Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_pilon, 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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 26
Found at i:2710760 original size:69 final size:69
Alignment explanation
Indices: 2710652--2710836 Score: 218
Period size: 69 Copynumber: 2.8 Consensus size: 69
2710642 TTGATCTCAC
* * * * *
2710652 TTGAAATTGTTT-TC-CTAAAAATAAA-TTTTGTCTCGCTTGATATAGTTTCTCTTGAAACATAA
1 TTGAAATTATTTCTCTCTAAAAAAAAAGTTTTGCCTCGCTTGAAACAGTTTCTCTTGAAACATAA
2710714 ACCT
66 ACCT
* * *
2710718 TTGACATTATTTCTCTCTAAAAAAAAAGTTTTGCCTCGCTTGAAACAATTTCTGTTGAAACATAA
1 TTGAAATTATTTCTCTCTAAAAAAAAAGTTTTGCCTCGCTTGAAACAGTTTCTCTTGAAACATAA
*
2710783 GCCT
66 ACCT
* * * *
2710787 TTGAAATTATTTCTCT-T-GAAAAAAAGTTTCGCCTTGCTTGAGACAGTTTC
1 TTGAAATTATTTCTCTCTAAAAAAAAAGTTTTGCCTCGCTTGAAACAGTTTC
2710837 CTTTGAAGCC
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
66 10 0.10
67 30 0.30
68 11 0.11
69 50 0.50
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (69 bp):
TTGAAATTATTTCTCTCTAAAAAAAAAGTTTTGCCTCGCTTGAAACAGTTTCTCTTGAAACATAA
ACCT
Found at i:2710909 original size:66 final size:65
Alignment explanation
Indices: 2710823--2710983 Score: 166
Period size: 66 Copynumber: 2.5 Consensus size: 65
2710813 TTTCGCCTTG
* * ** *
2710823 CTTGAGACAGTTTCCTTTGAA-GCCCATATTTCAAATTTGTTTCACTTGAAACA-AAATTGATCT
1 CTTGAGATAGTTTCCCTTGAATGCAAAT-TTTCAAA-TTGTTTCACTCGAAACAGAAATTGATCT
2710886 CA
64 CA
* * * *
2710888 CTTGAGATAGTTTTCCCTTGAAATGCAAATTTTGAAATTGTTTCCCTCGAAACAGAATTTTATCT
1 CTTGAGATAG-TTTCCCTTG-AATGCAAATTTTCAAATTGTTTCACTCGAAACAGAAATTGATCT
2710953 CA
64 CA
* *
2710955 CCTGAGATAGTTTCTCTTGAAT-CAAATTT
1 CTTGAGATAGTTTCCCTTGAATGCAAATTT
2710984 CTTTCCACTC
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
64 7 0.09
65 12 0.15
66 31 0.38
67 27 0.33
68 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (65 bp):
CTTGAGATAGTTTCCCTTGAATGCAAATTTTCAAATTGTTTCACTCGAAACAGAAATTGATCTCA
Found at i:2712973 original size:96 final size:96
Alignment explanation
Indices: 2712809--2713001 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
2712799 TTGGTTAAAT
2712809 ACGCTAAGGTCTCTATACCTTTAGCGTGTTTTACGACTAAGTCATATAGTTGTGGGCTAATTACC
1 ACGCTAAGGTCTCTATACCTTTAGCGTGTTTTACGACTAAGTCATATAGTTGTGGGCTAATTACC
2712874 CACAGGTCCCTAACCTTGATGCAACTATCTA
66 CACAGGTCCCTAACCTTGATGCAACTATCTA
2712905 ACGCTAAGGTCTCTATACCTTTAGCGTGTTTTACGACTAAGTCATATAGTTGTGGGCTAATTACC
1 ACGCTAAGGTCTCTATACCTTTAGCGTGTTTTACGACTAAGTCATATAGTTGTGGGCTAATTACC
2712970 CACAGGTCCCTAACCTTGATGCAACTATCTA
66 CACAGGTCCCTAACCTTGATGCAACTATCTA
2713001 A
1 A
2713002 GTCCTAGTCA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (96 bp):
ACGCTAAGGTCTCTATACCTTTAGCGTGTTTTACGACTAAGTCATATAGTTGTGGGCTAATTACC
CACAGGTCCCTAACCTTGATGCAACTATCTA
Found at i:2713173 original size:18 final size:17
Alignment explanation
Indices: 2713141--2713175 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2713131 TCACTAGATA
2713141 CTTTGTTTAGATGTTTT
1 CTTTGTTTAGATGTTTT
*
2713158 CTTTGATTTAGGTGTTTT
1 CTTTG-TTTAGATGTTTT
2713176 GTTTCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.06, G:0.20, T:0.63
Consensus pattern (17 bp):
CTTTGTTTAGATGTTTT
Found at i:2714167 original size:76 final size:76
Alignment explanation
Indices: 2714075--2714226 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
2714065 TCAATGTTCG
2714075 ATAAATGTATCATAATTTAATTTTCTATTCAAATTTCAATTTCCACTATTATAACAACATATAAG
1 ATAAATGTATCATAATTTAATTTTCTATTCAAATTTCAATTTCCACTATTATAACAACATATAAG
2714140 CGACTACATAT
66 CGACTACATAT
2714151 ATAAATGTATCATAATTTAATTTTCTATTCAAATTTCAATTTCCACTATTATAACAACATATAAG
1 ATAAATGTATCATAATTTAATTTTCTATTCAAATTTCAATTTCCACTATTATAACAACATATAAG
2714216 CGACTACATAT
66 CGACTACATAT
2714227 CAATTTTGGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (76 bp):
ATAAATGTATCATAATTTAATTTTCTATTCAAATTTCAATTTCCACTATTATAACAACATATAAG
CGACTACATAT
Found at i:2714540 original size:33 final size:33
Alignment explanation
Indices: 2714498--2714561 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
2714488 TCGTTTTTCA
2714498 AAAAAAGACGTTATGAAAAACATCACTATCATC
1 AAAAAAGACGTTATGAAAAACATCACTATCATC
2714531 AAAAAAGACGTTATGAAAAACATCACTATCA
1 AAAAAAGACGTTATGAAAAACATCACTATCA
2714562 ATTTTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.20
Consensus pattern (33 bp):
AAAAAAGACGTTATGAAAAACATCACTATCATC
Found at i:2715230 original size:2 final size:2
Alignment explanation
Indices: 2715223--2715271 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2715213 AATTTAGAGA
2715223 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
2715265 AT AT AT A
1 AT AT AT A
2715272 AACATCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2715639 original size:40 final size:41
Alignment explanation
Indices: 2715595--2715672 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
2715585 CATCAAATAA
* *
2715595 TAATGGGCATCAATTTGGTGT-AGAAAATCGAAGGATACAT
1 TAATGAGCATCAATTTGGTGTAAAAAAATCGAAGGATACAT
*
2715635 TAATGAGCATCAATTTGGTGTAAAAAAATCGAATGATA
1 TAATGAGCATCAATTTGGTGTAAAAAAATCGAAGGATA
2715673 ATTTGAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 20 0.59
41 14 0.41
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (41 bp):
TAATGAGCATCAATTTGGTGTAAAAAAATCGAAGGATACAT
Found at i:2715865 original size:9 final size:9
Alignment explanation
Indices: 2715851--2715875 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2715841 GATATTTTTA
2715851 ATTTTATTT
1 ATTTTATTT
2715860 ATTTTATTT
1 ATTTTATTT
2715869 ATTTTAT
1 ATTTTAT
2715876 AATATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTATTT
Found at i:2734550 original size:19 final size:19
Alignment explanation
Indices: 2734526--2734584 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
2734516 ACTGATACTC
2734526 CTCTTGATAGGTATCGATA
1 CTCTTGATAGGTATCGATA
*
2734545 CTCTTGCTAGGTATCGATA
1 CTCTTGATAGGTATCGATA
*
2734564 CTGCTTTAATAGGTATCGATA
1 CT-C-TTGATAGGTATCGATA
2734585 TTGTTCGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 20 0.57
20 1 0.03
21 14 0.40
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (19 bp):
CTCTTGATAGGTATCGATA
Found at i:2738854 original size:17 final size:18
Alignment explanation
Indices: 2738821--2738863 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2738811 CAAACAAATT
2738821 CAAATTC-AATCAATCCA
1 CAAATTCAAATCAATCCA
*
2738838 CAAATTCAAAT-ATTCCA
1 CAAATTCAAATCAATCCA
2738855 -AAATTCAAA
1 CAAATTCAAA
2738864 AAGTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 12 0.50
18 3 0.12
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (18 bp):
CAAATTCAAATCAATCCA
Found at i:2740597 original size:20 final size:20
Alignment explanation
Indices: 2740560--2740598 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2740550 AGATTGAGTG
* * *
2740560 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
2740580 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2740599 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:2750721 original size:44 final size:44
Alignment explanation
Indices: 2750658--2750749 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
2750648 ACTGCGGAGA
2750658 CAAAATAATCTCTTAGACCTTACATTAAAGATCATATTATTAAT
1 CAAAATAATCTCTTAGACCTTACATTAAAGATCATATTATTAAT
2750702 CAAAATAATCTCTTAGACCTTACATTAAAGATCATATTATTAAT
1 CAAAATAATCTCTTAGACCTTACATTAAAGATCATATTATTAAT
2750746 CAAA
1 CAAA
2750750 TACTTGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (44 bp):
CAAAATAATCTCTTAGACCTTACATTAAAGATCATATTATTAAT
Found at i:2755133 original size:19 final size:19
Alignment explanation
Indices: 2755079--2755134 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 19
2755069 CTGTAAAATT
2755079 AATAAATAATAAT-AT-TA
1 AATAAATAATAATAATATA
*
2755096 AAT-AATAAT--TATTAT-
1 AATAAATAATAATAATATA
2755111 AATAAATAATAATAATATA
1 AATAAATAATAATAATATA
2755130 AATAA
1 AATAA
2755135 CCCAGACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 1 0.03
15 4 0.13
16 13 0.42
17 3 0.10
18 5 0.16
19 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAATAATAATAATATA
Found at i:2755134 original size:22 final size:25
Alignment explanation
Indices: 2755080--2755134 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 25
2755070 TGTAAAATTA
2755080 ATAAATAATAATATTAAATAATAAT
1 ATAAATAATAATATTAAATAATAAT
*
2755105 -TATTATAATAA-A-T-AATAATAAT
1 ATA-AATAATAATATTAAATAATAAT
2755127 ATAAATAA
1 ATAAATAA
2755135 CCCAGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
22 13 0.50
23 3 0.12
24 3 0.12
25 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAAATAATAATATTAAATAATAAT
Found at i:2756035 original size:41 final size:42
Alignment explanation
Indices: 2755985--2756066 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
2755975 CGAAGGTCTT
* *
2755985 ATAGTTGACCTGAAGGACTTAA-CATCTTGCTCGAAAGACTG
1 ATAGATGACCCGAAGGACTTAATCATCTTGCTCGAAAGACTG
*
2756026 ATAGATGACCCGAAGGATTTAATCATCTTGCTCGAAAGACT
1 ATAGATGACCCGAAGGACTTAATCATCTTGCTCGAAAGACT
2756067 TATTGATGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 19 0.51
42 18 0.49
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
ATAGATGACCCGAAGGACTTAATCATCTTGCTCGAAAGACTG
Found at i:2756060 original size:258 final size:258
Alignment explanation
Indices: 2755278--2756707 Score: 1870
Period size: 258 Copynumber: 5.6 Consensus size: 258
2755268 AACTTGAATT
* * **
2755278 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGGAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
* ** *
2755343 TA-TCAGGTAAGAAACTGTGGAAATTACTTTCTTACTTTTCAAAATTTTCATTCTT-TGAAAATA
66 TACT-AGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATT-TTCTGAAAATA
* *
2755406 TTAAATGAGAAACTTTGAAAATCACTTTCTTAT-TTCTA-AAAATCATGTGAAAACAT-ATTGCC
129 TTAAATGAGAAACTTTGAAAATCACTTTCTCATATT-TAGAAAATCATGTGAAAACATCA-TACC
* * * * * *
2755468 CAAAGGTCTTATAGTTGGCATGAATGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAC
192 CGAAGGTCTTATAGTTGGCCTGAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCGAA
2755533 GG
257 GG
* * *
2755535 ATTTAATCATCATGCTCGAAAGACTTACTGGTGGCCCAAAGGAGTTACCAATTTTGGAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
* * * *
2755600 TAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTTGGAAATAT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA-TTTTCTGAAAATAT
* * * * *
2755665 TAAATGAGAAATTTTGAAAATTACTTT-TCTTATTT-----TTCA----AAAACATCATACCTGA
130 TAAATGAGAAACTTTGAAAATCACTTTCTCATATTTAGAAAATCATGTGAAAACATCATACCCGA
* * * *
2755720 AGGTCTTATA-TATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGA
195 AGGTCTTATAGT-TGGCCTGAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
* * **
2755784 ATTTAACCATCATGCTCGAAAGATTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
*
2755849 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTT-CATTTTCAAAAATTTCATTTTTTGAAAATAT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTAC-TTTTCAAAAATTTCATTTTCTGAAAATAT
* * *
2755913 TAAATGAGAAACTTTGAAAATCGCTTTCTCATATTTAGAAAATCATTTGAAAACATCATGCCCGA
130 TAAATGAGAAACTTTGAAAATCACTTTCTCATATTTAGAAAATCATGTGAAAACATCATACCCGA
* *
2755978 AGGTCTTATAGTTGACCTGAAGGACTTAACATCTTGCTCGAAAGACTGATAGATGACCCGAAGG
195 AGGTCTTATAGTTGGCCTGAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
* * * * * *
2756042 ATTTAATCATCTTGCTCGAAAGACTTATTGATGGCCCTAAAGACTTACCAATTTTAGAAATAGTA
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
* * * *
2756107 AACTGGGTAAGAAACTTTGGAAATCTCTTTCTAACTTTTCAAAACA-TTCATTTTCTGAAAATAT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA-ATTTCATTTTCTGAAAATAT
* * * *
2756171 TAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTACTCGA
130 TAAATGAGAAACTTTGAAAATCACTTTCTCATATTTAGAAAATCATGTGAAAACATCATACCCGA
* ** * * * *
2756236 AGGTCGTATAGACGGCCTGAAGGACTTAATATCTTGCTTGAAAGACTGACAAATGACCCAAAGG
195 AGGTCTTATAGTTGGCCTGAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
* * * * *
2756300 ATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCAAAGGACTTATCGATATTGGAAATAGTT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
* *
2756365 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCATTTTCTAAAAATATT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
* * *
2756430 AAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAA
131 AAATGAGAAACTTTGAAAATCACTTTCTCATATTTAGAAAATCATGTGAAAACATCATACCCGAA
** * * ** * * *
2756495 GGTCTTATAGGCGACCCGAATTACTTAACATCTTGCTCGAAAGACTGATAGATGACCTGAAAG
196 GGTCTTATAGTTGGCCTGAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
**
2756558 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAAAT
1 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
* * * *
2756623 TAATAGGTAAGAAACTCTGGAAATCGTTTTCTAACTTTTCAAAAATTTCATTTTCTGAAAATATT
66 TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
2756688 AAATGAGAAACTTTGAAAAT
131 AAATGAGAAACTTTGAAAAT
2756708 TTCTTTTCTC
Statistics
Matches: 1030, Mismatches: 122, Indels: 41
0.86 0.10 0.03
Matches are distributed among these distances:
248 39 0.04
249 179 0.17
250 1 0.00
253 3 0.00
254 3 0.00
257 106 0.10
258 696 0.68
259 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (258 bp):
ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
TACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATT
AAATGAGAAACTTTGAAAATCACTTTCTCATATTTAGAAAATCATGTGAAAACATCATACCCGAA
GGTCTTATAGTTGGCCTGAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCGAAGG
Found at i:2758751 original size:18 final size:20
Alignment explanation
Indices: 2758728--2758765 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
2758718 ATTTGTTATA
2758728 TTTGTTCTT-T-TCTTTTTT
1 TTTGTTCTTCTCTCTTTTTT
*
2758746 TTTGTTGTTCTCTCTTTTTT
1 TTTGTTCTTCTCTCTTTTTT
2758766 CTTCTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTGTTCTTCTCTCTTTTTT
Found at i:2758768 original size:32 final size:30
Alignment explanation
Indices: 2758732--2758813 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 30
2758722 GTTATATTTG
* *
2758732 TTCTTTTCTTTTTTTTTGTTGTTCTCTCTTTT
1 TTCTTTTCTTTTTTTTT-AT-TTATCTCTTTT
* *
2758764 TTCTTCTCTTTTTTATTATTTATCTCTTTT
1 TTCTTTTCTTTTTTTTTATTTATCTCTTTT
2758794 TTC--TTCTTTTTTTATTATTT
1 TTCTTTTCTTTTTTT-TTATTT
2758814 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.19
29 6 0.14
30 13 0.30
31 1 0.02
32 15 0.35
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (30 bp):
TTCTTTTCTTTTTTTTTATTTATCTCTTTT
Found at i:2758803 original size:40 final size:43
Alignment explanation
Indices: 2758753--2758837 Score: 88
Period size: 40 Copynumber: 2.0 Consensus size: 43
2758743 TTTTTTGTTG
* * *
2758753 TTCTCTC-TTTTTTCTTCTCTTTTTTATTATTTATCTCT-TTTT
1 TTCTCTCTTTTTTTATTAT-TTTTTTATTATTTAACTCTCTTTT
* *
2758795 TC-T-TCTTTTTTTATTATTTTTTTATTTTTTAACTCTCTTTT
1 TTCTCTCTTTTTTTATTATTTTTTTATTATTTAACTCTCTTTT
2758836 TT
1 TT
2758838 TTAATATGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
40 19 0.54
41 15 0.43
42 1 0.03
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (43 bp):
TTCTCTCTTTTTTTATTATTTTTTTATTATTTAACTCTCTTTT
Found at i:2758808 original size:22 final size:21
Alignment explanation
Indices: 2758772--2758840 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
2758762 TTTTCTTCTC
*
2758772 TTTTTTA-TTATTTATCTCTT
1 TTTTTTATTTTTTTATCTCTT
* *
2758792 TTTTCTTCTTTTTTTAT-T-AT
1 TTTT-TTATTTTTTTATCTCTT
*
2758812 TTTTTTATTTTTTAACTCTCTT
1 TTTTTTATTTTTTTA-TCTCTT
2758834 TTTTTTA
1 TTTTTTA
2758841 ATATGAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.24
20 10 0.26
21 4 0.11
22 15 0.39
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTATTTTTTTATCTCTT
Found at i:2758824 original size:30 final size:29
Alignment explanation
Indices: 2758735--2758813 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
2758725 ATATTTGTTC
* * *
2758735 TTTTCTT-TTTTTTTGTT-GTTCTCTCTT
1 TTTTCTTCTTTTTTTATTATTTATCTCTT
2758762 TTTTCTTCTCTTTTTTATTATTTATCTCTT
1 TTTTCTTCT-TTTTTTATTATTTATCTCTT
2758792 TTTTCTTCTTTTTTTATTATTT
1 TTTTCTTCTTTTTTTATTATTT
2758814 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 7 0.15
28 1 0.02
29 21 0.46
30 17 0.37
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.77
Consensus pattern (29 bp):
TTTTCTTCTTTTTTTATTATTTATCTCTT
Found at i:2765882 original size:21 final size:21
Alignment explanation
Indices: 2765845--2765926 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
2765835 ATTTGGTGCA
*
2765845 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
2765865 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
*
2765886 GAAGGGGAACCGATTCCCCCCAC
1 G-A-GGGAACCGATTCCCCCCAT
* * *
2765909 AAGGGAATCGATACCCCC
1 GAGGGAACCGATTCCCCC
2765927 TAGGGTTCTG
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.20
21 22 0.44
22 2 0.04
23 16 0.32
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:2766304 original size:19 final size:18
Alignment explanation
Indices: 2766282--2766321 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2766272 AAAACACAAG
2766282 AATTTTCCAAAAAAAATAA
1 AATTTTCCAAAAAAAA-AA
* *
2766301 AATTTTCGAAATAAAAAA
1 AATTTTCCAAAAAAAAAA
2766319 AAT
1 AAT
2766322 GTTGATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (18 bp):
AATTTTCCAAAAAAAAAA
Found at i:2775796 original size:13 final size:12
Alignment explanation
Indices: 2775777--2775822 Score: 74
Period size: 13 Copynumber: 3.7 Consensus size: 12
2775767 TGTAAAATTA
2775777 ATAAATAATAAT
1 ATAAATAATAAT
2775789 ATTAAATAATAAT
1 A-TAAATAATAAT
2775802 AATAAATAATAAT
1 -ATAAATAATAAT
2775815 ATAAATAA
1 ATAAATAA
2775823 CCCGGACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.28
13 22 0.69
14 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:2776725 original size:415 final size:415
Alignment explanation
Indices: 2775955--2776778 Score: 1468
Period size: 415 Copynumber: 2.0 Consensus size: 415
2775945 GAGCTCATTT
2775955 AATTGCATTAATTTAGTTCTTTAATTGACATTGATTGTTCTTGTGTTTATGTGGCATTTACCAAT
1 AATTGCATTAATTTAGTTCTTTAATTGACATTGATTGTTCTTGTGTTTATGTGGCATTTACCAAT
*
2776020 GCTAAGGGGACGATCAACGATGTTGATACGACATTCTACATATGAATGATGACATGGTATATGGG
66 GCTAAGGGGACGATCAACGATGTTGATACGACATTCTACATATGAATGATGACATGATATATGGG
2776085 TTGAATTGATTTTTTCCAGCCGAATTTGATATCATAGTTGATTTTTTACTAAGTTCAAAGACATA
131 TTGAATTGATTTTTTCCAGCCGAATTTGATATCATAGTTGATTTTTTACTAAGTTCAAAGACATA
2776150 ATTGATTCTAATTTAAGGTTCAAGTACATCCTTAATATTTAAGAAAAAATAGGAAATTATTATTT
196 ATTGATTCTAATTTAAGGTTCAAGTACATCCTTAATATTTAAGAAAAAATAGGAAATTATTATTT
* * *
2776215 TTAAAATATTAATAAACTATTAAAATTGTTGAGGAGGTGGTCGGGTTGTAGTTTTAGTCGTCTCT
261 TTAAAATATTAATAAACTATTAAAATTGTTGAGGAGGTAGTAGGGTAGTAGTTTTAGTCGTCTCT
* *
2776280 TCTCTTATGATCTCTCCTGCATGGCTATTTATAGTTCTCTGGGCTTGGCCTTGGGTAGGAGTTGT
326 TCTCTTATGATCTCTCCTGCATGGCTATTTATAGTGCTCTAGGCTTGGCCTTGGGTAGGAGTTGT
2776345 CATTCCACTAATCCTTATTTTCTAC
391 CATTCCACTAATCCTTATTTTCTAC
*
2776370 AATTGCATTAATTTCGTTCTTTAATTGACATTGATTGTTCTTGTGTTTATGTGGCATTTACCAAT
1 AATTGCATTAATTTAGTTCTTTAATTGACATTGATTGTTCTTGTGTTTATGTGGCATTTACCAAT
* * *
2776435 GCTAAGGTGACGATCAACGATGTTGATACGACATTCTACATATGAATGATTATATGATATATGGG
66 GCTAAGGGGACGATCAACGATGTTGATACGACATTCTACATATGAATGATGACATGATATATGGG
*
2776500 TTGAATTGATTTTTTCCAGCCGAATTTGATATCATAGTTGATTTTTTTCTAAGTTCAAAGACATA
131 TTGAATTGATTTTTTCCAGCCGAATTTGATATCATAGTTGATTTTTTACTAAGTTCAAAGACATA
* * * *
2776565 TTTGATTCTAATTTAAGGTTCAAGTACTTCTTTAATATTTAAGAAATAATAGGAAATTATTATTT
196 ATTGATTCTAATTTAAGGTTCAAGTACATCCTTAATATTTAAGAAAAAATAGGAAATTATTATTT
*
2776630 TTTAAATATTAATAAACTATTAAAATTGTTGAGGAGGTAGTAGGGTAGTAGTTTTAGTCGTCTCT
261 TTAAAATATTAATAAACTATTAAAATTGTTGAGGAGGTAGTAGGGTAGTAGTTTTAGTCGTCTCT
* * * *
2776695 TTTGTTATGATCTTTCCTGCATGGCTATTTATAGTGCTCTAGGCTTGGCCTTGGGTAGGGGTTGT
326 TCTCTTATGATCTCTCCTGCATGGCTATTTATAGTGCTCTAGGCTTGGCCTTGGGTAGGAGTTGT
2776760 CATTCCACTAATCCTTATT
391 CATTCCACTAATCCTTATT
2776779 AGTTTTTCTT
Statistics
Matches: 389, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
415 389 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (415 bp):
AATTGCATTAATTTAGTTCTTTAATTGACATTGATTGTTCTTGTGTTTATGTGGCATTTACCAAT
GCTAAGGGGACGATCAACGATGTTGATACGACATTCTACATATGAATGATGACATGATATATGGG
TTGAATTGATTTTTTCCAGCCGAATTTGATATCATAGTTGATTTTTTACTAAGTTCAAAGACATA
ATTGATTCTAATTTAAGGTTCAAGTACATCCTTAATATTTAAGAAAAAATAGGAAATTATTATTT
TTAAAATATTAATAAACTATTAAAATTGTTGAGGAGGTAGTAGGGTAGTAGTTTTAGTCGTCTCT
TCTCTTATGATCTCTCCTGCATGGCTATTTATAGTGCTCTAGGCTTGGCCTTGGGTAGGAGTTGT
CATTCCACTAATCCTTATTTTCTAC
Found at i:2780869 original size:26 final size:26
Alignment explanation
Indices: 2780813--2780870 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2780803 TTACTCTAAA
2780813 TTTT-TTTAGAAAAAATCATTTCAAG
1 TTTTCTTTAGAAAAAATCATTTCAAG
* *
2780838 TATTTCTTTA-AAAAAATTATTTCTTAG
1 T-TTTCTTTAGAAAAAATCATTTC-AAG
2780865 TTTTCT
1 TTTTCT
2780871 CTTTCTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 20 0.71
27 7 0.25
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTTCTTTAGAAAAAATCATTTCAAG
Found at i:2781195 original size:31 final size:31
Alignment explanation
Indices: 2781154--2781220 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
2781144 TTGAAACTTA
* * *
2781154 CAATATAGTCCCCTAACATTTAGTCTGTTTG
1 CAATACAGTCCCCCAACATTTAGTCCGTTTG
2781185 CAATACAGTCCCCCAACATTTAGTCCGTTTG
1 CAATACAGTCCCCCAACATTTAGTCCGTTTG
2781216 CAATA
1 CAATA
2781221 TGGTCTCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (31 bp):
CAATACAGTCCCCCAACATTTAGTCCGTTTG
Found at i:2783178 original size:31 final size:31
Alignment explanation
Indices: 2783143--2783208 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2783133 GGTTACGTCA
* *
2783143 GGGACCATATTGTAAACGGACTAAATGTTAG
1 GGGACCATATTGCAAACAGACTAAATGTTAG
** * *
2783174 GGGACTGTATTGCAAATAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTAG
2783205 GGGA
1 GGGA
2783209 TTGTATTGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTAG
Found at i:2783935 original size:14 final size:14
Alignment explanation
Indices: 2783916--2783962 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
2783906 CTCAATTAAT
2783916 TTTATGTTTGTTCG
1 TTTATGTTTGTTCG
*
2783930 TTTATGCTTGTTCG
1 TTTATGTTTGTTCG
* *
2783944 TTTACGTTCGTTCG
1 TTTATGTTTGTTCG
2783958 TTTAT
1 TTTAT
2783963 CATTTTAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.09, C:0.13, G:0.19, T:0.60
Consensus pattern (14 bp):
TTTATGTTTGTTCG
Found at i:2788072 original size:14 final size:14
Alignment explanation
Indices: 2788032--2788078 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2788022 CTCAATTAAT
*
2788032 TTTATGTTCGTTCG
1 TTTATATTCGTTCG
* *
2788046 TTCATGCTT-GTTCG
1 TTTAT-ATTCGTTCG
2788060 TTTATATTCGTTCG
1 TTTATATTCGTTCG
2788074 TTTAT
1 TTTAT
2788079 CATTTTAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (14 bp):
TTTATATTCGTTCG
Found at i:2789897 original size:21 final size:21
Alignment explanation
Indices: 2789867--2789909 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2789857 ATCTACAAAA
2789867 TGTATATACGTTCAATTTACT
1 TGTATATACGTTCAATTTACT
*
2789888 TGTATGTACGTTCAATTTACT
1 TGTATATACGTTCAATTTACT
2789909 T
1 T
2789910 TGGGAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (21 bp):
TGTATATACGTTCAATTTACT
Found at i:2792660 original size:31 final size:32
Alignment explanation
Indices: 2792582--2792673 Score: 108
Period size: 27 Copynumber: 3.1 Consensus size: 32
2792572 GAATAAATTA
* *
2792582 AAAATTATCATTAAATTTTATCAGA----TA-
1 AAAATGATCATTAAATTTTATCAAACTTTTAC
2792609 AAAATGATCATTAAATTTTATCAAA-TTGTTAC
1 AAAATGATCATTAAATTTTATCAAACTT-TTAC
2792641 AAAATGATCATT-AATTTTATCAAACTTTTAC
1 AAAATGATCATTAAATTTTATCAAACTTTTAC
2792672 AA
1 AA
2792674 TTATTATAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
27 23 0.40
31 20 0.35
32 14 0.25
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (32 bp):
AAAATGATCATTAAATTTTATCAAACTTTTAC
Found at i:2795315 original size:59 final size:60
Alignment explanation
Indices: 2795215--2795345 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 60
2795205 ATACCATATG
* * * * *
2795215 TCCCTAAACTATGATCTTCATTTTAAATTAGGTTCTAAACTTTTGAAGAT-TCTAATTTCA
1 TCCCCAAACTATGATCTTCATTTTAAATTAGATCCTAAACTTTTGAACATATC-AAATTCA
* * * *
2795275 TCTCCAAACTATGCT-TTCATTTTAAATTA-ATCCCTGAACTTTTGATCATATCAAATTCA
1 TCCCCAAACTATGATCTTCATTTTAAATTAGAT-CCTAAACTTTTGAACATATCAAATTCA
2795334 TCCCCAAACTAT
1 TCCCCAAACTAT
2795346 AACTCTTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
58 1 0.02
59 44 0.75
60 14 0.24
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (60 bp):
TCCCCAAACTATGATCTTCATTTTAAATTAGATCCTAAACTTTTGAACATATCAAATTCA
Found at i:2796613 original size:45 final size:45
Alignment explanation
Indices: 2796509--2796594 Score: 122
Period size: 43 Copynumber: 1.9 Consensus size: 45
2796499 GATCCGAATA
* *
2796509 TATTAATATTTTAAAATAATTAAAATAATATATATTTTATAATTTTT
1 TATT-ATATTTTAAACT-GTTAAAATAATATATATTTTATAATTTTT
2796556 TATTATATTTTAAACTGTTAAAATAAT-T-TATTTTATAAT
1 TATTATATTTTAAACTGTTAAAATAATATATATTTTATAAT
2796595 AAAATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 11 0.30
44 1 0.03
45 10 0.27
46 11 0.30
47 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (45 bp):
TATTATATTTTAAACTGTTAAAATAATATATATTTTATAATTTTT
Found at i:2796634 original size:21 final size:22
Alignment explanation
Indices: 2796603--2796647 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2796593 ATAAAATTTT
*
2796603 TATATTTTTAATAAT-TAAAGAA
1 TATATTTTTAACAATATAAA-AA
2796625 TATA-TTTTAACAATATAAAAA
1 TATATTTTTAACAATATAAAAA
2796646 TA
1 TA
2796648 AAAATTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TATATTTTTAACAATATAAAAA
Found at i:2797019 original size:2 final size:2
Alignment explanation
Indices: 2796979--2797008 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2796969 ACGCACATAC
2796979 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
2797009 GCTATTATAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2803769 original size:21 final size:21
Alignment explanation
Indices: 2803743--2803783 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2803733 TCGTAGTTTC
2803743 TTTTGAGCATTCGATTCATGA
1 TTTTGAGCATTCGATTCATGA
*
2803764 TTTTGAGCATTTGATTCATG
1 TTTTGAGCATTCGATTCATG
2803784 GTTATTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (21 bp):
TTTTGAGCATTCGATTCATGA
Found at i:2805373 original size:42 final size:44
Alignment explanation
Indices: 2805302--2805392 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 44
2805292 AAGGTAATTA
* * *
2805302 GCGGCTTTTGTATCCAAAAACGCAGTTATAGAT-TTGATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCAGTTATAGATCTTGACCTATT
*
2805345 GCGGCGTTTGT-TCCAAAAATGCCA-TTATAGATCTTGACCTATT
1 GCGGCGTTTGTATCCAAAAACG-CAGTTATAGATCTTGACCTATT
2805388 GCGGC
1 GCGGC
2805393 ATTTTTTGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 17 0.40
43 25 0.60
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (44 bp):
GCGGCGTTTGTATCCAAAAACGCAGTTATAGATCTTGACCTATT
Found at i:2805705 original size:22 final size:21
Alignment explanation
Indices: 2805661--2805724 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
2805651 TAATATATAT
* *
2805661 TAAATATAAAAATATCAAAAAA
1 TAAA-ATAAATATATTAAAAAA
2805683 TAATAATTAAAT-TATTAAAAAA
1 TAA-AA-TAAATATATTAAAAAA
*
2805705 TAAAATATATATATTAAAAA
1 TAAAATAAATATATTAAAAA
2805725 CACTATCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 4 0.11
21 11 0.31
22 16 0.44
23 5 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATAAATATATTAAAAAA
Found at i:2805709 original size:29 final size:29
Alignment explanation
Indices: 2805652--2805722 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
2805642 TATTTTTAAT
2805652 AATATATATTAAATATAAAAATATCAAAA
1 AATATATATTAAATATAAAAATATCAAAA
2805681 AATA-ATAATTAAATTATTAAAAA-AT-AAAA
1 AATATAT-ATTAAA-TA-TAAAAATATCAAAA
*
2805710 TATATATATTAAA
1 AATATATATTAAA
2805723 AACACTATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
28 2 0.05
29 23 0.62
30 6 0.16
31 6 0.16
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
AATATATATTAAATATAAAAATATCAAAA
Found at i:2805720 original size:24 final size:22
Alignment explanation
Indices: 2805677--2805724 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
2805667 TAAAAATATC
2805677 AAAAAATAATAATTAAATTATT
1 AAAAAATAATAATTAAATTATT
*
2805699 AAAAAATAA-AA-TATATATATT
1 AAAAAATAATAATTAAAT-TATT
2805720 AAAAA
1 AAAAA
2805725 CACTATCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 9 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAATAATAATTAAATTATT
Found at i:2805929 original size:21 final size:21
Alignment explanation
Indices: 2805905--2806064 Score: 91
Period size: 20 Copynumber: 7.8 Consensus size: 21
2805895 CGCAACATAG
2805905 TTTCCAAATTCGCAACGCGAA
1 TTTCCAAATTCGCAACGCGAA
* ** *
2805926 TTTCCCAAATTCCCAAC-TTAT
1 TTT-CCAAATTCGCAACGCGAA
* * *
2805947 TTTCTGAAA-TCACAACGCGGA
1 TTTC-CAAATTCGCAACGCGAA
*** *
2805968 TTT-CTTTTTTGCAACGC-AA
1 TTTCCAAATTCGCAACGCGAA
* *
2805987 TTTTCCAAATTTGCAACGTG-A
1 -TTTCCAAATTCGCAACGCGAA
**
2806008 TTTTAAAATTCGCAACGCG-A
1 TTTCCAAATTCGCAACGCGAA
*
2806028 TTTCCAAATTCGCAACACGGAA
1 TTTCCAAATTCGCAACGC-GAA
2806050 TTT-CAAATTCGCAAC
1 TTTCCAAATTCGCAAC
2806065 TTGATTTCTG
Statistics
Matches: 102, Mismatches: 28, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
19 1 0.01
20 48 0.47
21 37 0.36
22 16 0.16
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (21 bp):
TTTCCAAATTCGCAACGCGAA
Found at i:2806022 original size:20 final size:20
Alignment explanation
Indices: 2805986--2806084 Score: 85
Period size: 20 Copynumber: 4.8 Consensus size: 20
2805976 TTGCAACGCA
*
2805986 ATTTTCCAAATTTGCAACGTG
1 ATTTT-CAAATTCGCAACGTG
* *
2806007 ATTTTAAAATTCGCAACGCG
1 ATTTTCAAATTCGCAACGTG
*
2806027 ATTTCCAAATTCGCAACACG-G
1 ATTTTCAAATTCGC-A-ACGTG
* *
2806048 AATTTCAAATTCGCAACTTG
1 ATTTTCAAATTCGCAACGTG
*
2806068 A-TTTCTGAATTCGCAAC
1 ATTTTC-AAATTCGCAAC
2806085 ACAAGTTTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.09
20 37 0.57
21 19 0.29
22 3 0.05
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (20 bp):
ATTTTCAAATTCGCAACGTG
Found at i:2806058 original size:41 final size:40
Alignment explanation
Indices: 2805978--2806172 Score: 140
Period size: 40 Copynumber: 4.8 Consensus size: 40
2805968 TTTCTTTTTT
* * ** * *
2805978 GCAACGCAATTTTCCAAATTTGCAACGTGATTTTAAAATTC
1 GCAACGCGA-TTTCCAAATTCGCAACACGAATTTCAAATTC
2806019 GCAACGCGATTTCCAAATTCGCAACACGGAATTTCAAATTC
1 GCAACGCGATTTCCAAATTCGCAACAC-GAATTTCAAATTC
** ** ***
2806060 GCAACTTGATTTCTGAATTCGCAACAC-AAGTTTCCTTTTC
1 GCAACGCGATTTCCAAATTCGCAACACGAA-TTTCAAATTC
** * * * **
2806100 GCAACAAGATTTTCTAATTCGCAACACGAATTTTATTTTC
1 GCAACGCGATTTCCAAATTCGCAACACGAATTTCAAATTC
* * * *
2806140 GCAACTCGATTTTCGAATTCGCAACATGAATTT
1 GCAACGCGATTTCCAAATTCGCAACACGAATTT
2806173 TAATTTTGCA
Statistics
Matches: 127, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 81 0.64
41 44 0.35
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (40 bp):
GCAACGCGATTTCCAAATTCGCAACACGAATTTCAAATTC
Found at i:2806113 original size:20 final size:19
Alignment explanation
Indices: 2806085--2806203 Score: 64
Period size: 20 Copynumber: 6.2 Consensus size: 19
2806075 AATTCGCAAC
*
2806085 ACAAG-TTTCCTTTTCGCA
1 ACAAGATTTTCTTTTCGCA
*
2806103 ACAAGATTTTCTAATTCGCA
1 ACAAGATTTTCT-TTTCGCA
* *
2806123 ACACGAATTTTATTTTCGCA
1 ACAAG-ATTTTCTTTTCGCA
** **
2806143 ACTCGATTTTCGAATTCGCA
1 ACAAGATTTTC-TTTTCGCA
* *
2806163 ACATGAATTTTAATTTT-GCA
1 ACAAG-ATTTT-CTTTTCGCA
* *
2806183 AC-AGCTTTTATTTTCGCA
1 ACAAGATTTTCTTTTCGCA
2806201 ACA
1 ACA
2806204 CAAATGTTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
17 5 0.06
18 14 0.18
19 11 0.14
20 34 0.44
21 13 0.17
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (19 bp):
ACAAGATTTTCTTTTCGCA
Found at i:2806119 original size:40 final size:40
Alignment explanation
Indices: 2806016--2806185 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
2806006 GATTTTAAAA
** * * **
2806016 TTCGCAACGCGATTTCCAAATTCGCAACACGGAATTTCAAA
1 TTCGCAACAAGATTTTCTAATTCGCAACAC-GAATTTCATT
** *
2806057 TTCGCAACTTGA-TTTCTGAATTCGCAACAC-AAGTTTCCTT
1 TTCGCAACAAGATTTTCT-AATTCGCAACACGAA-TTTCATT
*
2806097 TTCGCAACAAGATTTTCTAATTCGCAACACGAATTTTATT
1 TTCGCAACAAGATTTTCTAATTCGCAACACGAATTTCATT
** * * *
2806137 TTCGCAACTCGATTTTCGAATTCGCAACATGAATTTTAATT
1 TTCGCAACAAGATTTTCTAATTCGCAACACGAA-TTTCATT
2806178 TT-GCAACA
1 TTCGCAACA
2806186 GCTTTTATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.02
40 68 0.64
41 37 0.35
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (40 bp):
TTCGCAACAAGATTTTCTAATTCGCAACACGAATTTCATT
Found at i:2807125 original size:24 final size:24
Alignment explanation
Indices: 2807110--2807165 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2807100 CAGTATTCGA
*
2807110 AATTTGATCTTGGTCAATACTCTG
1 AATTTGATCTTGGTCAATATTCTG
* *
2807134 ACTTTGATCTTGGTCAATATTCAG
1 AATTTGATCTTGGTCAATATTCTG
*
2807158 ATTTTGAT
1 AATTTGAT
2807166 GATATTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (24 bp):
AATTTGATCTTGGTCAATATTCTG
Found at i:2809449 original size:12 final size:12
Alignment explanation
Indices: 2809434--2809467 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2809424 GGGAAATCAA
2809434 AATCAAAATCGT
1 AATCAAAATCGT
*
2809446 AATCAAAATTGT
1 AATCAAAATCGT
2809458 AATCAAAATC
1 AATCAAAATC
2809468 AAAATCCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (12 bp):
AATCAAAATCGT
Found at i:2809761 original size:20 final size:20
Alignment explanation
Indices: 2809733--2809786 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2809723 TGATTGTTGT
*
2809733 GAAAGTCAAATTTGCAACAC
1 GAAAATCAAATTTGCAACAC
*
2809753 GAAAATCAAATTCGCAACAC
1 GAAAATCAAATTTGCAACAC
*
2809773 GAAAATCGAATTTG
1 GAAAATCAAATTTG
2809787 ACATGCGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (20 bp):
GAAAATCAAATTTGCAACAC
Found at i:2809863 original size:20 final size:20
Alignment explanation
Indices: 2809840--2809886 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2809830 CAATCGCAAC
*
2809840 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
**
2809860 GCGAATTTGGTTTTCGCATT
1 GCGAATTTGACTTTCGCATT
2809880 GCGAATT
1 GCGAATT
2809887 AAATTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:2809893 original size:20 final size:20
Alignment explanation
Indices: 2809851--2809894 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2809841 CGAATTTGAC
* ***
2809851 TTTCGCGTTGCGAATTTGGT
1 TTTCGCATTGCGAATTAAAT
2809871 TTTCGCATTGCGAATTAAAT
1 TTTCGCATTGCGAATTAAAT
2809891 TTTC
1 TTTC
2809895 TTAAAGGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (20 bp):
TTTCGCATTGCGAATTAAAT
Found at i:2809969 original size:15 final size:15
Alignment explanation
Indices: 2809951--2809979 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2809941 TACAAATTGA
2809951 AATTAAACAAAAAAC
1 AATTAAACAAAAAAC
2809966 AATTAAACAAAAAA
1 AATTAAACAAAAAA
2809980 AAAATTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (15 bp):
AATTAAACAAAAAAC
Found at i:2809985 original size:16 final size:15
Alignment explanation
Indices: 2809950--2809982 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2809940 ATACAAATTG
2809950 AAATTAAACAAAAAA
1 AAATTAAACAAAAAA
*
2809965 CAATTAAACAAAAAA
1 AAATTAAACAAAAAA
2809980 AAA
1 AAA
2809983 ATTCTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (15 bp):
AAATTAAACAAAAAA
Found at i:2810609 original size:21 final size:21
Alignment explanation
Indices: 2810585--2810635 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2810575 AGGTGGATCC
2810585 TGAACGATGGAAGGGGCCTCT
1 TGAACGATGGAAGGGGCCTCT
* * * *
2810606 TGAATGATGGGAGGGTCTTCT
1 TGAACGATGGAAGGGGCCTCT
2810627 TGAACGATG
1 TGAACGATG
2810636 ACAGGTGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.25
Consensus pattern (21 bp):
TGAACGATGGAAGGGGCCTCT
Found at i:2810662 original size:21 final size:21
Alignment explanation
Indices: 2810638--2810678 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2810628 GAACGATGAC
*
2810638 AGGTGAATCCTGAACAATGGG
1 AGGTGAATCATGAACAATGGG
* *
2810659 AGGTGGATCATGAATAATGG
1 AGGTGAATCATGAACAATGG
2810679 TAAGTGGATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.34, T:0.22
Consensus pattern (21 bp):
AGGTGAATCATGAACAATGGG
Found at i:2810996 original size:21 final size:21
Alignment explanation
Indices: 2810972--2811025 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2810962 TAAAACAATC
* *
2810972 TCACGTAGAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
2810993 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
* *
2811014 CCACATAAAGCA
1 TCACGTAAAGCA
2811026 CCATTGTCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:2811078 original size:42 final size:43
Alignment explanation
Indices: 2810986--2811081 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
2810976 GTAGAGCAGC
*
2810986 TACCTCATCACGTAAAGTAGATACCTCACCACATAAAGCACCA
1 TACCTCATCACGTAAAATAGATACCTCACCACATAAAGCACCA
** * * * * *
2811029 T-TGTCATCGCGTAAAATAGCTACCTCTCCACGTAAA-CACCG
1 TACCTCATCACGTAAAATAGATACCTCACCACATAAAGCACCA
2811070 TACCTCATCACG
1 TACCTCATCACG
2811082 CCATGCACCA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
41 5 0.12
42 35 0.85
43 1 0.02
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (43 bp):
TACCTCATCACGTAAAATAGATACCTCACCACATAAAGCACCA
Found at i:2811122 original size:21 final size:21
Alignment explanation
Indices: 2811098--2811147 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2811088 ACCATTGTCG
*
2811098 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
** *
2811119 TCACACAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
2811140 TCACGTAA
1 TCACGTAA
2811148 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.34, G:0.12, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:2811321 original size:42 final size:42
Alignment explanation
Indices: 2811262--2811359 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
2811252 GTGATGGAAT
* * * **
2811262 AGGTGATGGCTCTCGGTGTCTAGGTATATAATTGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCAGCTCGATC
*
2811304 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCAGCTCGATC
*
2811346 AAGTGATGGCTCTC
1 AGGTGATGGCTCTC
2811360 AAAGTGGGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCAGCTCGATC
Found at i:2812875 original size:20 final size:20
Alignment explanation
Indices: 2812852--2812889 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2812842 TTTGAAACTT
2812852 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
2812872 AAATTCGCAACGCGAAAA
1 AAATTCGCAACACGAAAA
2812890 CTAAAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:2813547 original size:20 final size:20
Alignment explanation
Indices: 2813524--2813565 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2813514 TGCAATTTCA
* *
2813524 GAAACTGAGTTGCGAATTTG
1 GAAACAGAGTTGCGAAATTG
*
2813544 GAAACAGTGTTGCGAAATTG
1 GAAACAGAGTTGCGAAATTG
2813564 GA
1 GA
2813566 GTTCGTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (20 bp):
GAAACAGAGTTGCGAAATTG
Found at i:2813934 original size:23 final size:22
Alignment explanation
Indices: 2813908--2813960 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
2813898 ATTTTTTACT
2813908 ATTTTTATTTTTAATAATTTATG
1 ATTTTTATTTTT-ATAATTTATG
* * *
2813931 ATTTATCATTTTTTTAGTTTATG
1 ATTT-TTATTTTTATAATTTATG
2813954 ATGTTTT
1 AT-TTTT
2813961 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.66
Consensus pattern (22 bp):
ATTTTTATTTTTATAATTTATG
Found at i:2819024 original size:16 final size:17
Alignment explanation
Indices: 2818974--2819025 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
2818964 TAAAAAAATA
2818974 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
2818991 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
2819006 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
2819022 AATT
1 AATT
2819026 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:2819039 original size:32 final size:32
Alignment explanation
Indices: 2818974--2819039 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
2818964 TAAAAAAATA
* **
2818974 AATTTGAAAGTTAGAGTGATTAAATTAGGAGT
1 AATTTGAAAGTTAGAGTAATTAAATTAAAAGT
2819006 AATTTGAAAGTTA-AGTAATTAAATTAAAAAGT
1 AATTTGAAAGTTAGAGTAATTAAATT-AAAAGT
2819038 AA
1 AA
2819040 ATTTTTGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (32 bp):
AATTTGAAAGTTAGAGTAATTAAATTAAAAGT
Found at i:2820418 original size:27 final size:28
Alignment explanation
Indices: 2820362--2820418 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
2820352 ATTTAAATTT
*
2820362 AAATATTTAATAGATTCAATTTTTTAAA
1 AAATATTTAATAGATTCAATTATTTAAA
* *
2820390 AAATA-TTAATA-ATTTAATCTATTTCAA
1 AAATATTTAATAGATTCAAT-TATTTAAA
2820417 AA
1 AA
2820419 TGTTATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATATTTAATAGATTCAATTATTTAAA
Found at i:2820418 original size:28 final size:28
Alignment explanation
Indices: 2820362--2820418 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
2820352 ATTTAAATTT
*
2820362 AAATATTTAATAGATTCAATTTTTTAAA
1 AAATATTTAATAGATTCAATTTTTCAAA
*
2820390 AAATA-TTAATA-ATTTAATCTATTTCAAA
1 AAATATTTAATAGATTCAAT-T-TTTCAAA
2820418 A
1 A
2820419 TGTTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 6 0.24
27 7 0.28
28 12 0.48
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATATTTAATAGATTCAATTTTTCAAA
Found at i:2821583 original size:16 final size:16
Alignment explanation
Indices: 2821562--2821594 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2821552 ACATACATAT
*
2821562 ATTTTTATATTATTAA
1 ATTTTTATATTAATAA
2821578 ATTTTTATATTAATAA
1 ATTTTTATATTAATAA
2821594 A
1 A
2821595 ATTCTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTATATTAATAA
Found at i:2826608 original size:19 final size:19
Alignment explanation
Indices: 2826568--2826609 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
2826558 AAGTTTTCAT
*
2826568 TAAATAAATAATTCAATTA
1 TAAATAAATAATTAAATTA
*
2826587 TAAAT-AATTATTAAATTGA
1 TAAATAAATAATTAAATT-A
2826606 TAAA
1 TAAA
2826610 GGACTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAATAAATAATTAAATTA
Found at i:2828194 original size:36 final size:38
Alignment explanation
Indices: 2828121--2828194 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
2828111 AACACTAAAC
2828121 CTAGGAAGAGTAAAATATGATTTTACCCTAAAGTTTTG
1 CTAGGAAGAGTAAAATATGATTTTACCCTAAAGTTTTG
2828159 CTAGG-AGAGTAAAATATGATTTTA-CCTAAAGTTTTG
1 CTAGGAAGAGTAAAATATGATTTTACCCTAAAGTTTTG
2828195 ATGGTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 12 0.33
37 19 0.53
38 5 0.14
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (38 bp):
CTAGGAAGAGTAAAATATGATTTTACCCTAAAGTTTTG
Found at i:2829427 original size:3 final size:3
Alignment explanation
Indices: 2829419--2829499 Score: 100
Period size: 3 Copynumber: 27.7 Consensus size: 3
2829409 TTATATATTA
2829419 AAT AAT AAT AAAT AAT AAT AAT AAT -AT AAT -AT AAAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
2829464 -AT AAAT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AA
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2829500 CCAGGATGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
2 10 0.14
3 53 0.76
4 7 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2829459 original size:26 final size:28
Alignment explanation
Indices: 2829419--2829495 Score: 103
Period size: 26 Copynumber: 3.0 Consensus size: 28
2829409 TTATATATTA
*
2829419 AATAATAATA-AATAATAATAATAATAT
1 AATAATAAAATAATAATAATAATAATAT
2829446 AAT-AT-AAATAATAATAAT-ATAA-AT
1 AATAATAAAATAATAATAATAATAATAT
2829470 AATAATAAAATAATAATAA-AATAATA
1 AATAATAAAATAATAATAATAATAATA
2829496 ATAACCAGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
24 5 0.11
25 8 0.18
26 27 0.61
27 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAATAAAATAATAATAATAATAATAT
Found at i:2829499 original size:11 final size:11
Alignment explanation
Indices: 2829418--2829499 Score: 103
Period size: 11 Copynumber: 7.1 Consensus size: 11
2829408 ATTATATATT
2829418 AAATAATAATAA
1 AAATAATAAT-A
2829430 ATAATAATAATA
1 A-AATAATAATA
*
2829442 ATATAAT-ATAA
1 AAATAATAAT-A
2829453 ATAATAATAATA
1 A-AATAATAATA
2829465 TAAATAATAATA
1 -AAATAATAATA
2829477 AAATAATAATA
1 AAATAATAATA
2829488 AAATAATAATA
1 AAATAATAATA
2829499 A
1 A
2829500 CCAGGATGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.03
11 30 0.48
12 19 0.30
13 12 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATAATAATA
Found at i:2829893 original size:41 final size:41
Alignment explanation
Indices: 2829848--2829949 Score: 96
Period size: 42 Copynumber: 2.5 Consensus size: 41
2829838 AAGGTCTTAT
*
2829848 AGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTATCATCTCGCTCAAAAGACTGAC
* * * * * * * *
2829889 AGATGACCCCAAAGATTTAATCATTTTGTTCAAAAGACTTAC
1 AGATGGCCCGAAGGACTT-ATCATCTCGCTCAAAAGACTGAC
* *
2829931 TGATGGCCTGAAGGACTTA
1 AGATGGCCCGAAGGACTTA
2829950 CCAATTTGGG
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
41 15 0.33
42 30 0.67
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCTCGCTCAAAAGACTGAC
Found at i:2830170 original size:260 final size:256
Alignment explanation
Indices: 2829620--2830524 Score: 1131
Period size: 260 Copynumber: 3.5 Consensus size: 256
2829610 GTCTCAAGTG
* * * * * * *
2829620 AGACTGACATATAACCTGAAGGATTTAATAATCATGCTCGAAAGACTTACTGATGGCCCAAATGG
1 AGACTGACAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAA-GG
*
2829685 -CTCACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAA
65 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAA
*
2829749 AATTTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTGCTTTTCTCATTTTTCAAAAA
130 AAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATT-CTTTTCTCATTTTTCAAAAA
* * * * *
2829814 CATCATATGAAAACATCTTTCCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTCGCTCG
194 CATCA-A--AAAA-ATCATGCCCAAAGATCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCG
2829879 AA
255 AA
* ** * *
2829881 AGACTGACAGATGACCCCAAAGATTTAATCATTTTGTTCAAAAGACTTACTGATGGCCTGAAGGA
1 AGACTGACAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGA
* *
2829946 CTTACCAATTTGGGAAATAGTTTACTAGGTAATAAAC-TTGGAAATCACTTTCTTACTTTTCAAA
66 CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTC-AA
* * * *
2830010 AAATTTCATTTTCTCAAAACATTAAATGAGAAACCTTGAAAATTACTTTTATCATTGTTCGAAAA
130 AAATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATT-CTTTTCTCATTTTTC-AAAA
* * * *
2830075 ACCTTCCAAAAAAATAATGCCCAAAGATCTTATAGATGGCACAAAGGACTTAACATCTTGCTCGA
193 A-CAT-CAAAAAAATCATGCCCAAAGATCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCGA
2830140 A
256 A
* * **
2830141 AGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAATA
1 AGACTGACAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGA
* * ** *
2830206 CTTACTAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGTTTTCTTATTTTTCAAA
66 CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAA
* * *
2830271 AATTTCATTTTCTGAAAATATTAAATGAG-AA-TTGTGAAAATTGTGTTTCTTATTTTTCAAAAA
131 AATTTCATTTTCTGAAAACATTAAATGAGAAACTT-TGAAAATTCT-TTTCTCATTTTTCAAAAA
* * * *
2830334 TCAT-ATGAAAACATCATGGCCGAAGGA-CTTATAGATGGCCCGAAGGACTTAACATCTTGCTTG
194 -CATCA--AAAAAATCAT-GCCCAAAGATCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCG
2830397 AA
255 AA
* * * *
2830399 AGACTGACATATGACCCGAAAGATTTAATCCTCATGCTTGAAAA-ACTTACTGATGGCCCTAAGG
1 AGACTGACAGATGACCCGAAAGATTTAATCATCATGC-TCAAAAGACTTACTGATGGCCCGAAGG
* * *
2830463 ACTTACTAATTTTGGAAATAGTTTAATAGGTAAGAAACTTTGGAAATCACTTTTTTACTTTT
65 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTT
2830525 TTACTTTGGA
Statistics
Matches: 556, Mismatches: 76, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
256 1 0.00
258 159 0.29
259 31 0.06
260 190 0.34
261 165 0.30
262 5 0.01
263 3 0.01
264 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (256 bp):
AGACTGACAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGA
CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAA
AATTTCATTTTCTGAAAACATTAAATGAGAAACTTTGAAAATTCTTTTCTCATTTTTCAAAAACA
TCAAAAAAATCATGCCCAAAGATCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCGAA
Found at i:2830179 original size:42 final size:41
Alignment explanation
Indices: 2830118--2830202 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
2830108 AGATGGCACA
*
2830118 AAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCG
1 AAGGACTTAACATCATGCTCGAAAGACTGACAGATGACCCG
* * * *
2830159 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCG
1 AAGGACTTAA-CATCATGCTCGAAAGACTGACAGATGACCCG
2830201 AA
1 AA
2830203 ATACTTACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 9 0.24
42 29 0.76
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
AAGGACTTAACATCATGCTCGAAAGACTGACAGATGACCCG
Found at i:2830417 original size:41 final size:42
Alignment explanation
Indices: 2830367--2830467 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
2830357 AGGACTTATA
* * *
2830367 GATGGCCCGAAGGACTTAA-CATCTTGCTTGAAAGACTGACAT
1 GATGACCCGAAGGACTTAATCATCATGCTTGAAAAACTGAC-T
* * * *
2830409 -ATGACCCGAAAGATTTAATCCTCATGCTTGAAAAACTTACT
1 GATGACCCGAAGGACTTAATCATCATGCTTGAAAAACTGACT
* *
2830450 GATGGCCCTAAGGACTTA
1 GATGACCCGAAGGACTTA
2830468 CTAATTTTGG
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
GATGACCCGAAGGACTTAATCATCATGCTTGAAAAACTGACT
Found at i:2830530 original size:28 final size:28
Alignment explanation
Indices: 2830499--2830552 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2830489 TAGGTAAGAA
**
2830499 ACTTTGGAAATCACTTTTTTACTTTTTT
1 ACTTTGGAAATCACTTTCGTACTTTTTT
2830527 ACTTTGGAAATCACTTTCGTACTTTT
1 ACTTTGGAAATCACTTTCGTACTTTT
2830553 CAAAATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (28 bp):
ACTTTGGAAATCACTTTCGTACTTTTTT
Found at i:2839648 original size:174 final size:177
Alignment explanation
Indices: 2839358--2839708 Score: 681
Period size: 174 Copynumber: 2.0 Consensus size: 177
2839348 CTAAACCGTC
2839358 TGCCCTTTTTTTGTGAGAGTTCTCAAACTCTCTCTTTCGGTCGCCTCCTTCAAAGCTAGAGGGCC
1 TGCCCTTTTTTTGTGAGAGTTCTCAAACTCTCTCTTTCGGTCGCCTCCTTCAAAGCTAGAGGGCC
2839423 CCTCGCTGGTGCCGGCCACCATGTTTTGGTGGTTATCTCTATCTCCGATAGCC-TTCCCCTTGG-
66 CCTCGCTGGTGCCGGCCACCATGTTTTGGTGGTTATCTCTATCTCCGATAGCCTTTCCCCTTGGC
2839486 CAGAGAACCC-AAACAGACCCCAAATAGAATCTCATCTCTTCCAAAA
131 CAGAGAACCCAAAACAGACCCCAAATAGAATCTCATCTCTTCCAAAA
2839532 TGCCCTTTTTTTGTGAGAGTTCTCAAACTCTCTCTTTCGGTCGCCTCCTTCAAAGCTAGAGGGCC
1 TGCCCTTTTTTTGTGAGAGTTCTCAAACTCTCTCTTTCGGTCGCCTCCTTCAAAGCTAGAGGGCC
2839597 CCTCGCTGGTGCCGGCCACCATGTTTTGGTGGTTATCTCTATCTCCGATAGCCTTTCCCCTTGGC
66 CCTCGCTGGTGCCGGCCACCATGTTTTGGTGGTTATCTCTATCTCCGATAGCCTTTCCCCTTGGC
2839662 CAGAGAACCCAAAACAGACCCCAAATAGAATCTCATCTCTTCCAAAA
131 CAGAGAACCCAAAACAGACCCCAAATAGAATCTCATCTCTTCCAAAA
2839709 CCCCTACTTC
Statistics
Matches: 174, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
174 118 0.68
175 10 0.06
176 10 0.06
177 36 0.21
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (177 bp):
TGCCCTTTTTTTGTGAGAGTTCTCAAACTCTCTCTTTCGGTCGCCTCCTTCAAAGCTAGAGGGCC
CCTCGCTGGTGCCGGCCACCATGTTTTGGTGGTTATCTCTATCTCCGATAGCCTTTCCCCTTGGC
CAGAGAACCCAAAACAGACCCCAAATAGAATCTCATCTCTTCCAAAA
Found at i:2840727 original size:3 final size:3
Alignment explanation
Indices: 2840719--2840788 Score: 72
Period size: 3 Copynumber: 22.7 Consensus size: 3
2840709 ATATGCATTA
*
2840719 AAT AAT AAT AAT AAAT ATT AAT AAT AAAT AAT AAT AAT -AT AA- ATAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT
*
2840765 AAAT AAT AAT AAA AAT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AAT AA
2840789 CCCAGACAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 3 0.05
3 45 0.79
4 8 0.14
5 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2840735 original size:13 final size:13
Alignment explanation
Indices: 2840717--2840788 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
2840707 ATATATGCAT
2840717 TAAATAATAATAA
1 TAAATAATAATAA
*
2840730 TAAATATTAATAA
1 TAAATAATAATAA
2840743 TAAATAATAATAA
1 TAAATAATAATAA
2840756 T--AT-A-AAT-A
1 TAAATAATAATAA
2840764 TAAATAATAATAA
1 TAAATAATAATAA
2840777 -AAATAATAATAA
1 TAAATAATAATAA
2840789 CCCAGACAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
8 2 0.04
9 3 0.06
10 3 0.06
11 3 0.06
12 15 0.29
13 26 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATAATAATAA
Found at i:2840740 original size:10 final size:10
Alignment explanation
Indices: 2840719--2840785 Score: 70
Period size: 10 Copynumber: 6.8 Consensus size: 10
2840709 ATATGCATTA
2840719 AATAAT-AAT
1 AATAATAAAT
*
2840728 AATAA-ATATT
1 AATAATA-AAT
2840738 AATAATAAAT
1 AATAATAAAT
2840748 AATAATAATAT
1 AATAATAA-AT
2840759 AA-ATATAAAT
1 AATA-ATAAAT
2840769 AATAATAAA-
1 AATAATAAAT
2840778 AATAATAA
1 AATAATAA
2840786 TAACCCAGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
9 13 0.26
10 27 0.54
11 10 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAAAT
Found at i:2840742 original size:16 final size:16
Alignment explanation
Indices: 2840719--2840788 Score: 89
Period size: 15 Copynumber: 4.7 Consensus size: 16
2840709 ATATGCATTA
2840719 AATAATAATAATAAAT
1 AATAATAATAATAAAT
2840735 -AT--TAATAATAAAT
1 AATAATAATAATAAAT
2840748 AATAATAAT-ATAAAT
1 AATAATAATAATAAAT
2840763 -ATAAATAATAATAAA-
1 AAT-AATAATAATAAAT
2840778 AATAATAATAA
1 AATAATAATAA
2840789 CCCAGACAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.23
14 4 0.08
15 22 0.46
16 11 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATAATAATAAAT
Found at i:2840769 original size:18 final size:15
Alignment explanation
Indices: 2840719--2840788 Score: 88
Period size: 16 Copynumber: 4.5 Consensus size: 15
2840709 ATATGCATTA
2840719 AATAATAATAATAAAT
1 AATAATAATAA-AAAT
*
2840735 ATTAATAATAAATAAT
1 AATAATAATAAA-AAT
*
2840751 AATAAT-ATAAATAT
1 AATAATAATAAAAAT
2840765 AAATAATAATAAAAAT
1 -AATAATAATAAAAAT
2840781 AATAATAA
1 AATAATAA
2840789 CCCAGACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
14 2 0.04
15 20 0.43
16 25 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATAATAAAAAT
Found at i:2849036 original size:12 final size:12
Alignment explanation
Indices: 2849015--2849044 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2849005 GAAAGTATGG
2849015 GAAAAATAGAGA
1 GAAAAATAGAGA
*
2849027 GAAAACTAGAGA
1 GAAAAATAGAGA
2849039 GAAAAA
1 GAAAAA
2849045 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:2849161 original size:19 final size:20
Alignment explanation
Indices: 2849117--2849173 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
2849107 GCCTTCAAAT
2849117 TCTTAAAAAC-AAGTTAAAACA
1 TCTT-AAAACTAA-TTAAAACA
*
2849138 TCTTAAACCTAATTAAAACA
1 TCTTAAAACTAATTAAAACA
*
2849158 -CTTAAAACTATTTAAA
1 TCTTAAAACTAATTAAA
2849174 CTAAAATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
20 12 0.38
21 6 0.19
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.30
Consensus pattern (20 bp):
TCTTAAAACTAATTAAAACA
Found at i:2849240 original size:71 final size:74
Alignment explanation
Indices: 2849141--2849329 Score: 237
Period size: 76 Copynumber: 2.6 Consensus size: 74
2849131 TAAAACATCT
* * *
2849141 TAAACCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATATCT--AA-AAA-A-TAATATTTA
1 TAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATTAATA-TAA
*
2849200 AAATAATATTC
64 AAATAATATCC
2849211 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATTAAATATAA
1 TAAA-CCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATT-AATATAA
2849276 AAATAATATCC
64 AAATAATATCC
* *
2849287 TAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATAC
1 T-AAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
2849330 ATAGATAAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
70 9 0.09
71 32 0.31
73 2 0.02
74 3 0.03
75 1 0.01
76 50 0.48
77 7 0.07
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.30
Consensus pattern (74 bp):
TAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATTAATATAAAA
ATAATATCC
Found at i:2849301 original size:76 final size:71
Alignment explanation
Indices: 2849142--2849365 Score: 236
Period size: 76 Copynumber: 3.0 Consensus size: 71
2849132 AAAACATCTT
* * *
2849142 AAACCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATATCTAAAAAATAATATTTAAAATAA
1 AAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAATAATATTAAAAATAA
*
2849206 TATTCTA
65 TATCCTA
*
2849213 AATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA-AGATTAAATATAAA
1 AAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AATA-A-T--AT-TAAA
2849277 AATAATATCCTA
60 AATAATATCCTA
* * * * *
2849289 AAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACATAGATAAAATATAATGTTTAAAA
1 AAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--A-AAAA-ATAATATTAAAAA
*
2849354 TATTATCCTA
62 TAATATCCTA
2849364 AA
1 AA
2849366 CTTGAGTTTA
Statistics
Matches: 129, Mismatches: 12, Indels: 20
0.80 0.07 0.12
Matches are distributed among these distances:
70 5 0.04
71 39 0.30
72 3 0.02
73 1 0.01
75 18 0.14
76 54 0.42
78 3 0.02
79 5 0.04
80 1 0.01
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (71 bp):
AAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAATATTAAAAATAAT
ATCCTA
Found at i:2859304 original size:59 final size:59
Alignment explanation
Indices: 2859212--2859340 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
2859202 CGTAGTGCAA
* * * * **
2859212 TCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
2859271 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
2859330 TCCCGAATATG
1 TCCCGAATATG
2859341 CAGCATGCTG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:2867913 original size:30 final size:32
Alignment explanation
Indices: 2867853--2867913 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
2867843 CAACCATTCA
* * *
2867853 CAACTTTCTCTAAAATTACCGAATTGGTCCCC
1 CAACTTTCTCGAAAATTACCAAAATGGTCCCC
2867885 CAACTTT-TCGAAAATTA-CAAAATGGTCCC
1 CAACTTTCTCGAAAATTACCAAAATGGTCCC
2867914 TAAATTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 10 0.38
31 9 0.35
32 7 0.27
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (32 bp):
CAACTTTCTCGAAAATTACCAAAATGGTCCCC
Found at i:2868993 original size:110 final size:112
Alignment explanation
Indices: 2868790--2869011 Score: 385
Period size: 110 Copynumber: 2.0 Consensus size: 112
2868780 TCCAACATTT
*
2868790 TAAAAATGTGAAAATAATATTTTTATTTACTTATTTTCGTGATCCATATGTAATTTTTTAAAATT
1 TAAAAATATGAAAATAATATTTTTATTTACTTATTTTCGTGATCCATATGTAATTTTTTAAAATT
*
2868855 ACATTTTGGTCCCTAAACTTTTCAAAG-TT-TACTTTGGTCACCAAA
66 ACATTTTGGTCCCTAAAATTTTCAAAGTTTATACTTTGGTCACCAAA
*
2868900 TAAAAATATGAAAATAATATTTTTATTTACTTATTTTCGTGATCCGTATGTAATTTTTTAAAATT
1 TAAAAATATGAAAATAATATTTTTATTTACTTATTTTCGTGATCCATATGTAATTTTTTAAAATT
**
2868965 ACATTTTGGTCCCTAAAATTTTTTAAGTTTATACTTTGGTCACCAAA
66 ACATTTTGGTCCCTAAAATTTTCAAAGTTTATACTTTGGTCACCAAA
2869012 CTTTACCAAA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 87 0.83
111 2 0.02
112 16 0.15
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (112 bp):
TAAAAATATGAAAATAATATTTTTATTTACTTATTTTCGTGATCCATATGTAATTTTTTAAAATT
ACATTTTGGTCCCTAAAATTTTCAAAGTTTATACTTTGGTCACCAAA
Found at i:2879496 original size:19 final size:21
Alignment explanation
Indices: 2879472--2879523 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2879462 CGGCCAAGAG
*
2879472 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2879491 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2879512 CATGTATTTTCA
1 CATGTATTTTCA
2879524 AGGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2880251 original size:13 final size:12
Alignment explanation
Indices: 2880235--2880305 Score: 72
Period size: 13 Copynumber: 5.6 Consensus size: 12
2880225 GTGCAAAAAG
*
2880235 AAAGATAAAGACA
1 AAAGA-AAAGAAA
*
2880248 AAAGAAGAGAAA
1 AAAGAAAAGAAA
2880260 AAA-AATAAGAAA
1 AAAGAA-AAGAAA
2880272 AGAAGAAAAGAAGA
1 A-AAGAAAAGAA-A
2880286 AAAGAAAAGAAA
1 AAAGAAAAGAAA
2880298 AAGAGAAA
1 AA-AGAAA
2880306 GCAAGCCAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 2 0.04
12 17 0.34
13 27 0.54
14 4 0.08
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:2880263 original size:30 final size:29
Alignment explanation
Indices: 2880229--2880297 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2880219 ATTGGAGTGC
2880229 AAAAAGAAAGATAAAG-ACAAAAGAAGAGAA
1 AAAAAGAAAGA-AAAGAACAAAAGAAGA-AA
*
2880259 AAAAA-ATAAGAAAAGAAGAAAAGAAGAAA
1 AAAAAGA-AAGAAAAGAACAAAAGAAGAAA
2880288 AGAAAAGAAA
1 A-AAAAGAAA
2880298 AAGAGAAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 8 0.24
30 25 0.74
31 1 0.03
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (29 bp):
AAAAAGAAAGAAAAGAACAAAAGAAGAAA
Found at i:2880305 original size:8 final size:8
Alignment explanation
Indices: 2880247--2880291 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
2880237 AGATAAAGAC
2880247 AAAAGAAG
1 AAAAGAAG
*
2880255 AGAA-AA-
1 AAAAGAAG
*
2880261 AAAATAAG
1 AAAAGAAG
2880269 AAAAGAAG
1 AAAAGAAG
2880277 AAAAGAAG
1 AAAAGAAG
2880285 AAAAGAA
1 AAAAGAA
2880292 AAGAAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 3 0.09
7 4 0.12
8 25 0.78
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:2883490 original size:21 final size:19
Alignment explanation
Indices: 2883443--2883494 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
2883433 CGACCAAGAG
*
2883443 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
* *
2883462 AATATATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
2883483 CATGTATTTTCA
1 CATGTATTTTCA
2883495 AAGGGGTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 9 0.35
20 2 0.08
21 15 0.58
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:2885127 original size:29 final size:29
Alignment explanation
Indices: 2885074--2885139 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
2885064 GTGATGTGAC
*
2885074 CTATGAGATCATATGAAATATTATATG-A
1 CTATGTGATCATATGAAATATTATATGTA
*
2885102 CTATGTGATTATATGAAA-ATGATATATGTA
1 CTATGTGATCATATGAAATAT--TATATGTA
2885132 -TATGTGAT
1 CTATGTGAT
2885140 ATGTAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
28 16 0.48
29 14 0.42
30 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (29 bp):
CTATGTGATCATATGAAATATTATATGTA
Found at i:2885442 original size:23 final size:23
Alignment explanation
Indices: 2885411--2885470 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
2885401 TGTTATAAGT
*
2885411 GGTCATTCGGGACATTTCTACGC
1 GGTCCTTCGGGACATTTCTACGC
* *
2885434 GGTCCTTCGGGATATTTTTACGC
1 GGTCCTTCGGGACATTTCTACGC
2885457 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
2885471 AAGTCTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTACGC
Found at i:2890482 original size:14 final size:15
Alignment explanation
Indices: 2890465--2890505 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2890455 TAAAAATATG
2890465 GAAAATTAAAT-ACT
1 GAAAATTAAATGACT
*
2890479 GAAAATTAGATGACT
1 GAAAATTAAATGACT
2890494 -AAAATATAAATG
1 GAAAAT-TAAATG
2890506 CAGGAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (15 bp):
GAAAATTAAATGACT
Found at i:2891262 original size:18 final size:18
Alignment explanation
Indices: 2891239--2891274 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2891229 AAGTTTCATT
2891239 TCCTCACGTGGGTGTACG
1 TCCTCACGTGGGTGTACG
2891257 TCCTCACGTGGGTGTACG
1 TCCTCACGTGGGTGTACG
2891275 AGATTTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (18 bp):
TCCTCACGTGGGTGTACG
Found at i:2893909 original size:64 final size:65
Alignment explanation
Indices: 2893830--2893960 Score: 255
Period size: 64 Copynumber: 2.0 Consensus size: 65
2893820 CTCTCTGAAT
2893830 TTTATGCTTTATCTTTTATTCTGCTCCTTAATTCTTTATATAATTGTGATGTATTAGCA-CTTGA
1 TTTATGCTTTATCTTTTATTCTGCTCCTTAATTCTTTATATAATTGTGATGTATTAGCAGCTTGA
2893894 TTTATGCTTTATCTTTTATTCTGCTCCTTAATTCTTTATATAATTGTGATGTATTAGCAGCTTGA
1 TTTATGCTTTATCTTTTATTCTGCTCCTTAATTCTTTATATAATTGTGATGTATTAGCAGCTTGA
2893959 TT
1 TT
2893961 AATCATTGTA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 59 0.89
65 7 0.11
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.53
Consensus pattern (65 bp):
TTTATGCTTTATCTTTTATTCTGCTCCTTAATTCTTTATATAATTGTGATGTATTAGCAGCTTGA
Found at i:2895036 original size:19 final size:20
Alignment explanation
Indices: 2895012--2895049 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2895002 ATTCAAAACT
2895012 TATTTTT-AAAATTATAAAA
1 TATTTTTCAAAATTATAAAA
2895031 TATTTTTCAAAATTATAAA
1 TATTTTTCAAAATTATAAA
2895050 TTTATGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTTTCAAAATTATAAAA
Found at i:2900218 original size:6 final size:6
Alignment explanation
Indices: 2900207--2900242 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
2900197 CTTAATTCTG
*
2900207 AAAATT AAAATT AAAATT AAAATT TAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
2900243 TAAAGACCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AAAATT
Found at i:2900243 original size:12 final size:12
Alignment explanation
Indices: 2900208--2900246 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2900198 TTAATTCTGA
*
2900208 AAATTAAAATTA
1 AAATTAAAATTT
2900220 AAATTAAAATTT
1 AAATTAAAATTT
2900232 AAATTAAAATTT
1 AAATTAAAATTT
2900244 AAA
1 AAA
2900247 GACCTGATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:2900483 original size:18 final size:18
Alignment explanation
Indices: 2900460--2900510 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2900450 TTTAGAAAAG
*
2900460 AAAAATAATAAAATATAA
1 AAAAATAATAAAATAGAA
** *
2900478 AAAAATGTTAAAAGAGAA
1 AAAAATAATAAAATAGAA
2900496 AATAAA-AATAAAATA
1 AA-AAATAATAAAATA
2900511 ATAATAAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAATAATAAAATAGAA
Found at i:2900519 original size:21 final size:21
Alignment explanation
Indices: 2900495--2900549 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2900485 TTAAAAGAGA
2900495 AAATAAAAATAAAATAATAA-T
1 AAATAAAAATAAAAT-ATAATT
***
2900516 AAATAAAAGGGAAATATAATT
1 AAATAAAAATAAAATATAATT
2900537 AAATAATAAATAA
1 AAATAA-AAATAA
2900550 TAGTAGTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATAAAAATAAAATATAATT
Found at i:2900613 original size:18 final size:18
Alignment explanation
Indices: 2900592--2900634 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2900582 GTTATTTTTA
2900592 AAATAAAAG-ATAAGAATT
1 AAATAAAAGTA-AAGAATT
*
2900610 AAATAAAAGTAAATAATT
1 AAATAAAAGTAAAGAATT
2900628 AAATAAA
1 AAATAAA
2900635 TAATATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGTAAAGAATT
Found at i:2901607 original size:16 final size:16
Alignment explanation
Indices: 2901596--2901632 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
2901586 AAAAATAACA
2901596 AAATGAATAAATAAAT
1 AAATGAATAAATAAAT
2901612 AAATGAAAATAAATAAAT
1 AAATG--AATAAATAAAT
2901630 AAA
1 AAA
2901633 ATGGCATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AAATGAATAAATAAAT
Found at i:2901623 original size:14 final size:13
Alignment explanation
Indices: 2901604--2901634 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2901594 CAAAATGAAT
2901604 AAATAAATAAATGA
1 AAATAAATAAAT-A
2901618 AAATAAATAAATA
1 AAATAAATAAATA
2901631 AAAT
1 AAAT
2901635 GGCATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:2901729 original size:34 final size:36
Alignment explanation
Indices: 2901660--2901734 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 36
2901650 AATAATATTA
* *
2901660 TATATATTTTCAAAAAATGCTTTCAAAACCATATAT
1 TATATATGTTCAAAAAATGCTTTCAAAAACATATAT
*
2901696 TATATATGTTC-AAAAATGTTTTCAAAAAC-TATAT
1 TATATATGTTCAAAAAATGCTTTCAAAAACATATAT
2901730 TATAT
1 TATAT
2901735 TAATATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 10 0.28
35 16 0.44
36 10 0.28
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (36 bp):
TATATATGTTCAAAAAATGCTTTCAAAAACATATAT
Found at i:2904582 original size:34 final size:32
Alignment explanation
Indices: 2904520--2904588 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
2904510 ACCTTACAAC
* *
2904520 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
2904552 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
2904586 TCC
1 TCC
2904589 TCTTTACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:2904998 original size:21 final size:21
Alignment explanation
Indices: 2904954--2905029 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2904944 TTGCAACCTT
* * *
2904954 GATGCATGGATGTATGG-TAG
1 GATGCATCGATGCATGGCAAG
2904974 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
2904995 GATGCATCGATGCATGGCAAT
1 GATGCATCGATGCATGGCAAG
2905016 GATGCATCGATGCA
1 GATGCATCGATGCA
2905030 CTAATTGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 15 0.29
21 36 0.71
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.24
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:2905235 original size:30 final size:30
Alignment explanation
Indices: 2905201--2905260 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2905191 AACTTTGAAT
2905201 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
2905231 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
2905261 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:2905448 original size:30 final size:30
Alignment explanation
Indices: 2905414--2905470 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
2905404 AACTTTGAAT
2905414 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
2905444 AAATTCAATTCAAGTCCAAAAACATTT
1 AAATTCAATTCAAATCCAAAAACATTT
2905471 GAAAAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:2905478 original size:30 final size:30
Alignment explanation
Indices: 2905402--2905478 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
2905392 GAAACCTTTT
2905402 AAAAC-TTTGAATAAATTCAATTCAAATCCA
1 AAAACATTTGAA-AAATTCAATTCAAATCCA
* *
2905432 AAAACATTTTG-CAAATTCAATTCAAGTCCA
1 AAAACA-TTTGAAAAATTCAATTCAAATCCA
2905462 AAAACATTTGAAAAATT
1 AAAACATTTGAAAAATT
2905479 GGTTTTGGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.10
30 33 0.80
32 4 0.10
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAACATTTGAAAAATTCAATTCAAATCCA
Found at i:2905838 original size:229 final size:231
Alignment explanation
Indices: 2905437--2905896 Score: 906
Period size: 229 Copynumber: 2.0 Consensus size: 231
2905427 ATCCAAAAAC
2905437 ATTTTGCAAATTCAATTCAAGTCCAAAAACATTTGAAAAATTGGTTTTGGCAAAACTCCCCCTTA
1 ATTTTGCAAATTCAATTCAAGTCCAAAAACATTTGAAAAATTGGTTTTGGCAAAACTCCCCCTTA
2905502 ATAAAATGTTTAATGAAAAAGATATCAATTGTTACCAATTGTTGGAAAATATATGAAAATGTTAA
66 ATAAAATGTTTAATGAAAAAGATATCAATTGTTACCAATTGTTGGAAAATATATGAAAATGTTAA
2905567 GCTCCCCCTTTTTCATTAAGAAATTGAATTTTTCAAACCATAACTTCT-CCCCTTTTTGTTATAT
131 GCTCCCCCTTTTTCATTAAGAAATTGAATTTTTCAAACCATAACTTCTCCCCCTTTTTGTTATAT
2905631 C-AAAATAATTCAATCTTTGAAGTTCAAAATAACTT
196 CAAAAATAATTCAATCTTTGAAGTTCAAAATAACTT
2905666 ATTTTGCAAATTCAATTCAAGTCCAAAAACATTTGAAAAATTGGTTTTGGCAAAACTCCCCCTTA
1 ATTTTGCAAATTCAATTCAAGTCCAAAAACATTTGAAAAATTGGTTTTGGCAAAACTCCCCCTTA
2905731 ATAAAATGTTTAATGAAAAAGATATCAATTGTTACCAATTGTTGGAAAATATATGAAAATGTTAA
66 ATAAAATGTTTAATGAAAAAGATATCAATTGTTACCAATTGTTGGAAAATATATGAAAATGTTAA
2905796 GCTCCCCCTTTTTCATTAAGAAATTGAATTTTTCAAACCATAACTTCTCCCCCTTTTTGTTATAT
131 GCTCCCCCTTTTTCATTAAGAAATTGAATTTTTCAAACCATAACTTCTCCCCCTTTTTGTTATAT
2905861 CAAAAATAATTCAATCTTTGAAGTTCAAAATAACTT
196 CAAAAATAATTCAATCTTTGAAGTTCAAAATAACTT
2905897 TGGAGAGTAA
Statistics
Matches: 229, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
229 178 0.78
230 17 0.07
231 34 0.15
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (231 bp):
ATTTTGCAAATTCAATTCAAGTCCAAAAACATTTGAAAAATTGGTTTTGGCAAAACTCCCCCTTA
ATAAAATGTTTAATGAAAAAGATATCAATTGTTACCAATTGTTGGAAAATATATGAAAATGTTAA
GCTCCCCCTTTTTCATTAAGAAATTGAATTTTTCAAACCATAACTTCTCCCCCTTTTTGTTATAT
CAAAAATAATTCAATCTTTGAAGTTCAAAATAACTT
Found at i:2906847 original size:19 final size:20
Alignment explanation
Indices: 2906804--2906851 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2906794 TCTAAATCCT
*
2906804 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
2906824 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
2906843 TTTTCAAAA
1 TTTTCAAAA
2906852 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:2908190 original size:21 final size:21
Alignment explanation
Indices: 2908146--2908221 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
2908136 TTGCAGCCTT
*
2908146 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
2908166 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
2908187 GATGCATCGATGCATGGCAAT
1 GATGCATCGATGCATGGCAAG
2908208 GATGCATCGATGCA
1 GATGCATCGATGCA
2908222 CTAATTGCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:2908301 original size:13 final size:13
Alignment explanation
Indices: 2908283--2908315 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2908273 GCATTAGTAT
2908283 GGATGCACTGCAG
1 GGATGCACTGCAG
2908296 GGATGCACTGCAG
1 GGATGCACTGCAG
2908309 GGATGCA
1 GGATGCA
2908316 TGGATGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.39, T:0.15
Consensus pattern (13 bp):
GGATGCACTGCAG
Found at i:2908440 original size:30 final size:30
Alignment explanation
Indices: 2908406--2908465 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2908396 AACTGTGAAT
2908406 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
2908436 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
2908466 CTTTAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Done.