Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 76 of 91
Found at i:27964013 original size:26 final size:26
Alignment explanation
Indices: 27963984--27964075 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
27963974 AAAAGCACTA
** *
27963984 AAGGTGTTCAAAGTACAAAAGCGCCC
1 AAGGTGTTCAAAGTGTAGAAGCGCCC
* * *
27964010 AAGGGTGTTCCAAGCGTAGAAGTGCCC
1 AA-GGTGTTCAAAGTGTAGAAGCGCCC
* *
27964037 AAGGTGTTCCAAGTGTAGAAGCGCCT
1 AAGGTGTTCAAAGTGTAGAAGCGCCC
*
27964063 AGGGTGTTCAAAG
1 AAGGTGTTCAAAG
27964076 CGTGAAAACT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 34 0.63
27 20 0.37
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (26 bp):
AAGGTGTTCAAAGTGTAGAAGCGCCC
Found at i:27964036 original size:27 final size:27
Alignment explanation
Indices: 27964006--27964164 Score: 101
Period size: 27 Copynumber: 6.0 Consensus size: 27
27963996 GTACAAAAGC
27964006 GCCCAAGGGTGTTCCAAGCGTAGAAGT
1 GCCCAAGGGTGTTCCAAGCGTAGAAGT
* *
27964033 GCCCAA-GGTGTTCCAAGTGTAGAAGC
1 GCCCAAGGGTGTTCCAAGCGTAGAAGT
* * * *
27964059 G-CCTAGGGTGTTCAAAGCGTGAAAACT
1 GCCCAAGGGTGTTCCAAGCGT-AGAAGT
** ** * *
27964086 -TTCAAAAGTGTTCTAAGCATAGAAGT
1 GCCCAAGGGTGTTCCAAGCGTAGAAGT
* * * * * *
27964112 GCCCAAGAGTATTCTAAACGCAAAAGT
1 GCCCAAGGGTGTTCCAAGCGTAGAAGT
*
27964139 GCTCCAA-GGTGTTCCAAGCGAAGAAG
1 GC-CCAAGGGTGTTCCAAGCGTAGAAG
27964165 CGCTTAGGGC
Statistics
Matches: 97, Mismatches: 30, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
25 3 0.03
26 35 0.36
27 55 0.57
28 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (27 bp):
GCCCAAGGGTGTTCCAAGCGTAGAAGT
Found at i:27968469 original size:52 final size:52
Alignment explanation
Indices: 27968403--27968503 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 52
27968393 ATATTACTCT
*
27968403 ATTGGTCGCAAGCTTTATCGCTCAACTT-TTGGCCATAGTTTGCTATTCACAA
1 ATTGGCCGCAAGCTTTATCGCTC-ACTTCTTGGCCATAGTTTGCTATTCACAA
* *
27968455 ATTGGCCGCAAGCTTTATTGTTCACTTCTTGGCCATAGTTTGCTATTCA
1 ATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGCTATTCA
27968504 TAATTAGGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 4 0.09
52 41 0.91
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
ATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGCTATTCACAA
Found at i:27969278 original size:27 final size:27
Alignment explanation
Indices: 27969216--27969552 Score: 70
Period size: 27 Copynumber: 12.5 Consensus size: 27
27969206 CAAATTACAT
* * *
27969216 TAAGATTGTTTCAAATGCGAAAGTGCC
1 TAAGAGTGTTCCAAATGCGAAAGCGCC
* * * *
27969243 CAAGGGTGTTCCAAATGTGGAAGCGCC
1 TAAGAGTGTTCCAAATGCGAAAGCGCC
* * *
27969270 TAAGAGTGTTTCAAGTGCAAATATGC-CC
1 TAAGAGTGTTCCAAATGCGAA-A-GCGCC
* * *
27969298 -AAGAGTATTCCAAACGTAGAAATGC-CC
1 TAAGAGTGTTCCAAATG-CGAAA-GCGCC
* * *
27969325 -AAG-GTCGTTACAAACGCGAAAGCACC
1 TAAGAGT-GTTCCAAATGCGAAAGCGCC
* *** * * *
27969351 -AAGGGTGTTCCTCGTACGGAAGTGCC
1 TAAGAGTGTTCCAAATGCGAAAGCGCC
* * * * *
27969377 TAAGGGTGTTCCAAGTACGGAAGCACC
1 TAAGAGTGTTCCAAATGCGAAAGCGCC
* * *
27969404 TAAGAATGTTCTAAGTGC-AGAAGCGCC
1 TAAGAGTGTTCCAAATGCGA-AAGCGCC
* * *
27969431 TAGGTGTGTTCCAAGTATG-G-AAGTGCC
1 TAAGAGTGTTCCAA--ATGCGAAAGCGCC
* * * *
27969458 CAAG-GTGTTCCAAGTGTGAAAAGCACC
1 TAAGAGTGTTCCAAATGCG-AAAGCGCC
* *
27969485 -CAGAGGTGTTCCAAATGCGGAAA-CACC
1 TAAGA-GTGTTCCAAATGC-GAAAGCGCC
* * *
27969512 -CAGAGGTGTTCCAAATGCGGAAGCACC
1 TAAGA-GTGTTCCAAATGCGAAAGCGCC
* *
27969539 CAAGGGTGTTCCAA
1 TAAGAGTGTTCCAA
27969553 GCATAGAAGC
Statistics
Matches: 232, Mismatches: 59, Indels: 38
0.71 0.18 0.12
Matches are distributed among these distances:
24 2 0.01
25 3 0.01
26 36 0.16
27 165 0.71
28 21 0.09
29 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (27 bp):
TAAGAGTGTTCCAAATGCGAAAGCGCC
Found at i:27969494 original size:54 final size:54
Alignment explanation
Indices: 27969378--27969623 Score: 196
Period size: 54 Copynumber: 4.6 Consensus size: 54
27969368 GGAAGTGCCT
* * * * * *
27969378 AAGGGTGTTCCAAGTACGGAAGCACCTAAGAATGTTCTAAGTG-CAGAAGC-GCC
1 AAGGGTGTTCCAAGTATGGAAGCACCCAAG-GTGTTCCAAGTGTGAGAAGCACCC
* ** *
27969431 TAGGTGTGTTCCAAGTATGGAAGTGCCCAAGGTGTTCCAAGTGTGAAAAGCACCC
1 AAGG-GTGTTCCAAGTATGGAAGCACCCAAGGTGTTCCAAGTGTGAGAAGCACCC
* ** * * *
27969486 -AGAGGTGTTCCAAATGCGGAAACACCCAGAGGTGTTCCAAATGCG-GAAGCACCC
1 AAG-GGTGTTCCAAGTATGGAAGCACCCA-AGGTGTTCCAAGTGTGAGAAGCACCC
* * * * *
27969540 AAGGGTGTTCCAAGCATAGAAGCACCTAGGGTGTTCCAAGTGT-AGAAGCTCCC
1 AAGGGTGTTCCAAGTATGGAAGCACCCAAGGTGTTCCAAGTGTGAGAAGCACCC
* * * *
27969593 AAGGGTATTCCAAGTGTAGAAGCACCTAAGG
1 AAGGGTGTTCCAAGTATGGAAGCACCCAAGG
27969624 GTGCTCTAGA
Statistics
Matches: 152, Mismatches: 34, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
53 60 0.39
54 73 0.48
55 19 0.12
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (54 bp):
AAGGGTGTTCCAAGTATGGAAGCACCCAAGGTGTTCCAAGTGTGAGAAGCACCC
Found at i:27969561 original size:27 final size:27
Alignment explanation
Indices: 27969378--27969626 Score: 175
Period size: 27 Copynumber: 9.3 Consensus size: 27
27969368 GGAAGTGCCT
*** *
27969378 AAGGGTGTTCCAAGTACGGAAGCACCT
1 AAGGGTGTTCCAAGTGTAGAAGCACCC
** * * *
27969405 AAGAATGTTCTAAGTGCAGAAGC-GCC
1 AAGGGTGTTCCAAGTGTAGAAGCACCC
* * * **
27969431 TAGGTGTGTTCCAAGTATGGAAGTGCCC
1 AAGG-GTGTTCCAAGTGTAGAAGCACCC
*
27969459 AA-GGTGTTCCAAGTGTGAAAAGCACCC
1 AAGGGTGTTCCAAGTGT-AGAAGCACCC
* ** *
27969486 -AGAGGTGTTCCAAATGCGGAAACACCC
1 AAG-GGTGTTCCAAGTGTAGAAGCACCC
* **
27969513 -AGAGGTGTTCCAAATGCGGAAGCACCC
1 AAG-GGTGTTCCAAGTGTAGAAGCACCC
**
27969540 AAGGGTGTTCCAAGCATAGAAGCA-CC
1 AAGGGTGTTCCAAGTGTAGAAGCACCC
* *
27969566 TAGGGTGTTCCAAGTGTAGAAGCTCCC
1 AAGGGTGTTCCAAGTGTAGAAGCACCC
* *
27969593 AAGGGTATTCCAAGTGTAGAAGCACCT
1 AAGGGTGTTCCAAGTGTAGAAGCACCC
27969620 AAGGGTG
1 AAGGGTG
27969627 CTCTAGAAAA
Statistics
Matches: 173, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
26 38 0.22
27 118 0.68
28 17 0.10
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (27 bp):
AAGGGTGTTCCAAGTGTAGAAGCACCC
Found at i:27972245 original size:19 final size:19
Alignment explanation
Indices: 27972223--27972259 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
27972213 CAAAGCCAAC
27972223 TCTGCTACTGGCAGCCATA
1 TCTGCTACTGGCAGCCATA
27972242 TCTGCTACTGGCAGCCAT
1 TCTGCTACTGGCAGCCAT
27972260 TTTTGATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.32, G:0.22, T:0.27
Consensus pattern (19 bp):
TCTGCTACTGGCAGCCATA
Found at i:27973008 original size:26 final size:25
Alignment explanation
Indices: 27972962--27973019 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
27972952 ACCAATCTTT
* *
27972962 CAAAAAAAAAACCAGATTCAAACAA
1 CAAAAAAAAAACCAAAATCAAACAA
* *
27972987 CAAAAAAAAAACCACAAATCAACCAC
1 CAAAAAAAAAACCA-AAATCAAACAA
27973013 CAAAAAA
1 CAAAAAA
27973020 GCCTAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.69, C:0.24, G:0.02, T:0.05
Consensus pattern (25 bp):
CAAAAAAAAAACCAAAATCAAACAA
Found at i:27973635 original size:21 final size:19
Alignment explanation
Indices: 27973597--27973637 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
27973587 CTATGATTCT
*
27973597 AATTTATATATTTATAATA
1 AATTAATATATTTATAATA
27973616 AATTAATATATTATATTAATA
1 AATTAATATATT-TA-TAATA
27973637 A
1 A
27973638 GTTTACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 2 0.11
21 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAATATATTTATAATA
Found at i:27974631 original size:32 final size:32
Alignment explanation
Indices: 27974553--27974631 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
27974543 ATTCGAGTTG
* * * *
27974553 AATTTTAAATAAATT-TTTTAATAAATAATTT
1 AATTTTAAATATATTATATTAATAAAAAATCT
* *
27974584 AA-CTTGAATATTATTATATTAATAAAAAATCT
1 AATTTTAAATA-TATTATATTAATAAAAAATCT
27974616 AATTTTAAATATATTA
1 AATTTTAAATATATTA
27974632 AAAAATATTG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
30 6 0.16
31 5 0.14
32 20 0.54
33 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (32 bp):
AATTTTAAATATATTATATTAATAAAAAATCT
Found at i:27993191 original size:12 final size:13
Alignment explanation
Indices: 27993174--27993205 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27993164 CTGCCTCCCT
27993174 AACAACAAAGAA-
1 AACAACAAAGAAC
27993186 AACAAC-AAGAAC
1 AACAACAAAGAAC
27993198 AACAACAA
1 AACAACAA
27993206 CCAAACCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 12 0.67
13 1 0.06
ACGTcount: A:0.72, C:0.22, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAACAAAGAAC
Found at i:28003826 original size:46 final size:46
Alignment explanation
Indices: 28003774--28003865 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
28003764 GAATAAAAAA
*
28003774 AATCGAATATTTATATTATATATATAAAAGGAAGTCTCAACGAACT
1 AATCGAATATTTATATTACATATATAAAAGGAAGTCTCAACGAACT
28003820 AATCGAATATTTATATTACATATATAAAAGGAAGTCTCAACGAACT
1 AATCGAATATTTATATTACATATATAAAAGGAAGTCTCAACGAACT
28003866 TTCACATTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.32
Consensus pattern (46 bp):
AATCGAATATTTATATTACATATATAAAAGGAAGTCTCAACGAACT
Found at i:28006829 original size:22 final size:21
Alignment explanation
Indices: 28006778--28006831 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
28006768 AGAAACTAGG
*
28006778 ACTAAAAATTAAGATAAAAAT
1 ACTAAAAAGTAAGATAAAAAT
* * *
28006799 AATGGAAAAGTAAGCCTAAAAAT
1 ACT-AAAAAGTAAG-ATAAAAAT
28006822 ACTAAAAAGT
1 ACTAAAAAGT
28006832 TAAAAAGTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 2 0.08
22 14 0.56
23 9 0.36
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.20
Consensus pattern (21 bp):
ACTAAAAAGTAAGATAAAAAT
Found at i:28010011 original size:5 final size:5
Alignment explanation
Indices: 28009988--28010060 Score: 53
Period size: 5 Copynumber: 14.6 Consensus size: 5
28009978 TAGACACCAA
* * *
28009988 AAAAT -AAAT AAAA- AAATT AAATT ATAAT AAAAT AAAAT AAAATAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAA-AT AAAAT
* *
28010038 ATAA- AATAT AAAAT ATAAAT AAA
1 AAAAT AAAAT AAAAT A-AAAT AAA
28010061 GAAAATAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 9 0.17
5 32 0.59
6 11 0.20
7 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AAAAT
Found at i:28010036 original size:7 final size:7
Alignment explanation
Indices: 28010024--28010056 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28010014 ATAAAATAAA
28010024 ATAAAAT
1 ATAAAAT
28010031 ATAAAAT
1 ATAAAAT
28010038 ATAAAAT
1 ATAAAAT
28010045 ATAAAAT
1 ATAAAAT
28010052 ATAAA
1 ATAAA
28010057 TAAAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATAAAAT
Found at i:28010068 original size:13 final size:12
Alignment explanation
Indices: 28009986--28010077 Score: 55
Period size: 13 Copynumber: 7.5 Consensus size: 12
28009976 TGTAGACACC
28009986 AAAAAATAAATA
1 AAAAAATAAATA
*
28009998 AAAAAATTAAATT
1 AAAAAA-TAAATA
* *
28010011 ATAATA-AAAT-
1 AAAAAATAAATA
*
28010021 AAAATA-AAATA
1 AAAAAATAAATA
*
28010032 TAAAATATAAAATA
1 -AAAAAAT-AAATA
*
28010046 TAAAATATAAATA
1 -AAAAAATAAATA
*
28010059 AAGAAAATAATTA
1 AA-AAAATAAATA
28010072 AAAAAA
1 AAAAAA
28010078 AAAGAAAAGG
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.13
11 4 0.06
12 18 0.26
13 24 0.35
14 13 0.19
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:28010368 original size:21 final size:20
Alignment explanation
Indices: 28010339--28010377 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28010329 GCCCCGGCAG
28010339 GGAGAAAGAAGAGAAAGAGAA
1 GGAGAAAGAA-AGAAAGAGAA
*
28010360 GGAGGAAGAAAGAAAGAG
1 GGAGAAAGAAAGAAAGAG
28010378 GAAAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (20 bp):
GGAGAAAGAAAGAAAGAGAA
Found at i:28010429 original size:17 final size:17
Alignment explanation
Indices: 28010409--28010448 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28010399 CGGGGGAAAG
*
28010409 AAAGGAGAAGAAAGAGA
1 AAAGGAAAAGAAAGAGA
*
28010426 AAAGAAAAAGAAAGAGA
1 AAAGGAAAAGAAAGAGA
28010443 AGAAGG
1 A-AAGG
28010449 GGGGAGCGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAAGGAAAAGAAAGAGA
Found at i:28010451 original size:47 final size:52
Alignment explanation
Indices: 28010351--28010497 Score: 144
Period size: 51 Copynumber: 2.8 Consensus size: 52
28010341 AGAAAGAAGA
*
28010351 GAAAGAGAAGGAGGAAGAAAGAAAGAGGAAAAAGAAAGAAGAAGCCAACGGGG
1 GAAAGAGAAGGAGGAAGAAAGAAAGAAGAAAAAGAAAGAAGAAG-CAACGGGG
*
28010404 GAAAGA-AAGGA-GAAGAAAGAGAA-AAGAAAAAGAAAG-AGAAG-AAGGGGG
1 GAAAGAGAAGGAGGAAGAAAGA-AAGAAGAAAAAGAAAGAAGAAGCAACGGGG
** * *
28010452 GAGCG-GCCAGGAGAGAAAGAAAGAAAGAAAGAGAAAGAAAGAAGAA
1 GAAAGAG-AAGGAG-G-AAGAAAGAAAG-AAGAAAAAGAAAGAAGAA
28010498 AGAGAAAAGA
Statistics
Matches: 79, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
48 9 0.11
49 4 0.05
50 5 0.06
51 24 0.30
52 15 0.19
53 18 0.23
54 4 0.05
ACGTcount: A:0.59, C:0.04, G:0.37, T:0.00
Consensus pattern (52 bp):
GAAAGAGAAGGAGGAAGAAAGAAAGAAGAAAAAGAAAGAAGAAGCAACGGGG
Found at i:28010474 original size:4 final size:4
Alignment explanation
Indices: 28010465--28010527 Score: 59
Period size: 4 Copynumber: 17.5 Consensus size: 4
28010455 CGGCCAGGAG
*
28010465 AGAA AGAA AGAA AGAA AG-- AGAA AGAA AG-A AGAA AGAG A-AA AG-A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
28010508 A-AA AGAA AGAG AG-A AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AG
28010528 GGGGAGCGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
2 2 0.04
3 11 0.23
4 35 0.73
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28010498 original size:17 final size:17
Alignment explanation
Indices: 28010463--28010527 Score: 96
Period size: 17 Copynumber: 3.7 Consensus size: 17
28010453 AGCGGCCAGG
28010463 AGAGAAAGAAAGAAAGAA
1 AGAGAAAGAAAG-AAGAA
28010481 AGAGAAAGAAAGAAGAA
1 AGAGAAAGAAAGAAGAA
28010498 AGAGAAAAGAAA-AAGAA
1 AGAG-AAAGAAAGAAGAA
28010515 AGAGAGAAGAAAG
1 AGAGA-AAGAAAG
28010528 GGGGAGCGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.02
17 24 0.55
18 19 0.43
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAGAAGAA
Found at i:28010514 original size:28 final size:29
Alignment explanation
Indices: 28010465--28010527 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
28010455 CGGCCAGGAG
*
28010465 AGAAAGAAAGAAAGAAAGAGAAAGAAAGA
1 AGAAAGAAAGAAAGAAAAAGAAAGAAAGA
* *
28010494 AGAAAGAGA-AAAGAAAAAGAAAGAGAGA
1 AGAAAGAAAGAAAGAAAAAGAAAGAAAGA
28010522 AGAAAG
1 AGAAAG
28010528 GGGGAGCGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (29 bp):
AGAAAGAAAGAAAGAAAAAGAAAGAAAGA
Found at i:28010553 original size:4 final size:4
Alignment explanation
Indices: 28010544--28010605 Score: 51
Period size: 4 Copynumber: 16.2 Consensus size: 4
28010534 CGGCTGGGAG
* * * *
28010544 AGAA AGAA AG-- AGAA AAAA AGAA AGAG AGAA AGAA AAAGA AGAA AAAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA
28010591 AGAA A-AA A-AA AGAA A
1 AGAA AGAA AGAA AGAA A
28010606 AAAAATGGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
2 2 0.04
3 6 0.13
4 35 0.76
5 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28010565 original size:14 final size:14
Alignment explanation
Indices: 28010546--28010595 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
28010536 GCTGGGAGAG
28010546 AAAGAAAGAGAAAA
1 AAAGAAAGAGAAAA
28010560 AAAGAAAGAGAGAAA
1 AAAGAAAGAGA-AAA
*
28010575 GAA-AAAGAAGAAAA
1 AAAGAAAG-AGAAAA
28010589 AAAGAAA
1 AAAGAAA
28010596 AAAAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAGAAAA
Found at i:28010567 original size:18 final size:18
Alignment explanation
Indices: 28010544--28010605 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
28010534 CGGCTGGGAG
28010544 AGAAAGAAAGAGAAAAAA
1 AGAAAGAAAGAGAAAAAA
*
28010562 AGAAAGAGAGAAAGAAAAAGA
1 AGAAAGA-A-AGAGAAAAA-A
* *
28010583 AGAAAAAAAGAAAAAAAA
1 AGAAAGAAAGAGAAAAAA
28010601 AGAAA
1 AGAAA
28010606 AAAAATGGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 13 0.35
19 8 0.22
20 9 0.24
21 7 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGAGAAAAAA
Found at i:28010585 original size:21 final size:21
Alignment explanation
Indices: 28010546--28010610 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
28010536 GCTGGGAGAG
* *
28010546 AAAGAAAGAGAAAAAAAGAAAG
1 AAAGAAAGA-AAAAGAAGAAAA
*
28010568 AGAGAAAGAAAAAGAAGAAAA
1 AAAGAAAGAAAAAGAAGAAAA
*
28010589 AAAGAAAAAAAAAGAA-AAAA
1 AAAGAAAGAAAAAGAAGAAAA
28010609 AA
1 AA
28010611 TGGAGAAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 6 0.16
21 24 0.63
22 8 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAAGAAAA
Found at i:28010593 original size:8 final size:8
Alignment explanation
Indices: 28010544--28010609 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 8
28010534 CGGCTGGGAG
28010544 AGAAAGAAA
1 AGAAA-AAA
28010553 GAGAAAAAA
1 -AGAAAAAA
28010562 AGAAAGAGAGAA
1 AG-AA-A-A-AA
28010574 AGAAAAAGA
1 AGAAAAA-A
28010583 AGAAAAAA
1 AGAAAAAA
28010591 AGAAAAAAAA
1 AG--AAAAAA
28010601 AGAAAAAA
1 AGAAAAAA
28010609 A
1 A
28010610 ATGGAGAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
8 13 0.27
9 14 0.29
10 15 0.31
11 3 0.06
12 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:28010604 original size:79 final size:78
Alignment explanation
Indices: 28010405--28010605 Score: 266
Period size: 79 Copynumber: 2.6 Consensus size: 78
28010395 CCAACGGGGG
*
28010405 AAAGAAAG-GAGAAGAAAGAGAAAAGAAAAAG-AAAGAGAAGAAGGGGGGAGCGGCCAGGAGAGA
1 AAAGAAAGAGAGAAGAAAGAGAAAAGAAAAAGAAAAGAGAAGAAAGGGGGAGCGGCCAGGAGAGA
28010468 AAGAAAGAAAGAA
66 AAGAAAGAAAGAA
* * **
28010481 AGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGGGAGCGGCTGGGAGAG
1 AAAGAAAGAGAGAAGAAAGAGAAAAGAAAAAGAAA-AGAGAAGAAAGGGGGAGCGGCCAGGAGAG
28010546 AAAGAAAGAGAA-AA
65 AAAGAAAGA-AAGAA
* * *
28010560 AAAGAAAGAGAGAAAGAAAAAGAAGAA-AAAAAGAAAAAAAAAGAAA
1 AAAGAAAGAGAG-AAGAAAGAGAA-AAGAAAAAGAAAAGAGAAGAAA
28010606 AAAAATGGAG
Statistics
Matches: 109, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
76 7 0.06
77 22 0.20
78 2 0.02
79 55 0.50
80 21 0.19
81 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (78 bp):
AAAGAAAGAGAGAAGAAAGAGAAAAGAAAAAGAAAAGAGAAGAAAGGGGGAGCGGCCAGGAGAGA
AAGAAAGAAAGAA
Found at i:28010606 original size:10 final size:10
Alignment explanation
Indices: 28010570--28010610 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
28010560 AAAGAAAGAG
*
28010570 AGAAAGAAAA
1 AGAAAAAAAA
28010580 AGAAGAAAAAA
1 AGAA-AAAAAA
28010591 AGAAAAAAAA
1 AGAAAAAAAA
28010601 AGAAAAAAAA
1 AGAAAAAAAA
28010611 TGGAGAAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:28011423 original size:4 final size:4
Alignment explanation
Indices: 28011385--28011463 Score: 53
Period size: 4 Copynumber: 20.8 Consensus size: 4
28011375 GATACGGATC
*
28011385 TAAA TAAA -AAA TAGAA -AAA -AAA T-AA TAATA AAAA TAAA TAAA T-AA
1 TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA
** * *
28011430 TCCA TAAA -AAA TAAA AAAA TAAA TATA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
28011464 GGTGATAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
3 17 0.29
4 37 0.63
5 5 0.08
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:28014251 original size:2 final size:2
Alignment explanation
Indices: 28014246--28014271 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28014236 ACAGTACGTT
28014246 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
28014272 ATACCTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28016872 original size:41 final size:41
Alignment explanation
Indices: 28016818--28016921 Score: 192
Period size: 41 Copynumber: 2.6 Consensus size: 41
28016808 TAATGTACAG
28016818 ATTATT-GAGGATTATTGGAGAGTCTTTAATGAAATTGACA
1 ATTATTGGAGGATTATTGGAGAGTCTTTAATGAAATTGACA
28016858 ATTATTGGAGGATTATTGGAGAGTCTTTAATGAAATTGACA
1 ATTATTGGAGGATTATTGGAGAGTCTTTAATGAAATTGACA
*
28016899 ATTGTTGGAGGATTATTGGAGAG
1 ATTATTGGAGGATTATTGGAGAG
28016922 GTGAAATTGC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 6 0.10
41 56 0.90
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (41 bp):
ATTATTGGAGGATTATTGGAGAGTCTTTAATGAAATTGACA
Found at i:28020822 original size:74 final size:76
Alignment explanation
Indices: 28020726--28020876 Score: 227
Period size: 74 Copynumber: 2.0 Consensus size: 76
28020716 AAATATCCAA
*
28020726 AATCTATACTTATAAATATGTATTCATTAAATGACGATCATTAAAATATTTTTTATTATAATT-A
1 AATCTATACTTATAAATATGTATTCATCAAATGACGATCATTAAAATATTTTTTATTAT-ATTAA
*
28020790 TTAGTAAGATTT
65 TTAGTAAAATTT
* * *
28020802 AATCT-TA-TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATATTAAT
1 AATCTATACTTATAAATATGTATTCATCAAATGACGATCATTAAAATATTTTTTATTATATTAAT
28020865 TAGTAAAATTT
66 TAGTAAAATTT
28020876 A
1 A
28020877 TTCCATTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
73 3 0.04
74 59 0.86
75 2 0.03
76 5 0.07
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (76 bp):
AATCTATACTTATAAATATGTATTCATCAAATGACGATCATTAAAATATTTTTTATTATATTAAT
TAGTAAAATTT
Found at i:28021015 original size:20 final size:21
Alignment explanation
Indices: 28020978--28021027 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
28020968 AATATGTTAA
*
28020978 ATTAATTTTTTCAAGTTAAAT
1 ATTAATATTTTCAAGTTAAAT
*
28020999 TTTAATATTTT-AAGTTAAAT
1 ATTAATATTTTCAAGTTAAAT
28021019 ATTAATATT
1 ATTAATATT
28021028 CATCAAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTAATATTTTCAAGTTAAAT
Found at i:28031894 original size:60 final size:59
Alignment explanation
Indices: 28031761--28031894 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
28031751 CTAGAAAGAA
** * * * *
28031761 AAACTTTTAAGCATTTTAAATTTTTTAGAGTGGTTTTTGATTCACGAAGAAAAACTTTT
1 AAACTTTTAAGCATTTTAAACATTTTACAGTGATTTTTGATACACGAAAAAAAACTTTT
* * * * * *
28031820 AAGCGTTTTGAGCATTTTGAGCATTTTACAGTGATTTTTGATACATGAAAAAAAATTTTT
1 AAAC-TTTTAAGCATTTTAAACATTTTACAGTGATTTTTGATACACGAAAAAAAACTTTT
28031880 AAACATTTTAAGCAT
1 AAAC-TTTTAAGCAT
28031895 CCTTTGCCAA
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
59 3 0.05
60 56 0.95
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (59 bp):
AAACTTTTAAGCATTTTAAACATTTTACAGTGATTTTTGATACACGAAAAAAAACTTTT
Found at i:28032076 original size:22 final size:22
Alignment explanation
Indices: 28032026--28032091 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28032016 CCGGTTTTCG
* *
28032026 GACATTGTATGATTAGTTTTAA
1 GACATTATATGATTAGTTTTTA
* * *
28032048 AATATTATGTGATTAGTTTTTA
1 GACATTATATGATTAGTTTTTA
* *
28032070 GACATTACATGATTAATTTTTA
1 GACATTATATGATTAGTTTTTA
28032092 AGTATTGCGT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (22 bp):
GACATTATATGATTAGTTTTTA
Found at i:28032122 original size:23 final size:23
Alignment explanation
Indices: 28032095--28032148 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
28032085 ATTTTTAAGT
**
28032095 ATTGCGTGACTTGTTAATATGAC
1 ATTGCGTGACCGGTTAATATGAC
*
28032118 ATTGCGTGACCGGTTGATATGAC
1 ATTGCGTGACCGGTTAATATGAC
*
28032141 ATTACGTG
1 ATTGCGTG
28032149 TGACTAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (23 bp):
ATTGCGTGACCGGTTAATATGAC
Found at i:28032306 original size:22 final size:22
Alignment explanation
Indices: 28032237--28032320 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
28032227 GGATGCCACG
* * *
28032237 CAATGCTTAAAAATTAGTCACA
1 CAATACTTAAAAATCAGTTACA
* * *
28032259 TAATACTTAAAAATCAATCT-CT
1 CAATACTTAAAAATCAGT-TACA
28032281 CAATACTTAAAAATCAGTTACA
1 CAATACTTAAAAATCAGTTACA
*
28032303 CAATA-TCTAAAAACCAGT
1 CAATACT-TAAAAATCAGT
28032321 AATGCAATAC
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
21 2 0.04
22 47 0.96
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (22 bp):
CAATACTTAAAAATCAGTTACA
Found at i:28037687 original size:22 final size:22
Alignment explanation
Indices: 28037662--28037742 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
28037652 TAATCACTGT
* * *
28037662 GTGACTGGTTTTTAAGTATTAC
1 GTGACTGATTTTTAAGCATTGC
* *
28037684 GTGA-TTAGTTTT-AGACATTGC
1 GTGACTGATTTTTAAG-CATTGC
*
28037705 GTGACTGATTTTTAGGCATTGC
1 GTGACTGATTTTTAAGCATTGC
*
28037727 GTGATTGATTTTTAAG
1 GTGACTGATTTTTAAG
28037743 TAATGCCTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
22 30 0.65
23 1 0.02
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (22 bp):
GTGACTGATTTTTAAGCATTGC
Found at i:28037785 original size:23 final size:23
Alignment explanation
Indices: 28037759--28037833 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
28037749 CTAAGTCCTA
28037759 CAATGCTTTACTAACTAA-TCACG
1 CAATGCTTTACTAAC-AAGTCACG
*
28037782 CAATGCTTTACTAACAAGTCAAG
1 CAATGCTTTACTAACAAGTCACG
* *
28037805 CAATGCCTTACTAACAAGTTACG
1 CAATGCTTTACTAACAAGTCACG
28037828 CAATGC
1 CAATGC
28037834 CTATCAACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 2 0.04
23 45 0.96
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (23 bp):
CAATGCTTTACTAACAAGTCACG
Found at i:28037868 original size:26 final size:26
Alignment explanation
Indices: 28037825--28038052 Score: 169
Period size: 26 Copynumber: 9.3 Consensus size: 26
28037815 CTAACAAGTT
28037825 ACGCAATGCC-TATC---AACTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
* **
28037847 ACACAATGTTTTATCAGAAACTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
* * *
28037873 ACGCAATACCTTATCAAAAACTAATC
1 ACGCAATGCCTTATCAGAAACTAGTC
**
28037899 ACGCAATG-C---TCA-AAGTTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
*
28037920 ACACAATGCC-TATC---AACTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
* * **
28037942 AAGTAATGTTTTATCAGAAACTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
* *
28037968 ACGTAATACCTTATCAGAAA-TAAGTC
1 ACGCAATGCCTTATCAGAAACT-AGTC
* *
28037994 ACGTAATACCTTATCAGAAACTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
* * *
28038020 ACACAATGTCTTATCAAAAACTAGTC
1 ACGCAATGCCTTATCAGAAACTAGTC
28038046 ACGCAAT
1 ACGCAAT
28038053 ACCCAAAGTC
Statistics
Matches: 162, Mismatches: 31, Indels: 22
0.75 0.14 0.10
Matches are distributed among these distances:
21 13 0.08
22 22 0.14
23 8 0.05
24 2 0.01
25 2 0.01
26 114 0.70
27 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.26
Consensus pattern (26 bp):
ACGCAATGCCTTATCAGAAACTAGTC
Found at i:28037906 original size:52 final size:52
Alignment explanation
Indices: 28037839--28038052 Score: 187
Period size: 52 Copynumber: 4.3 Consensus size: 52
28037829 AATGCCTATC
* *
28037839 AACTAGTCACACAATGTTTTATCAGAAACTAGTCACGCAATACCTTATCAAA
1 AACTAGTCACGCAATGTTTTATCAGAAACTAGTCACACAATACCTTATCAAA
* * ** *
28037891 AACTAATCACGCAATG----CTCA-AAGTTAGTCACACAATGCC-TATC---
1 AACTAGTCACGCAATGTTTTATCAGAAACTAGTCACACAATACCTTATCAAA
* * ** *
28037934 AACTAGTCAAGTAATGTTTTATCAGAAACTAGTCACGTAATACCTTATCAGA
1 AACTAGTCACGCAATGTTTTATCAGAAACTAGTCACACAATACCTTATCAAA
* *** **
28037986 AA-TAAGTCACGTAATACCTTATCAGAAACTAGTCACACAATGTCTTATCAAA
1 AACT-AGTCACGCAATGTTTTATCAGAAACTAGTCACACAATACCTTATCAAA
28038038 AACTAGTCACGCAAT
1 AACTAGTCACGCAAT
28038053 ACCCAAAGTC
Statistics
Matches: 125, Mismatches: 26, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
43 13 0.10
46 4 0.03
47 18 0.14
48 17 0.14
49 4 0.03
51 1 0.01
52 67 0.54
53 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (52 bp):
AACTAGTCACGCAATGTTTTATCAGAAACTAGTCACACAATACCTTATCAAA
Found at i:28038095 original size:21 final size:21
Alignment explanation
Indices: 28038041--28038097 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28038031 TATCAAAAAC
*
28038041 TAGTCACGCAATACCCAAAGT
1 TAGTCACGCAATGCCCAAAGT
* * *
28038062 CAGTCACGTAATGTCCAAAGT
1 TAGTCACGCAATGCCCAAAGT
28038083 TAGTCACGCAATGCC
1 TAGTCACGCAATGCC
28038098 TAAAAACTAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (21 bp):
TAGTCACGCAATGCCCAAAGT
Found at i:28057204 original size:2 final size:2
Alignment explanation
Indices: 28057199--28057241 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28057189 CACACATGTG
28057199 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
28057241 T
1 T
28057242 GAAATCATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28065434 original size:2 final size:2
Alignment explanation
Indices: 28065427--28065507 Score: 103
Period size: 2 Copynumber: 41.0 Consensus size: 2
28065417 ACACAAATAC
* *
28065427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
28065468 AT -T AGT NC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28065508 TTATTTATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
1 2 0.03
2 65 0.96
3 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:28066720 original size:20 final size:19
Alignment explanation
Indices: 28066697--28066745 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
28066687 TAAAAGAATC
28066697 AAAATTTATTTAAATTTTTT
1 AAAATTTATTT-AATTTTTT
* *
28066717 AAAAATAATTTAATTTTTT
1 AAAATTTATTTAATTTTTT
28066736 AAAATATTAT
1 AAAAT-TTAT
28066746 ATATTATGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAATTTATTTAATTTTTT
Found at i:28071703 original size:4 final size:4
Alignment explanation
Indices: 28071694--28071749 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
28071684 AATAAACCCA
* * * *
28071694 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
28071742 GTAT ATAT
1 ATAT ATAT
28071750 GTGGTACATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:28073237 original size:26 final size:26
Alignment explanation
Indices: 28073201--28073255 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
28073191 AGAAAAGAGT
28073201 ATGCTTGGTGAGGGCGTGGTTTGCAG
1 ATGCTTGGTGAGGGCGTGGTTTGCAG
28073227 ATGCTTGGTGAGGGCGTGGTTTGCAG
1 ATGCTTGGTGAGGGCGTGGTTTGCAG
28073253 ATG
1 ATG
28073256 AAAATGGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.13, C:0.11, G:0.45, T:0.31
Consensus pattern (26 bp):
ATGCTTGGTGAGGGCGTGGTTTGCAG
Found at i:28075376 original size:33 final size:33
Alignment explanation
Indices: 28075331--28075400 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
28075321 CTATTCATCC
*
28075331 AAACCATTGTTTGTTGCAGTAGTGTTGCAGCTT
1 AAACCATGGTTTGTTGCAGTAGTGTTGCAGCTT
*
28075364 AAACCATGGTTTGTTGCAGTAGTGTTGCGGCTT
1 AAACCATGGTTTGTTGCAGTAGTGTTGCAGCTT
28075397 AAAC
1 AAAC
28075401 TTAAACCTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (33 bp):
AAACCATGGTTTGTTGCAGTAGTGTTGCAGCTT
Found at i:28081812 original size:3 final size:3
Alignment explanation
Indices: 28081804--28081841 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
28081794 TATCGAGATG
28081804 AGA AGA AGA AGA AGA AGA AGA AGAA AGA A-A AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AG
28081842 GAATAGGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:28085213 original size:7 final size:7
Alignment explanation
Indices: 28085192--28085234 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
28085182 TATTTGCTTT
28085192 TTTATTA
1 TTTATTA
28085199 -TT-TTA
1 TTTATTA
28085204 TTTATTA
1 TTTATTA
28085211 TTTATTA
1 TTTATTA
28085218 TTTATTA
1 TTTATTA
28085225 TTTATTA
1 TTTATTA
28085232 TTT
1 TTT
28085235 CATTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 3 0.09
6 4 0.12
7 27 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:28085439 original size:30 final size:29
Alignment explanation
Indices: 28085404--28085465 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
28085394 AAAATGTATA
28085404 TTTTATTATT-TATTTATTATTT-TTATTTCT
1 TTTTATTATTATATTT-TT-TTTCTTATTT-T
28085434 TTTTATTATTATATTTTTTTTCTTATTTT
1 TTTTATTATTATATTTTTTTTCTTATTTT
28085463 TTT
1 TTT
28085466 ATTTCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 7 0.23
30 18 0.60
31 5 0.17
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTTATTATTATATTTTTTTTCTTATTTT
Found at i:28085503 original size:39 final size:37
Alignment explanation
Indices: 28085402--28085504 Score: 104
Period size: 38 Copynumber: 2.8 Consensus size: 37
28085392 AAAAAATGTA
*
28085402 TATT-TTATTATTTATTTATTA-TTTTTATTTCTTTT
1 TATTATTATAATTTATTTATTATTTTTTATTTCTTTT
* * *
28085437 TATTATTATATTTTTTTTCTTATTTTTTTATTTCTTTAT
1 TATTATTATAATTTATTTATTA-TTTTTTATTTCTTT-T
* *
28085476 TATTCTTCATAATTTATTT-TTACTTTTTA
1 TATTATT-ATAATTTATTTATTATTTTTTA
28085505 CAATTTTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
35 4 0.07
36 13 0.24
38 19 0.35
39 10 0.18
40 9 0.16
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (37 bp):
TATTATTATAATTTATTTATTATTTTTTATTTCTTTT
Found at i:28085552 original size:4 final size:4
Alignment explanation
Indices: 28085543--28085576 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
28085533 TAATATTATC
28085543 ATTT ATTT ATTT ATTT ATTT -TTT ATTT -TTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
28085577 TCTAACACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
ATTT
Found at i:28085566 original size:7 final size:7
Alignment explanation
Indices: 28085543--28085577 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
28085533 TAATATTATC
28085543 ATTTATTT
1 ATTT-TTT
28085551 ATTTATTT
1 ATTT-TTT
28085559 ATTTTTT
1 ATTTTTT
28085566 ATTTTTT
1 ATTTTTT
28085573 ATTTT
1 ATTTT
28085578 CTAACACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.56
8 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
ATTTTTT
Found at i:28085859 original size:6 final size:6
Alignment explanation
Indices: 28085836--28085902 Score: 64
Period size: 6 Copynumber: 10.5 Consensus size: 6
28085826 GATCCAAATC
* *
28085836 CTTTTC CTTCTTT TTTTTT CTTTTT -TCTTTT CTTTCTTT CTTTTT CTTTTT
1 CTTTTT CTT-TTT CTTTTT CTTTTT CT-TTTT C-TT-TTT CTTTTT CTTTTT
28085887 CTTTTT CTTTCTT CTT
1 CTTTTT CTTT-TT CTT
28085903 CTCTCATAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
5 1 0.02
6 34 0.65
7 12 0.23
8 5 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:28085872 original size:26 final size:25
Alignment explanation
Indices: 28085836--28085899 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
28085826 GATCCAAATC
* *
28085836 CTTTTCCTTCTTTTTTTTTCTTTTTT
1 CTTTTCTTTCTTTCTTTTTC-TTTTT
28085862 CTTTTCTTTCTTTCTTTTTCTTTTT
1 CTTTTCTTTCTTTCTTTTTCTTTTT
28085887 CTTTTTCTTTCTT
1 C-TTTTCTTTCTT
28085900 CTTCTCTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (25 bp):
CTTTTCTTTCTTTCTTTTTCTTTTT
Found at i:28085897 original size:16 final size:16
Alignment explanation
Indices: 28085843--28085904 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
28085833 ATCCTTTTCC
*
28085843 TTCTTTTTTTTTCTTTT
1 TTCTTTCTTTTTC-TTT
*
28085860 TTCTTT-TCTTTCTTT
1 TTCTTTCTTTTTCTTT
28085875 CTT-TTTCTTTTTCTTT
1 -TTCTTTCTTTTTCTTT
*
28085891 TTCTTTCTTCTTCT
1 TTCTTTCTTTTTCT
28085905 CTCATAGCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 8 0.21
16 25 0.64
17 6 0.15
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTCTTTTTCTTT
Found at i:28085899 original size:30 final size:30
Alignment explanation
Indices: 28085838--28085896 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
28085828 TCCAAATCCT
28085838 TTTCCTTCTTTTTTTTTCTTTTTTCTTTTC
1 TTTCCTTCTTTTTTTTTCTTTTTTCTTTTC
*
28085868 TTTCTTTCTTTTTCTTTT-TCTTTTTCTTT
1 TTTCCTTCTTTTT-TTTTCT-TTTTTCTTT
28085897 CTTCTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (30 bp):
TTTCCTTCTTTTTTTTTCTTTTTTCTTTTC
Found at i:28086048 original size:35 final size:34
Alignment explanation
Indices: 28086009--28086079 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
28085999 CTCTCTTCAC
*
28086009 TTTCCCCTTTTTTCTTTCTCTT-TGTTCTTCTTCTT
1 TTTCCCCTTATTTCTTTCT-TTCTGTTCTT-TTCTT
*
28086044 TTTCCCCTTATTTCTTTCTTTCTTTTCTTTTCTT
1 TTTCCCCTTATTTCTTTCTTTCTGTTCTTTTCTT
28086078 TT
1 TT
28086080 CTTTCTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.70
Consensus pattern (34 bp):
TTTCCCCTTATTTCTTTCTTTCTGTTCTTTTCTT
Found at i:28086652 original size:8 final size:8
Alignment explanation
Indices: 28086641--28086720 Score: 57
Period size: 8 Copynumber: 10.8 Consensus size: 8
28086631 TTTTTTTTTA
28086641 ATTTTATT
1 ATTTTATT
28086649 ATTTT-TT
1 ATTTTATT
*
28086656 AATTT-TT
1 ATTTTATT
28086663 A-TTT-TT
1 ATTTTATT
* *
28086669 ATTATGTT
1 ATTTTATT
*
28086677 ATTTGATT
1 ATTTTATT
28086685 ATTTTA-T
1 ATTTTATT
28086692 -TTTTATT
1 ATTTTATT
28086699 ATTTTTATT
1 A-TTTTATT
28086708 -TTTTATT
1 ATTTTATT
*
28086715 TTTTTA
1 ATTTTA
28086721 AAATGAGTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
6 11 0.18
7 20 0.33
8 22 0.37
9 7 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
ATTTTATT
Found at i:28086662 original size:27 final size:25
Alignment explanation
Indices: 28086631--28086719 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 25
28086621 TTCTCTGTTC
28086631 TTTTTTTTTAATTTTATTATTTTTTAA
1 TTTTTTTTT-ATTTTATTATTTTTT-A
* * *
28086658 TTTTTATTTTTATTATGTTATTTGATTA
1 -TTTT-TTTTTATTTTATTATTT-TTTA
*
28086686 TTTTATTTTTATTATTTTTATTTTTTA
1 TTTT-TTTTTATT-TTATTATTTTTTA
28086713 TTTTTTT
1 TTTTTTT
28086720 AAAATGAGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.06
27 20 0.38
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTTTTATTTTATTATTTTTTA
Found at i:28086710 original size:6 final size:6
Alignment explanation
Indices: 28086631--28086717 Score: 61
Period size: 6 Copynumber: 13.7 Consensus size: 6
28086621 TTCTCTGTTC
* * *
28086631 TTTT-T TTTTAA TTTTAT TATT-T TTTAAT TTTTAT TTTTAT TATGTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T-T-TTAT
*
28086679 TTGATTAT TTTATTT TTATTAT TTTTATT TTTTAT TTTT
1 TT--TTAT TTT-TAT TT-TTAT TTTTA-T TTTTAT TTTT
28086718 TTAAAATGAG
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
5 7 0.11
6 30 0.46
7 16 0.25
8 12 0.18
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:28086950 original size:21 final size:22
Alignment explanation
Indices: 28086926--28086969 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
28086916 GGTTTTATGA
* *
28086926 ATGTATCCGGAGGTTTT-GAAG
1 ATGTACCCAGAGGTTTTAGAAG
*
28086947 ATGTACCCAGAGTTTTTAGAAG
1 ATGTACCCAGAGGTTTTAGAAG
28086969 A
1 A
28086970 AAATGTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (22 bp):
ATGTACCCAGAGGTTTTAGAAG
Found at i:28087088 original size:80 final size:80
Alignment explanation
Indices: 28086950--28087123 Score: 267
Period size: 80 Copynumber: 2.2 Consensus size: 80
28086940 TTTGAAGATG
* * * * * *
28086950 TACCCAGAGTTTTTAGAAGAAAATGTTGTTCCTCATCTCAGAATGATGCTACGTAACTTTGAAGA
1 TACCCAGAGGTTTTAGAAGAAAAGGTTGTTCCTCATCTCAAAATAAGGCTACGCAACTTTGAAGA
*
28087015 AATCTTGAAACAAAT
66 AATCTTGAAACAAAA
* *
28087030 TACCCGGAGGTTTTAGAAGAAAAGGTTGTTCCTCATCTCAAAATAAGGCTATGCAACTTTGAAGA
1 TACCCAGAGGTTTTAGAAGAAAAGGTTGTTCCTCATCTCAAAATAAGGCTACGCAACTTTGAAGA
28087095 AATCTTGAAACAAAA
66 AATCTTGAAACAAAA
28087110 TACCCAGAGGTTTT
1 TACCCAGAGGTTTT
28087124 TGAAATGTAC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (80 bp):
TACCCAGAGGTTTTAGAAGAAAAGGTTGTTCCTCATCTCAAAATAAGGCTACGCAACTTTGAAGA
AATCTTGAAACAAAA
Found at i:28087221 original size:30 final size:29
Alignment explanation
Indices: 28087187--28087283 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 29
28087177 GACTACGTAA
28087187 CTTAAATTCTCTCGTGCCAAGATAACTGGG
1 CTTAAA-TCTCTCGTGCCAAGATAACTGGG
* * *
28087217 CTTAAA-CGTCTTGGATGCC-AGCTATAGTGGG
1 CTTAAATC-TC-TCG-TGCCAAGATA-ACTGGG
*
28087248 CTTAAA-CATCTCGGTGCCAATATAACTGGG
1 CTTAAATC-TCTC-GTGCCAAGATAACTGGG
28087278 CTTAAA
1 CTTAAA
28087284 CATCTTGGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 28 0.53
31 22 0.42
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (29 bp):
CTTAAATCTCTCGTGCCAAGATAACTGGG
Found at i:28087248 original size:31 final size:31
Alignment explanation
Indices: 28087211--28088127 Score: 281
Period size: 31 Copynumber: 30.0 Consensus size: 31
28087201 TGCCAAGATA
*
28087211 ACTGGGCTTAAACGTCTTGGATGCCAGCTAT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * *
28087242 AGTGGGCTTAAACATCTCGG-TGCCA-ATAT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
*
28087271 AACTGGGCTTAAACATCTTGGATGCCAGCTAA
1 -ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * * *
28087303 ATTGGGCTTAAAC-TCCTTTTG-TGGCAACGTA-
1 ACTGGGCTTAAACAT-C-TTGGATGCCAGC-TAT
* * * * *
28087334 ATTGGACTTATACATCTTGGATGCCA-ATTT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* *
28087364 AATTGGGCTTAAATC-TCTT-TATGCCAATG-TA-
1 -ACTGGGCTTAAA-CATCTTGGATGCC-A-GCTAT
* * * * *
28087395 ATTAGACTTATACATCTTGGATGCCAG-TTT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * *
28087425 AATTGGGCTTAAATC-TCTTTG-TGCCAACGTA-
1 -ACTGGGCTTAAA-CATCTTGGATGCCAGC-TAT
* * *
28087456 ACTGGGCTTAAATATCTTGGATGCCAGTTAA
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* ** * * * * *
28087487 ATTGACCTTAAATATTTTTG-TGTCAAC-AT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * * * *
28087516 AACTAGACTTAAACATCTTGGATGCTAACTAA
1 -ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * * * *
28087548 ATTGGGCTTAATCGTCTT-TATGCCA-ATAT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* *
28087577 AACTGGGCTTAAACATCTTGGATGCCAGCAAA
1 -ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* *
28087609 ATTGGGCTTAAAC-TCCTTCG-TGCCAAAG-TA-
1 ACTGGGCTTAAACAT-CTTGGATGCC--AGCTAT
* * *
28087639 ACTGGACTTATACATCTTGGATGTCAG-TAT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * *
28087669 AACTTGGGCTTAAATC-TTTTTG-TGCCAAC-AT
1 -AC-TGGGCTTAAA-CATCTTGGATGCCAGCTAT
* *
28087700 AGCTGGGCTTAAACATCTTGGATGCCAGTTAA
1 A-CTGGGCTTAAACATCTTGGATGCCAGCTAT
* *
28087732 ATTGGGCTTAAAC-TCCTTCG-TGCCAAAG-TA-
1 ACTGGGCTTAAACAT-CTTGGATGCC--AGCTAT
* *
28087762 ACTGGACTTATACATCTTGGATGCCAG-TAT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* *
28087792 AACTTGGGCTTAAATC-TCTTTG-TGCCAAC-AT
1 -AC-TGGGCTTAAA-CATCTTGGATGCCAGCTAT
* * * * *
28087823 AGTTGGGTTTAAACATCTTGGATGGCAGTTAA
1 A-CTGGGCTTAAACATCTTGGATGCCAGCTAT
* * *
28087855 ATTGGGCTTAAACATCTTTG-TGCCA-ATAT
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * *
28087884 AACTGAGCTTAAAC-TCCTT-TATGCTAATG-TA-
1 -ACTGGGCTTAAACAT-CTTGGATGC-CA-GCTAT
* * * *
28087915 ACTGGACTTATACATCTTGGATGCCAGATAA
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* * * *
28087946 ATTAGGCTTAAATC-TCTTTG-TGCCAAC-AT
1 ACTGGGCTTAAA-CATCTTGGATGCCAGCTAT
* * * *
28087975 AGCTAGGCTTAAACATATTGGATGCTAGCTAA
1 A-CTGGGCTTAAACATCTTGGATGCCAGCTAT
* * * * *
28088007 ATTGGGCTTAATCGTCTT-TATGCCAAGATA-
1 ACTGGGCTTAAACATCTTGGATGCC-AGCTAT
* * * *
28088037 ATTGGACTTAAACATCTTGGATGCCAGCAAA
1 ACTGGGCTTAAACATCTTGGATGCCAGCTAT
* ** * *
28088068 ATTGGTATTAAACATCTTTG-TGCCAACGTA-
1 ACTGGGCTTAAACATCTTGGATGCCAGC-TAT
*
28088098 ACTGGACTTAAACATCTTGGATGCCAGCTA
1 ACTGGGCTTAAACATCTTGGATGCCAGCTA
28088128 AATTGAGCTT
Statistics
Matches: 647, Mismatches: 161, Indels: 157
0.67 0.17 0.16
Matches are distributed among these distances:
29 27 0.04
30 276 0.43
31 290 0.45
32 52 0.08
33 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (31 bp):
ACTGGGCTTAAACATCTTGGATGCCAGCTAT
Found at i:28087282 original size:61 final size:60
Alignment explanation
Indices: 28087200--28087897 Score: 693
Period size: 61 Copynumber: 11.4 Consensus size: 60
28087190 AAATTCTCTC
* * * * **
28087200 GTGCCAAGATAACTGGGCTTAAACGTCTTGGATGCCAGCTATAGTGGGCTTAAACATCTCG
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAAC-TCTTT
*
28087261 GTGCCAATATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCCTTTT
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAACT-C-TTT
* * * * * ** *
28087323 GTGGCAACGTAATTGGACTTATACATCTTGGATGCCAATTTAATTGGGCTTAAATCTCTTT
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAA-CTCTTT
* ** * * * * * *
28087384 ATGCCAATGTAATTAGACTTATACATCTTGGATGCCAGTTTAATTGGGCTTAAATCTCTTT
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAA-CTCTTT
* * * ** * *
28087445 GTGCCAACGTAACTGGGCTTAAATATCTTGGATGCCAGTTAAATTGACCTTAAATATTTTT
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAA-CTCTTT
* * * * * *
28087506 GTGTCAACATAACTAGACTTAAACATCTTGGATGCTAACTAAATTGGGCTTAATCGTCTTT
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAAC-TCTTT
* * * *
28087567 ATGCCAATATAACTGGGCTTAAACATCTTGGATGCCAGCAAAATTGGGCTTAAACTCCTTC
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAACT-CTTT
* * * *
28087628 GTGCCAA-AGTAACTGGACTTATACATCTTGGATGTCAG-TATAACTTGGGCTTAAATCTTTTT
1 GTGCCAACA-TAACTGGGCTTAAACATCTTGGATGCCAGCTA-AA-TTGGGCTTAAA-CTCTTT
* * *
28087690 GTGCCAACATAGCTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTCCTTC
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAACT-CTTT
* *
28087751 GTGCCAA-AGTAACTGGACTTATACATCTTGGATGCCAG-TATAACTTGGGCTTAAATCTCTTT
1 GTGCCAACA-TAACTGGGCTTAAACATCTTGGATGCCAGCTA-AA-TTGGGCTTAAA-CTCTTT
** * * *
28087813 GTGCCAACATAGTTGGGTTTAAACATCTTGGATGGCAGTTAAATTGGGCTTAAACATCTTT
1 GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAAC-TCTTT
* *
28087874 GTGCCAATATAACTGAGCTTAAAC
1 GTGCCAACATAACTGGGCTTAAAC
28087898 TCCTTTATGC
Statistics
Matches: 535, Mismatches: 83, Indels: 38
0.82 0.13 0.06
Matches are distributed among these distances:
60 10 0.02
61 373 0.70
62 140 0.26
63 12 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (60 bp):
GTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCTTT
Found at i:28087726 original size:123 final size:122
Alignment explanation
Indices: 28087187--28087888 Score: 771
Period size: 123 Copynumber: 5.7 Consensus size: 122
28087177 GACTACGTAA
* * * * * *
28087187 CTTAAAT-TCTCTCGTGCCAAGATAACTGGGCTTAAACGTCTTGGATGCCAGCTATAGTGGGCTT
1 CTTAAATCTCT-TTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTT
* *
28087251 AAACAT-C-TCGGTGCCAATATAACTGGGCTTAAACATCTTGGATGCCAGCTA-AATTGGG
65 AAAC-TCCTTC-GTGCCAATATAACTGGACTTATACATCTTGGATGCCAG-TATAATTGGG
* * * * * * *
28087309 CTTAAA-CTCCTTTTGTGGCAACGTAATTGGACTTATACATCTTGGATGCCAATTTAATTGGGCT
1 CTTAAATCT-C-TTTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCT
** * * * *
28087373 TAAA-TCTCTTTATGCCAATGTAATTAGACTTATACATCTTGGATGCCAGTTTAATTGGG
64 TAAACTC-CTTCGTGCCAATATAACTGGACTTATACATCTTGGATGCCAGTATAATTGGG
* * **
28087432 CTTAAATCTCTTTGTGCCAACGTAACTGGGCTTAAATATCTTGGATGCCAGTTAAATTGACCTTA
1 CTTAAATCTCTTTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTA
** * * * * * * *
28087497 AA-TATTTTTGTGTCAACATAACTAGACTTAAACATCTTGGATGCTAACTA-AATTGGG
66 AACT-CCTTCGTGCCAATATAACTGGACTTATACATCTTGGATGC-CAGTATAATTGGG
* * **
28087554 CTT-AATCGTCTTTATGCCAATATAACTGGGCTTAAACATCTTGGATGCCAGCAAAATTGGGCTT
1 CTTAAATC-TCTTTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTT
*
28087618 AAACTCCTTCGTGCCAA-AGTAACTGGACTTATACATCTTGGATGTCAGTATAACTTGGG
65 AAACTCCTTCGTGCCAATA-TAACTGGACTTATACATCTTGGATGCCAGTATAA-TTGGG
* *
28087677 CTTAAATCTTTTTGTGCCAACATAGCTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTA
1 CTTAAATCTCTTTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTA
28087742 AACTCCTTCGTGCCAA-AGTAACTGGACTTATACATCTTGGATGCCAGTATAACTTGGG
66 AACTCCTTCGTGCCAATA-TAACTGGACTTATACATCTTGGATGCCAGTATAA-TTGGG
** * *
28087800 CTTAAATCTCTTTGTGCCAACATAGTTGGGTTTAAACATCTTGGATGGCAGTTAAATTGGGCTTA
1 CTTAAATCTCTTTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTA
*
28087865 AACAT-CTTTGTGCCAATATAACTG
66 AAC-TCCTTCGTGCCAATATAACTG
28087889 AGCTTAAACT
Statistics
Matches: 492, Mismatches: 70, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
121 9 0.02
122 183 0.37
123 290 0.59
124 10 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (122 bp):
CTTAAATCTCTTTGTGCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTA
AACTCCTTCGTGCCAATATAACTGGACTTATACATCTTGGATGCCAGTATAATTGGG
Found at i:28087766 original size:184 final size:183
Alignment explanation
Indices: 28087201--28087897 Score: 739
Period size: 184 Copynumber: 3.8 Consensus size: 183
28087191 AATTCTCTCG
* * * * *
28087201 TGCC-AAGATAACTGGGCTTAAACGTCTTGGATGCCAGCTATAGTGGGCTTAAA-CATC-TCGGT
1 TGCCAAAG-TAACTGGACTTAAACATCTTGGATGCCAGCAAAATTGGGCTTAAATC-TCTTC-GT
* * * *
28087263 GCCAATATAACTGGGCTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAACTCCTTTTGTGGC
63 GCCAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAA-TCTTTTTGTGCC
* * * * *
28087328 AACGTAATTGGACTTATACATCTTGGATGCCAATTTAATTGGGCTTAAA-TCTCTTTA
127 AACATAACTGGACTTAAACATCTTGGATGCCAATTAAATTGGGCTTAAACTC-CTTCA
* * * * *** *
28087385 TGCCAATGTAATTAGACTTATACATCTTGGATGCCAGTTTAATTGGGCTTAAATCTCTTTGTGCC
1 TGCCAAAGTAACTGGACTTAAACATCTTGGATGCCAGCAAAATTGGGCTTAAATCTCTTCGTGCC
* * ** * *
28087450 AACGTAACTGGGCTTAAATATCTTGGATGCCAGTTAAATTGACCTTAAATATTTTTGTGTCAACA
66 AACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAATCTTTTTGTGCCAACA
* * * * *
28087515 TAACTAGACTTAAACATCTTGGATGCTAACTAAATTGGGCTTAATCGT-CTTTA
131 TAACTGGACTTAAACATCTTGGATGCCAATTAAATTGGGCTTAAAC-TCCTTCA
*
28087568 TGCCAATA-TAACTGGGCTTAAACATCTTGGATGCCAGCAAAATTGGGCTTAAA-CTCCTTCGTG
1 TGCCAA-AGTAACTGGACTTAAACATCTTGGATGCCAGCAAAATTGGGCTTAAATCT-CTTCGTG
* * * *
28087631 CCAA-AGTAACTGGACTTATACATCTTGGATGTCAGTATAACTTGGGCTTAAATCTTTTTGTGCC
64 CCAACA-TAACTGGGCTTAAACATCTTGGATGCCAGT-TAAATTGGGCTTAAATCTTTTTGTGCC
* * * *
28087695 AACATAGCTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTCCTTCG
127 AACATAACTGGACTTAAACATCTTGGATGCCAATTAAATTGGGCTTAAACTCCTTCA
* * * *
28087752 TGCCAAAGTAACTGGACTTATACATCTTGGATGCCAGTATAACTTGGGCTTAAATCTCTTTGTGC
1 TGCCAAAGTAACTGGACTTAAACATCTTGGATGCCAGCA-AAATTGGGCTTAAATCTCTTCGTGC
** * * *
28087817 CAACATAGTTGGGTTTAAACATCTTGGATGGCAGTTAAATTGGGCTTAAA-CATCTTTGTGCCAA
65 CAACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAATC-TTTTTGTGCCAA
*
28087881 TATAACT-GAGCTTAAAC
129 CATAACTGGA-CTTAAAC
28087898 TCCTTTATGC
Statistics
Matches: 425, Mismatches: 72, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
182 2 0.00
183 139 0.33
184 229 0.54
185 52 0.12
186 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (183 bp):
TGCCAAAGTAACTGGACTTAAACATCTTGGATGCCAGCAAAATTGGGCTTAAATCTCTTCGTGCC
AACATAACTGGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAATCTTTTTGTGCCAACA
TAACTGGACTTAAACATCTTGGATGCCAATTAAATTGGGCTTAAACTCCTTCA
Found at i:28087955 original size:61 final size:60
Alignment explanation
Indices: 28087861--28088144 Score: 251
Period size: 61 Copynumber: 4.7 Consensus size: 60
28087851 TTAAATTGGG
* * * *
28087861 CTTAAACATCTTTG-TGCCA-ATATAACTGAGCTTAAACTCCTTTATGCTAATGTAACTGGA
1 CTTAAACATCTTGGATGCCAGATA-AATTG-GCTTAAACTCCTTTATGCCAACGTAACTGGA
* * * *
28087921 CTTATACATCTTGGATGCCAGATAAATTAGGCTTAAA-TCTCTTTGTGCCAACATAGCTAGG-
1 CTTAAACATCTTGGATGCCAGATAAATT-GGCTTAAACTC-CTTTATGCCAACGTAACT-GGA
* * * * *
28087982 CTTAAACATATTGGATGCTAGCTAAATTGGGCTTAATCGT-CTTTATGCCAA-GATAATTGGA
1 CTTAAACATCTTGGATGCCAGATAAATT-GGCTTAAAC-TCCTTTATGCCAACG-TAACTGGA
* *
28088043 CTTAAACATCTTGGATGCCAGCA-AAATTGGTATTAAACAT-CTTTGTGCCAACGTAACTGGA
1 CTTAAACATCTTGGATGCCAG-ATAAATTGG-CTTAAAC-TCCTTTATGCCAACGTAACTGGA
*
28088104 CTTAAACATCTTGGATGCCAGCTAAATTGAGCTTAAGACTC
1 CTTAAACATCTTGGATGCCAGATAAATTG-GCTTAA-ACTC
28088145 AAATCTTTCT
Statistics
Matches: 180, Mismatches: 28, Indels: 30
0.76 0.12 0.13
Matches are distributed among these distances:
60 18 0.10
61 151 0.84
62 10 0.06
63 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (60 bp):
CTTAAACATCTTGGATGCCAGATAAATTGGCTTAAACTCCTTTATGCCAACGTAACTGGA
Found at i:28088047 original size:152 final size:153
Alignment explanation
Indices: 28087703--28088049 Score: 459
Period size: 152 Copynumber: 2.3 Consensus size: 153
28087693 CCAACATAGC
* * * *
28087703 TGGGCTTAAACATCTTGGATGCC-AGTTAAATTGGGCTTAAACTCCTTCGTGCCAAAGTAACTGG
1 TGGGCTTAAACATCTT-TATGCCAAGAT-AATTGGACTTAAACTCCTTCATGCCAAAGTAACTGG
* * * * *
28087767 ACTTATACATCTTGGATGCCAGTATAACTTGGGCTTAAATCTCTTTGTGCCAACATAGTTGGGTT
64 ACTTATACATCTTGGATGCCAGTATAAATTAGGCTTAAATCTCTTTGTGCCAACATAGCTAGGCT
* *
28087832 TAAACATCTTGGATGGCAGTTAAAT
129 TAAACATATTGGATGGCAGCTAAAT
* * * * * *
28087857 TGGGCTTAAACATCTTTGTGCCAATATAACT-GAGCTTAAACTCCTTTATGCTAATGTAACTGGA
1 TGGGCTTAAACATCTTTATGCCAAGATAATTGGA-CTTAAACTCCTTCATGCCAAAGTAACTGGA
28087921 CTTATACATCTTGGATGCCAG-ATAAATTAGGCTTAAATCTCTTTGTGCCAACATAGCTAGGCTT
65 CTTATACATCTTGGATGCCAGTATAAATTAGGCTTAAATCTCTTTGTGCCAACATAGCTAGGCTT
28087985 AAACATATTGGAT-GCTAGCTAAAT
130 AAACATATTGGATGGC-AGCTAAAT
* *
28088009 TGGGCTTAATCGTCTTTATGCCAAGATAATTGGACTTAAAC
1 TGGGCTTAAACATCTTTATGCCAAGATAATTGGACTTAAAC
28088050 ATCTTGGATG
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
151 2 0.01
152 91 0.54
153 56 0.34
154 18 0.11
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (153 bp):
TGGGCTTAAACATCTTTATGCCAAGATAATTGGACTTAAACTCCTTCATGCCAAAGTAACTGGAC
TTATACATCTTGGATGCCAGTATAAATTAGGCTTAAATCTCTTTGTGCCAACATAGCTAGGCTTA
AACATATTGGATGGCAGCTAAAT
Found at i:28088054 original size:122 final size:122
Alignment explanation
Indices: 28087887--28088139 Score: 320
Period size: 122 Copynumber: 2.1 Consensus size: 122
28087877 CCAATATAAC
* * *
28087887 TGAGCTTAAAC-TCCTTTATGCTAATGTAACTGGACTTATACATCTTGGATGCCAG-ATAAATTA
1 TGAGCTTAATCGT-CTTTATGCCAATGTAACTGGACTTAAACATCTTGGATGCCAGCA-AAATT-
* * *
28087950 GG-CTTAAATC-TCTTTGTGCCAACATAGCTAGG-CTTAAACATATTGGATGCTAGCTAAAT
63 GGTATTAAA-CATCTTTGTGCCAACATAACT-GGACTTAAACATATTGGATGCCAGCTAAAT
* *
28088009 TGGGCTTAATCGTCTTTATGCCAA-GATAATTGGACTTAAACATCTTGGATGCCAGCAAAATTGG
1 TGAGCTTAATCGTCTTTATGCCAATG-TAACTGGACTTAAACATCTTGGATGCCAGCAAAATTGG
* *
28088073 TATTAAACATCTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCCAGCTAAAT
65 TATTAAACATCTTTGTGCCAACATAACTGGACTTAAACATATTGGATGCCAGCTAAAT
28088131 TGAGCTTAA
1 TGAGCTTAA
28088140 GACTCAAATC
Statistics
Matches: 114, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
121 6 0.05
122 106 0.93
123 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (122 bp):
TGAGCTTAATCGTCTTTATGCCAATGTAACTGGACTTAAACATCTTGGATGCCAGCAAAATTGGT
ATTAAACATCTTTGTGCCAACATAACTGGACTTAAACATATTGGATGCCAGCTAAAT
Found at i:28089384 original size:26 final size:24
Alignment explanation
Indices: 28089334--28089392 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
28089324 CTATAGCTCA
*
28089334 TTTTTTTCTCTTCTCTTTTTCCTC
1 TTTTTTTTTCTTCTCTTTTTCCTC
*
28089358 TTTTTTTTTGTTCTCTTTTTCATCTC
1 TTTTTTTTTCTTCTCTTTTTC--CTC
28089384 TTTTTTTTT
1 TTTTTTTTT
28089393 TTCATTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 19 0.61
26 12 0.39
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTCTTCTCTTTTTCCTC
Found at i:28094170 original size:27 final size:27
Alignment explanation
Indices: 28094139--28094194 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28094129 TTATTAGAAC
28094139 AAATATGAAATGATTGCATGTA-G-ATGA
1 AAATATGAAAT--TTGCATGTATGCATGA
*
28094166 AAATATGATATTTGCATGTATGCATGA
1 AAATATGAAATTTGCATGTATGCATGA
28094193 AA
1 AA
28094195 TGTTATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 9 0.35
26 1 0.04
27 16 0.62
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (27 bp):
AAATATGAAATTTGCATGTATGCATGA
Found at i:28096228 original size:7 final size:7
Alignment explanation
Indices: 28096207--28096242 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
28096197 TATTTGCTTT
28096207 TTTATTA
1 TTTATTA
28096214 -TT-TTA
1 TTTATTA
28096219 TTTATTA
1 TTTATTA
28096226 TTTATTA
1 TTTATTA
28096233 TTTATTA
1 TTTATTA
28096240 TTT
1 TTT
28096243 CATTTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 3 0.11
6 4 0.15
7 20 0.74
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTATTA
Found at i:28096438 original size:13 final size:12
Alignment explanation
Indices: 28096420--28096476 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
28096410 TATTTTATTA
28096420 TTTATTTATTATT
1 TTTATTTATT-TT
*
28096433 TTTATTTCTTTT
1 TTTATTTATTTT
28096445 TATTATTATATTTT
1 T-TTATT-TATTTT
*
28096459 TTT-CTTATTTT
1 TTTATTTATTTT
28096470 TTTATTT
1 TTTATTT
28096477 CTTTATTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.24
12 6 0.16
13 16 0.43
14 6 0.16
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:28096590 original size:23 final size:21
Alignment explanation
Indices: 28096552--28096597 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
28096542 ACATTATCAT
28096552 TTATTTATTTATTATTATTATTA
1 TTATTTATTTATTATT-TT-TTA
28096575 TTATTTATTT-TCTATTTTTTA
1 TTATTTATTTAT-TATTTTTTA
28096596 TT
1 TT
28096598 TTCTAACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.23
22 3 0.14
23 14 0.64
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTATTTATTATTTTTTA
Found at i:28096595 original size:14 final size:14
Alignment explanation
Indices: 28096550--28096602 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
28096540 TAACATTATC
*
28096550 ATTTATTTATTTATT
1 ATTTATTT-TCTATT
*
28096565 A-TTATTAT-TATT
1 ATTTATTTTCTATT
28096577 ATTTATTTTCTATT
1 ATTTATTTTCTATT
*
28096591 TTTTATTTTCTA
1 ATTTATTTTCTA
28096603 ACACTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 5 0.15
13 7 0.21
14 20 0.61
15 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTATTTTCTATT
Found at i:28096596 original size:27 final size:28
Alignment explanation
Indices: 28096534--28096597 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
28096524 TTGTATTATG
** *
28096534 ATTTTTTAACATTATCATTTATTTATTT
1 ATTTTTTATTATTATCATTTATTTATCT
* *
28096562 A-TTATTATTATTATTATTTATTT-TCT
1 ATTTTTTATTATTATCATTTATTTATCT
28096588 ATTTTTTATT
1 ATTTTTTATT
28096598 TTCTAACACT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 25 0.86
28 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.69
Consensus pattern (28 bp):
ATTTTTTATTATTATCATTTATTTATCT
Found at i:28096871 original size:10 final size:10
Alignment explanation
Indices: 28096856--28096922 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
28096846 TTGACCTAAA
*
28096856 TCTTTTTCCT
1 TCTTTTTCTT
28096866 TCTTTTT-TT
1 TCTTTTTCTT
*
28096875 T-TCTTT-TT
1 TCTTTTTCTT
28096883 T-TTTTTCTT
1 TCTTTTTCTT
28096892 TCTTTTTCCTTT
1 TCTTTTT-C-TT
28096904 TCTTTTTCTT
1 TCTTTTTCTT
*
28096914 TCTTATTCT
1 TCTTTTTCT
28096923 CTCCCAACCG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 11 0.22
9 5 0.10
10 22 0.45
11 2 0.04
12 9 0.18
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TCTTTTTCTT
Found at i:28096890 original size:22 final size:22
Alignment explanation
Indices: 28096865--28096917 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
28096855 ATCTTTTTCC
* * *
28096865 TTCTTTTTTTTTCTTTTTTTTT
1 TTCTTTCTTTTTCCTTTTCTTT
28096887 TTCTTTCTTTTTCCTTTTCTTT
1 TTCTTTCTTTTTCCTTTTCTTT
28096909 TTCTTTCTT
1 TTCTTTCTT
28096918 ATTCTCTCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTCTTTCTTTTTCCTTTTCTTT
Found at i:28096905 original size:12 final size:12
Alignment explanation
Indices: 28096856--28096911 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
28096846 TTGACCTAAA
28096856 TCTTTTTCCTTCT
1 TCTTTTTCCTT-T
* *
28096869 TTTTTTTTCTTT
1 TCTTTTTCCTTT
* *
28096881 TTTTTTTTC-TT
1 TCTTTTTCCTTT
28096892 TCTTTTTCCTTT
1 TCTTTTTCCTTT
28096904 TCTTTTTC
1 TCTTTTTC
28096912 TTTCTTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 9 0.24
12 20 0.53
13 9 0.24
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTCCTTT
Found at i:28096922 original size:16 final size:16
Alignment explanation
Indices: 28096865--28096922 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
28096855 ATCTTTTTCC
*
28096865 TTCTTTTTTTTTCTTT
1 TTCTTTTTCTTTCTTT
*
28096881 TTTTTTTTCTTTCTTT
1 TTCTTTTTCTTTCTTT
*
28096897 TTCCTTTTCTTT-TTCT
1 TTCTTTTTCTTTCTT-T
*
28096913 TTCTTATTCT
1 TTCTTTTTCT
28096923 CTCCCAACCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 2 0.06
16 33 0.94
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTCTTTCTTT
Found at i:28097049 original size:10 final size:10
Alignment explanation
Indices: 28097036--28097117 Score: 64
Period size: 10 Copynumber: 8.3 Consensus size: 10
28097026 TCTTTCCCCT
28097036 TCTTTCTTTC
1 TCTTTCTTTC
*
28097046 TCTTTCTTTT
1 TCTTTCTTTC
*
28097056 TCCTCTCTTTC
1 T-CTTTCTTTC
* *
28097067 CCCTTC-TT-
1 TCTTTCTTTC
28097075 TCTTTCTTTC
1 TCTTTCTTTC
28097085 T-TTTCTTT-
1 TCTTTCTTTC
28097093 TCTTTTCTTTC
1 TC-TTTCTTTC
*
28097104 TCCTTCTTCTC
1 TCTTTCTT-TC
28097115 TCT
1 TCT
28097118 CCCAATCGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
8 5 0.09
9 11 0.20
10 26 0.47
11 13 0.24
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TCTTTCTTTC
Found at i:28097067 original size:35 final size:33
Alignment explanation
Indices: 28097021--28097088 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 33
28097011 GGTGCCTCTC
28097021 TCCTCTCTTTCCCCTTCTTTCTTTCTCTTTCTTTT
1 TCCTCTCTTTCCCCTTCTTTC-TT-TCTTTCTTTT
28097056 TCCTCTCTTTCCCCTTCTTTCTTTCTTTCTTTT
1 TCCTCTCTTTCCCCTTCTTTCTTTCTTTCTTTT
28097089 CTTTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 10 0.30
34 2 0.06
35 21 0.64
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (33 bp):
TCCTCTCTTTCCCCTTCTTTCTTTCTTTCTTTT
Found at i:28097700 original size:19 final size:19
Alignment explanation
Indices: 28097673--28097710 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28097663 CCATTTGACT
28097673 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
28097692 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
28097711 GTTAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:28100684 original size:9 final size:9
Alignment explanation
Indices: 28100662--28100775 Score: 62
Period size: 9 Copynumber: 12.7 Consensus size: 9
28100652 TTCTCTGTTT
*
28100662 TTTTTTTTA
1 TTTTTATTA
*
28100671 ATTTTATTA
1 TTTTTATTA
28100680 TTTTTAATTAA
1 TTTTT-ATT-A
28100691 TTTTT-TTA
1 TTTTTATTA
*
28100699 -ATTT-TTA
1 TTTTTATTA
28100706 TTTTTATTA
1 TTTTTATTA
*
28100715 TGTTATT-TGA
1 T-TT-TTATTA
*
28100725 TTATT-TTA
1 TTTTTATTA
28100733 TTTTTATTA
1 TTTTTATTA
28100742 TTATTTATT-
1 TT-TTTATTA
*
28100751 TTATTTTTTA
1 TT-TTTATTA
28100761 TTTTTTATT-
1 -TTTTTATTA
28100770 TTTTTA
1 TTTTTA
28100776 AAATGGGTGT
Statistics
Matches: 84, Mismatches: 11, Indels: 21
0.72 0.09 0.18
Matches are distributed among these distances:
7 6 0.07
8 18 0.21
9 31 0.37
10 19 0.23
11 10 0.12
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTATTA
Found at i:28100700 original size:28 final size:26
Alignment explanation
Indices: 28100663--28100776 Score: 105
Period size: 27 Copynumber: 4.3 Consensus size: 26
28100653 TCTCTGTTTT
28100663 TTTTTTTAATTTTATTATTTTTAATTAA
1 TTTTTTTAATTTT-TTATTTTT-ATTAA
28100691 TTTTTTTAA-TTTTTATTTTTATT-A
1 TTTTTTTAATTTTTTATTTTTATTAA
* *
28100715 TGTTATTTGATTATTTTATTTTTATTATTA
1 T-TTTTTTAATT-TTTTATTTTTATTA--A
28100745 TTTATTTT-ATTTTTTA-TTTT-TT-A
1 TTT-TTTTAATTTTTTATTTTTATTAA
28100768 TTTTTTTAA
1 TTTTTTTAA
28100777 AATGGGTGTC
Statistics
Matches: 75, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.05
23 5 0.07
24 2 0.03
25 9 0.12
26 11 0.15
27 20 0.27
28 14 0.19
29 5 0.07
30 5 0.07
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTTTAATTTTTTATTTTTATTAA
Found at i:28100704 original size:29 final size:28
Alignment explanation
Indices: 28100663--28100776 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 28
28100653 TCTCTGTTTT
28100663 TTTTTTTAA-TTTTATTATTTTTAATTAA
1 TTTTTTTAATTTTTATT-TTTTTAATTAA
* *
28100691 TTTTTTTAATTTTTATTTTTATTATGTTAT
1 TTTTTTTAATTTTTATTTTT-TTA-ATTAA
* * *
28100721 TTGATTATTTTATTTTTATTATTATTTATTTTA
1 TT--TT-TTTAATTTTTATT-TT-TTTAATTAA
*
28100754 -TTTTTTATTTTTTATTTTTTTAA
1 TTTTTTTAATTTTTATTTTTTTAA
28100777 AATGGGTGTC
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
27 4 0.06
28 14 0.20
29 21 0.30
30 7 0.10
32 3 0.04
33 14 0.20
34 5 0.07
35 1 0.01
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTTTTAATTTTTATTTTTTTAATTAA
Found at i:28100742 original size:22 final size:22
Alignment explanation
Indices: 28100672--28100775 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 22
28100662 TTTTTTTTAA
* *
28100672 TTTTATTATTT-TTAATTAATT
1 TTTTATTATTTATTATTTTATT
* *
28100693 TTTT-TAATTT-TTATTTT-TA
1 TTTTATTATTTATTATTTTATT
* *
28100712 TTATGTTATTTGATTATTTTA-T
1 TTTTATTATTT-ATTATTTTATT
28100734 TTTTATTA-TTATTTATTTTATT
1 TTTTATTATTTA-TTATTTTATT
* *
28100756 TTTTATTTTTTATTTTTTTA
1 TTTTATTATTTATTATTTTA
28100776 AAATGGGTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.06
20 16 0.25
21 14 0.22
22 28 0.43
23 3 0.05
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTATTATTTATTATTTTATT
Found at i:28100746 original size:33 final size:34
Alignment explanation
Indices: 28100694--28100764 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
28100684 TAATTAATTT
*
28100694 TTTTAATTTTTATTTTTA-TTATGTTATTTGATTA
1 TTTTAATTTTTATTATTATTTATGTTATTT-ATTA
* *
28100728 TTTT-ATTTTTATTATTATTTATTTTATTTTTTA
1 TTTTAATTTTTATTATTATTTATGTTATTTATTA
28100761 TTTT
1 TTTT
28100765 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 19 0.58
34 14 0.42
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (34 bp):
TTTTAATTTTTATTATTATTTATGTTATTTATTA
Found at i:28100755 original size:34 final size:31
Alignment explanation
Indices: 28100660--28100764 Score: 93
Period size: 34 Copynumber: 3.1 Consensus size: 31
28100650 CCTTCTCTGT
* * *
28100660 TTTTTTTTTTAATTTTATTATTTTTAATTAATTT
1 TTTTATTTTT-ATTTTATTA-TTTT-ATTTATTA
*
28100694 TTTTAATTTTTATTTTTATTATGTTATTTGATTA
1 TTTT-ATTTTTA-TTTTATTATTTTATTT-ATTA
*
28100728 TTTTATTTTTATTATTATTTATTTTATTTTTTA
1 TTTTATTTTTATT-TTA-TTATTTTATTTATTA
28100761 TTTT
1 TTTT
28100765 TTATTTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.03
33 20 0.33
34 25 0.42
35 13 0.22
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (31 bp):
TTTTATTTTTATTTTATTATTTTATTTATTA
Found at i:28100759 original size:7 final size:7
Alignment explanation
Indices: 28100692--28100773 Score: 64
Period size: 7 Copynumber: 11.9 Consensus size: 7
28100682 TTTAATTAAT
28100692 TTTTTTA
1 TTTTTTA
*
28100699 ATTTTTA
1 TTTTTTA
28100706 -TTTTTA
1 TTTTTTA
*
28100712 TTATGTTA
1 TT-TTTTA
*
28100720 TTTGATTA
1 TTT-TTTA
28100728 TTTTATT-
1 TTTT-TTA
*
28100735 TTTATTA
1 TTTTTTA
*
28100742 TTATTTA
1 TTTTTTA
28100749 --TTTTA
1 TTTTTTA
28100754 TTTTTTA
1 TTTTTTA
28100761 TTTTTTA
1 TTTTTTA
28100768 TTTTTT
1 TTTTTT
28100774 TAAAATGGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.07
6 8 0.13
7 34 0.57
8 14 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:28103902 original size:13 final size:13
Alignment explanation
Indices: 28103884--28103929 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
28103874 AAAAAATATT
28103884 AAACATATAATTA
1 AAACATATAATTA
28103897 AAACATATAA-TA
1 AAACATATAATTA
* *
28103909 AGAACATATCATTT
1 A-AACATATAATTA
28103923 AAACATA
1 AAACATA
28103930 GTAAAGCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 3 0.10
13 24 0.83
14 2 0.07
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (13 bp):
AAACATATAATTA
Found at i:28104379 original size:26 final size:26
Alignment explanation
Indices: 28104343--28104419 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
28104333 GATGGGTATT
28104343 CATCAACTTTTGGTGGTAAAATTATC
1 CATCAACTTTTGGTGGTAAAATTATC
* *
28104369 CATCTACTTTTTGTGGTAAAATTATC
1 CATCAACTTTTGGTGGTAAAATTATC
* * **
28104395 CATCCACTTCTGGTGACAAAATTAT
1 CATCAACTTTTGGTGGTAAAATTAT
28104420 AATTAGAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (26 bp):
CATCAACTTTTGGTGGTAAAATTATC
Found at i:28104538 original size:59 final size:59
Alignment explanation
Indices: 28104475--28104588 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
28104465 TTTCATATCC
* *
28104475 ATGATCATAATTATTAAATAATGT-GACATTCACTTCAGGGAATAGATAGATTTATGACT
1 ATGATCATAATTATTAAATAATGTCG-CATTCACTTCAGGGAATAGACAAATTTATGACT
*
28104534 ATGATCATAATTATTAAATGATGTCGCATTCACTTCAGGGAATAGACAAATTTAT
1 ATGATCATAATTATTAAATAATGTCGCATTCACTTCAGGGAATAGACAAATTTAT
28104589 AATAATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 50 0.98
60 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (59 bp):
ATGATCATAATTATTAAATAATGTCGCATTCACTTCAGGGAATAGACAAATTTATGACT
Found at i:28104638 original size:61 final size:61
Alignment explanation
Indices: 28104555--28104702 Score: 287
Period size: 61 Copynumber: 2.4 Consensus size: 61
28104545 TATTAAATGA
*
28104555 TGTCGCATTCACTTCAGGGAATAGACAAATTTATAATAATTTTTTTTATTATTAACTCGTT
1 TGTCACATTCACTTCAGGGAATAGACAAATTTATAATAATTTTTTTTATTATTAACTCGTT
28104616 TGTCACATTCACTTCAGGGAATAGACAAATTTATAATAATTTTTTTTATTATTAACTCGTT
1 TGTCACATTCACTTCAGGGAATAGACAAATTTATAATAATTTTTTTTATTATTAACTCGTT
28104677 TGTCACATTCACTTCAGGGAATAGAC
1 TGTCACATTCACTTCAGGGAATAGAC
28104703 GTTATGATTT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 86 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (61 bp):
TGTCACATTCACTTCAGGGAATAGACAAATTTATAATAATTTTTTTTATTATTAACTCGTT
Found at i:28121171 original size:43 final size:43
Alignment explanation
Indices: 28121123--28121210 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
28121113 ATTTTTTATT
* *
28121123 TTGTTTT-TTTATACTTTTTCACGTACACTTTTTAATTCTTAAC
1 TTGTTTTCTTT-TACCTTTTCACGTACACTTTTTAACTCTTAAC
* *
28121166 TTGTTTTCTTTTACCTTTTCACGTATACTTTTTCACTCTTAAC
1 TTGTTTTCTTTTACCTTTTCACGTACACTTTTTAACTCTTAAC
28121209 TT
1 TT
28121211 TTAATCAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 37 0.93
44 3 0.08
ACGTcount: A:0.18, C:0.19, G:0.05, T:0.58
Consensus pattern (43 bp):
TTGTTTTCTTTTACCTTTTCACGTACACTTTTTAACTCTTAAC
Found at i:28121800 original size:20 final size:20
Alignment explanation
Indices: 28121743--28121802 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
28121733 ACATGGGCTC
* * *
28121743 CCCAAGGGTGCACTGGTGCT
1 CCCAAGGGAGCACCGGAGCT
* * *
28121763 CCCTAAAGAAGCATCGGAGCT
1 CCC-AAGGGAGCACCGGAGCT
28121784 CCCAAGGGAGCACCGGAGC
1 CCCAAGGGAGCACCGGAGC
28121803 CTCAATTGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.25, C:0.32, G:0.32, T:0.12
Consensus pattern (20 bp):
CCCAAGGGAGCACCGGAGCT
Found at i:28124827 original size:15 final size:15
Alignment explanation
Indices: 28124804--28124834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28124794 TTGGACTGCG
*
28124804 ACATGCAAAGTCTCC
1 ACATACAAAGTCTCC
28124819 ACATACAAAGTCTCC
1 ACATACAAAGTCTCC
28124834 A
1 A
28124835 TAAATATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.10, T:0.19
Consensus pattern (15 bp):
ACATACAAAGTCTCC
Found at i:28126638 original size:30 final size:31
Alignment explanation
Indices: 28126581--28126660 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
28126571 CTGTTGTTGC
*
28126581 AATAAATTCATGTTTCGATCATGA-CCCCAAA
1 AATAAATTCATG-TTCAATCATGACCCCCAAA
* * *
28126612 ATTTAATTCATGTTCAATCATTACCCCCAAA
1 AATAAATTCATGTTCAATCATGACCCCCAAA
28126643 AATAAATTCATGTTCAAT
1 AATAAATTCATGTTCAAT
28126661 TGTGTACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 9 0.21
31 33 0.79
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (31 bp):
AATAAATTCATGTTCAATCATGACCCCCAAA
Found at i:28145006 original size:2 final size:2
Alignment explanation
Indices: 28144999--28145034 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28144989 CGAAACAAAC
28144999 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
28145035 TTGTAATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28145786 original size:2 final size:2
Alignment explanation
Indices: 28145775--28145819 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
28145765 AATAAACAGG
28145775 TA TA -A 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
28145816 TA TA
1 TA TA
28145820 CCAAATTGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28150909 original size:2 final size:2
Alignment explanation
Indices: 28150902--28150945 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28150892 AGTCAAATTA
28150902 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
28150944 AT
1 AT
28150946 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28151069 original size:2 final size:2
Alignment explanation
Indices: 28151062--28151105 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28151052 AGTCAAAATA
28151062 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
28151104 AT
1 AT
28151106 TGAAATACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28164641 original size:139 final size:139
Alignment explanation
Indices: 28164385--28164667 Score: 521
Period size: 139 Copynumber: 2.0 Consensus size: 139
28164375 GAACCTTTTC
* *
28164385 CTACTTTAGATAAAGTGTAAAATTTAGTTCTTCGAAAAGAAAATTAGAGGAGTCTTTTGTTACAA
1 CTACCTTAGATAAAGTGTAAAATTTAGTTCTTCGAAAAGAAAATTAGAAGAGTCTTTTGTTACAA
* *
28164450 TCTAATAGGGATGTCAACGGGTCGGGTACCCTATAATTTCGAGGTACCCGAACCCTAACCCTATT
66 TCTAATAGGGATGTCAACGGGTCGGGTACCCTATAATTTCGAGATACCCGAACCCTAACCCCATT
28164515 AAAAATTAA
131 AAAAATTAA
28164524 CTACCTTAGATAAAGTGTAAAATTTAGTTCTTCGAAAAGAAAATTAGAAGAGTCTTTTGTTACAA
1 CTACCTTAGATAAAGTGTAAAATTTAGTTCTTCGAAAAGAAAATTAGAAGAGTCTTTTGTTACAA
*
28164589 TCTAATAGGGATGTCAACGGGTCGGGTACCCTATAATTTCGAGATACTCGAACCCTAACCCCATT
66 TCTAATAGGGATGTCAACGGGTCGGGTACCCTATAATTTCGAGATACCCGAACCCTAACCCCATT
28164654 AAAAATTAA
131 AAAAATTAA
28164663 CTACC
1 CTACC
28164668 CTAACCCTAT
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 139 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (139 bp):
CTACCTTAGATAAAGTGTAAAATTTAGTTCTTCGAAAAGAAAATTAGAAGAGTCTTTTGTTACAA
TCTAATAGGGATGTCAACGGGTCGGGTACCCTATAATTTCGAGATACCCGAACCCTAACCCCATT
AAAAATTAA
Found at i:28171492 original size:22 final size:23
Alignment explanation
Indices: 28171458--28171501 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
28171448 CAAATTAATA
28171458 CAATAAACTAACA-ACAATTAAC
1 CAATAAACTAACATACAATTAAC
*
28171480 CAATAAA-TCAACATGCAATTAA
1 CAATAAACT-AACATACAATTAA
28171502 AAAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.58
23 7 0.37
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.20
Consensus pattern (23 bp):
CAATAAACTAACATACAATTAAC
Found at i:28214714 original size:29 final size:29
Alignment explanation
Indices: 28214682--28214746 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
28214672 CAACATTAAT
* *
28214682 TATAATAGCTTATTTGAATCAAATAAAAG
1 TATAATAGCTTAATTAAATCAAATAAAAG
**
28214711 TAT-ATGAGCTTAATTAAATGTAATAAAAG
1 TATAAT-AGCTTAATTAAATCAAATAAAAG
*
28214740 AATAATA
1 TATAATA
28214747 ATTTATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.07
29 25 0.86
30 2 0.07
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.34
Consensus pattern (29 bp):
TATAATAGCTTAATTAAATCAAATAAAAG
Found at i:28220821 original size:25 final size:24
Alignment explanation
Indices: 28220792--28220846 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
28220782 CTGAATAATT
*
28220792 AAAAAAA-ACTAAAAAAAAAAGAA
1 AAAAAAATAATAAAAAAAAAAGAA
*
28220815 AAGAAAAATAATTAAAAAAAAAGAA
1 AA-AAAAATAATAAAAAAAAAAGAA
28220840 AAAAAAA
1 AAAAAAA
28220847 GTATTGGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 10 0.36
25 16 0.57
ACGTcount: A:0.85, C:0.02, G:0.05, T:0.07
Consensus pattern (24 bp):
AAAAAAATAATAAAAAAAAAAGAA
Found at i:28222032 original size:13 final size:11
Alignment explanation
Indices: 28222008--28222078 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 11
28221998 TTTTAAGTTT
28222008 AAATAAATAAA
1 AAATAAATAAA
28222019 AAATATAATGAAA
1 AAATA-AAT-AAA
28222032 AAATAAA-AAA
1 AAATAAATAAA
28222042 TATAAT-AATAAAA
1 -A-AATAAAT-AAA
28222055 AAATACAATAAA
1 AAATA-AATAAA
*
28222067 ATAAAAAATAAA
1 A-AATAAATAAA
28222079 CTTCAAAAGC
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
10 3 0.06
11 11 0.22
12 19 0.38
13 17 0.34
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:28222037 original size:20 final size:19
Alignment explanation
Indices: 28222007--28222078 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 19
28221997 TTTTTAAGTT
28222007 TAAATAAATAAAAAATATAA
1 TAAA-AAATAAAAAATATAA
28222027 TGAAAAAATAAAAAATATAA
1 T-AAAAAATAAAAAATATAA
*
28222047 TAATAAAA-AAATACAATAAAA
1 TAA-AAAATAAA-A-AATATAA
28222068 TAAAAAATAAA
1 TAAAAAATAAA
28222079 CTTCAAAAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
19 5 0.11
20 26 0.57
21 15 0.33
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (19 bp):
TAAAAAATAAAAAATATAA
Found at i:28222055 original size:23 final size:21
Alignment explanation
Indices: 28222007--28222069 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
28221997 TTTTTAAGTT
*
28222007 TAAATAAAT-AAAAAATATAA
1 TAAAAAAATAAAAAAATATAA
*
28222027 TGAAAAAATAAAAAATATAATAA
1 TAAAAAAATAAAAAA-AT-ATAA
28222050 TAAAAAAATACAATAAAATA
1 TAAAAAAATA-AA-AAAATA
28222070 AAAAATAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 7 0.20
21 5 0.14
22 2 0.06
23 14 0.40
24 4 0.11
25 3 0.09
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATATAA
Found at i:28224741 original size:13 final size:14
Alignment explanation
Indices: 28224723--28224760 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28224713 AATCTTGTTT
28224723 TTTTAAAT-TTTCA
1 TTTTAAATATTTCA
*
28224736 TTTTAAATATTTTA
1 TTTTAAATATTTCA
*
28224750 TTATAAATATT
1 TTTTAAATATT
28224761 AATTAGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAAATATTTCA
Found at i:28230876 original size:33 final size:33
Alignment explanation
Indices: 28230839--28230923 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
28230829 TATATATAGA
28230839 ACCCAAAAAAAAAAAAGAAAATTTTTATTGGCT
1 ACCCAAAAAAAAAAAAGAAAATTTTTATTGGCT
* *
28230872 ACCCAAAAAAAAGAAAGAAATTTTTTATTGGCT
1 ACCCAAAAAAAAAAAAGAAAATTTTTATTGGCT
28230905 ACCC-AAAAAAAAAAAGAAA
1 ACCCAAAAAAAAAAAAGAAA
28230924 GAAATTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 14 0.29
33 35 0.71
ACGTcount: A:0.58, C:0.13, G:0.09, T:0.20
Consensus pattern (33 bp):
ACCCAAAAAAAAAAAAGAAAATTTTTATTGGCT
Found at i:28238516 original size:2 final size:2
Alignment explanation
Indices: 28238504--28238547 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
28238494 TTGTCTCTGC
* * *
28238504 CT CT CT GT CT CT CT CT CT CT CT CT CT GT CT CT CG CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28238546 CT
1 CT
28238548 GTAAGCACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.48
Consensus pattern (2 bp):
CT
Found at i:28238942 original size:2 final size:2
Alignment explanation
Indices: 28238937--28238962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28238927 TAATCAAAAT
28238937 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
28238963 GATACTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28239480 original size:34 final size:34
Alignment explanation
Indices: 28239437--28239510 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
28239427 AAATAGTTTA
28239437 TCCACCACGTATTTCTGCTGGCATCAGATACCCC
1 TCCACCACGTATTTCTGCTGGCATCAGATACCCC
28239471 TCCACCACGTATTTCTGCTGGCATCAGATACCCC
1 TCCACCACGTATTTCTGCTGGCATCAGATACCCC
28239505 TCCACC
1 TCCACC
28239511 TCAAAGTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.26
Consensus pattern (34 bp):
TCCACCACGTATTTCTGCTGGCATCAGATACCCC
Found at i:28241818 original size:19 final size:20
Alignment explanation
Indices: 28241786--28241824 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
28241776 TCACCATTAT
28241786 TTCAAATGTCATGAT-TTCA
1 TTCAAATGTCATGATATTCA
* *
28241805 TTCAAATTTTATGATATTCA
1 TTCAAATGTCATGATATTCA
28241825 ATATTTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (20 bp):
TTCAAATGTCATGATATTCA
Found at i:28245111 original size:2 final size:2
Alignment explanation
Indices: 28245104--28245143 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28245094 AGCATAAAAA
28245104 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28245144 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.