTATATGTGATTAGAAAGAACTTAG
3643531 CAGAGTTTCC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 38 0.61
64 24 0.39
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (64 bp):
TTCAATTCTCTGTTCGATCCTTCATTAGACTTTAGTTCATTATATGTGATTAGAAAGAACTTAG
Found at i:3649334 original size:1 final size:1
Alignment explanation
Indices: 3649328--3649352 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3649318 AGCAAGGAGA
3649328 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
3649353 ATGAATTGGA
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:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3652244 original size:28 final size:27
Alignment explanation
Indices: 3652213--3652304 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
3652203 AAAACGGGAC
3652213 TTTTGGATATCTGGGGGCAAAATGGTAA
1 TTTTGGATATC-GGGGGCAAAATGGTAA
**
3652241 TTTTGGACTCGCGGGGGCAAAATGGTAA
1 TTTTGGA-TATCGGGGGCAAAATGGTAA
* * *
3652269 CTTTCGGTGATATCGGGGTCAAAA-GGGAA
1 -TTT-TG-GATATCGGGGGCAAAATGGTAA
3652298 TTTTGGA
1 TTTTGGA
3652305 AAATTCGAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 26 0.50
29 9 0.17
30 12 0.23
31 2 0.04
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (27 bp):
TTTTGGATATCGGGGGCAAAATGGTAA
Found at i:3652359 original size:30 final size:28
Alignment explanation
Indices: 3652325--3652477 Score: 75
Period size: 30 Copynumber: 5.2 Consensus size: 28
3652315 GTAAAATAAT
3652325 AATTTTTGGTGAAATAGAGGTCAAAAATGG
1 AATTTTTGGTGAAATAGAGGT--AAAATGG
*
3652355 AA-TTTT-G-GAAAGTTTAGGGGTAAAATGG
1 AATTTTTGGTGAAA---TAGAGGTAAAATGG
* * *
3652383 TAATATTTGGTGAAATCGGGGTTAAAAATGG
1 -AATTTTTGGTGAAATAGAGG-T-AAAATGG
* *
3652414 AA-TTTT-G-GAAAGTTCGGAGGCAAAATGG
1 AATTTTTGGTGAAA--T-AGAGGTAAAATGG
* *
3652442 TAATTTTTGGTAAAATTGAGGTTAAAATGG
1 -AATTTTTGGTGAAATAGAGG-TAAAATGG
3652472 AATTTT
1 AATTTT
3652478 GGAAAGTTTG
Statistics
Matches: 96, Mismatches: 10, Indels: 35
0.68 0.07 0.25
Matches are distributed among these distances:
27 8 0.08
28 16 0.17
29 27 0.28
30 29 0.30
31 9 0.09
32 7 0.07
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (28 bp):
AATTTTTGGTGAAATAGAGGTAAAATGG
Found at i:3652376 original size:59 final size:58
Alignment explanation
Indices: 3652254--3652627 Score: 387
Period size: 59 Copynumber: 6.4 Consensus size: 58
3652244 TGGACTCGCG
* * * * * * * * *
3652254 GGGGCAAAATGGTAACTTTCGGTGATATCGGGGTCAAAAGGGAATTTTGGAAA-ATTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTAAAAATGGAATTTTGGAAAGTTTA
** *
3652311 GAGGGTAAAATAATAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGT-AAAAATGGAATTTTGGAAAGTTTA
* * *
3652371 GGGGTAAAATGGTAATATTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TAAAAATGGAATTTTGGAAAGTTTA
* * * * *
3652429 GGAGGCAAAATGGTAATTTTTGGTAAAATTGAGGTTAAAATGGAATTTTGGAAAGTTTG
1 GG-GGTAAAATGGTAATTTTTGGTGAAATCGAGGTAAAAATGGAATTTTGGAAAGTTTA
* * * *
3652488 GGGGTAAAATGGTAATTTTTTGGTAAAATCGGGGTTAAAATGCAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGAGGTAAAAATGGAATTTTGGAAAGTTTA
* * * * *
3652547 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATATG-ATTTCGAAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TAAAAAT-GGAATTTTGGAAAGTTTA
3652605 GAGGGTAAAATGGTAATTTTTGG
1 G-GGGTAAAATGGTAATTTTTGG
3652628 ACAATTCAGG
Statistics
Matches: 267, Mismatches: 40, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
57 1 0.00
58 79 0.30
59 183 0.69
60 4 0.01
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:3652469 original size:117 final size:116
Alignment explanation
Indices: 3652254--3652585 Score: 434
Period size: 117 Copynumber: 2.8 Consensus size: 116
3652244 TGGACTCGCG
* * * * * *
3652254 GGGGCAAAATGGTAACTTTCGGTGATATCGGGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAA
1 GGGGTAAAATGGTAACTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAA
** *
3652319 AATAATAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTA
66 AATGGTAATTTTTGGTGAAATAGAGGT-TAAAATGGAATTTTGGAAAGTTTA
3652371 GGGGTAAAATGGTAA-TATTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCG-GAGG
1 GGGGTAAAATGGTAACT-TTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCGAG-GG
* * * *
3652434 CAAAATGGTAATTTTTGGTAAAATTGAGGTTAAAATGGAATTTTGGAAAGTTTG
63 TAAAATGGTAATTTTTGGTGAAATAGAGGTTAAAATGGAATTTTGGAAAGTTTA
* * * **
3652488 GGGGTAAAATGGTAATTTTTTGGTAAAATCGGGGTTAAAATGCAATTTTGGAAAGTTTAAGGGTA
1 GGGGTAAAATGGTAA-CTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTA
*
3652553 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAA
65 AAATGGTAATTTTTGGTGAAATAGAGGTTAAAA
3652586 ATATGATTTC
Statistics
Matches: 189, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
116 1 0.01
117 121 0.64
118 66 0.35
119 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (116 bp):
GGGGTAAAATGGTAACTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAA
AATGGTAATTTTTGGTGAAATAGAGGTTAAAATGGAATTTTGGAAAGTTTA
Found at i:3652537 original size:176 final size:176
Alignment explanation
Indices: 3652255--3652627 Score: 473
Period size: 176 Copynumber: 2.1 Consensus size: 176
3652245 GGACTCGCGG
* * * * *
3652255 GGGCAAAATGGTAACTTTCGGTGATATCGGGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAAA
1 GGGCAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAAA
* * *
3652320 ATAATAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTA
66 ATAATAATTTTTGGTAAAATAGAGGTCAAAAATGCAATTTTGGAAAGTTTAAGGGTAAAATGGTA
* * *
3652385 ATATTTGGTGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTCG-
131 ATATTTGGTGAAATCGAGGTTAAAAATAGG-ATTTCGAAAAGTTCGA
* * * * * *
3652430 GAGGCAAAATGGTAATTTTTGGTAAAATTGAGGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAA
1 G-GGCAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAA
** * * *
3652495 AATGGTAATTTTTTGGTAAAATCGGGGT-TAAAATGCAATTTTGGAAAGTTTAAGGGTAAAATGG
65 AATAATAA-TTTTTGGTAAAATAGAGGTCAAAAATGCAATTTTGGAAAGTTTAAGGGTAAAATGG
* *
3652559 TAATTTTTGGTGAAATCGAGGTTAAAAATATGATTTCGAAAAGTTCGA
129 TAATATTTGGTGAAATCGAGGTTAAAAATAGGATTTCGAAAAGTTCGA
*
3652607 GGGTAAAATGGTAATTTTTGG
1 GGGCAAAATGGTAATTTTTGG
3652628 ACAATTCAGG
Statistics
Matches: 169, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
175 1 0.01
176 150 0.89
177 18 0.11
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (176 bp):
GGGCAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAAA
ATAATAATTTTTGGTAAAATAGAGGTCAAAAATGCAATTTTGGAAAGTTTAAGGGTAAAATGGTA
ATATTTGGTGAAATCGAGGTTAAAAATAGGATTTCGAAAAGTTCGA
Found at i:3652625 original size:117 final size:116
Alignment explanation
Indices: 3652259--3652627 Score: 429
Period size: 117 Copynumber: 3.1 Consensus size: 116
3652249 TCGCGGGGGC
* * * * * * ** **
3652259 AAAATGGTAACTTTCGGTGATATCGGGGTCAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAA
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGG
* *
3652324 TAATTTTTGGTGAAATAGAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGT
66 TAATTTTTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTGA-GGGT
* ** *
3652376 AAAATGGTAATATTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGAGGCAAAAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTTAAG-GGTAAAAT
* * *
3652440 GGTAATTTTTGGTAAAATTGAGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGT
64 GGTAATTTTTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAG-TTGAGGGT
* *
3652493 AAAATGGTAATTTTTTGGTAAAATCGGGGTTAAAATGCAATTTTGGAAAGTTTAAGGGTAAAATG
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
* * * *
3652558 GTAATTTTTGGTGAAATCGAGGTTAAAAATATG-ATTTCGAAAAGTTCGAGGGT
65 GTAATTTTTGGTGAAATAGAGGTTAAAAAT-GGAATTTTGGAAAGTT-GAGGGT
3652611 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
3652628 ACAATTCAGG
Statistics
Matches: 214, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
117 117 0.55
118 96 0.45
119 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (116 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGG
TAATTTTTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTGAGGGT
Found at i:3654428 original size:6 final size:6
Alignment explanation
Indices: 3654417--3654475 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
3654407 TGAAATTTGA
* * *
3654417 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AGGTAGAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
3654465 ATAAAT TTAAA
1 TTAAAT TTAAA
3654476 ATCAATTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
5 8 0.20
6 29 0.71
8 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:3669620 original size:24 final size:24
Alignment explanation
Indices: 3669577--3669639 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
3669567 TAGAGTAATA
* * *
3669577 AGAATTTGACTCAAATAAATAAAC
1 AGAATTTAACTGAAACAAATAAAC
* *
3669601 AGAATTTAATTGAAACAAATAAAT
1 AGAATTTAACTGAAACAAATAAAC
*
3669625 AGAGTTTAACTGAAA
1 AGAATTTAACTGAAA
3669640 GATTATTTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (24 bp):
AGAATTTAACTGAAACAAATAAAC
Found at i:3671596 original size:24 final size:24
Alignment explanation
Indices: 3671568--3671626 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3671558 TAGAGTAATA
*
3671568 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* * *
3671592 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAT
*
3671616 AGAATTTAACT
1 AGAGTTTAACT
3671627 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:3671629 original size:24 final size:24
Alignment explanation
Indices: 3671580--3671630 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3671570 AGTTTGACTC
* * *
3671580 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAACTG
3671604 AAACAAATAAACAGAATTTAACTG
1 AAACAAATAAACAGAATTTAACTG
3671628 AAA
1 AAA
3671631 GATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:3676792 original size:28 final size:27
Alignment explanation
Indices: 3676761--3676820 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 27
3676751 AAAGTATTAA
3676761 TTTTATTTTATTTTTATAT-TTAATAATT
1 TTTTATTTT-TTTTTATATATTAA-AATT
*
3676789 TTTTA-TTTTTTTTATTTATTAAAATT
1 TTTTATTTTTTTTTATATATTAAAATT
3676815 TTTTAT
1 TTTTAT
3676821 ATAGTCATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 17 0.59
27 7 0.24
28 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTATTTTTTTTTATATATTAAAATT
Found at i:3676804 original size:24 final size:25
Alignment explanation
Indices: 3676766--3676820 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
3676756 ATTAATTTTA
*
3676766 TTTTA-TTTTTATATTTA-ATAATT
1 TTTTATTTTTTATATTTATAAAATT
*
3676789 TTTTATTTTTTTTATTTATTAAAATT
1 TTTTATTTTTTATATTTA-TAAAATT
3676815 TTTTAT
1 TTTTAT
3676821 ATAGTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 11 0.41
26 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTATTTTTTATATTTATAAAATT
Found at i:3685211 original size:64 final size:64
Alignment explanation
Indices: 3685138--3685265 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
3685128 ACAAGTGTTG
* *
3685138 ATGCAATAATAAGTATATTGCGCTTTT-AGAAAGAGAACTCAAGTTCGAATCGTAGAGATGACAT
1 ATGCAATAATAAGTATATTGCGCTTTTCA-AAAAAAAACTCAAGTTCGAATCGTAGAGATGACAT
3685202 ATGCAATAATAAGTATATTGCGCTTTTCAAAAAAAAACTCAAGTTCGAATCGTAGAGATGACAT
1 ATGCAATAATAAGTATATTGCGCTTTTCAAAAAAAAACTCAAGTTCGAATCGTAGAGATGACAT
3685266 TATAAAGAGG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 60 0.98
65 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (64 bp):
ATGCAATAATAAGTATATTGCGCTTTTCAAAAAAAAACTCAAGTTCGAATCGTAGAGATGACAT
Found at i:3686631 original size:6 final size:6
Alignment explanation
Indices: 3686620--3686644 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3686610 GAAAAGTAAT
3686620 GAAATG GAAATG GAAATG GAAATG G
1 GAAATG GAAATG GAAATG GAAATG G
3686645 CAGAAAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:3688161 original size:7 final size:7
Alignment explanation
Indices: 3688144--3688180 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
3688134 TATTCAACTG
3688144 AAATT-A
1 AAATTAA
*
3688150 AAATTGA
1 AAATTAA
3688157 AAATTAA
1 AAATTAA
3688164 AAATTAA
1 AAATTAA
3688171 AAA-TAA
1 AAATTAA
3688177 AAAT
1 AAAT
3688181 GAATTTGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (7 bp):
AAATTAA
Found at i:3690913 original size:16 final size:17
Alignment explanation
Indices: 3690878--3690916 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
3690868 GCGTTTAGAG
*
3690878 ATAAAACATCAAACTAAA
1 ATAAAACA-CAAAATAAA
3690896 ATAAAACA-AAAATAAA
1 ATAAAACACAAAATAAA
3690912 ATAAA
1 ATAAA
3690917 TAAGTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (17 bp):
ATAAAACACAAAATAAA
Found at i:3691676 original size:6 final size:6
Alignment explanation
Indices: 3691665--3691689 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3691655 GAAAAGTAAT
3691665 GAAATG GAAATG GAAATG GAAATG G
1 GAAATG GAAATG GAAATG GAAATG G
3691690 CAGAAAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:3692358 original size:60 final size:58
Alignment explanation
Indices: 3692249--3692391 Score: 135
Period size: 60 Copynumber: 2.4 Consensus size: 58
3692239 CAAGAACATA
* * * * * *
3692249 TCAAGGACTAACTAGGACAAAAAGAAGTTTAAGCCCCAATTTAAGAACAATTTCTAAGT
1 TCAAGGCCTAACT-TGAAAAAAAAAAGTTTAAGCCCCAATTTAAGAACAATTACCAAGT
* * * **
3692308 TTAGGGCCTAACTTGGATAAAAAAAAAGTTTATG-CCCAATTATGGGAACAATTACCAAGT
1 TCAAGGCCTAACTT-GA-AAAAAAAAAGTTTAAGCCCCAATT-TAAGAACAATTACCAAGT
*
3692368 TCAAGGTCTAACTTGAAAAAAAAA
1 TCAAGGCCTAACTTGAAAAAAAAA
3692392 TTAAACCCTA
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
58 8 0.12
59 21 0.31
60 38 0.57
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.24
Consensus pattern (58 bp):
TCAAGGCCTAACTTGAAAAAAAAAAGTTTAAGCCCCAATTTAAGAACAATTACCAAGT
Found at i:3696168 original size:18 final size:18
Alignment explanation
Indices: 3696142--3696210 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
3696132 GGGGTAGAAT
*
3696142 TTAACAAAAATAAATTTC
1 TTAATAAAAATAAATTTC
3696160 TTAATAAAAACTAAATTT-
1 TTAATAAAAA-TAAATTTC
* *
3696178 GTAGATAACAAT-AATTTC
1 TTA-ATAAAAATAAATTTC
3696196 TTAAATAAATAATAA
1 TT-AATAAA-AATAA
3696211 TTTTAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 5 0.12
18 17 0.43
19 17 0.43
20 1 0.03
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (18 bp):
TTAATAAAAATAAATTTC
Found at i:3703343 original size:21 final size:21
Alignment explanation
Indices: 3703315--3703386 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3703305 TCACTGGTTA
3703315 GGCACAAAGCCTGATAACACC
1 GGCACAAAGCCTGATAACACC
*
3703336 GACACAAAG-CT--T-ACTA--
1 GGCACAAAGCCTGATAAC-ACC
*
3703352 GGCACAAAGCCTAATAACACC
1 GGCACAAAGCCTGATAACACC
3703373 GGCACAAAGCCTGA
1 GGCACAAAGCCTGA
3703387 ATTTGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
16 8 0.20
17 4 0.10
18 2 0.05
19 2 0.05
20 4 0.10
21 21 0.51
ACGTcount: A:0.40, C:0.31, G:0.18, T:0.11
Consensus pattern (21 bp):
GGCACAAAGCCTGATAACACC
Found at i:3704142 original size:19 final size:19
Alignment explanation
Indices: 3704118--3704155 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3704108 TTTATGAGTG
*
3704118 TAATTTACTCAATAAAATT
1 TAATTTACTAAATAAAATT
*
3704137 TAATTTACTAAATATAATT
1 TAATTTACTAAATAAAATT
3704156 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATTTACTAAATAAAATT
Found at i:3705608 original size:6 final size:6
Alignment explanation
Indices: 3705584--3705623 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
3705574 ATAAAATTAT
3705584 TAAATA TTAAAT- T-AATA TAAATA TAAATA TAAAT- TAAATA
1 TAAATA -TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
3705624 ATTAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
4 3 0.10
5 7 0.23
6 15 0.50
7 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATA
Found at i:3705621 original size:17 final size:16
Alignment explanation
Indices: 3705567--3705630 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
3705557 AAAACTAAAA
3705567 TAAATATATAAAATT-AT
1 TAAATAT-T-AAATTAAT
3705584 TAAATATTAAATTAAT
1 TAAATATTAAATTAAT
3705600 ATAAATA-TAAATATAAAT
1 -TAAATATTAAAT-T-AAT
3705618 TAAATAATTAAAT
1 TAAAT-ATTAAAT
3705631 ATCTTAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.12
16 8 0.20
17 19 0.46
18 4 0.10
19 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATATTAAATTAAT
Found at i:3709713 original size:57 final size:57
Alignment explanation
Indices: 3709652--3709761 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
3709642 AAAATCGGAC
* * *
3709652 AAAAAAAA-TTTAGGTATCAAATTAAAAAGATGT-CAAGTTCAAATATCAAATTAGACA
1 AAAAAAAATTTTA-ATATCAAATTAAAAA-ATATACAAATTCAAATATCAAATTAGACA
* *
3709709 AAAAAAAATTTTAATATTAAATTAAAAAATATACAAATTCAGATATCAAATTA
1 AAAAAAAATTTTAATATCAAATTAAAAAATATACAAATTCAAATATCAAATTA
3709762 AACCAAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 3 0.07
57 39 0.85
58 4 0.09
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.29
Consensus pattern (57 bp):
AAAAAAAATTTTAATATCAAATTAAAAAATATACAAATTCAAATATCAAATTAGACA
Found at i:3710336 original size:14 final size:14
Alignment explanation
Indices: 3710317--3710355 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3710307 TTAATTTTAT
3710317 ATTTTATATATAAA
1 ATTTTATATATAAA
* *
3710331 ATTTTATAAATAAT
1 ATTTTATATATAAA
3710345 ATATTTATATA
1 AT-TTTATATA
3710356 ATCTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTATATATAAA
Found at i:3714875 original size:12 final size:12
Alignment explanation
Indices: 3714848--3714883 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3714838 ACGGGTAGAA
*
3714848 GAAGATAGACGAT
1 GAAGA-AGAAGAT
3714861 GAAGAAGAAGAT
1 GAAGAAGAAGAT
3714873 GAAGAAGAAGA
1 GAAGAAGAAGA
3714884 ACAAATTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.56, C:0.03, G:0.33, T:0.08
Consensus pattern (12 bp):
GAAGAAGAAGAT
Found at i:3718811 original size:855 final size:855
Alignment explanation
Indices: 3717144--3718854 Score: 3179
Period size: 855 Copynumber: 2.0 Consensus size: 855
3717134 AAATTAAATT
*
3717144 TTTTTCAAAAATAAATATAATTATATTTTGTGCGTGCAAACTACACGAAAAAATTATAAATTATT
1 TTTTTCAAAAATAAATATAATTATATTTTGTGCATGCAAACTACACGAAAAAATTATAAATTATT
3717209 TTTCAGATGGGCGACTCCTTCGAGATCAGGAGAACAAAGACGATGCTCGTATATCGCCAAATGAT
66 TTTCAGATGGGCGACTCCTTCGAGATCAGGAGAACAAAGACGATGCTCGTATATCGCCAAATGAT
*
3717274 TAAGGCACACTCCAGGAACAACGTAAAATACTATTCTAAATTTATTGTTTTTTAAATTACAATAT
131 TAAGGCACACTCCAGGAACAACGTAAAATACTATTCTAAATTTATTATTTTTTAAATTACAATAT
3717339 TTAAGTACTACAAATATTTTTTATTACGACATTTAAAATAAATTTATTTAACTATATAAATTATC
196 TTAAGTACTACAAATATTTTTTATTACGACATTTAAAATAAATTTATTTAACTATATAAATTATC
* *
3717404 GATATTGTGTAGTTTGTGTGGATGTCGTATTCGGGAAAGACGTTACGACAGTTATTCCAACGTGG
261 GATACTGTGTAGTTTGTGTAGATGTCGTATTCGGGAAAGACGTTACGACAGTTATTCCAACGTGG
*
3717469 TTCCACCAGCTACAACTAATACGCTCTACCAACATCCCGTTGCTTAATTTTTCAATGGTTGAGTG
326 TTCCACCAGCTACAACTAATACGCTCTACCAACATCCCGTTGCTTAATTTTTCAACGGTTGAGTG
* *
3717534 GCGCAATGCTAATCGAGTTTTGAGACAGTTTGGGCCCATTCAACATATTTCGTACCCTCCACAAA
391 GCGCAATGCTAACCGAGTTTTGAGACAGTTTAGGCCCATTCAACATATTTCGTACCCTCCACAAA
3717599 ACTTCGATGACAATCACGACATTAACAAAAGGATAAAGACAATAAGAATTGGGTTGTCGTACATG
456 ACTTCGATGACAATCACGACATTAACAAAAGGATAAAGACAATAAGAATTGGGTTGTCGTACATG
3717664 GTCAATACCTCACTTTGTGGAACGCCCAACTTGAGAAGCAACCTCGCTTACATGTCTATGTTAGA
521 GTCAATACCTCACTTTGTGGAACGCCCAACTTGAGAAGCAACCTCGCTTACATGTCTATGTTAGA
3717729 AGTTTCATGCCTTCGCCCGAGCATCGAAGTCGGTACACGACGAACGAGAAATCATTTATATATAA
586 AGTTTCATGCCTTCGCCCGAGCATCGAAGTCGGTACACGACGAACGAGAAATCATTTATATATAA
* *
3717794 TGGCTAGTTTATGATGGGCCCGCCGCACATATGCCGATAGGGATCTCGATAACACGAGGCTCGGC
651 TGGCTAGTTTATGATGGGCCCCCCGCACATATGCCGATAGGGATCTCGATAACACGAGGCTCGAC
*
3717859 TCAAGCACGCAGTTATCGAGGTCCATCGTTCAGTGTAACCTAACCTATCTCAAACCCCAAGCCCA
716 TCAAGCACACAGTTATCGAGGTCCATCGTTCAGTGTAACCTAACCTATCTCAAACCCCAAGCCCA
*
3717924 AGCCTCAACATTCGATGTCCAAAACATACTCATACCTTCCCTATCCCCAACAACCACCATCTTTC
781 AGCCTCAACATTCAATGTCCAAAACATACTCATACCTTCCCTATCCCCAACAACCACCATCTTTC
3717989 TTCGAGGGCA
846 TTCGAGGGCA
*
3717999 TTTTTCAAAAATAAATATAATTATATTTTGTGCATGCAAACTATACGAAAAAATTATAAATTATT
1 TTTTTCAAAAATAAATATAATTATATTTTGTGCATGCAAACTACACGAAAAAATTATAAATTATT
3718064 TTTCAGATGGGCGACTCCTTCGAGATCAGGAGAACAAAGACGATGCTCGTATATCGCCAAATGAT
66 TTTCAGATGGGCGACTCCTTCGAGATCAGGAGAACAAAGACGATGCTCGTATATCGCCAAATGAT
*
3718129 TAAGGCACACTCCGGGAACAACGTAAAATACTATTCTAAATTTATTATTTTTTAAATTACAATAT
131 TAAGGCACACTCCAGGAACAACGTAAAATACTATTCTAAATTTATTATTTTTTAAATTACAATAT
*
3718194 TTAAGTACTACAAATATTTTTTATTGCGACATTTAAAATAAATTTATTTAACTATATAAATTATC
196 TTAAGTACTACAAATATTTTTTATTACGACATTTAAAATAAATTTATTTAACTATATAAATTATC
* **
3718259 GATACTGTGTAGTTTGTGTAGATGTCGTATTCGGGGAAGACGTTACGACAGTTATTCCAGTGTGG
261 GATACTGTGTAGTTTGTGTAGATGTCGTATTCGGGAAAGACGTTACGACAGTTATTCCAACGTGG
* *
3718324 TTCCACCAGCTACAACTAATGCGGTCTACCAACATCCCGTTGCTTAATTTTTCAACGGTTGAGTG
326 TTCCACCAGCTACAACTAATACGCTCTACCAACATCCCGTTGCTTAATTTTTCAACGGTTGAGTG
3718389 GCGCAATGCTAACCGAGTTTTGAGACAGTTTAGGCCCATTCAACATATTTCGTACCCTCCACAAA
391 GCGCAATGCTAACCGAGTTTTGAGACAGTTTAGGCCCATTCAACATATTTCGTACCCTCCACAAA
*
3718454 ACTTCGATGACAATCACGTCATTAACAAAAGGATAAAGACAATAAGAATTGGGTTGTCGTACATG
456 ACTTCGATGACAATCACGACATTAACAAAAGGATAAAGACAATAAGAATTGGGTTGTCGTACATG
* *
3718519 GTCAATACCTCACTTTGTGGAGCGCCCAACTTGAGAAGCGACCTCGCTTACATGTCTATGTTAGA
521 GTCAATACCTCACTTTGTGGAACGCCCAACTTGAGAAGCAACCTCGCTTACATGTCTATGTTAGA
**
3718584 AGTTTCATGCCTTCGCCCGAGCATCGAAGTCGGTACACGGTGAACGAGAAATCATTTATATATAA
586 AGTTTCATGCCTTCGCCCGAGCATCGAAGTCGGTACACGACGAACGAGAAATCATTTATATATAA
3718649 TGGCTAGTTTATGATGGGCCCCCCGCACATATGCCGATAGGGATCTCGATAACACGAGGCTCGAC
651 TGGCTAGTTTATGATGGGCCCCCCGCACATATGCCGATAGGGATCTCGATAACACGAGGCTCGAC
3718714 TCAAGCACACAGTTATCGAGGTCCATCGTTCAGTGTAACCTAACCTATCTCAAACCCCAAGCCCA
716 TCAAGCACACAGTTATCGAGGTCCATCGTTCAGTGTAACCTAACCTATCTCAAACCCCAAGCCCA
* * *
3718779 AGCCTCAACATTCAATGTCCGAAACGTACTCATACCTTCCCTATCCCCAACAACCATCATCTTTC
781 AGCCTCAACATTCAATGTCCAAAACATACTCATACCTTCCCTATCCCCAACAACCACCATCTTTC
3718844 TTCGAGGGCA
846 TTCGAGGGCA
3718854 T
1 T
3718855 CTTTGGTGCA
Statistics
Matches: 829, Mismatches: 27, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
855 829 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (855 bp):
TTTTTCAAAAATAAATATAATTATATTTTGTGCATGCAAACTACACGAAAAAATTATAAATTATT
TTTCAGATGGGCGACTCCTTCGAGATCAGGAGAACAAAGACGATGCTCGTATATCGCCAAATGAT
TAAGGCACACTCCAGGAACAACGTAAAATACTATTCTAAATTTATTATTTTTTAAATTACAATAT
TTAAGTACTACAAATATTTTTTATTACGACATTTAAAATAAATTTATTTAACTATATAAATTATC
GATACTGTGTAGTTTGTGTAGATGTCGTATTCGGGAAAGACGTTACGACAGTTATTCCAACGTGG
TTCCACCAGCTACAACTAATACGCTCTACCAACATCCCGTTGCTTAATTTTTCAACGGTTGAGTG
GCGCAATGCTAACCGAGTTTTGAGACAGTTTAGGCCCATTCAACATATTTCGTACCCTCCACAAA
ACTTCGATGACAATCACGACATTAACAAAAGGATAAAGACAATAAGAATTGGGTTGTCGTACATG
GTCAATACCTCACTTTGTGGAACGCCCAACTTGAGAAGCAACCTCGCTTACATGTCTATGTTAGA
AGTTTCATGCCTTCGCCCGAGCATCGAAGTCGGTACACGACGAACGAGAAATCATTTATATATAA
TGGCTAGTTTATGATGGGCCCCCCGCACATATGCCGATAGGGATCTCGATAACACGAGGCTCGAC
TCAAGCACACAGTTATCGAGGTCCATCGTTCAGTGTAACCTAACCTATCTCAAACCCCAAGCCCA
AGCCTCAACATTCAATGTCCAAAACATACTCATACCTTCCCTATCCCCAACAACCACCATCTTTC
TTCGAGGGCA
Found at i:3726264 original size:29 final size:30
Alignment explanation
Indices: 3726230--3726287 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
3726220 TTATGTATAA
*
3726230 AATTACACA-AAATTAAAATTCATATATTT
1 AATTACACATAAACTAAAATTCATATATTT
*
3726259 AATTACACATTAAACTATAATTCATATAT
1 AATTACACA-TAAACTAAAATTCATATAT
3726288 AGATTTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTACACATAAACTAAAATTCATATATTT
Found at i:3728821 original size:50 final size:50
Alignment explanation
Indices: 3728767--3728865 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
3728757 ATTAATAATG
* *
3728767 TTAACAAAATGATAATTAATTAATTAAAATTTAATAATTTAATAATATTT
1 TTAACAAAATAATAATTAATTAATTAAAATTAAATAATTTAATAATATTT
* *
3728817 TTAACAACATAATAATTAATTAATTAAAATTAAATATTTTAATAATATT
1 TTAACAAAATAATAATTAATTAATTAAAATTAAATAATTTAATAATATT
3728866 ATCTTACCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (50 bp):
TTAACAAAATAATAATTAATTAATTAAAATTAAATAATTTAATAATATTT
Found at i:3729017 original size:30 final size:30
Alignment explanation
Indices: 3728983--3729046 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3728973 GAAAAAAATT
* * * * *
3728983 AAAAAAAATAGAATTGAGAATTTAGAATAA
1 AAAAAAAAGAGAATTAACAATTGAAAATAA
*
3729013 AAAAAATAGAGAATTAACAATTGAAAATAA
1 AAAAAAAAGAGAATTAACAATTGAAAATAA
3729043 AAAA
1 AAAA
3729047 TTGAGAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (30 bp):
AAAAAAAAGAGAATTAACAATTGAAAATAA
Found at i:3729050 original size:14 final size:14
Alignment explanation
Indices: 3729031--3729060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3729021 GAGAATTAAC
3729031 AATTGAAAATAAAA
1 AATTGAAAATAAAA
*
3729045 AATTGAGAATAAAA
1 AATTGAAAATAAAA
3729059 AA
1 AA
3729061 GTAAGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (14 bp):
AATTGAAAATAAAA
Found at i:3739376 original size:18 final size:18
Alignment explanation
Indices: 3739330--3739377 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
3739320 AAATTTGAGA
*
3739330 AGATTTGA-ATAAAAAAT
1 AGATTTGATTTAAAAAAT
* *
3739347 AAATTT-ATTTAAAATAT
1 AGATTTGATTTAAAAAAT
3739364 AGATTTGATTTAAA
1 AGATTTGATTTAAA
3739378 TATTTAAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 1 0.04
17 17 0.68
18 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (18 bp):
AGATTTGATTTAAAAAAT
Found at i:3743517 original size:19 final size:20
Alignment explanation
Indices: 3743489--3743535 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
3743479 ATTGTACCAG
*
3743489 TTTTATAATTTTA-TAATTT
1 TTTTAAAATTTTATTAATTT
3743508 TTTTAAAATTTTATTAATTT
1 TTTTAAAATTTTATTAATTT
3743528 TTATTAAA
1 TT-TTAAA
3743536 TCAACGTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 8 0.32
21 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATTTTATTAATTT
Found at i:3747462 original size:5 final size:5
Alignment explanation
Indices: 3747452--3747476 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3747442 TTAAACCTGA
3747452 GCCCG GCCCG GCCCG GCCCG GCCCG
1 GCCCG GCCCG GCCCG GCCCG GCCCG
3747477 ATCTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.40, T:0.00
Consensus pattern (5 bp):
GCCCG
Done.