Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013729.1 Kokia drynarioides strain JFW-HI SEQ_128757, 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: 97013
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:323 original size:30 final size:30
Alignment explanation
Indices: 287--533 Score: 187
Period size: 30 Copynumber: 8.3 Consensus size: 30
277 TTTGACAGAG
* * *
287 AAGTTTAGGGGTTAAAATGTAATTTTTGTA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
* ** *
317 AAGTTT-AGGGTTAAAATGTGCTTTTAGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
* * * * *
346 AGGTTCAAAGGTGAAAATGTAATTTTGGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
* * *
376 AAGTTT--GGGATAAAAATGTGATTTTAGAA
1 AAGTTTAAGGG-TCAAAATGTAATTTTTGAA
* * * * *
405 AAGTTTATGGGTTAAAATATAATTTTGGAG
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
* * *
435 AAGTTTAAGAGTCAAAATGTAATTTTGGAG
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
* *
465 AAGTTTAAGGGTCAAAATGCAATTTTGGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
* * * * *
495 AAGCTCAGGGGTCAAAATGCAA-TTTTGGA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAA
524 AAGTTTAAGG
1 AAGTTTAAGG
534 ACCTTCTGGG
Statistics
Matches: 175, Mismatches: 38, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
28 2 0.01
29 56 0.32
30 114 0.65
31 3 0.02
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
AAGTTTAAGGGTCAAAATGTAATTTTTGAA
Found at i:392 original size:59 final size:59
Alignment explanation
Indices: 300--497 Score: 191
Period size: 59 Copynumber: 3.3 Consensus size: 59
290 TTTAGGGGTT
* * * * *
300 AAAATGTAATTTTTGTAAAGTTTAGGGTTAAAATGTGCTTTTAGAAAGGTTCAAAGGTG
1 AAAATGTAATTTTGGAAAAGTTTAGGGTAAAAATGTGATTTTAGAAAAGTTCAAAGGTG
* ** *
359 AAAATGTAATTTTGGAAAAGTTT-GGGATAAAAATGTGATTTTAGAAAAGTTTATGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGG-TAAAAATGTGATTTTAGAAAAGTTCAAAGGTG
* * * * * * * * * *
418 AAAATATAATTTTGGAGAAGTTTAAGAGTCAAAATGTAATTTTGGAGAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTAAAAATGTGATTTTAGAAAAGTTCAAAGGTG
*
478 AAAATGCAATTTTGGAAAAG
1 AAAATGTAATTTTGGAAAAG
498 CTCAGGGGTC
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
58 3 0.03
59 67 0.58
60 43 0.37
61 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTAAAAATGTGATTTTAGAAAAGTTCAAAGGTG
Found at i:452 original size:89 final size:88
Alignment explanation
Indices: 359--532 Score: 215
Period size: 90 Copynumber: 2.0 Consensus size: 88
349 TTCAAAGGTG
** * * * *
359 AAAATGTAATTTTGGAAAAGTTT-GGGATAAAAATGTGATTTTAGAAAAGTTTATGGGTTAAAAT
1 AAAATGTAATTTTGGAAAAGTTTAGGG-TAAAAATGCAATTTTAGAAAAGCTCAGGGGTCAAAAT
*
423 ATAATTTTGGAGAAGTTTAAGAGTC
65 ACAATTTTGGA-AAGTTTAAGAGTC
* * *
448 AAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATGCAATTTTGGAAAAGCTCAGGGGTCAAAAT
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTAAAAATGCAATTTTAGAAAAGCTCAGGGGTCAAAAT
*
513 GCAATTTTGGAAAGTTTAAG
65 ACAATTTTGGAAAGTTTAAG
533 GACCTTCTGG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
89 31 0.43
90 38 0.53
91 3 0.04
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (88 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTAAAAATGCAATTTTAGAAAAGCTCAGGGGTCAAAATA
CAATTTTGGAAAGTTTAAGAGTC
Found at i:2462 original size:17 final size:17
Alignment explanation
Indices: 2421--2455 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2411 GTGGACATTT
*
2421 TAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
2438 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
2455 T
1 T
2456 TTATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:2991 original size:47 final size:48
Alignment explanation
Indices: 2877--3000 Score: 160
Period size: 47 Copynumber: 2.6 Consensus size: 48
2867 GGATGTTACA
* *
2877 CCACCACTTTTGCAGATAAATTGCCATATAAAAATTATTATGGACAAG
1 CCACCACTTTTGCAGATAAACTGCCACATAAAAATTATTATGGACAAG
* * * * *
2925 CCACCACTTTTGCAAATAAACTGCCACATTATAA-TATTGTGGACAAT
1 CCACCACTTTTGCAGATAAACTGCCACATAAAAATTATTATGGACAAG
* *
2972 CCACCATTTTTGTAGATAAACTGCCACAT
1 CCACCACTTTTGCAGATAAACTGCCACAT
3001 CTTTCACCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
47 37 0.56
48 29 0.44
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (48 bp):
CCACCACTTTTGCAGATAAACTGCCACATAAAAATTATTATGGACAAG
Found at i:6883 original size:13 final size:13
Alignment explanation
Indices: 6848--6886 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
6838 AAATATCTCT
6848 AGAATTTTTTTGAA
1 AGAATTTTTTT-AA
* *
6862 ATAAATTTTTTAA
1 AGAATTTTTTTAA
6875 AGAATTTTTTTA
1 AGAATTTTTTTA
6887 CAACTTTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AGAATTTTTTTAA
Found at i:7070 original size:21 final size:22
Alignment explanation
Indices: 7029--7070 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
7019 TAAATATTAG
*
7029 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
7051 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
7071 ATCTAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:7166 original size:17 final size:17
Alignment explanation
Indices: 7098--7155 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
7088 TAACCACTTT
*
7098 AATATTAAATT-AATAA
1 AATATTAAATTAAATTA
* *
7114 AATATT--ATTAAGTCA
1 AATATTAAATTAAATTA
*
7129 AGTATTAAATTAAATTA
1 AATATTAAATTAAATTA
7146 AATATTAAAT
1 AATATTAAAT
7156 CAATTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
14 3 0.09
15 8 0.24
16 6 0.18
17 16 0.48
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (17 bp):
AATATTAAATTAAATTA
Found at i:17170 original size:81 final size:80
Alignment explanation
Indices: 16919--17186 Score: 285
Period size: 84 Copynumber: 3.3 Consensus size: 80
16909 TTCCCTCCAT
* * *
16919 TTAACAGATTTTATTCTACTTTGATTTTATTTCAAAATGAGAATAAGTTAAATAAATCTGTTTCG
1 TTAATAGATTTTATTCTA-TTTGATTTTGTTTCAAAAT-AAAATAAGTTAAATAAATCTGTTTCG
*
16984 AGATTTATTCCTGTCG-
64 AGATTTATTCCCGTCGA
* * * *
17000 TTCAATAGATTTTATTTCATATTTGGATTTTGGTTCTAAATAATAATTAAG-TAAATCAATCTAT
1 TT-AATAGATTTTA-TTC-TATTT-GATTTTGTTTCAAAATAA-AA-TAAGTTAAATAAATCTGT
*
17064 TTCG-GAATTTATT-CC-TAGCA
60 TTCGAG-ATTTATTCCCGTCG-A
* *
17084 TTTAATAGATTTTATTCTAGTTTGATTTTGTTTCCAAATAAAATAAGTTGAATAAATCTGTTTCG
1 -TTAATAGATTTTATTCTA-TTTGATTTTGTTTCAAAATAAAATAAGTTAAATAAATCTGTTTCG
17149 AGATTTATTCCCGTCGA
64 AGATTTATTCCCGTCGA
*
17166 TTAATAGATTATATTCTATTT
1 TTAATAGATTTTATTCTATTT
17187 TTGGATTTTA
Statistics
Matches: 156, Mismatches: 16, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
80 7 0.04
81 42 0.27
82 34 0.22
83 17 0.11
84 50 0.32
85 6 0.04
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (80 bp):
TTAATAGATTTTATTCTATTTGATTTTGTTTCAAAATAAAATAAGTTAAATAAATCTGTTTCGAG
ATTTATTCCCGTCGA
Found at i:21074 original size:27 final size:27
Alignment explanation
Indices: 21028--21113 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
21018 AGATCTGTCG
*
21028 AATAACGAATAATGCAATAAAGATCGCC
1 AATAAC-AATAATGCGATAAAGATCGCC
* * * *
21056 AATATCAATAATGTGATAAAGAACACC
1 AATAACAATAATGCGATAAAGATCGCC
*
21083 AATAACATATAATGCGATAGAGATCGCC
1 AATAACA-ATAATGCGATAAAGATCGCC
21111 AAT
1 AAT
21114 CCTCTCGATA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 23 0.49
28 24 0.51
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (27 bp):
AATAACAATAATGCGATAAAGATCGCC
Found at i:21405 original size:43 final size:43
Alignment explanation
Indices: 21303--21478 Score: 171
Period size: 43 Copynumber: 4.1 Consensus size: 43
21293 ATCATGCTCT
* *
21303 CAATCAATCACATACTATCAATATTAGGAAACAATG-T--TC-
1 CAATCAATCTCATACTTTCAATATTAGGAAACAATGTTCCTCA
* * * *
21342 CAATCATTTGTTCATGTACTTTCAATAATAGGAAACAATGTTCCACA
1 CAATCA-AT-CTCA--TACTTTCAATATTAGGAAACAATGTTCCTCA
* * * *
21389 CAATCAATGTCATACTTTCAATTTTAAGAAACAATGTTCCTCT
1 CAATCAATCTCATACTTTCAATATTAGGAAACAATGTTCCTCA
* * *
21432 CAATCAATCTCATGCTTTTAATTTTAGGAAACAATGTTCCTCA
1 CAATCAATCTCATACTTTCAATATTAGGAAACAATGTTCCTCA
21475 CAAT
1 CAAT
21479 GTCATTTAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
39 6 0.05
40 1 0.01
41 2 0.02
43 90 0.81
44 1 0.01
45 3 0.03
46 2 0.02
47 6 0.05
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (43 bp):
CAATCAATCTCATACTTTCAATATTAGGAAACAATGTTCCTCA
Found at i:28989 original size:33 final size:34
Alignment explanation
Indices: 28925--28989 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
28915 TGAGCCAGAC
* *
28925 GCCCAACTGTTGCTCCCAAGCCATGCTTGTTGTA
1 GCCCAACTGTTGCTCCCAACCCATGCCTGTTGTA
* *
28959 GCCCAATTGTTGCTGCC-ACCCATGCCTGTTG
1 GCCCAACTGTTGCTCCCAACCCATGCCTGTTG
28990 CTGGAATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.15, C:0.34, G:0.22, T:0.29
Consensus pattern (34 bp):
GCCCAACTGTTGCTCCCAACCCATGCCTGTTGTA
Found at i:33102 original size:37 final size:37
Alignment explanation
Indices: 33052--33126 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
33042 AATGGTTGAT
33052 TCAAAACTAGTTGTGAATCAAGTGTAAGAACTTCAAC
1 TCAAAACTAGTTGTGAATCAAGTGTAAGAACTTCAAC
*
33089 TCAAAACTAGTTGTGAATCAGGTGTAAGAACTTCAAC
1 TCAAAACTAGTTGTGAATCAAGTGTAAGAACTTCAAC
33126 T
1 T
33127 GATCATTCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (37 bp):
TCAAAACTAGTTGTGAATCAAGTGTAAGAACTTCAAC
Found at i:33589 original size:19 final size:20
Alignment explanation
Indices: 33565--33606 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
33555 TTTTGAGGAA
33565 GTGTCTGATATAGAC-TTAT
1 GTGTCTGATATAGACTTTAT
*
33584 GTGTCTGATATAGGCTTTAT
1 GTGTCTGATATAGACTTTAT
33604 GTG
1 GTG
33607 GGAAGAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (20 bp):
GTGTCTGATATAGACTTTAT
Found at i:34250 original size:30 final size:30
Alignment explanation
Indices: 34214--34275 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
34204 GCTAATTCTA
*
34214 TCCTACAACCACTTG-GAAATGTGGGGGGTG
1 TCCTACAACCACTTGAAAAATGT-GGGGGTG
*
34244 TCCTACAGCCACTTGAAAAATGTGGGGGTG
1 TCCTACAACCACTTGAAAAATGTGGGGGTG
34274 TC
1 TC
34276 TTTCTAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (30 bp):
TCCTACAACCACTTGAAAAATGTGGGGGTG
Found at i:34882 original size:21 final size:21
Alignment explanation
Indices: 34858--34905 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
34848 GAAGTAAGAT
*
34858 TTGTTTTGGTAGAAAAGTCAC
1 TTGTATTGGTAGAAAAGTCAC
**
34879 TTGTATTGGTAGAACTGTCAC
1 TTGTATTGGTAGAAAAGTCAC
34900 TTGTAT
1 TTGTAT
34906 CGATAGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
TTGTATTGGTAGAAAAGTCAC
Found at i:34912 original size:21 final size:21
Alignment explanation
Indices: 34874--34913 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34864 TGGTAGAAAA
* *
34874 GTCACTTGTATTGGTAGAACT
1 GTCACTTGTATCGATAGAACT
34895 GTCACTTGTATCGATAGAA
1 GTCACTTGTATCGATAGAA
34914 GTCTGCACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
GTCACTTGTATCGATAGAACT
Found at i:35219 original size:29 final size:29
Alignment explanation
Indices: 35177--35235 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
35167 TTTAGGTGTT
*
35177 ACACCCCCACATTTGC-AAGTGGTTGTAGG
1 ACACCCCCACATTT-CTAAGTGGTTCTAGG
35206 ACACCCCCACATTTCTAAGTGGTTCTAGG
1 ACACCCCCACATTTCTAAGTGGTTCTAGG
35235 A
1 A
35236 TGGTTTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (29 bp):
ACACCCCCACATTTCTAAGTGGTTCTAGG
Found at i:37434 original size:82 final size:81
Alignment explanation
Indices: 37323--38139 Score: 666
Period size: 82 Copynumber: 10.0 Consensus size: 81
37313 AATAGAATTT
* * * *
37323 AATTAATTCTTGTTTGGAAACAAAATCAAAATCAAATCAATTCTGTTGAACGACGGGAATAAATC
1 AATTAATTATTGTTTGGAAACAAAATCAAAAT-AAATAAAATCTGTTGAACGACAGGAATAAATC
37388 CCGAAACAGAATTATTC
65 CCGAAACAGAATTATTC
* * * * * ** * *
37405 AATTCATTCTTGTTTGGAAACAAAATCAAAATCAAATCAAATATGTTGAATG-GTGAAAATATAT
1 AATTAATTATTGTTTGGAAACAAAATCAAAAT-AAATAAAATCTGTTGAACGACAG-GAATAAAT
* *
37469 ACCAAAACAGAATTATTC
64 CCCGAAACAGAATTATTC
* * * *
37487 AATTAACTATTGTTTGGAAACAAAATCAAAATCAAATCAAATCTATTGAACGGCAGGAATAAATC
1 AATTAATTATTGTTTGGAAACAAAATCAAAAT-AAATAAAATCTGTTGAACGACAGGAATAAATC
* * *
37552 TCGAAACAAAATTATTT
65 CCGAAACAGAATTATTC
* * * *
37569 AATTTAATTCTTGTTTAGAAACAAAATCAAAATCAAATCAAAA-CTCTTGAACGACGGGAATAAA
1 AA-TTAATTATTGTTTGGAAACAAAATCAAAAT-AAAT-AAAATCTGTTGAACGACAGGAATAAA
* *
37633 TCCCGAAACATAATTATTT
63 TCCCGAAACAGAATTATTC
* * * * *
37652 AATTTTAATTCTTGTTTAGAAACAAAATCAAAAT---T---A----TTGAATGGCAAGAATAAAT
1 AA--TTAATTATTGTTTGGAAACAAAATCAAAATAAATAAAATCTGTTGAACGACAGGAATAAAT
* * *
37707 CCCAAAACATAATTATTT
64 CCCGAAACAGAATTATTC
* * * * *
37725 AATTTTAATTCTTCTTTGGAAACAAAATCAAAATCAAT----TTTGTTGAACGACAAGAATAAAT
1 AA--TTAATTATTGTTTGGAAACAAAATCAAAATAAATAAAATCTGTTGAACGACAGGAATAAAT
* ** *
37786 CCCAAAATGGAACTATTC
64 CCCGAAACAGAATTATTC
* ** *
37804 AATTAATTATTATTTGGAAACAAAATTCAAATATAAAGTAAAATCTGTTGAAC-AGTGGAAACAA
1 AATTAATTATTGTTTGGAAACAAAA-TCAAA-ATAAA-TAAAATCTGTTGAACGACAGG-AATAA
* * *
37868 ATCCTGAAATAGAATTATTT
62 ATCCCGAAACAGAATTATTC
* * *
37888 AATTAATTATTATTTGAAAACAAAATCCAAATATAGAATAAAATCTGTTGAACGGC-GAGAATAA
1 AATTAATTATTGTTTGGAAACAAAAT-CAAA-ATA-AATAAAATCTGTTGAACGACAG-GAATAA
* *
37952 ATCTCGAAACAGATTTATTC
62 ATCCCGAAACAGAATTATTC
* ** * *
37972 AATTCATTATTAATTGGAAACAAAATAAAAATAGAATAAAATCTGTTAAAC-AGCAGGAATAAAT
1 AATTAATTATTGTTTGGAAACAAAATCAAAATA-AATAAAATCTGTTGAACGA-CAGGAATAAAT
38036 CCCGAAACAGAATTATTC
64 CCCGAAACAGAATTATTC
** ** * * *
38054 ACCTAATTATTGTTCAGAAACAAAATCAAAATAGAATAAAATATGTTGAACAACAGAAATAAATC
1 AATTAATTATTGTTTGGAAACAAAATCAAAATA-AATAAAATCTGTTGAACGACAGGAATAAATC
38119 CCGAAACA-AATTTATTC
65 CCGAAACAGAA-TTATTC
38136 AATT
1 AATT
38140 TTAATTTTTA
Statistics
Matches: 616, Mismatches: 91, Indels: 56
0.81 0.12 0.07
Matches are distributed among these distances:
73 64 0.10
76 2 0.00
77 21 0.03
78 5 0.01
79 36 0.06
80 2 0.00
81 3 0.00
82 250 0.41
83 78 0.13
84 152 0.25
85 3 0.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (81 bp):
AATTAATTATTGTTTGGAAACAAAATCAAAATAAATAAAATCTGTTGAACGACAGGAATAAATCC
CGAAACAGAATTATTC
Found at i:39568 original size:29 final size:29
Alignment explanation
Indices: 39504--39571 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
39494 ATCAAAATCA
* * *
39504 AACTTTTGGAAATTTGAGGTCGAAAATGT
1 AACTTTTGGAAATTTGAGGGCAAAAAGGT
*
39533 GACTTTTGGAAATTTGAGGGCAAAAAGGT
1 AACTTTTGGAAATTTGAGGGCAAAAAGGT
*
39562 AATTTTTGGA
1 AACTTTTGGA
39572 TGCTTAGGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (29 bp):
AACTTTTGGAAATTTGAGGGCAAAAAGGT
Found at i:39586 original size:29 final size:28
Alignment explanation
Indices: 39554--39685 Score: 115
Period size: 29 Copynumber: 4.5 Consensus size: 28
39544 ATTTGAGGGC
*
39554 AAAAAGGTAATTTTTGGATGCTTAGGGAG
1 AAAATGGTAATTTTTGGATG-TTAGGGAG
* * **
39583 AAAATGGTAA-TTTTGGAAAAGTTCGGGTT
1 AAAATGGTAATTTTTGG--ATGTTAGGGAG
39612 AAAATGGTAATTTTTGGATGTTCGAGGGA-
1 AAAATGGTAATTTTTGGATGTT--AGGGAG
* * *
39641 AAATTGGTAATTTTTTGGATGCTCGGGAG
1 AAAATGGTAA-TTTTTGGATGTTAGGGAG
39670 CAAAATGGTAATTTTT
1 -AAAATGGTAATTTTT
39686 AAACGTTCGA
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
28 14 0.17
29 38 0.46
30 31 0.37
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.36
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGATGTTAGGGAG
Found at i:39656 original size:30 final size:30
Alignment explanation
Indices: 39552--39685 Score: 104
Period size: 30 Copynumber: 4.6 Consensus size: 30
39542 AAATTTGAGG
* *
39552 GCAAAAAGGTAA-TTTTTGGATGCTTAGGGA
1 GCAAAATGGTAATTTTTTGGATGC-TCGGGA
* *
39582 G-AAAATGGTAA--TTTTGGAAAAGTTCGGG-
1 GCAAAATGGTAATTTTTTGG--ATGCTCGGGA
** *
39610 TTAAAATGGTAA-TTTTTGGATGTTCGAGG-
1 GCAAAATGGTAATTTTTTGGATGCTCG-GGA
39639 G-AAAATTGGTAATTTTTTGGATGCTCGGGA
1 GCAAAA-TGGTAATTTTTTGGATGCTCGGGA
39669 GCAAAATGGTAATTTTT
1 GCAAAATGGTAATTTTT
39686 AAACGTTCGA
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
28 16 0.18
29 33 0.38
30 34 0.39
31 4 0.05
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.35
Consensus pattern (30 bp):
GCAAAATGGTAATTTTTTGGATGCTCGGGA
Found at i:39667 original size:58 final size:58
Alignment explanation
Indices: 39552--39685 Score: 141
Period size: 58 Copynumber: 2.3 Consensus size: 58
39542 AAATTTGAGG
* *
39552 GCAAAAAGGTAATTTTTGGATGCTTAGGGAGAAAATGGTAATTTTGGAAAAGTTCGGG-
1 GCAAAATGGTAATTTTTGGATGCTTAGGGAGAAAATGGTAATTTTGG-AAAGCTCGGGA
** * *
39610 TTAAAATGGTAATTTTTGGATG-TTCGAGGGA-AAATTGGTAATTTTTTGG-ATGCTCGGGA
1 GCAAAATGGTAATTTTTGGATGCTT--AGGGAGAAAATGGTAA--TTTTGGAAAGCTCGGGA
39669 GCAAAATGGTAATTTTT
1 GCAAAATGGTAATTTTT
39686 AAACGTTCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
57 2 0.03
58 35 0.56
59 20 0.32
60 6 0.10
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.35
Consensus pattern (58 bp):
GCAAAATGGTAATTTTTGGATGCTTAGGGAGAAAATGGTAATTTTGGAAAGCTCGGGA
Found at i:39702 original size:29 final size:28
Alignment explanation
Indices: 39583--39804 Score: 96
Period size: 30 Copynumber: 7.5 Consensus size: 28
39573 GCTTAGGGAG
* *
39583 AAAATGGTAATTTTGGAAAAGTTCG-GGTT
1 AAAATGGTAATTTT--TAAAGTTCGAGGTC
* * *
39612 AAAATGGTAATTTTTGGATGTTCGAGG-G
1 AAAATGGTAATTTTT-AAAGTTCGAGGTC
* * * *
39640 AAAATTGGTAATTTTTTGGATGCTCG-GGAGC
1 AAAA-TGGTAA-TTTTT-AAAGTTCGAGG-TC
39671 AAAATGGTAATTTTTAAACGTTCGAGGTC
1 AAAATGGTAATTTTTAAA-GTTCGAGGTC
* * * * *
39700 AAAAATGGAAATTTTGAAAAGTTTAGGGGTA
1 -AAAATGGTAATTTT-TAAAG-TTCGAGGTC
*
39731 AAAAT-GTAATTTTTGAGAAGCTCGAGGGTC
1 AAAATGGTAATTTTT-A-AAGTTCGA-GGTC
*
39761 AAAAT-GTGATTTTTGAGAAGTTCGAGGGTC
1 AAAATGGTAATTTTT-A-AAGTTCGA-GGTC
*
39791 AAAAT-ATAATTTTT
1 AAAATGGTAATTTTT
39805 TGTGAAGCTT
Statistics
Matches: 154, Mismatches: 25, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
28 11 0.07
29 44 0.29
30 86 0.56
31 13 0.08
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAATGGTAATTTTTAAAGTTCGAGGTC
Found at i:39705 original size:30 final size:31
Alignment explanation
Indices: 39671--39804 Score: 129
Period size: 30 Copynumber: 4.5 Consensus size: 31
39661 GCTCGGGAGC
39671 AAAATGGTAATTTTT-A-AACGTTCGA-GGTCA
1 AAAAT-GTAATTTTTGAGAA-GTTCGAGGGTCA
* * * *
39701 AAAATGGAAATTTTGAAAAGTT-TAGGGGT-A
1 AAAATGTAATTTTTGAGAAGTTCGA-GGGTCA
*
39731 AAAATGTAATTTTTGAGAAGCTCGAGGGTC-
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTCA
*
39761 AAAATGTGATTTTTGAGAAGTTCGAGGGTC-
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTCA
*
39791 AAAATATAATTTTT
1 AAAATGTAATTTTT
39805 TGTGAAGCTT
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
29 8 0.09
30 72 0.84
31 6 0.07
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (31 bp):
AAAATGTAATTTTTGAGAAGTTCGAGGGTCA
Found at i:39826 original size:31 final size:31
Alignment explanation
Indices: 39711--39835 Score: 114
Period size: 30 Copynumber: 4.1 Consensus size: 31
39701 AAAATGGAAA
* * * *
39711 TTTTGAAAAGTTTAG-GGGTAAAAATGTAAT
1 TTTTGAGAAGCTTAGAGGGTCAAAATATAAT
* * *
39741 TTTTGAGAAGC-TCGAGGGTCAAAATGTGAT
1 TTTTGAGAAGCTTAGAGGGTCAAAATATAAT
*
39771 TTTTGAGAAG-TTCGAGGGTCAAAATATAATT
1 TTTTGAGAAGCTTAGAGGGTCAAAATATAA-T
* * *
39802 TTTTGTGAAGCTTAG-GGGTTAAAATATATT
1 TTTTGAGAAGCTTAGAGGGTCAAAATATAAT
39832 TTTT
1 TTTT
39836 AAAAGAAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.03
30 53 0.66
31 22 0.28
32 3 0.04
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (31 bp):
TTTTGAGAAGCTTAGAGGGTCAAAATATAAT
Found at i:41645 original size:17 final size:17
Alignment explanation
Indices: 41620--41652 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41610 ATTCTTTTTA
41620 AATTCAAAATAAATTTG
1 AATTCAAAATAAATTTG
*
41637 AATTTAAAATAAATTT
1 AATTCAAAATAAATTT
41653 AAAAATTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTCAAAATAAATTTG
Found at i:42277 original size:49 final size:49
Alignment explanation
Indices: 42223--42602 Score: 250
Period size: 49 Copynumber: 7.7 Consensus size: 49
42213 CGCCGTTGTA
* * * *
42223 GCCTCAACCTTTCCCTTCATATCTCCATGGTACCAAGTTTGTCTTTACG
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAAGTTTGTCGTTGCG
* * * ** *
42272 GCCTCAACCTTTCCCATCACATCTTCTTAAGTACCGGGTTT-TTGTTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCAT-GGTACCAAGTTTGTCGTTGCG
* *
42321 ACCTCAACCTTTCCCTTCGA-ATCTTCATGGTACCAGGTTTGTCGTTGCG
1 GCCTCAACCTTTCCCTTC-ACATCTTCATGGTACCAAGTTTGTCGTTGCG
* * * * * ***
42370 ACCTCAACCTTTCCCATCACATCTTCTTAGGTATCGAGTTCACCGTTGCG
1 GCCTCAACCTTTCCCTTCACATCTTCAT-GGTACCAAGTTTGTCGTTGCG
** * * * * *
42420 GCCTCAACCTTTCCCTTCGTATCTACATGGTACCGAA-TTCGCCATTGCA
1 GCCTCAACCTTTCCCTTCACATCTTCATGGTACC-AAGTTTGTCGTTGCG
** * * * * * * *
42469 GCCTCAACCTTTTACATCACATCTTCTAAGGTA-CTAGATTCGCCATCGCG
1 GCCTCAACCTTTCCCTTCACATCTTC-ATGGTACCAAG-TTTGTCGTTGCG
* * * *
42519 GCCTCAATCC-TTCCCTTAATC-TCTTCATGGTACTAGGTTCGTCGTTGCG
1 GCCTCAA-CCTTTCCCTTCA-CATCTTCATGGTACCAAGTTTGTCGTTGCG
* * *
42568 GCCTCTACCTTTCCCATCACATCTTCTTAGGTACC
1 GCCTCAACCTTTCCCTTCACATCTTCAT-GGTACC
42603 GGATTCGTTG
Statistics
Matches: 255, Mismatches: 61, Indels: 29
0.74 0.18 0.08
Matches are distributed among these distances:
48 15 0.06
49 151 0.59
50 86 0.34
51 3 0.01
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.34
Consensus pattern (49 bp):
GCCTCAACCTTTCCCTTCACATCTTCATGGTACCAAGTTTGTCGTTGCG
Found at i:42288 original size:99 final size:99
Alignment explanation
Indices: 42124--42715 Score: 518
Period size: 99 Copynumber: 6.0 Consensus size: 99
42114 CGTCGTTGTG
* * ** * * * *
42124 GCCTCAACATTTCCCTTTATATCTTCATGGTA-TTGGATTCGCCAATGCGACCTCAA-TTCTTCC
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGG-TTCGTCATTGCGGCCTCAACCT-TTCC
* * *
42187 CATCGCATCTTCTAAGGTACTGGATTCGCCGTTGTA
64 CATCACATCTTCTAAGGTACCGGATTCGCCGTTGCA
* * * * *
42223 GCCTCAACCTTTCCCTTCATATCTCCATGGTACCAAGTTTGTCTTTACGGCCTCAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCA
* ***
42288 TCACATCTTCTTAA-GTACCGGGTT-TTTGTTGC-
66 TCACATCTTC-TAAGGTACCGGATTCGCCGTTGCA
* * *
42320 GACCTCAACCTTTCCCTTCGA-ATCTTCATGGTACCAGGTTTGTCGTTGCGACCTCAACCTTTCC
1 G-CCTCAACCTTTCCCTTC-ATATCTTCATGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCC
* * * *
42384 CATCACATCTTCTTAGGTATC-GAGTTCACCGTTGCG
64 CATCACATCTTCTAAGGTACCGGA-TTCGCCGTTGCA
* * * * * **
42420 GCCTCAACCTTTCCCTTCGTATCTACATGGTACC-GAATTCGCCATTGCAGCCTCAACCTTTTAC
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAG-GTTCGTCATTGCGGCCTCAACCTTTCCC
** * * *
42484 ATCACATCTTCTAAGGTACTAGATTCGCCATCGCG
65 ATCACATCTTCTAAGGTACCGGATTCGCCGTTGCA
* * * * *
42519 GCCTCAATCC-TTCCCTTAATCTCTTCATGGTACTAGGTTCGTCGTTGCGGCCTCTACCTTTCCC
1 GCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCC
* ** *
42583 ATCACATCTTCTTAGGTACCGGATTCGTTGTCGCA
65 ATCACATCTTCTAAGGTACCGGATTCGCCGTTGCA
* * * * ** * * *
42618 GCCTCAATCTTTCCTTTCATCTTTTCATGGTACTGGGTTCGCCATTGCGGCTTTAACCTTTCCCA
1 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCA
* *
42683 TCACATATTTTAAGGTACCGGATTCGCCGTTGC
66 TCACATCTTCTAAGGTACCGGATTCGCCGTTGC
42716 GGGTTCAATC
Statistics
Matches: 396, Mismatches: 82, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
97 4 0.01
98 79 0.20
99 302 0.76
100 11 0.03
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (99 bp):
GCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCA
TCACATCTTCTAAGGTACCGGATTCGCCGTTGCA
Found at i:42624 original size:198 final size:197
Alignment explanation
Indices: 42169--42730 Score: 580
Period size: 198 Copynumber: 2.8 Consensus size: 197
42159 GATTCGCCAA
* * * * *
42169 TGCGACCTCAA-TTCTTCCCATCGCATCTTCTAAGGTACTGGATTCGCCGTTGTAGCCTCAACCT
1 TGCGACCTCAACCT-TTCCCATCACATCTTCTTAGGTACCGGATTCGCCGTTGCAGCCTCAACCT
* * * * *
42233 TTCCCTTCATATCTCCATGGTACC-AAGTTTGTCTTTACGGCCTCAACCTTTCCCATCACATCTT
65 TTCCCTTCATATCTACATGGTACCGAA-TTCGCCATTGCGGCCTCAACCTTTCCCATCACATCTT
* *** *
42297 CTTAA-GTACCGGGTT-TTTGTTGCGACCTCAA-CCTTTCCCTTCGAATCTTCATGGTACCAGGT
129 C-TAAGGTACCGGATTCGCCGTTGCGGCCTCAATCC-TTCCCTTC-AATCTTCATGGTACCAGGT
*
42359 TTGTCGT
191 TCGTCGT
* * *
42366 TGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTATC-GAGTTCACCGTTGCGGCCTCAACCT
1 TGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGA-TTCGCCGTTGCAGCCTCAACCT
* * **
42430 TTCCCTTCGTATCTACATGGTACCGAATTCGCCATTGCAGCCTCAACCTTTTACATCACATCTTC
65 TTCCCTTCATATCTACATGGTACCGAATTCGCCATTGCGGCCTCAACCTTTCCCATCACATCTTC
** * * *
42495 TAAGGTACTAGATTCGCCATCGCGGCCTCAATCCTTCCCTT-AATCTCTTCATGGTACTAGGTTC
130 TAAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCTTCAA--TCTTCATGGTACCAGGTTC
42559 GTCGT
193 GTCGT
* * ** * *
42564 TGCGGCCTCTACCTTTCCCATCACATCTTCTTAGGTACCGGATTCGTTGTCGCAGCCTCAATCTT
1 TGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGATTCGCCGTTGCAGCCTCAACCTT
* * * * * ** * * * *
42629 TCCTTTCATCTTTTCATGGTACTGGGTTCGCCATTGCGGCTTTAACCTTTCCCATCACATATTTT
66 TCCCTTCATATCTACATGGTACCGAATTCGCCATTGCGGCCTCAACCTTTCCCATCACATCTTCT
**
42694 AAGGTACCGGATTCGCCGTTGCGGGTTCAATCCTTCC
131 AAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCC
42731 TTGTCAAACC
Statistics
Matches: 298, Mismatches: 58, Indels: 17
0.80 0.16 0.05
Matches are distributed among these distances:
196 7 0.02
197 111 0.37
198 176 0.59
199 4 0.01
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (197 bp):
TGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGATTCGCCGTTGCAGCCTCAACCTT
TCCCTTCATATCTACATGGTACCGAATTCGCCATTGCGGCCTCAACCTTTCCCATCACATCTTCT
AAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCTTCAATCTTCATGGTACCAGGTTCGTC
GT
Found at i:46563 original size:30 final size:28
Alignment explanation
Indices: 46529--46584 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
46519 TTAAAATCGA
46529 ACTTTTGGAAAATTTGAGGACGAAAATGTG
1 ACTTTTGG-AAATTTGAGGAC-AAAATGTG
* *
46559 ACTTTTGGAAGTTTGAGGGCAAAATG
1 ACTTTTGGAAATTTGAGGACAAAATG
46585 GTAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 10 0.42
30 8 0.33
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (28 bp):
ACTTTTGGAAATTTGAGGACAAAATGTG
Found at i:46593 original size:29 final size:29
Alignment explanation
Indices: 46561--46857 Score: 175
Period size: 30 Copynumber: 10.1 Consensus size: 29
46551 AAAATGTGAC
*
46561 TTTTGGAAGTTTGAGGGCAAAATGGTAAT
1 TTTTGGAAGTTCGAGGGCAAAATGGTAAT
* * * *
46590 TTTTAGATGCTCGAGAGCAAAATGGTAA-
1 TTTTGGAAGTTCGAGGGCAAAATGGTAAT
*
46618 TTTTGGAAAAGTTCG-GGTCAAAATGGTAAT
1 TTTTGG--AAGTTCGAGGGCAAAATGGTAAT
* *
46648 TTTTGGATGTTCGAGGCCAAAATGGTAAT
1 TTTTGGAAGTTCGAGGGCAAAATGGTAAT
* **
46677 TTTCT-GAATGCTCGAGGTAAAAATGGTAAT
1 TTT-TGGAA-GTTCGAGGGCAAAATGGTAAT
* * *
46707 TTTTAGATGTTCG-GGGTCAAAATAGTAATT
1 TTTTGGAAGTTCGAGGG-CAAAATGGTAA-T
* *
46737 TTTTAGAAGTT-TA-GGCTAAAAT-GTAAT
1 TTTTGGAAGTTCGAGGGC-AAAATGGTAAT
* *
46764 TTTTGAGAAGCTCGAGGGTCAAAAT-GTGAT
1 TTTTG-GAAGTTCGAGGG-CAAAATGGTAAT
* * *
46794 TTTCGATAAGTTTG-GGAGTCAAAAT-GTAAT
1 TTTTG-GAAGTTCGAGG-G-CAAAATGGTAAT
* **
46824 TTTTACGAAGTTTAAGGGTCAAAAT-GTAAT
1 TTTT-GGAAGTTCGAGGG-CAAAATGGTAAT
46854 TTTT
1 TTTT
46858 AAAGGAAAAT
Statistics
Matches: 214, Mismatches: 36, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
27 5 0.02
28 23 0.11
29 78 0.36
30 105 0.49
31 3 0.01
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTCGAGGGCAAAATGGTAAT
Found at i:46649 original size:58 final size:59
Alignment explanation
Indices: 46578--46857 Score: 227
Period size: 58 Copynumber: 4.8 Consensus size: 59
46568 AGTTTGAGGG
* *
46578 CAAAATGGTAATTTTTAGATGCTCGAGAG-CAAAATGGTAATTTTGGAAAAGTTCGGGT
1 CAAAATGGTAATTTTTAGATGCTCGAGGGTCAAAATGGTAATTTTTGAAAAGTTCGGGT
* * * * *
46636 CAAAATGGTAATTTTTGGATGTTCGA-GGCCAAAATGGTAATTTTCTG-AATGCTCGAGGT
1 CAAAATGGTAATTTTTAGATGCTCGAGGGTCAAAATGGTAATTTT-TGAAAAGTTCG-GGT
* * * * * **
46695 AAAAATGGTAATTTTTAGATGTTCG-GGGTCAAAATAGTAATTTTTTAGAAGTTTAGG-
1 CAAAATGGTAATTTTTAGATGCTCGAGGGTCAAAATGGTAATTTTTGAAAAGTTCGGGT
* * * * *
46752 CTAAAAT-GTAATTTTTGAGAAGCTCGAGGGTCAAAAT-GTGATTTTCGATAAGTTTGGGAGT
1 C-AAAATGGTAATTTTT-AGATGCTCGAGGGTCAAAATGGTAATTTTTGAAAAG-TTCGG-GT
* * **
46813 CAAAAT-GTAATTTTTACGAAGTTTAAGGGTCAAAAT-GTAATTTTT
1 CAAAATGGTAATTTTTA-GATGCTCGAGGGTCAAAATGGTAATTTTT
46858 AAAGGAAAAT
Statistics
Matches: 180, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
57 10 0.06
58 71 0.39
59 60 0.33
60 38 0.21
61 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (59 bp):
CAAAATGGTAATTTTTAGATGCTCGAGGGTCAAAATGGTAATTTTTGAAAAGTTCGGGT
Found at i:46758 original size:88 final size:86
Alignment explanation
Indices: 46551--46857 Score: 261
Period size: 88 Copynumber: 3.5 Consensus size: 86
46541 TTTGAGGACG
* * * *
46551 AAAATGTGACTTTTGGAAGTTTGAGGGC-AAAATGGTAATTTTT-AGATGCTCGAGAG-CAAAAT
1 AAAATGTAATTTTTAGAAGTTT-AAGGCTAAAAT-GTAATTTTTGAGATGCTCGAG-GTCAAAAT
* * *
46613 GGTAATTTTGGAAAAGTTC-GGGTC
63 GGTAATTTT-TAGATGTTCGGGGTC
* * ** * *
46637 AAAATGGTAATTTTTGGATGTTCGAGGCCAAAATGGTAATTTTCTGA-ATGCTCGAGGTAAAAAT
1 AAAAT-GTAATTTTTAGAAGTTTAAGGCTAAAAT-GTAATTTT-TGAGATGCTCGAGGTCAAAAT
46701 GGTAATTTTTAGATGTTCGGGGTC
63 GGTAATTTTTAGATGTTCGGGGTC
*
46725 AAAATAGTAATTTTTTAGAAGTTT-AGGCTAAAATGTAATTTTTGAGAAGCTCGAGGGTCAAAAT
1 AAAAT-GTAA-TTTTTAGAAGTTTAAGGCTAAAATGTAATTTTTGAGATGCTCGA-GGTCAAAAT
* * *
46789 -GTGA-TTTTCGATAAGTTTGGGAGTC
63 GGTAATTTTTAGAT--GTTCGGG-GTC
*
46814 AAAATGTAATTTTTACGAAGTTTAAGGGTCAAAATGTAATTTTT
1 AAAATGTAATTTTTA-GAAGTTTAAGGCT-AAAATGTAATTTTT
46858 AAAGGAAAAT
Statistics
Matches: 185, Mismatches: 21, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
86 18 0.10
87 58 0.31
88 72 0.39
89 23 0.12
90 14 0.08
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (86 bp):
AAAATGTAATTTTTAGAAGTTTAAGGCTAAAATGTAATTTTTGAGATGCTCGAGGTCAAAATGGT
AATTTTTAGATGTTCGGGGTC
Found at i:48628 original size:17 final size:17
Alignment explanation
Indices: 48597--48652 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
48587 GATCATTCTT
*
48597 TTTAAA-TTCAAATAAA
1 TTTAAATTTAAAATAAA
48613 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
48630 TTTGAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
48647 TTTAAA
1 TTTAAA
48653 AATACTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 6 0.17
17 30 0.83
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:49203 original size:32 final size:32
Alignment explanation
Indices: 49147--49207 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
49137 AGGAGTCTTT
* *
49147 AAATTAATTTGAATTGAATCAAATCAAATCAA
1 AAATCAATTTGAATTGAATAAAATCAAATCAA
49179 AAATCAATTTG-ATTGGAATAAAATCAAAT
1 AAATCAATTTGAATT-GAATAAAATCAAAT
49208 TGAGATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (32 bp):
AAATCAATTTGAATTGAATAAAATCAAATCAA
Found at i:50384 original size:9 final size:9
Alignment explanation
Indices: 50370--50395 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
50360 TACTTATTTA
50370 AATAATGAC
1 AATAATGAC
50379 AATAATGAC
1 AATAATGAC
50388 AATAATGA
1 AATAATGA
50396 AAATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (9 bp):
AATAATGAC
Found at i:51732 original size:22 final size:21
Alignment explanation
Indices: 51682--51734 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
51672 TGTACTGAAA
*
51682 TTATTTCTTTTTGTTTTTTAT
1 TTATTTATTTTTGTTTTTTAT
51703 TCTA-TTATTTTTAGTTTTATT-T
1 T-TATTTATTTTT-GTTTT-TTAT
51725 TTATTTATTT
1 TTATTTATTT
51735 AAAAATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 10 0.37
22 15 0.56
23 2 0.07
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (21 bp):
TTATTTATTTTTGTTTTTTAT
Found at i:53683 original size:19 final size:19
Alignment explanation
Indices: 53661--53705 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53651 TTATATTAGG
53661 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
53680 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
53699 ATTTAAT
1 ATTTAAT
53706 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:54548 original size:21 final size:21
Alignment explanation
Indices: 54522--54562 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54512 TTCTATTTCT
*
54522 TTTAATTCTATTTTTTTTATC
1 TTTAATTCTATTTCTTTTATC
*
54543 TTTAATTCTGTTTCTTTTAT
1 TTTAATTCTATTTCTTTTAT
54563 TTTTCCTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTAATTCTATTTCTTTTATC
Found at i:56130 original size:21 final size:21
Alignment explanation
Indices: 56105--56154 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
56095 GAATTCAAGC
*
56105 AGCAATCTATAAATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
* **
56126 AGCAAACTTTGGATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
*
56147 AGAAAACT
1 AGCAAACT
56155 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (21 bp):
AGCAAACTATAAATTTTCAAA
Found at i:60000 original size:9 final size:8
Alignment explanation
Indices: 59985--60040 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
59975 GGCAACCCAA
59985 ATTTTTTT
1 ATTTTTTT
59993 ATTTTTTT
1 ATTTTTTT
**
60001 ATTTTACT
1 ATTTTTTT
60009 ATCTTATTTT
1 AT-TT-TTTT
*
60019 ATTTATTT
1 ATTTTTTT
*
60027 ATTTATTT
1 ATTTTTTT
60035 ATTTTT
1 ATTTTT
60041 GTCCAGGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 32 0.80
9 4 0.10
10 4 0.10
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTT
Found at i:61605 original size:19 final size:19
Alignment explanation
Indices: 61583--61627 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
61573 TTATATTAGG
61583 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
61602 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
61621 ATTTAAT
1 ATTTAAT
61628 TTATGCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:62470 original size:21 final size:21
Alignment explanation
Indices: 62430--62488 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
62420 TTCGACTTCC
62430 CTATTTTCTATT-TCTTTTAATT
1 CTATTTTCT-TTAT-TTTTAATT
62452 CTATTTTCTTTATTTTTAATT
1 CTATTTTCTTTATTTTTAATT
62473 -T-TGTTTCTTTTATTTT
1 CTAT-TTTC-TTTATTTT
62489 CCCTTAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 18 0.53
22 10 0.29
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (21 bp):
CTATTTTCTTTATTTTTAATT
Found at i:63529 original size:20 final size:20
Alignment explanation
Indices: 63504--63543 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
63494 TTCGAACCTA
63504 ACAATTAATCTAATATTGTG
1 ACAATTAATCTAATATTGTG
63524 ACAATTAATCTAATATTGTG
1 ACAATTAATCTAATATTGTG
63544 TATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
ACAATTAATCTAATATTGTG
Found at i:65298 original size:20 final size:19
Alignment explanation
Indices: 65275--65313 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
65265 CTAAACAATT
65275 TTATAGAAAT-CATACAAAAA
1 TTATA-AAATGCAT-CAAAAA
65295 TTATAAAATGCATCAAAAA
1 TTATAAAATGCATCAAAAA
65314 GTCCCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (19 bp):
TTATAAAATGCATCAAAAA
Found at i:65574 original size:9 final size:9
Alignment explanation
Indices: 65560--65718 Score: 73
Period size: 9 Copynumber: 17.6 Consensus size: 9
65550 ACTTTATAAA
65560 ATTTTATAT
1 ATTTTATAT
65569 ATTTTATAT
1 ATTTTATAT
* *
65578 -TTTTTTACG
1 ATTTTATA-T
*
65587 ATTTTTATAAA
1 A-TTTTAT-AT
65598 ATTTTATAT
1 ATTTTATAT
*
65607 TTTTTATAT
1 ATTTTATAT
* *
65616 -TTTTTTACG
1 ATTTTATA-T
65625 ATTTTTATAT
1 A-TTTTATAT
*
65635 ATTTTCTA-
1 ATTTTATAT
*
65643 ATTTTAAAT
1 ATTTTATAT
65652 ATTTTA-AT
1 ATTTTATAT
* *
65660 TTTTTATTAAA
1 ATTTTA-T-AT
65671 ATTTTATA-
1 ATTTTATAT
*
65679 ATATTTATAG
1 AT-TTTATAT
*
65689 CTTTTAT-T
1 ATTTTATAT
65697 GATTTTA-AT
1 -ATTTTATAT
65706 ATTTTATA-
1 ATTTTATAT
65714 ATTTT
1 ATTTT
65719 TAATAAAAAC
Statistics
Matches: 115, Mismatches: 19, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
8 38 0.33
9 49 0.43
10 9 0.08
11 18 0.16
12 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTATAT
Found at i:65574 original size:19 final size:19
Alignment explanation
Indices: 65552--65723 Score: 82
Period size: 19 Copynumber: 9.5 Consensus size: 19
65542 TTCTTATGAC
*
65552 TTTATAAAATTTTATATAT
1 TTTATAATATTTTATATAT
* * *
65571 TTTATATTTTTTTACGAT-T
1 TTTATAATATTTTA-TATAT
* *
65590 TTTATAAAATTTTATATTT
1 TTTATAATATTTTATATAT
* * *
65609 TTTATATTTTTTTACGAT-T
1 TTTATAATATTTTA-TATAT
*
65628 TTTAT-ATATTTTCTA-AT
1 TTTATAATATTTTATATAT
*
65645 TTTA-AATATTTTA-ATTT
1 TTTATAATATTTTATATAT
*
65662 TTTATTAAAATTTTATA-AT
1 TTTA-TAATATTTTATATAT
**
65681 ATTTAT-AGCTTTTAT-TGA-
1 -TTTATAATATTTTATAT-AT
65699 TTT-TAATATTTTATA-AT
1 TTTATAATATTTTATATAT
65716 TTT-TAATA
1 TTTATAATA
65724 AAAACATGGG
Statistics
Matches: 114, Mismatches: 24, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
16 3 0.03
17 36 0.32
18 14 0.12
19 52 0.46
20 9 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATAATATTTTATATAT
Found at i:65594 original size:38 final size:38
Alignment explanation
Indices: 65552--65684 Score: 159
Period size: 38 Copynumber: 3.6 Consensus size: 38
65542 TTCTTATGAC
65552 TTTATAAAATTTTATATATTTTATATTTTTTTACGATT
1 TTTATAAAATTTTATATATTTTATATTTTTTTACGATT
*
65590 TTTATAAAATTTTATATTTTTTATATTTTTTTACGATT
1 TTTATAAAATTTTATATATTTTATATTTTTTTACGATT
* * * *
65628 TTTAT-ATATTTTCTA-ATTTTA-AATATTTTA--ATTT
1 TTTATAAAATTTTATATATTTTATATTTTTTTACGA-TT
65662 TTTATTAAAATTTTATAATATTT
1 TTTA-TAAAATTTTAT-ATATTT
65685 ATAGCTTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 6 0.07
35 8 0.10
36 12 0.15
37 9 0.11
38 46 0.56
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (38 bp):
TTTATAAAATTTTATATATTTTATATTTTTTTACGATT
Found at i:65861 original size:90 final size:87
Alignment explanation
Indices: 65731--65924 Score: 271
Period size: 90 Copynumber: 2.2 Consensus size: 87
65721 ATAAAAACAT
* *
65731 GGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTAC
1 GGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTAC
* *
65796 CTAATTGAGTGCAAAAAAGAGTAA
66 CTAAATGAGTG-AAAAAAAAG-AA
* * * *
65820 GGGCTTAATTGCTATTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTA
1 GGGCTTAATTGCT-TTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTA
*
65885 CCTAAATGAGTGAAAAAAAAGCA
65 CCTAAATGAGTGAAAAAAAAGAA
65908 GGGACTTAATTGCTTTT
1 GGG-CTTAATTGCTTTT
65925 CTAAAAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
88 7 0.07
89 30 0.32
90 57 0.61
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.38
Consensus pattern (87 bp):
GGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTAC
CTAAATGAGTGAAAAAAAAGAA
Found at i:65935 original size:90 final size:89
Alignment explanation
Indices: 65731--65950 Score: 241
Period size: 90 Copynumber: 2.5 Consensus size: 89
65721 ATAAAAACAT
* * ** * *
65731 GGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTAC
1 GGGCTTAATTGCTATTTTAAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTAC
* *
65796 CTAATTGAGTGCAAAAAAGAGTAA
66 CTAAATGAGTGCAAAAAAAAGTAA
** * * *
65820 GGGCTTAATTGCTATTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTA
1 GGGCTTAATTGCTA-TTTTAAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTA
*
65885 CCTAAATGAGTG-AAAAAAAAG-CA
65 CCTAAATGAGTGCAAAAAAAAGTAA
*
65908 GGGACTTAATTGCT-TTTCTAAAAAAAAGTTTGAGAG-CTTTTTG
1 GGG-CTTAATTGCTATTT-T-AAAAAAAGTTTGAGGGTCTTTTTG
65951 CACCATTAAG
Statistics
Matches: 113, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
87 3 0.03
88 12 0.11
89 42 0.37
90 56 0.50
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (89 bp):
GGGCTTAATTGCTATTTTAAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTAC
CTAAATGAGTGCAAAAAAAAGTAA
Found at i:72110 original size:20 final size:20
Alignment explanation
Indices: 72066--72114 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
72056 CGTTAAAGAG
*
72066 TTTGATTTTAATTCAAATAAG
1 TTTGA-TTTAATTCAAATAAA
**
72087 TTTGATTTAATTTGAATAAA
1 TTTGATTTAATTCAAATAAA
72107 TTTG-TTTA
1 TTTGATTTA
72115 GAAATCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 16 0.64
21 5 0.20
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTGATTTAATTCAAATAAA
Found at i:73488 original size:16 final size:14
Alignment explanation
Indices: 73432--73490 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 14
73422 TTGCTTTTGG
73432 ACAGTT-CACATATA
1 ACAGTTCCACATA-A
*
73446 ATAGTTCTCACATAA
1 ACAGTTC-CACATAA
*
73461 ACAATT-CACATACA
1 ACAGTTCCACATA-A
73475 ACAGTTCGCACATAA
1 ACAGTTC-CACATAA
73490 A
1 A
73491 TAGATCATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
13 6 0.17
14 11 0.31
15 7 0.19
16 12 0.33
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (14 bp):
ACAGTTCCACATAA
Found at i:73535 original size:29 final size:28
Alignment explanation
Indices: 73503--73571 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
73493 GATCATAGAT
* *
73503 AATAGTCAACACATAATCAGTTCGCATAC
1 AATAGTC-ACACATAACCAATTCGCATAC
* *
73532 AATAGTTCACATATAACCAATTTGCATAC
1 AATAG-TCACACATAACCAATTCGCATAC
73561 AATAGTTCACA
1 AATAG-TCACA
73572 TGTAATCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 33 0.94
30 2 0.06
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.28
Consensus pattern (28 bp):
AATAGTCACACATAACCAATTCGCATAC
Found at i:74602 original size:23 final size:23
Alignment explanation
Indices: 74550--74603 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
74540 ACAAATAAAT
* *
74550 AAAATTAAATTGAAATTAACGAA
1 AAAATAAAATTGAAATAAACGAA
*
74573 AAAATAAAATT-AAATAAAGGAA
1 AAAATAAAATTGAAATAAACGAA
74595 AAATATAAA
1 AAA-ATAAA
74604 TAGCATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (23 bp):
AAAATAAAATTGAAATAAACGAA
Found at i:74604 original size:22 final size:23
Alignment explanation
Indices: 74550--74604 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
74540 ACAAATAAAT
*
74550 AAAAT-TAAATTGAAATTAACGA
1 AAAATATAAATTGAAATAAACGA
*
74572 AAAA-ATAAAATT-AAATAAAGGA
1 AAAATAT-AAATTGAAATAAACGA
74594 AAAATATAAAT
1 AAAATATAAAT
74605 AGCATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAATATAAATTGAAATAAACGA
Found at i:74740 original size:26 final size:25
Alignment explanation
Indices: 74711--74761 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
74701 AAGAATAATA
*
74711 AATAAAAATTAA-ATACTAAATAAAAT
1 AATAAAAA-TAATATA-TAAAAAAAAT
*
74737 AATACAAATAATATATAAAAAAAAT
1 AATAAAAATAATATATAAAAAAAAT
74762 TGGGACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (25 bp):
AATAAAAATAATATATAAAAAAAAT
Found at i:74866 original size:30 final size:29
Alignment explanation
Indices: 74830--74897 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
74820 AAATGGGGCA
74830 AAATAAAATAAAGGACTA-A-ATTAAAAAAG
1 AAATAAAATAAA-G-CTACACATTAAAAAAG
* *
74859 CAAATAAATTAAAGCTACACATTAAAATAG
1 -AAATAAAATAAAGCTACACATTAAAAAAG
74889 AAATAAAAT
1 AAATAAAAT
74898 GAAATTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 3 0.09
29 10 0.30
30 20 0.61
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (29 bp):
AAATAAAATAAAGCTACACATTAAAAAAG
Found at i:76062 original size:16 final size:16
Alignment explanation
Indices: 76036--76068 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
76026 ATTTGGGCTA
76036 GGGTTTTTTT-GTTTT
1 GGGTTTTTTTGGTTTT
76051 GGGTTTTATTTGGTTTT
1 GGGTTTT-TTTGGTTTT
76068 G
1 G
76069 TTTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (16 bp):
GGGTTTTTTTGGTTTT
Found at i:80154 original size:191 final size:196
Alignment explanation
Indices: 79788--80240 Score: 502
Period size: 195 Copynumber: 2.3 Consensus size: 196
79778 AAACCGACAC
* * * * * **
79788 GATGGCTGAGGTACCGAATATGTTGCGACTCCTCAACAGCTCGTGCAAGAAGCATCGTGAGTCAG
1 GATGGATGAGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGAAGCATCGTGA--C--
* * * * * *
79853 AAAATGAGAAAAGAAATATGGATCCTAAATGGATTACTGGCCCTACGATTATTGAGATTTATGCA
62 ---ATG-GGAAAGAAATATGGATCCTAAATGGATTACAGGCCCTACGATGACTGAGATCTATACA
* * * *
79918 TAAGTGCATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAG-T-TA-TATGCACAGA
123 TAAGTGCATACTCTCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATAGTATACACAAA
* *
79980 TACCGTATT
188 CACCGTACT
* * * * *
79989 GATGGATGAGGTACCGCATATGTTGTGAGTCCTCGATAGCTTGTGTGAGCAGCATCGTGACATGG
1 GATGGATGAGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGAAGCATCGTGACATGG
* * * *
80054 GAAAGAGATATGGATCCTAAATGGATTACAGGCCCTACGATGACTGGGA-CTATAC-TTATTGCA
66 GAAAGAAATATGGATCCTAAATGGATTACAGGCCCTACGATGACTGAGATCTATACATAAGTGCA
* *
80117 TACTCTCGACAGCTCGTGTGAGCAGCATTATTAGGGAACAGTTTATAGTATATACAAACACCGTA
131 TACTCTCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAG-TTATAGTATACACAAACACCGTA
80182 CT
195 CT
* *
80184 GATGGCTGGGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGAAGCATCG
1 GATGGATGAGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGAAGCATCG
80241 AGTACTGGTA
Statistics
Matches: 213, Mismatches: 35, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
191 44 0.21
192 4 0.02
193 45 0.21
194 5 0.02
195 64 0.30
199 1 0.00
201 50 0.23
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (196 bp):
GATGGATGAGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGAAGCATCGTGACATGG
GAAAGAAATATGGATCCTAAATGGATTACAGGCCCTACGATGACTGAGATCTATACATAAGTGCA
TACTCTCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATAGTATACACAAACACCGTAC
T
Found at i:86434 original size:32 final size:32
Alignment explanation
Indices: 86393--86461 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
86383 CATCATTTAC
86393 ATATCCAACAAACTTGAAA-CATAATAAATTCA
1 ATATCCAAC-AACTTGAAAGCATAATAAATTCA
* *
86425 ATATCCAACAACTTTAAAGCATAATAATTTCA
1 ATATCCAACAACTTGAAAGCATAATAAATTCA
86457 ATATC
1 ATATC
86462 AATATCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.29
Consensus pattern (32 bp):
ATATCCAACAACTTGAAAGCATAATAAATTCA
Found at i:90085 original size:13 final size:14
Alignment explanation
Indices: 90067--90100 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
90057 ATATTAAAAA
90067 CTTAAA-CACAATT
1 CTTAAACCACAATT
90080 CTTAAACCCACAATT
1 CTTAAA-CCACAATT
90095 CTTAAA
1 CTTAAA
90101 GCTAGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (14 bp):
CTTAAACCACAATT
Found at i:90116 original size:25 final size:25
Alignment explanation
Indices: 90088--90138 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
90078 TTCTTAAACC
90088 CACAATTCTTAAAGCTAGATAAAAG
1 CACAATTCTTAAAGCTAGATAAAAG
90113 CACAATTCTTAAAGCTAGATAAAAG
1 CACAATTCTTAAAGCTAGATAAAAG
90138 C
1 C
90139 CACACACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (25 bp):
CACAATTCTTAAAGCTAGATAAAAG
Found at i:93275 original size:3 final size:3
Alignment explanation
Indices: 93267--93300 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
93257 CAATAATGTA
* *
93267 AAT AAT AAT AAT AAT AAT AAT AGT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
93301 GAAGTGATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93301 original size:12 final size:12
Alignment explanation
Indices: 93258--93301 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
93248 CACCTATTTC
93258 AATAAT-GTAAAT
1 AATAATAGT-AAT
*
93270 AATAATAATAAT
1 AATAATAGTAAT
*
93282 AATAATAGTAGT
1 AATAATAGTAAT
93294 AATAATAG
1 AATAATAG
93302 AAGTGATAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 27 0.96
13 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (12 bp):
AATAATAGTAAT
Done.