Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 189 of 218
Found at i:56234532 original size:11 final size:11
Alignment explanation
Indices: 56234511--56234571 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
56234501 TAATAATACT
*
56234511 ATAATAGCAAA
1 ATAACAGCAAA
*
56234522 ATAACATCAAA
1 ATAACAGCAAA
**
56234533 ATGGCAGCAAA
1 ATAACAGCAAA
*
56234544 A-AACAACAAA
1 ATAACAGCAAA
*
56234554 ATAGCAGCAAA
1 ATAACAGCAAA
*
56234565 ACAACAG
1 ATAACAG
56234572 TGAAAAAAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
10 7 0.19
11 30 0.81
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.10
Consensus pattern (11 bp):
ATAACAGCAAA
Found at i:56234553 original size:21 final size:22
Alignment explanation
Indices: 56234516--56234570 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
56234506 ATACTATAAT
* * *
56234516 AGCAAAATAACATCAAAATGGC
1 AGCAAAACAACAACAAAATAGC
56234538 AGCAAAA-AACAACAAAATAGC
1 AGCAAAACAACAACAAAATAGC
56234559 AGCAAAACAACA
1 AGCAAAACAACA
56234571 GTGAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.62, C:0.20, G:0.11, T:0.07
Consensus pattern (22 bp):
AGCAAAACAACAACAAAATAGC
Found at i:56234922 original size:60 final size:62
Alignment explanation
Indices: 56234836--56235005 Score: 168
Period size: 60 Copynumber: 2.8 Consensus size: 62
56234826 AGGTTTGAAC
* * * * ** *
56234836 TTTTTTTGTCCAAATTAAGTCATGAACTTGA-CAGTTGTTCCCACATTGGGGCCTGAA-CCT
1 TTTTTTTGTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATTGGGACCTGAATCCT
* * **
56234896 TTTTTTTGTCCAAGTTAGGCCTTGAACTT-AGCAAATGTTCCCACGTTGGGACTTGAATTTT
1 TTTTTTTGTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATTGGGACCTGAATCCT
* * *
56234957 TTTTCTTTGGTCCAAGTTAGGCCTTAAACTTG-GCAACTGTTCTCACATT
1 TTTT-TTT-GTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATT
56235006 AGAATTTGAA
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
59 1 0.01
60 46 0.51
61 5 0.06
62 3 0.03
63 35 0.39
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (62 bp):
TTTTTTTGTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATTGGGACCTGAATCCT
Found at i:56235015 original size:63 final size:61
Alignment explanation
Indices: 56234895--56235023 Score: 159
Period size: 63 Copynumber: 2.1 Consensus size: 61
56234885 GGCCTGAACC
* * * * *
56234895 TTTTTTTTGTCCAAGTTAGGCCTTGAACTTAGCAAATGTTCCCACGTTGGGACTTGAATTT
1 TTTTTTTTGTCCAAGTTAGGCCTTAAACTTAGCAAATGTTCCCACATTAGAACTTGAACTT
* * * *
56234956 TTTTTCTTTGGTCCAAGTTAGGCCTTAAACTTGGCAACTGTTCTCACATTAGAATTTGAACTT
1 TTTTT-TTT-GTCCAAGTTAGGCCTTAAACTTAGCAAATGTTCCCACATTAGAACTTGAACTT
56235019 TTTTT
1 TTTTT
56235024 ATTCAAGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 5 0.09
62 3 0.05
63 49 0.86
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (61 bp):
TTTTTTTTGTCCAAGTTAGGCCTTAAACTTAGCAAATGTTCCCACATTAGAACTTGAACTT
Found at i:56239023 original size:34 final size:35
Alignment explanation
Indices: 56238980--56239052 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 35
56238970 TTTCTTTCTT
* *
56238980 AATTTA-TTTTTTCCTAATGATAAATTTGGCCCTC
1 AATTTATTTTTTTCATAATGATAAATTTGACCCTC
*
56239014 AATTTATTTTTTTTCATAATGATAAATTTGACTCTC
1 AATTTA-TTTTTTTCATAATGATAAATTTGACCCTC
56239050 AAT
1 AAT
56239053 ATTTATACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 6 0.18
36 28 0.82
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (35 bp):
AATTTATTTTTTTCATAATGATAAATTTGACCCTC
Found at i:56242640 original size:3 final size:3
Alignment explanation
Indices: 56242632--56242660 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56242622 TCTTCAACTC
56242632 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
56242661 AAATCTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:56249929 original size:15 final size:16
Alignment explanation
Indices: 56249904--56249933 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56249894 TGTTTAGTTT
56249904 TTATATTTTAATTTAG
1 TTATATTTTAATTTAG
56249920 TTAT-TTTTAATTTA
1 TTATATTTTAATTTA
56249934 AAATTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATATTTTAATTTAG
Found at i:56252453 original size:20 final size:18
Alignment explanation
Indices: 56252430--56252526 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 18
56252420 TTTCTCAATA
56252430 AAAATTTTAAAATGATTTT
1 AAAATTTTAAAAT-ATTTT
* *
56252449 CAAAAATTCAAAATAATTTT
1 -AAAATTTTAAAAT-ATTTT
*
56252469 TAAATTTTAAAATATTTAT
1 AAAATTTTAAAATATTT-T
*
56252488 AAAAATTCTAAAA-A-TTT
1 -AAAATTTTAAAATATTTT
* *
56252505 -ATATTTTAAAAAATTTAT
1 AAAATTTTAAAATATTT-T
56252523 AAAA
1 AAAA
56252527 ATTCTAAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
15 9 0.15
16 1 0.02
17 3 0.05
18 7 0.12
19 14 0.23
20 26 0.43
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
AAAATTTTAAAATATTTT
Found at i:56252521 original size:35 final size:36
Alignment explanation
Indices: 56252467--56252543 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
56252457 CAAAATAATT
* *
56252467 TTTAAATTTTAAAATATTTATAAAAATTCTAAA-AA
1 TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
56252502 TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
1 TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
*
56252538 TATATA
1 TTTATA
56252544 AAGAAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 31 0.82
36 7 0.18
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (36 bp):
TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
Found at i:56252526 original size:10 final size:10
Alignment explanation
Indices: 56252470--56252529 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
56252460 AATAATTTTT
56252470 AAATTT-TAA
1 AAATTTATAA
56252479 AATATTTATAA
1 AA-ATTTATAA
*
56252490 AAA-TTCTAA
1 AAATTTATAA
56252499 AAATTTAT--
1 AAATTTATAA
*
56252507 -ATTTTA-AA
1 AAATTTATAA
56252515 AAATTTATAA
1 AAATTTATAA
56252525 AAATT
1 AAATT
56252530 CTAAAGAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
7 5 0.12
9 15 0.38
10 15 0.38
11 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATTTATAA
Found at i:56253017 original size:15 final size:16
Alignment explanation
Indices: 56252997--56253030 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
56252987 GGTCATGACT
56252997 AAAAAATTAA-AATTA
1 AAAAAATTAAGAATTA
56253012 AAAAAATTAAGAATTA
1 AAAAAATTAAGAATTA
56253028 AAA
1 AAA
56253031 TTGATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAAATTAAGAATTA
Found at i:56256644 original size:44 final size:43
Alignment explanation
Indices: 56256549--56256674 Score: 157
Period size: 43 Copynumber: 2.9 Consensus size: 43
56256539 TCGTACAATG
* * * *
56256549 CCAATGTCCCAGACGTGGTCTTACATGTAAT-TAAATATCGATG
1 CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAA-ATCGATA
* *
56256592 CCACTGTCCTAGACAG-GGTCTTACACGAAAGTCTCAAATCGATA
1 CCAATGTCCCAGAC-GTGGTCTTACACGAAA-TCTCAAATCGATA
56256636 CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAAATC
1 CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAAATC
56256675 AAAATCCTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
43 34 0.48
44 34 0.48
45 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAAATCGATA
Found at i:56264101 original size:19 final size:19
Alignment explanation
Indices: 56264074--56264117 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
56264064 TTAGCTTTTT
*
56264074 AGAGCTTAATCCGGGTTTA
1 AGAGTTTAATCCGGGTTTA
*
56264093 AGAGTTTAATCTGGGTTTA
1 AGAGTTTAATCCGGGTTTA
56264112 AGAGTT
1 AGAGTT
56264118 GATTTAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (19 bp):
AGAGTTTAATCCGGGTTTA
Found at i:56281232 original size:12 final size:12
Alignment explanation
Indices: 56281217--56281265 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
56281207 TTCAGTTTCC
56281217 GGTTTGGTCTCT
1 GGTTTGGTCTCT
56281229 GGTTTGGTCTCCT
1 GGTTTGGTCT-CT
*
56281242 -GTTTGGCCTCT
1 GGTTTGGTCTCT
*
56281253 TGTTTGGTCTCT
1 GGTTTGGTCTCT
56281265 G
1 G
56281266 ATTTAGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.31, T:0.49
Consensus pattern (12 bp):
GGTTTGGTCTCT
Found at i:56281245 original size:24 final size:24
Alignment explanation
Indices: 56281218--56281263 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56281208 TCAGTTTCCG
*
56281218 GTTTGGTCTCTGGTTTGGTCTCCT
1 GTTTGGCCTCTGGTTTGGTCTCCT
*
56281242 GTTTGGCCTCTTGTTTGGTCTC
1 GTTTGGCCTCTGGTTTGGTCTC
56281264 TGATTTAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.28, T:0.50
Consensus pattern (24 bp):
GTTTGGCCTCTGGTTTGGTCTCCT
Found at i:56282639 original size:18 final size:18
Alignment explanation
Indices: 56282600--56282646 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
56282590 TAACTTTCTT
* *
56282600 TATATATTCTTAAAAGAG
1 TATATATTTTTAAAAGAA
56282618 TATATATTTTTAAAA-ATA
1 TATATATTTTTAAAAGA-A
*
56282636 TATACATTTTT
1 TATATATTTTT
56282647 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (18 bp):
TATATATTTTTAAAAGAA
Found at i:56283172 original size:45 final size:44
Alignment explanation
Indices: 56283106--56283200 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
56283096 GGATTAGAGG
* * * *
56283106 TGTAATGTAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
56283151 TGTAATGGAATAAAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGCAAAACACTGTTTGGTTGAA
56283195 TGTAAT
1 TGTAAT
56283201 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAAAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:56283383 original size:18 final size:17
Alignment explanation
Indices: 56283362--56283396 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56283352 TTATTATTTA
*
56283362 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56283380 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56283397 GGTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56283390 original size:28 final size:27
Alignment explanation
Indices: 56283320--56283392 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
56283310 TTTATTATCA
*
56283320 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
56283348 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
56283375 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
56283393 AAATGGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:56283509 original size:144 final size:147
Alignment explanation
Indices: 56283281--56283552 Score: 469
Period size: 144 Copynumber: 1.9 Consensus size: 147
56283271 ATGATTATTG
56283281 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
56283346 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGGTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
56283411 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
56283430 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
56283492 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTA
56283553 ATATTCTTAT
Statistics
Matches: 119, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
144 90 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:56283527 original size:18 final size:17
Alignment explanation
Indices: 56283506--56283540 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56283496 TTATTATTAA
*
56283506 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56283524 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56283541 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56287111 original size:13 final size:14
Alignment explanation
Indices: 56287093--56287121 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56287083 GTTTGAGATT
56287093 ATTATATTA-AAAA
1 ATTATATTATAAAA
56287106 ATTATATTATAAAA
1 ATTATATTATAAAA
56287120 AT
1 AT
56287122 AATTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATATTATAAAA
Found at i:56287115 original size:18 final size:18
Alignment explanation
Indices: 56287092--56287146 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
56287082 TGTTTGAGAT
56287092 TATTATATTAAAAAATTA
1 TATTATATTAAAAAATTA
56287110 TATTATA--AAAATAATT-
1 TATTATATTAAAA-AATTA
* *
56287126 TATGTATTTTATAAAATTA
1 TAT-TATATTAAAAAATTA
56287145 TA
1 TA
56287147 GCAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 11 0.37
19 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TATTATATTAAAAAATTA
Found at i:56287266 original size:14 final size:15
Alignment explanation
Indices: 56287231--56287268 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
56287221 TTTACATGTT
56287231 ATAAATTT-TTTATA
1 ATAAATTTATTTATA
*
56287245 ATATATTTATTTATA
1 ATAAATTTATTTATA
56287260 A-AAATTTAT
1 ATAAATTTAT
56287269 GATCAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAATTTATTTATA
Found at i:56288084 original size:17 final size:18
Alignment explanation
Indices: 56288062--56288104 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
56288052 GTTTAGAAAT
*
56288062 TATTTTTATCAT-ACTAA
1 TATTTTTATAATAACTAA
*
56288079 TATTTTTATAATAATTAA
1 TATTTTTATAATAACTAA
56288097 TATTTTTA
1 TATTTTTA
56288105 AAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTTATAATAACTAA
Found at i:56289818 original size:31 final size:31
Alignment explanation
Indices: 56289783--56289880 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 31
56289773 TAAATACGAC
56289783 TAAGGCAAGTGCACCTATCGAACATAGTGAG
1 TAAGGCAAGTGCACCTATCGAACATAGTGAG
* * * *
56289814 TAAGG---GT-CA-CTAAACTAACTATAAATACGAC
1 TAAGGCAAGTGCACCT-ATCGAAC-AT-AGT--GAG
56289845 TAAGGCAAGTGCACCTATCGAACATAGTGAG
1 TAAGGCAAGTGCACCTATCGAACATAGTGAG
56289876 TAAGG
1 TAAGG
56289881 AATATTGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
26 2 0.04
27 7 0.14
28 4 0.08
29 2 0.04
31 19 0.39
33 2 0.04
34 4 0.08
35 7 0.14
36 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (31 bp):
TAAGGCAAGTGCACCTATCGAACATAGTGAG
Found at i:56289853 original size:62 final size:62
Alignment explanation
Indices: 56289756--56289880 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
56289746 AACAACTAAT
56289756 GGTCACTAAACTAACTATAAATACGACTAAGGCAAGTGCACCTATCGAACATAGTGAGTAAG
1 GGTCACTAAACTAACTATAAATACGACTAAGGCAAGTGCACCTATCGAACATAGTGAGTAAG
56289818 GGTCACTAAACTAACTATAAATACGACTAAGGCAAGTGCACCTATCGAACATAGTGAGTAAG
1 GGTCACTAAACTAACTATAAATACGACTAAGGCAAGTGCACCTATCGAACATAGTGAGTAAG
56289880 G
1 G
56289881 AATATTGTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (62 bp):
GGTCACTAAACTAACTATAAATACGACTAAGGCAAGTGCACCTATCGAACATAGTGAGTAAG
Found at i:56290605 original size:22 final size:24
Alignment explanation
Indices: 56290580--56290626 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
56290570 CACAAGATAT
56290580 AAAGAAACTT-AATAAA-A-CTTCG
1 AAAGAAA-TTAAATAAAGATCTTCG
56290602 AAAGAAATTAAATAAAGATCTTCG
1 AAAGAAATTAAATAAAGATCTTCG
56290626 A
1 A
56290627 TCTTGAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 13 0.59
23 1 0.05
24 6 0.27
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (24 bp):
AAAGAAATTAAATAAAGATCTTCG
Found at i:56295228 original size:23 final size:24
Alignment explanation
Indices: 56295200--56295247 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
56295190 GTTTTGGTGC
*
56295200 TGTTATTTTTG-TGCTGTTTTTGT
1 TGTTATTTTTGCTACTGTTTTTGT
*
56295223 TGTTATTTTTGCTATTGTTTTTGT
1 TGTTATTTTTGCTACTGTTTTTGT
56295247 T
1 T
56295248 ATTTGTACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (24 bp):
TGTTATTTTTGCTACTGTTTTTGT
Found at i:56295246 original size:21 final size:22
Alignment explanation
Indices: 56295200--56295251 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
56295190 GTTTTGGTGC
*
56295200 TGTTATTTTTGTGCTGTTTTTGT
1 TGTTA-TTTTGTGCTATTTTTGT
56295223 TGTTATTTT-TGCTATTGTTT-T
1 TGTTATTTTGTGCTATT-TTTGT
56295244 TGTTATTT
1 TGTTATTT
56295252 GTACTGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 15 0.56
22 7 0.26
23 5 0.19
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.71
Consensus pattern (22 bp):
TGTTATTTTGTGCTATTTTTGT
Found at i:56299753 original size:10 final size:11
Alignment explanation
Indices: 56299728--56299753 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56299718 TGATATCTCT
56299728 TTTTTTAAATA
1 TTTTTTAAATA
56299739 TTTTTTAAATA
1 TTTTTTAAATA
56299750 TTTT
1 TTTT
56299754 ACTATACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:56301795 original size:20 final size:20
Alignment explanation
Indices: 56301780--56301820 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
56301770 TCTTTTTATA
56301780 TTTTATAGATTTTTTTGAAAT
1 TTTTATA-ATTTTTTTGAAAT
*
56301801 TTTTATAATTTTTTTAAAAT
1 TTTTATAATTTTTTTGAAAT
56301821 ATATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTTTGAAAT
Found at i:56301812 original size:18 final size:18
Alignment explanation
Indices: 56301791--56301858 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 18
56301781 TTTATAGATT
56301791 TTTTTGAAATTTTTATAA
1 TTTTTGAAATTTTTATAA
* * *
56301809 TTTTTTTAAA-ATATATAA
1 -TTTTTGAAATTTTTATAA
* *
56301827 ATTTTGGAATTTTTATAAA
1 TTTTTGAAATTTTTAT-AA
56301846 TATTTTG-AATTTT
1 T-TTTTGAAATTTT
56301859 AAAAATTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 6 0.16
18 10 0.27
19 16 0.43
20 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTTGAAATTTTTATAA
Found at i:56301857 original size:19 final size:19
Alignment explanation
Indices: 56301822--56301876 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
56301812 TTTTAAAATA
*
56301822 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
56301840 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
56301858 TAAAAATTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
56301877 AATTTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 15 0.47
19 15 0.47
20 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:56301859 original size:18 final size:18
Alignment explanation
Indices: 56301822--56301876 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
56301812 TTTTAAAATA
*
56301822 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAA-TTT
56301840 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
*
56301858 TAAAAATTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
56301877 AATTTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:56301865 original size:36 final size:36
Alignment explanation
Indices: 56301792--56301865 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
56301782 TTATAGATTT
* * *
56301792 TTTTGAAATTTTTATAATTTTTTTAAAATATATAAA
1 TTTTGAAATTTTTATAAATATTTTAAAATATAAAAA
* * * *
56301828 TTTTGGAATTTTTATAAATATTTTGAATTTTAAAAA
1 TTTTGAAATTTTTATAAATATTTTAAAATATAAAAA
56301864 TT
1 TT
56301866 ATTTTGAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (36 bp):
TTTTGAAATTTTTATAAATATTTTAAAATATAAAAA
Found at i:56303612 original size:10 final size:11
Alignment explanation
Indices: 56303587--56303620 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
56303577 AAATAAATTG
*
56303587 AAGAAAAAAGA
1 AAGAAAGAAGA
56303598 AAGAAAGAA-A
1 AAGAAAGAAGA
56303608 AAGAAAGAAGA
1 AAGAAAGAAGA
56303619 AA
1 AA
56303621 AATGAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:56303630 original size:14 final size:13
Alignment explanation
Indices: 56303586--56303622 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
56303576 CAAATAAATT
56303586 GAAGAAAAAAGAAA
1 GAAG-AAAAAGAAA
56303600 GAAAGAAAAAGAAA
1 G-AAGAAAAAGAAA
56303614 GAAGAAAAA
1 GAAGAAAAA
56303623 TGAGAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAGAAA
Found at i:56306420 original size:36 final size:36
Alignment explanation
Indices: 56306374--56306482 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
56306364 GGTAGCTTTA
*
56306374 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
56306410 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
56306446 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
56306482 G
1 G
56306483 TTAGTCTTAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:56306430 original size:21 final size:20
Alignment explanation
Indices: 56306402--56306467 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
56306392 AGTGAAAAAG
56306402 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
56306422 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
56306438 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
56306458 TGATCAAGTG
1 TGAT-AAGTG
56306468 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:56306441 original size:82 final size:84
Alignment explanation
Indices: 56306338--56306571 Score: 226
Period size: 82 Copynumber: 2.8 Consensus size: 84
56306328 TTTGAGTACT
* *
56306338 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC--TAGCTACACTTATCTGATCAAGTGAAAAAGT
56306403 GATAAGTG-C-TA-T-ACTTA
64 GATAAGTGTCTTACTAACTTA
*
56306420 TCTGATCAAGTGAAAAAGTGATAA---GT-GCTA--T--ACTTATCTGATCAAGTGACAAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
56306477 TAAGTGTTAGTCTTAGCTACACTTA
66 TAA--G-T-GTCTTA-CTA-ACTTA
* * * *
56306502 TCTAATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTAGCTACACTTATCTGATCAAGTGAAAAAGTG
56306565 ATAAGTG
65 ATAAGTG
56306572 ATCATATGTA
Statistics
Matches: 125, Mismatches: 8, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
72 28 0.22
74 2 0.02
75 1 0.01
76 3 0.02
77 1 0.01
78 4 0.03
79 2 0.02
80 1 0.01
82 49 0.39
85 3 0.02
86 2 0.02
87 4 0.03
89 11 0.09
90 2 0.02
91 12 0.10
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (84 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
TAAGTGTCTTACTAACTTA
Found at i:56311211 original size:51 final size:51
Alignment explanation
Indices: 56311070--56311275 Score: 197
Period size: 51 Copynumber: 4.1 Consensus size: 51
56311060 TACTTATGAA
* * * *
56311070 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTA-TCGATAGA-TGATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAT-GACT-TTGGT
* * *
56311121 CACATGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGATGACTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATGACTTTGGT
* * * *
56311172 TACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTGGA-AAGC-TTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATGA-CTTTGGT
** * **
56311222 CACGTGTGTAGTACTATGTATAGGCTACTACATGTA-TCGGATGACAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACT-GGATGACTTTGGT
56311273 CAC
1 CAC
56311276 AGATGACAAT
Statistics
Matches: 129, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 40 0.31
51 83 0.64
52 5 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGATGACTTTGGT
Found at i:56311264 original size:101 final size:101
Alignment explanation
Indices: 56311071--56311266 Score: 234
Period size: 101 Copynumber: 1.9 Consensus size: 101
56311061 ACTTATGAAC
* * * *
56311071 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCGATAGATGATGGTCACATGTGTAGTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAATCGAAAGAT-ATGATCACATGTGTAGTACT
* **
56311136 ATGTGCAGGCTACTATGCGTACTGGATGACTTTGGTT
65 ATGTACAGGCTACTACACGTACTGGATGACTTTGGTT
* * * *
56311173 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTGGAAAGCT-TGATCACGTGTGTAGTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAA-TCGAAAGATATGATCACATGTGTAGTACT
* *
56311237 ATGTATAGGCTACTACATGTA-TCGGATGAC
65 ATGTACAGGCTACTACACGTACT-GGATGAC
56311267 AATGGTCACA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
100 1 0.01
101 40 0.51
102 32 0.41
103 6 0.08
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (101 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAATCGAAAGATATGATCACATGTGTAGTACTA
TGTACAGGCTACTACACGTACTGGATGACTTTGGTT
Found at i:56311282 original size:16 final size:16
Alignment explanation
Indices: 56311261--56311292 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56311251 ACATGTATCG
56311261 GATGACAATGGTCACA
1 GATGACAATGGTCACA
56311277 GATGACAATGGTCACA
1 GATGACAATGGTCACA
56311293 TGGGTGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (16 bp):
GATGACAATGGTCACA
Found at i:56313752 original size:19 final size:19
Alignment explanation
Indices: 56313729--56313771 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
56313719 ATTTTTATAA
56313729 TTTTTCA-TAAAAAATATT
1 TTTTTCATTAAAAAATATT
* *
56313747 TATTTTTATTAAAAATTATT
1 T-TTTTCATTAAAAAATATT
56313767 TTTTT
1 TTTTT
56313772 GAGTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.43
20 11 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTCATTAAAAAATATT
Found at i:56327807 original size:31 final size:31
Alignment explanation
Indices: 56327767--56327834 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
56327757 TTAATAGCCT
*
56327767 AGTGACTTAAATAAAAACTTCTGAATTGTTC
1 AGTGACTTAAATAAAAACTTCTGAATAGTTC
* * *
56327798 AGTGGCTTAAATGAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTCTGAATAGTTC
56327829 AGTGAC
1 AGTGAC
56327835 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTCTGAATAGTTC
Found at i:56329250 original size:3 final size:3
Alignment explanation
Indices: 56329244--56329277 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56329234 AATAATGATG
56329244 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
56329278 GAGTTGCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:56332785 original size:14 final size:14
Alignment explanation
Indices: 56332766--56332796 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56332756 GGAATTGTTT
*
56332766 TAATCTAAATTTAC
1 TAATCTAAATTAAC
56332780 TAATCTAAATTAAC
1 TAATCTAAATTAAC
56332794 TAA
1 TAA
56332797 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:56339208 original size:16 final size:17
Alignment explanation
Indices: 56339189--56339230 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
56339179 TAAATGAAAT
*
56339189 TTTATTTAATTTTAGC-
1 TTTAATTAATTTTAGCA
56339205 TTTAAGTT-ATTTTAGCA
1 TTTAA-TTAATTTTAGCA
56339222 TTTAATTAA
1 TTTAATTAA
56339231 ATGGAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTAATTAATTTTAGCA
Found at i:56340712 original size:14 final size:14
Alignment explanation
Indices: 56340690--56340741 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
56340680 GATGCAAGGT
56340690 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
* *
56340703 TTTAAGGTTTAAGA
1 TTTAAGGTTTAGGG
*
56340717 TTTAAGATTTAGGG
1 TTTAAGGTTTAGGG
*
56340731 TTTGAGGTTTA
1 TTTAAGGTTTA
56340742 ATGTTCAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.16
14 26 0.84
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:56340727 original size:28 final size:27
Alignment explanation
Indices: 56340690--56340742 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
56340680 GATGCAAGGT
56340690 TTTAAGTTTAGGGTTTAAGGTTTAAGA
1 TTTAAGTTTAGGGTTTAAGGTTTAAGA
*
56340717 TTTAAGATTTAGGGTTTGAGGTTTAA
1 TTTAAG-TTTAGGGTTTAAGGTTTAA
56340743 TGTTCAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (27 bp):
TTTAAGTTTAGGGTTTAAGGTTTAAGA
Found at i:56340741 original size:21 final size:21
Alignment explanation
Indices: 56340685--56340742 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
56340675 ATCAAGATGC
* *
56340685 AAGGTTTTAAG-TTTAGGGTTT
1 AAGG-TTTAAGATTTAAGATTT
56340706 AAGGTTTAAGATTTAAGATTT
1 AAGGTTTAAGATTTAAGATTT
* * *
56340727 AGGGTTTGAGGTTTAA
1 AAGGTTTAAGATTTAA
56340743 TGTTCAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (21 bp):
AAGGTTTAAGATTTAAGATTT
Found at i:56342281 original size:14 final size:16
Alignment explanation
Indices: 56342251--56342283 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56342241 AAAATCTTTC
56342251 AAAAATAAGAAATTAA
1 AAAAATAAGAAATTAA
56342267 AAAAATAA-AAA-TAA
1 AAAAATAAGAAATTAA
56342281 AAA
1 AAA
56342284 TAAAAGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAATAAGAAATTAA
Found at i:56345536 original size:28 final size:30
Alignment explanation
Indices: 56345495--56345561 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 30
56345485 TTCTTATATA
*
56345495 TATTTTATTAAATAT-AAAAAAGTTAACAT
1 TATTTTATTAAATATAAAAAAACTTAACAT
56345524 TATTTT-TTAAATATAAAAAAACTTAACAT
1 TATTTTATTAAATATAAAAAAACTTAACAT
56345553 TATTTTATT
1 TATTTTATT
56345562 TAAACACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 8 0.23
29 25 0.71
30 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
TATTTTATTAAATATAAAAAAACTTAACAT
Found at i:56350081 original size:19 final size:21
Alignment explanation
Indices: 56350021--56350075 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
56350011 ATTGTTGAGG
* *
56350021 ATATGCAGTTTTAGATATG--
1 ATATGCAATCTTAGATATGAT
56350040 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
56350061 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
56350076 AGATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:56350097 original size:23 final size:24
Alignment explanation
Indices: 56350033--56350098 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 24
56350023 ATGCAGTTTT
56350033 AGATATG--ATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
56350052 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
56350076 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
56350099 GATTTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.17
21 12 0.30
23 12 0.30
24 9 0.22
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:56350523 original size:11 final size:11
Alignment explanation
Indices: 56350507--56350539 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
56350497 GTAGAGAGCA
56350507 TTTGTTTTTTT
1 TTTGTTTTTTT
56350518 TTTGTTTTTTT
1 TTTGTTTTTTT
56350529 TTAT-TTTTTTT
1 TT-TGTTTTTTT
56350540 CCTTTCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:56351036 original size:4 final size:4
Alignment explanation
Indices: 56351016--56351072 Score: 64
Period size: 4 Copynumber: 14.5 Consensus size: 4
56351006 GCTTTGCATG
* * *
56351016 TTAT TGAT TTA- TT-T TTAT TTAT TTAT TTAT TTAT TTAT TTGT TTGT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
56351062 TTAT ATTAT TT
1 TTAT -TTAT TT
56351073 CTATGCCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 4 0.09
4 38 0.83
5 4 0.09
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:56351120 original size:19 final size:20
Alignment explanation
Indices: 56351079--56351120 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
56351069 ATTTCTATGC
* *
56351079 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
56351099 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
56351118 CAT
1 CAT
56351121 CACATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:56352311 original size:13 final size:13
Alignment explanation
Indices: 56352293--56352323 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56352283 TAGTTACAAA
56352293 TATTTTTAATATT
1 TATTTTTAATATT
56352306 TATTTTTAATATT
1 TATTTTTAATATT
56352319 T-TTTT
1 TATTTT
56352324 ATTATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTTTAATATT
Found at i:56359092 original size:25 final size:27
Alignment explanation
Indices: 56359043--56359094 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
56359033 TATAAAGTTT
* *
56359043 AATTTATTAATAATTTATATGTTTTCC
1 AATTTATTAATAATGTACATGTTTTCC
56359070 AATTTA-TAAT-ATGTACATGTTTTCC
1 AATTTATTAATAATGTACATGTTTTCC
56359095 TTGTTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 4 0.17
27 6 0.26
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.52
Consensus pattern (27 bp):
AATTTATTAATAATGTACATGTTTTCC
Found at i:56362456 original size:50 final size:50
Alignment explanation
Indices: 56362334--56362582 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
56362324 GATAATAACA
* * * ** * *
56362334 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
56362385 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
56362435 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
56362485 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
56362540 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
56362583 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:56362510 original size:100 final size:104
Alignment explanation
Indices: 56362333--56362582 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
56362323 TGATAATAAC
* **
56362333 ATGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
56362398 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
56362435 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
56362498 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
56362540 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56362583 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:56362698 original size:13 final size:13
Alignment explanation
Indices: 56362677--56362708 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56362667 GCTTAGATCA
*
56362677 TCATCAAATAAAT
1 TCATAAAATAAAT
56362690 TCATAAAATAAAT
1 TCATAAAATAAAT
56362703 TCATAA
1 TCATAA
56362709 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56362956 original size:30 final size:30
Alignment explanation
Indices: 56362920--56362977 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56362910 CCTCGACTCT
* *
56362920 AACTTTTTCAAAATTATAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
56362950 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
56362978 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:56366323 original size:14 final size:15
Alignment explanation
Indices: 56366304--56366332 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56366294 ATTATAAAAA
56366304 TTTAAAAAG-ATATT
1 TTTAAAAAGAATATT
56366318 TTTAAAAAGAATATT
1 TTTAAAAAGAATATT
56366333 AAAATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTAAAAAGAATATT
Found at i:56369311 original size:9 final size:9
Alignment explanation
Indices: 56369294--56369339 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
56369284 GTGATTCAAC
56369294 TCGGTTAAT
1 TCGGTTAAT
*
56369303 TCGGGTAAT
1 TCGGTTAAT
*
56369312 TCAGTTAAT
1 TCGGTTAAT
*
56369321 TCGGATAAT
1 TCGGTTAAT
56369330 TCGGTTAAT
1 TCGGTTAAT
56369339 T
1 T
56369340 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (9 bp):
TCGGTTAAT
Found at i:56370426 original size:17 final size:17
Alignment explanation
Indices: 56370406--56370555 Score: 114
Period size: 17 Copynumber: 8.7 Consensus size: 17
56370396 AAAAATTTTG
*
56370406 TTTTGAAAACACGAGAA
1 TTTTGAAAACACGAAAA
***
56370423 TTTTG-AAACA--ATTT
1 TTTTGAAAACACGAAAA
*
56370437 TTTTTGAAAACATGAAAAA
1 TT-TTGAAAACACG-AAAA
* *
56370456 TTTTTAAAACACGAGAA
1 TTTTGAAAACACGAAAA
56370473 TTTT-AGAAACACGAAAA
1 TTTTGA-AAACACGAAAA
56370490 TTCTT-AAAACACGAAAA
1 TT-TTGAAAACACGAAAA
*
56370507 TTTTTGAAAACACGACAA
1 -TTTTGAAAACACGAAAA
56370525 TTTTG-AAACACGAGAAA
1 TTTTGAAAACACGA-AAA
56370542 TTTTTTGAAAACAC
1 --TTTTGAAAACAC
56370556 AAATTTTTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
14 3 0.03
15 3 0.03
16 19 0.18
17 44 0.41
18 25 0.23
19 8 0.07
20 6 0.06
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:56370464 original size:18 final size:17
Alignment explanation
Indices: 56370437--56370772 Score: 128
Period size: 17 Copynumber: 18.5 Consensus size: 17
56370427 GAAACAATTT
*
56370437 TTTTTGAAAACATGAAAAA
1 TTTTT-AAAACACG-AAAA
*
56370456 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
56370473 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
*
56370490 TTCTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
56370507 TTTTTGAAAACACGACAA
1 TTTTT-AAAACACGAAAA
*
56370525 -TTTTGAAACACGAGAAA
1 TTTTTAAAACACGA-AAA
*
56370542 TTTTTTGAAAACAC-AAATTT
1 -TTTTT-AAAACACGAAA--A
* **
56370562 TTTTTGAAACAC-AATTT
1 TTTTTAAAACACGAA-AA
56370579 TTTTTGAAAACAC-AGAAA
1 TTTTT-AAAACACGA-AAA
* * *
56370597 TTTGTGAAACACGAGAATTT
1 TTTTTAAAACACGA-AA--A
*
56370617 TTTTTAAAAACACGGAAAGT
1 TTTTT-AAAACAC-GAAA-A
* *
56370637 TTTTTGAAAACATGGAAATTT
1 TTTTT-AAAACA-CGAAA--A
*
56370658 TTTTTAAAACACGGAAA
1 TTTTTAAAACACGAAAA
* *
56370675 TTTTTGAAACACAAAGAA
1 TTTTTAAAACACGAA-AA
**
56370693 TTTTTTCAAAAACAAAAAAA
1 -TTTTT--AAAACACGAAAA
* * *
56370713 TTTTTGACACACCG-GAA
1 TTTTTAAAACA-CGAAAA
* *
56370730 TTTTTGAAAGCACGAAGA
1 TTTTT-AAAACACGAAAA
* *
56370748 TTTTT-GAACACGAAAT
1 TTTTTAAAACACGAAAA
56370764 TTTTTAAAA
1 TTTTTAAAA
56370773 ACAAAACAAA
Statistics
Matches: 243, Mismatches: 47, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
16 25 0.10
17 73 0.30
18 58 0.24
19 29 0.12
20 34 0.14
21 22 0.09
22 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:56370490 original size:34 final size:35
Alignment explanation
Indices: 56370437--56370617 Score: 127
Period size: 35 Copynumber: 5.1 Consensus size: 35
56370427 GAAACAATTT
* *
56370437 TTTTTGAAAACATGAAAAATTTTTAAAACACGAGAA
1 TTTTAGAAAACACG-AAAATTTTTAAAACACGAGAA
* *
56370473 TTTTAG-AAACACGAAAATTCTTAAAACACGAAAA
1 TTTTAGAAAACACGAAAATTTTTAAAACACGAGAA
* * *
56370507 TTTTTGAAAACACGACAA-TTTTGAAACACGAGAAA
1 TTTTAGAAAACACGAAAATTTTTAAAACACGAG-AA
* * * * ***
56370542 TTTTTTGAAAACAC-AAATTTTTTTTGAAACACAATTT
1 -TTTTAGAAAACACGAAA--ATTTTTAAAACACGAGAA
* * *
56370579 TTTTTGAAAACAC-AGAAATTTGTGAAACACGAGAA
1 TTTTAGAAAACACGA-AAATTTTTAAAACACGAGAA
56370614 TTTT
1 TTTT
56370618 TTTTAAAAAC
Statistics
Matches: 117, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
34 35 0.30
35 36 0.31
36 32 0.27
37 2 0.02
38 12 0.10
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (35 bp):
TTTTAGAAAACACGAAAATTTTTAAAACACGAGAA
Found at i:56370517 original size:52 final size:53
Alignment explanation
Indices: 56370406--56370555 Score: 175
Period size: 51 Copynumber: 2.9 Consensus size: 53
56370396 AAAAATTTTG
*** * *
56370406 TTTTGAAAACACGAGAATTTTGAAACA--ATTTTTTTTGAAAACATGAAAAAT
1 TTTTGAAAACACGAGAATTTTGAAACACGAAAATTCTTGAAAACACGAAAAAT
56370457 TTTT-AAAACACGAGAATTTTAGAAACACGAAAATTCTT-AAAACACG-AAAAT
1 TTTTGAAAACACGAGAATTTT-GAAACACGAAAATTCTTGAAAACACGAAAAAT
* *
56370508 TTTTGAAAACACGACAATTTTGAAACACGAGAAATTTTTTGAAAACAC
1 TTTTGAAAACACGAGAATTTTGAAACACGA-AAA-TTCTTGAAAACAC
56370556 AAATTTTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
50 16 0.19
51 28 0.33
52 25 0.29
53 9 0.11
54 7 0.08
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (53 bp):
TTTTGAAAACACGAGAATTTTGAAACACGAAAATTCTTGAAAACACGAAAAAT
Found at i:56370560 original size:52 final size:51
Alignment explanation
Indices: 56370406--56370563 Score: 166
Period size: 52 Copynumber: 3.1 Consensus size: 51
56370396 AAAAATTTTG
** *
56370406 TTTTGAAAACACGAGAATTTTG-AA-AC-AATTTTTTTTGAAAACATGAAAAAT
1 TTTTGAAAACACGAGAATTTTGAAACACGAAAATTTTTTGAAAAC---ACAAAT
*
56370457 TTTT-AAAACACGAGAATTTTAGAAACACGAAAA-TTCTT-AAAACACGAAAAT
1 TTTTGAAAACACGAGAATTTT-GAAACACGAAAATTTTTTGAAAACAC--AAAT
*
56370508 TTTTGAAAACACGACAATTTTGAAACACGAGAAATTTTTTGAAAACACAAAT
1 TTTTGAAAACACGAGAATTTTGAAACACGA-AAATTTTTTGAAAACACAAAT
56370560 TTTT
1 TTTT
56370564 TTTGAAACAC
Statistics
Matches: 91, Mismatches: 6, Indels: 19
0.78 0.05 0.16
Matches are distributed among these distances:
49 1 0.01
50 16 0.18
51 22 0.24
52 33 0.36
53 10 0.11
54 9 0.10
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (51 bp):
TTTTGAAAACACGAGAATTTTGAAACACGAAAATTTTTTGAAAACACAAAT
Found at i:56370698 original size:20 final size:19
Alignment explanation
Indices: 56370525--56370698 Score: 119
Period size: 20 Copynumber: 9.2 Consensus size: 19
56370515 AACACGACAA
*
56370525 TTTTG-AAACACGAGAAATT
1 TTTTGAAAACAC-AGAATTT
56370544 TTTTGAAAACACA-AATTTT
1 TTTTGAAAACACAGAA-TTT
*
56370563 TTTTG-AAACACA-ATTTT
1 TTTTGAAAACACAGAATTT
*
56370580 TTTTGAAAACACAGAA-AT
1 TTTTGAAAACACAGAATTT
*
56370598 TTGTG-AAACACGAGAATTTT
1 TTTTGAAAACAC-AGAA-TTT
* * *
56370618 TTTTAAAAACACGGAAAGTT
1 TTTTGAAAACACAG-AATTT
**
56370638 TTTTGAAAACATGGAAATTT
1 TTTTGAAAACACAG-AATTT
* * *
56370658 TTTTTAAAACACGGAA-AT
1 TTTTGAAAACACAGAATTT
*
56370676 TTTTGAAACACAAAGAATTT
1 TTTTGAAA-ACACAGAATTT
56370696 TTT
1 TTT
56370699 CAAAAACAAA
Statistics
Matches: 124, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
17 14 0.11
18 34 0.27
19 22 0.18
20 46 0.37
21 8 0.06
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (19 bp):
TTTTGAAAACACAGAATTT
Found at i:56370705 original size:38 final size:38
Alignment explanation
Indices: 56370507--56370724 Score: 148
Period size: 38 Copynumber: 5.8 Consensus size: 38
56370497 AACACGAAAA
* * *
56370507 TTTTTGAAAACAC-GACAA-TTTTGAAACAC-GAGAAAT
1 TTTTTAAAAACACAGA-AATTTTTGAAACACAAAGAATT
* * *
56370543 TTTTTGAAAACACA-AATTTTTTTTGAAACAC--A-ATTT
1 TTTTTAAAAACACAGAA--ATTTTTGAAACACAAAGAATT
* * *
56370579 TTTTTGAAAACACAGAAATTTGTGAAACAC-GAGAATTT
1 TTTTTAAAAACACAGAAATTTTTGAAACACAAAGAA-TT
* **
56370617 TTTTTAAAAACACGGAAAGTTTTTTGAAA-ACATGGAAATT
1 TTTTTAAAAACACAGAAA--TTTTTGAAACACAAAG-AATT
* *
56370657 TTTTTTAAAACACGGAAATTTTTGAAACACAAAGAATT
1 TTTTTAAAAACACAGAAATTTTTGAAACACAAAGAATT
* * * *
56370695 TTTTCAAAAACAAAAAAATTTTTGACACAC
1 TTTTTAAAAACACAGAAATTTTTGAAACAC
56370725 CGGAATTTTT
Statistics
Matches: 149, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
35 12 0.08
36 31 0.21
37 4 0.03
38 66 0.44
39 6 0.04
40 28 0.19
41 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (38 bp):
TTTTTAAAAACACAGAAATTTTTGAAACACAAAGAATT
Found at i:56370768 original size:16 final size:18
Alignment explanation
Indices: 56370729--56370767 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
56370719 ACACACCGGA
56370729 ATTTTTGAAAGCACGAAG
1 ATTTTTGAAAGCACGAAG
56370747 ATTTTTG-AA-CACGAA-
1 ATTTTTGAAAGCACGAAG
56370762 ATTTTT
1 ATTTTT
56370768 TAAAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 2 0.10
18 7 0.33
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
ATTTTTGAAAGCACGAAG
Found at i:56370827 original size:18 final size:17
Alignment explanation
Indices: 56370804--56370895 Score: 64
Period size: 18 Copynumber: 5.2 Consensus size: 17
56370794 AACATGGAAA
56370804 AAAACACGAAAATTTGTG
1 AAAACACGAAAATTT-TG
*
56370822 AAAACATGGAAAAAAAATTTT-
1 AAAACA-CG---A-AAATTTTG
*
56370843 -AAACACG-AATTTTTG
1 AAAACACGAAAATTTTG
*
56370858 AAAACATGAAAATTTTG
1 AAAACACGAAAATTTTG
*
56370875 AAAACACGGAAATTTTTG
1 AAAACAC-GAAAATTTTG
56370893 AAA
1 AAA
56370896 TAGGGGAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 6 0.10
16 6 0.10
17 13 0.22
18 18 0.31
19 2 0.03
20 5 0.09
22 2 0.03
23 6 0.10
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (17 bp):
AAAACACGAAAATTTTG
Found at i:56371083 original size:21 final size:22
Alignment explanation
Indices: 56371048--56371089 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
56371038 TGATCCTATT
56371048 AAAACACAAGAAATTTTTTAAA
1 AAAACACAAGAAATTTTTTAAA
56371070 AAAACACAAG-AATTTTTTAA
1 AAAACACAAGAAATTTTTTAA
56371090 TATTTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAACACAAGAAATTTTTTAAA
Found at i:56371227 original size:10 final size:10
Alignment explanation
Indices: 56371214--56371246 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
56371204 AAATTACTTA
*
56371214 AAATAAAATT
1 AAATTAAATT
56371224 AAATTAAATT
1 AAATTAAATT
56371234 AAATTAAATT
1 AAATTAAATT
56371244 AAA
1 AAA
56371247 AATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATTAAATT
Found at i:56371232 original size:15 final size:15
Alignment explanation
Indices: 56371214--56371246 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
56371204 AAATTACTTA
56371214 AAATAAAATTAAATT
1 AAATAAAATTAAATT
*
56371229 AAATTAAATTAAATT
1 AAATAAAATTAAATT
56371244 AAA
1 AAA
56371247 AATATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAAATTAAATT
Found at i:56371420 original size:12 final size:13
Alignment explanation
Indices: 56371403--56371465 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
56371393 AAATTGAACC
56371403 CTTTTTTTTTC-T
1 CTTTTTTTTTCTT
*
56371415 CTTTTTTCTTCTT
1 CTTTTTTTTTCTT
*
56371428 -TTTTTTCTTTTTT
1 CTTTTTT-TTTCTT
56371441 CTTTTTTTTTCCTT
1 CTTTTTTTTT-CTT
*
56371455 CTCTTTTTTTC
1 CTTTTTTTTTC
56371466 CTCTCTTCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 16 0.38
13 9 0.21
14 17 0.40
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTTTTTTTTCTT
Found at i:56371421 original size:9 final size:9
Alignment explanation
Indices: 56371407--56371448 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
56371397 TGAACCCTTT
56371407 TTTTTTCTC
1 TTTTTTCTC
56371416 TTTTTTCTTC
1 TTTTTTC-TC
*
56371426 TTTTTTTTC
1 TTTTTTCTC
56371435 TTTTTTCT-
1 TTTTTTCTC
56371443 TTTTTT
1 TTTTTT
56371449 TTCCTTCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 6 0.20
9 16 0.53
10 8 0.27
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:56371444 original size:16 final size:17
Alignment explanation
Indices: 56371418--56371449 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56371408 TTTTTCTCTT
56371418 TTTTCTTCTTTTTTTTC
1 TTTTCTTCTTTTTTTTC
56371435 TTTT-TTCTTTTTTTT
1 TTTTCTTCTTTTTTTT
56371450 TCCTTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTCTTCTTTTTTTTC
Found at i:56371449 original size:9 final size:9
Alignment explanation
Indices: 56371406--56371451 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 9
56371396 TTGAACCCTT
56371406 TTTTTTTCTC
1 TTTTTTT-TC
56371416 TTTTTTCTTC
1 TTTTTT-TTC
56371426 TTTTTTTTC
1 TTTTTTTTC
*
56371435 TTTTTTCT-
1 TTTTTTTTC
56371443 TTTTTTTTC
1 TTTTTTTTC
56371452 CTTCTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 7 0.22
9 10 0.31
10 14 0.44
11 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:56371464 original size:19 final size:18
Alignment explanation
Indices: 56371403--56371454 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
56371393 AAATTGAACC
56371403 CTTTTTTTTTCTCTTTTTT
1 CTTTTTTTTTC-CTTTTTT
*
56371422 CTTCTTTTTTTTCTTTTTT
1 CTT-TTTTTTTCCTTTTTT
56371441 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
56371455 CTCTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 10 0.33
19 13 0.43
20 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTTTTTTTCCTTTTTT
Found at i:56371949 original size:24 final size:25
Alignment explanation
Indices: 56371922--56371968 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56371912 CCTTTCTCCT
*
56371922 TCTTT-TATTTTTTTTCTTCTTTAC
1 TCTTTCTATTTTTTTTCCTCTTTAC
*
56371946 TCTTTCTCTTTTTTTTCCTCTTT
1 TCTTTCTATTTTTTTTCCTCTTT
56371969 TGCTTGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (25 bp):
TCTTTCTATTTTTTTTCCTCTTTAC
Found at i:56371984 original size:27 final size:26
Alignment explanation
Indices: 56371954--56372012 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
56371944 ACTCTTTCTC
*
56371954 TTTTTTTTCCTCTTTTGCTTGCTTGTT
1 TTTTTTTTCCTCTTTTGCCT-CTTGTT
*
56371981 TTTTTTTTCCTTTTTTGCCTCTTGTT
1 TTTTTTTTCCTCTTTTGCCTCTTGTT
*
56372007 TGTTTT
1 TTTTTT
56372013 GCTAGGTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.73
Consensus pattern (26 bp):
TTTTTTTTCCTCTTTTGCCTCTTGTT
Found at i:56372379 original size:29 final size:29
Alignment explanation
Indices: 56372337--56372442 Score: 124
Period size: 28 Copynumber: 3.6 Consensus size: 29
56372327 AAAACTTTTG
* *
56372337 GGGTTAAAGTATAATTTTGAGAACGTTTA
1 GGGTTAAAATATAATTTTGAGAAAGTTTA
*
56372366 GGGTTAAAATATAATTTT-AGAAAGTTAA
1 GGGTTAAAATATAATTTTGAGAAAGTTTA
* * *
56372394 GGGTTAAAATGTAATTTTGAAAAAATTTA
1 GGGTTAAAATATAATTTTGAGAAAGTTTA
*
56372423 GGGGTCAAAAATATAATTTT
1 -GGGT-TAAAATATAATTTT
56372443 AAAAAAAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
28 25 0.38
29 24 0.37
30 4 0.06
31 12 0.18
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.37
Consensus pattern (29 bp):
GGGTTAAAATATAATTTTGAGAAAGTTTA
Found at i:56373263 original size:85 final size:85
Alignment explanation
Indices: 56373116--56373281 Score: 271
Period size: 85 Copynumber: 2.0 Consensus size: 85
56373106 ATAAAAGTAG
*
56373116 GAGTCAAAAAGGTTGTTTGTTTGTTATGAAACGGAGATTCCTCCTTATCATATTCGCCTGTAAAA
1 GAGTCAAAAAGGTTGTTTGTTTGTTATGAAACGGAGAGTCCTCCTTATCATATTCGCCTGTAAAA
56373181 ATAGTCTTAGGGATAAATAT
66 ATAGTCTTAGGGATAAATAT
* * **
56373201 GAGTCAAAAAGGTTGTTTGTTTGTTATGTAAA-GGAGAGTCCTCTTTTTCATATTCGTTTGTAAA
1 GAGTCAAAAAGGTTGTTTGTTTGTTATG-AAACGGAGAGTCCTCCTTATCATATTCGCCTGTAAA
56373265 AATAGTCTTAGGGATAA
65 AATAGTCTTAGGGATAA
56373282 GTCAAAAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 72 0.96
86 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (85 bp):
GAGTCAAAAAGGTTGTTTGTTTGTTATGAAACGGAGAGTCCTCCTTATCATATTCGCCTGTAAAA
ATAGTCTTAGGGATAAATAT
Found at i:56375432 original size:42 final size:42
Alignment explanation
Indices: 56375373--56375458 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
56375363 TTTTATGAAC
56375373 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCTGCTTGAAATT
1 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCTGCTTGAAATT
56375415 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCTGCTTGAAATT
1 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCTGCTTGAAATT
56375457 GA
1 GA
56375459 CATTGCTGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (42 bp):
GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCTGCTTGAAATT
Found at i:56386148 original size:11 final size:11
Alignment explanation
Indices: 56386133--56386190 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
56386123 AAAGTAAAAA
56386133 AAAAAGTATTTT
1 AAAAA-TATTTT
56386145 AAAAATATTTT
1 AAAAATATTTT
* *
56386156 --TAA-ATTTA
1 AAAAATATTTT
56386164 AAAAAGTATTTT
1 AAAAA-TATTTT
56386176 AAAAATATTTT
1 AAAAATATTTT
56386187 AAAA
1 AAAA
56386191 TTAAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 4 0.11
9 2 0.05
10 2 0.05
11 16 0.42
12 14 0.37
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56386170 original size:31 final size:31
Alignment explanation
Indices: 56386111--56386199 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 31
56386101 TAAAATACCA
*
56386111 AAAAATATTTTAAAAGTAAAAAAAAAAGTATTTT
1 AAAAATATTTTAAAA-T--TAAAAAAAGTATTTT
* *
56386145 AAAAATATTTTTAAATTTAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAGTATTTT
56386176 AAAAATATTTTAAAATTAAAAAAA
1 AAAAATATTTTAAAATTAAAAAAA
56386200 TTTATAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.70
33 1 0.02
34 14 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAATATTTTAAAATTAAAAAAAGTATTTT
Found at i:56386196 original size:17 final size:18
Alignment explanation
Indices: 56386174--56386207 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56386164 AAAAAGTATT
*
56386174 TTAAAAATATTT-TAAAA
1 TTAAAAAAATTTATAAAA
56386191 TTAAAAAAATTTATAAA
1 TTAAAAAAATTTATAAA
56386208 TAAATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAAAAAATTTATAAAA
Found at i:56386214 original size:31 final size:29
Alignment explanation
Indices: 56386132--56386207 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 29
56386122 AAAAGTAAAA
*
56386132 AAAAAAGTATTTTAAAAATATTTTTAAATTT
1 AAAAAAG-ATTTTAAAAATA-TTTTAAAATT
56386163 AAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAAAG-ATTTTAAAAATATTTTAAAATT
56386193 AAAAAA-ATTTATAAA
1 AAAAAAGATTT-TAAA
56386208 TAAATATATT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 4 0.09
29 4 0.09
30 15 0.35
31 20 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAAAGATTTTAAAAATATTTTAAAATT
Found at i:56386747 original size:111 final size:109
Alignment explanation
Indices: 56386429--56386837 Score: 592
Period size: 111 Copynumber: 3.8 Consensus size: 109
56386419 TTGGGGGAAA
* * * *
56386429 TTTTTTAACTTTTCTCGTATACTGATACCTGTTATTGACACGAAAAAAGTAAAAAAAAAATTCTC
1 TTTTTTTACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAAATTCCC
* * * *
56386494 ACAAAAAAGGTGGTGCCGACCGTTGGTAGGCCACCA-CAA-TTT
66 CCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTT
*
56386536 TTTTTTTACTTTTTTCGTATACT-AGTACCTGCTATTGACACGAAAAAAGTGAAAAAAAAATT-C
1 TTTTTTTACTTTTTTCGTATACTGA-TACCTGCTATTGACACGAAAAAAGTAAAAAAAAAATTCC
*
56386599 CCCATAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTT
65 CCCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTT
* *
56386644 TTTTTTTACTTTTTTCGTATATTGATACCAGCTATTGACACGAAAAAAGTAAAAAAAAAACTCTC
1 TTTTTTTACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAAA-T-TC
* * *
56386709 CCCCCAAAAAGATGGTGCCGGCCATTGGCAAGCCACCACCAATTTT
64 CCCCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTT
** * *
56386755 TTTTTTTACTTTTTTTATATACTGATACCTGCTATTGACACGAAAAAAGTGAAAAAAAAATTTCC
1 TTTTTTTACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAAATTCCC
56386820 CCAAAAAAGGTGGTGCCG
66 CCAAAAAAGGTGGTGCCG
56386838 ACTAGAGGTG
Statistics
Matches: 270, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
106 33 0.12
107 59 0.22
108 58 0.21
109 21 0.08
110 2 0.01
111 97 0.36
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (109 bp):
TTTTTTTACTTTTTTCGTATACTGATACCTGCTATTGACACGAAAAAAGTAAAAAAAAAATTCCC
CCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAATTTT
Found at i:56387041 original size:11 final size:11
Alignment explanation
Indices: 56387025--56387050 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56387015 TTAAAAATAA
56387025 AAAAGTATTTT
1 AAAAGTATTTT
56387036 AAAAGTATTTT
1 AAAAGTATTTT
56387047 AAAA
1 AAAA
56387051 ATAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:56397230 original size:22 final size:24
Alignment explanation
Indices: 56397177--56397230 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
56397167 ATGATAATGG
* *
56397177 AAAATTTTCCATTTAGGTCCCTTT
1 AAAATTTTCCATTTAAGTCCCTTC
56397201 AAAATTTT-CATTTAAG-CCCTTC
1 AAAATTTTCCATTTAAGTCCCTTC
*
56397223 AAAGTTTT
1 AAAATTTT
56397231 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 7 0.26
24 8 0.30
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (24 bp):
AAAATTTTCCATTTAAGTCCCTTC
Found at i:56397414 original size:17 final size:18
Alignment explanation
Indices: 56397387--56397427 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56397377 CGGCCCTCCT
* * *
56397387 AAAATATTTTTTTACTCA
1 AAAACATTTTTTAACTAA
56397405 AAAACATTTTTTAACTAA
1 AAAACATTTTTTAACTAA
56397423 AAAAC
1 AAAAC
56397428 TTGGTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAACATTTTTTAACTAA
Found at i:56398046 original size:23 final size:24
Alignment explanation
Indices: 56398014--56398064 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
56398004 TAATGGAAAA
*
56398014 TTTTCTATTTAGGTCCATTTAAA-T
1 TTTTCTATTTAAGT-CATTTAAAGT
*
56398038 TTTTC-ATTTAAGTCTTTTAAAGT
1 TTTTCTATTTAAGTCATTTAAAGT
56398061 TTTT
1 TTTT
56398065 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTTCTATTTAAGTCATTTAAAGT
Found at i:56399044 original size:6 final size:6
Alignment explanation
Indices: 56399033--56399077 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
56399023 CACGTACTCA
*
56399033 TTTCAT TTTCAT TTCCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
56399078 TTGAAACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTCAT
Found at i:56414782 original size:62 final size:62
Alignment explanation
Indices: 56414708--56414840 Score: 155
Period size: 62 Copynumber: 2.1 Consensus size: 62
56414698 GAGCTTGATT
* * * *
56414708 AAAATTTTCAAAAA-TTTGAAGGGGCCTAATT-AAATATTTCTAAAAACTTCAA-GAGAGAAATG
1 AAAATTTCCAAAAATTTTG-ACGGACCTAATTAAAAT-TTTCTAAAAACTTCAATG-GAGAAATC
* * *
56414770 AAAATTTCCAAAAATTTTGACGGACTTAATTAAAATTTTCTAAAAATTTCAATGGAGAATTC
1 AAAATTTCCAAAAATTTTGACGGACCTAATTAAAATTTTCTAAAAACTTCAATGGAGAAATC
56414832 AAAATTTCC
1 AAAATTTCC
56414841 CATTTTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
62 52 0.85
63 9 0.15
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (62 bp):
AAAATTTCCAAAAATTTTGACGGACCTAATTAAAATTTTCTAAAAACTTCAATGGAGAAATC
Found at i:56414807 original size:31 final size:31
Alignment explanation
Indices: 56414678--56414818 Score: 81
Period size: 32 Copynumber: 4.5 Consensus size: 31
56414668 GATTAATGAG
* * *
56414678 AATTTCCAAAAATTTTAACAGAGCTTGATTAA
1 AATTTCCAAAAATTTTGACGGA-CTTAATTAA
* * * *
56414710 AATTTTCAAAAA-TTTGAAGGGGCCTAATTAA
1 AATTTCCAAAAATTTTG-ACGGACTTAATTAA
* * * * ** *
56414741 ATATTTCTAAAAA-CTTCAAGAGA-GAAATGAA
1 A-ATTTCCAAAAATTTTGACG-GACTTAATTAA
56414772 AATTTCCAAAAATTTTGACGGACTTAATTAA
1 AATTTCCAAAAATTTTGACGGACTTAATTAA
*
56414803 AATTTTCTAAAAATTT
1 AA-TTTCCAAAAATTT
56414819 CAATGGAGAA
Statistics
Matches: 79, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
30 12 0.15
31 30 0.38
32 37 0.47
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
AATTTCCAAAAATTTTGACGGACTTAATTAA
Found at i:56417853 original size:13 final size:13
Alignment explanation
Indices: 56417835--56417859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56417825 TCAAACTATC
56417835 AAATTTTCACACG
1 AAATTTTCACACG
56417848 AAATTTTCACAC
1 AAATTTTCACAC
56417860 ATATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:56423438 original size:20 final size:19
Alignment explanation
Indices: 56423391--56423438 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
56423381 TTTCACAAAA
* *
56423391 AAAGAAAGAATTTTGATATT
1 AAAGAAA-AATTTAGATAAT
*
56423411 AAATAAAAATTTAGTATAAT
1 AAAGAAAAATTTAG-ATAAT
56423431 AAAGAAAA
1 AAAGAAAA
56423439 GCTTAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAGAAAAATTTAGATAAT
Found at i:56424383 original size:40 final size:40
Alignment explanation
Indices: 56424328--56424407 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
56424318 ACCAGATGAC
56424328 TCAATTGCCTTTTCCTTATGCTTTCTTTTCTGTTTTCTTT
1 TCAATTGCCTTTTCCTTATGCTTTCTTTTCTGTTTTCTTT
56424368 TCAATTGCCTTTTCCTTATGCTTTCTTTTCTGTTTTCTTT
1 TCAATTGCCTTTTCCTTATGCTTTCTTTTCTGTTTTCTTT
56424408 CTCGCGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.62
Consensus pattern (40 bp):
TCAATTGCCTTTTCCTTATGCTTTCTTTTCTGTTTTCTTT
Found at i:56434203 original size:24 final size:25
Alignment explanation
Indices: 56434176--56434223 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
56434166 ATTAAGACTC
56434176 AATC-ACTAAATATAATTTTTTTTA
1 AATCAACTAAATATAATTTTTTTTA
56434200 AATCAACTAAATATAATTTTTTTT
1 AATCAACTAAATATAATTTTTTTT
56434224 CCTTTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (25 bp):
AATCAACTAAATATAATTTTTTTTA
Found at i:56444025 original size:158 final size:159
Alignment explanation
Indices: 56443710--56444069 Score: 562
Period size: 158 Copynumber: 2.3 Consensus size: 159
56443700 AAGTGAGAAA
* * *
56443710 AAGCCAGTGGAGTGCTTATTGTGTCATGGTCCGCATAAGTTGCGGAAGTGTCCAAGGAAGTCTGT
1 AAGCGAGTGGAGTGCTTCTTGTGTCATGGTCTGCATAAGTTGCGGAAGTGTCCAAGGAAGTCTGT
* * * * *
56443775 CATCGAAGGAAAAGATAGAGTAGACAAGGAGCCCAAGAAGTTTGGTTTGAGTAAGGGAAAAGTCG
66 CATCGAAGGAAAAGATAGAGCAGACAAAGAGCCCAAGAAGTTTGGTTCGAGTAAAGGAAAAGTCA
*
56443840 AAGCCAAGAGGGCAAAGAGGAGTAAAAAG
131 AAGCCAAGAGGGCAAAGAGGAGCAAAAAG
56443869 AAGCGAGTGGAGTGCTTCTTGTGTCATGGTCTGCATAAGTTGCGGAAGTGTCCAAGGAAGTCTGT
1 AAGCGAGTGGAGTGCTTCTTGTGTCATGGTCTGCATAAGTTGCGGAAGTGTCCAAGGAAGTCTGT
*
56443934 CATCGAAGGAAACG-TAGAGCAGACAAAGAGCCCAAGAAGTTTGGTTCGAGTAAAGGAAAAGTCA
66 CATCGAAGGAAAAGATAGAGCAGACAAAGAGCCCAAGAAGTTTGGTTCGAGTAAAGGAAAAGTCA
56443998 AAGCCAAGAGGGCAAAGAGGAGCAAAAAG
131 AAGCCAAGAGGGCAAAGAGGAGCAAAAAG
* ** * * *
56444027 AAACGAGTAAAGTGCTTCTTGTG-CCTGGTCTACATGAGTTGCG
1 AAGCGAGTGGAGTGCTTCTTGTGTCATGGTCTGCATAAGTTGCG
56444070 AAATTGTCTA
Statistics
Matches: 185, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
157 17 0.09
158 93 0.50
159 75 0.41
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.20
Consensus pattern (159 bp):
AAGCGAGTGGAGTGCTTCTTGTGTCATGGTCTGCATAAGTTGCGGAAGTGTCCAAGGAAGTCTGT
CATCGAAGGAAAAGATAGAGCAGACAAAGAGCCCAAGAAGTTTGGTTCGAGTAAAGGAAAAGTCA
AAGCCAAGAGGGCAAAGAGGAGCAAAAAG
Found at i:56446006 original size:17 final size:17
Alignment explanation
Indices: 56445986--56446019 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56445976 CTTGTAAATC
*
56445986 ATTTATTTTAAATTGTT
1 ATTTACTTTAAATTGTT
*
56446003 ATTTGCTTTAAATTGTT
1 ATTTACTTTAAATTGTT
56446020 TTGCATATAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (17 bp):
ATTTACTTTAAATTGTT
Found at i:56453114 original size:305 final size:306
Alignment explanation
Indices: 56452538--56453121 Score: 757
Period size: 305 Copynumber: 1.9 Consensus size: 306
56452528 TGTATATCAT
* * * * * * *
56452538 ATACTATAAATTCTATCACACGTGTATGCATGTGGAAACTATATAGTTAGAACGCAAATTTGTGT
1 ATACTAGAAACTCCATCACACGAGTATGCATGTAGAAACCATATAGTTAGAACACAAATTTGTGT
* * * *
56452603 TTTAAAATAACAACAATAAGAAATGAAATGTGTGGTTAGAAACTAAATAATAATCATATGAAATA
66 TTTAAAATAACAACAATAAGAAATGAAATGTATGATTAGAAACTAAATAATAATAACATGAAATA
* * * *
56452668 TGTACAATATTAAAATAAAAAATATGGTTTTAAATTGTAAGTAAAACAATATTTAAATACATGAA
131 TGTACAATATTAAAATAAAAAATA-GGTATTAAATTGTAAATAAAACAATATTTAAACACATAAA
* *
56452733 TACATCAGATTAAGAGGACTAAATGAATACAACTATTTATCATGGTATTGTCATCAATTTTAAGT
195 TACATCAGATTAAAAGGACTAAATGAATACAACTATTTATCATGGTATTGTCATCAATTCTAAGT
56452798 TGGCGTCGAGTTAATTTGTAACACCATATCAATCAACAATTTTATTA
260 TGGCGTCGAGTTAATTTGTAACACCATATCAATCAACAATTTTATTA
* *
56452845 ATACTAGAAACTCCATCATACGAGTATGCATGTAGAAACCATGTAGTTA-AAGCACAAATTTGTG
1 ATACTAGAAACTCCATCACACGAGTATGCATGTAGAAACCATATAGTTAGAA-CACAAATTTGTG
* * * *
56452909 -TTTAATAATAACATACAATAA-ATTATGAAATGTATGATTTGGAACTAATTAATAATAACATGA
65 TTTTAA-AATAACA-ACAATAAGA-AATGAAATGTATGATTAGAAACTAAATAATAATAACATGA
* * ** *
56452972 AATATGTACGATATTAAAATAAAAAATA-G-ATTAAATTGTAAATGAAAGTATTTTTAAACACAT
127 AATATGTACAATATTAAAATAAAAAATAGGTATTAAATTGTAAATAAAACAATATTTAAACACAT
* ** * * *
56453035 AAATACATTAGATTAAAATTATTAAATGAATACAATTATTTGTCATGGTATTGTCATC-ATTCCT
192 AAATACATCAGATTAAAAGGACTAAATGAATACAACTATTTATCATGGTATTGTCATCAATT-CT
*
56453099 AAGTTGGTGTCGAGTTAATTTGT
256 AAGTTGGCGTCGAGTTAATTTGT
56453122 GGTACCATCT
Statistics
Matches: 237, Mismatches: 35, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
304 3 0.01
305 100 0.42
306 8 0.03
307 60 0.25
308 66 0.28
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (306 bp):
ATACTAGAAACTCCATCACACGAGTATGCATGTAGAAACCATATAGTTAGAACACAAATTTGTGT
TTTAAAATAACAACAATAAGAAATGAAATGTATGATTAGAAACTAAATAATAATAACATGAAATA
TGTACAATATTAAAATAAAAAATAGGTATTAAATTGTAAATAAAACAATATTTAAACACATAAAT
ACATCAGATTAAAAGGACTAAATGAATACAACTATTTATCATGGTATTGTCATCAATTCTAAGTT
GGCGTCGAGTTAATTTGTAACACCATATCAATCAACAATTTTATTA
Found at i:56453800 original size:89 final size:88
Alignment explanation
Indices: 56453707--56453889 Score: 199
Period size: 89 Copynumber: 2.1 Consensus size: 88
56453697 TAAATATATT
** * *
56453707 TTTTAATATAAAATA-TTTTATTCACCCAAATCAAGGGTGTGATAAAA-CTTAGTATTAATAATG
1 TTTTAATATAAAATATTTTTAAACACCCAAA-C-A-CGTGTGATAAAATCTTAGTATTAATAATA
56453770 TTGTTGATTGAGTTGGTGTCACAAAA
63 TTGTTGATTGAGTTGGTGTCACAAAA
* *** ** * *
56453796 TTTTATTATATGTTATTTTTAAACATGCATACACGTGTGATAAAATTTTTAGTATTAATAATATT
1 TTTTAATATAAAATATTTTTAAACACCCAAACACGTGTGATAAAA-TCTTAGTATTAATAATATT
*
56453861 GTTGATTGAGTTGGTGTCACAAAT
65 GTTGATTGAGTTGGTGTCACAAAA
56453885 TTTTA
1 TTTTA
56453890 TTGCATATTC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
87 11 0.14
88 1 0.01
89 56 0.72
90 10 0.13
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (88 bp):
TTTTAATATAAAATATTTTTAAACACCCAAACACGTGTGATAAAATCTTAGTATTAATAATATTG
TTGATTGAGTTGGTGTCACAAAA
Found at i:56453904 original size:89 final size:87
Alignment explanation
Indices: 56453743--56453910 Score: 246
Period size: 89 Copynumber: 1.9 Consensus size: 87
56453733 CAAATCAAGG
* * *
56453743 GTGTGATAAAACTTAGTATTAATAATGTTGTTGATTGAGTTGGTGTCACAAAATTTTATTATATG
1 GTGTGATAAAACTTAGTATTAATAATATTGTTGATTGAGTTGGTGTCACAAAATTTTATTACATA
56453808 TTATTTTTAAACATGCATACAC
66 TTATTTTTAAACATGCATACAC
* * *
56453830 GTGTGATAAAATTTTTAGTATTAATAATATTGTTGATTGAGTTGGTGTCACAAATTTTTATTGCA
1 GTGTGATAAAA--CTTAGTATTAATAATATTGTTGATTGAGTTGGTGTCACAAAATTTTATTACA
* *
56453895 TATTCTTTTTAGACAT
64 TATTATTTTTAAACAT
56453911 ATCTCTATGT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
87 11 0.15
89 60 0.85
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (87 bp):
GTGTGATAAAACTTAGTATTAATAATATTGTTGATTGAGTTGGTGTCACAAAATTTTATTACATA
TTATTTTTAAACATGCATACAC
Found at i:56456977 original size:7 final size:7
Alignment explanation
Indices: 56456965--56457005 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
56456955 TATTTATTTT
56456965 ATTTATA
1 ATTTATA
56456972 ATTTATA
1 ATTTATA
56456979 ATTTATA
1 ATTTATA
56456986 ATTTAATA
1 ATTT-ATA
56456994 ATTTATA
1 ATTTATA
56457001 TATTT
1 -ATTT
56457006 TTATTTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 21 0.66
8 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTATA
Found at i:56457011 original size:22 final size:21
Alignment explanation
Indices: 56456961--56457012 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
56456951 ATAATATTTA
56456961 TTTTATTT-ATAATTTATAAT
1 TTTTATTTAATAATTTATAAT
*
56456981 TTATAATTTAATAATTTATATAT
1 TT-TTATTTAATAATTTATA-AT
56457004 TTTTATTTA
1 TTTTATTTA
56457013 TTCAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 5 0.19
22 16 0.59
23 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATTTAATAATTTATAAT
Found at i:56457141 original size:18 final size:18
Alignment explanation
Indices: 56457107--56457140 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56457097 TGTGTTATAA
56457107 ATTACATAATATAAAAAC
1 ATTACATAATATAAAAAC
56457125 ATTACA-AATATAAAAA
1 ATTACATAATATAAAAA
56457141 AGAAACTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTACATAATATAAAAAC
Found at i:56458609 original size:33 final size:33
Alignment explanation
Indices: 56458572--56458639 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
56458562 GCAATATCAC
56458572 ATTACATCTCTAAGATGACGCTTTCAATCTTGT
1 ATTACATCTCTAAGATGACGCTTTCAATCTTGT
* *
56458605 ATTACATCTTTAAGGTGACGCTTTCAATCTTGT
1 ATTACATCTCTAAGATGACGCTTTCAATCTTGT
56458638 AT
1 AT
56458640 ACTTGTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (33 bp):
ATTACATCTCTAAGATGACGCTTTCAATCTTGT
Found at i:56460178 original size:9 final size:9
Alignment explanation
Indices: 56460164--56460192 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
56460154 CAAGATCTCT
56460164 TTATTTTCA
1 TTATTTTCA
56460173 TTATTTTCA
1 TTATTTTCA
56460182 TTATTTTCA
1 TTATTTTCA
56460191 TT
1 TT
56460193 TTCACTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTTTCA
Found at i:56461315 original size:18 final size:18
Alignment explanation
Indices: 56461292--56461327 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
56461282 TGAGAATTCT
56461292 TTAAATTAAAGAAACTTC
1 TTAAATTAAAGAAACTTC
56461310 TTAAATTAAAGAAACTTC
1 TTAAATTAAAGAAACTTC
56461328 GGGTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
TTAAATTAAAGAAACTTC
Found at i:56466069 original size:14 final size:15
Alignment explanation
Indices: 56466050--56466078 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56466040 GTAATATGCC
56466050 AAAATTGCT-GAAAG
1 AAAATTGCTGGAAAG
56466064 AAAATTGCTGGAAAG
1 AAAATTGCTGGAAAG
56466079 CCATAATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.21
Consensus pattern (15 bp):
AAAATTGCTGGAAAG
Found at i:56469316 original size:27 final size:26
Alignment explanation
Indices: 56469258--56469309 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
56469248 ATATTAAGAA
* *
56469258 AAACATTTTTTATGAAAAAAAAATCT
1 AAACATTCTTTATGAAAAAAAAATCC
56469284 AAACATTCTTTATG-AAAAAAAATCC
1 AAACATTCTTTATGAAAAAAAAATCC
56469309 A
1 A
56469310 GGTACATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.31
Consensus pattern (26 bp):
AAACATTCTTTATGAAAAAAAAATCC
Found at i:56469843 original size:31 final size:31
Alignment explanation
Indices: 56469815--56469911 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 31
56469805 TTAATTATGA
56469815 ATATAAAATATTTTTAATACAATCATTATAT
1 ATATAAAATATTTTTAATACAATCATTATAT
* ** *
56469846 ATATTAAATATAGGTTAAT----T-A-T-GA-
1 ATATAAAATAT-TTTTAATACAATCATTATAT
56469870 ATATAAAATATTTTTAATACAATCATTATAT
1 ATATAAAATATTTTTAATACAATCATTATAT
*
56469901 ATATTAAATAT
1 ATATAAAATAT
56469912 AGGGTAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
23 5 0.10
24 10 0.21
25 1 0.02
26 1 0.02
27 2 0.04
28 2 0.04
29 1 0.02
30 1 0.02
31 20 0.42
32 5 0.10
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (31 bp):
ATATAAAATATTTTTAATACAATCATTATAT
Found at i:56469871 original size:55 final size:56
Alignment explanation
Indices: 56469805--56469923 Score: 222
Period size: 55 Copynumber: 2.1 Consensus size: 56
56469795 AAAAAAAAGA
56469805 TTAATTATGAATATAAAATATTTTTAATACAATCATTATATATATTAAATATA-GG
1 TTAATTATGAATATAAAATATTTTTAATACAATCATTATATATATTAAATATAGGG
56469860 TTAATTATGAATATAAAATATTTTTAATACAATCATTATATATATTAAATATAGGG
1 TTAATTATGAATATAAAATATTTTTAATACAATCATTATATATATTAAATATAGGG
*
56469916 TAAATTAT
1 TTAATTAT
56469924 TAAAATGTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 53 0.85
56 9 0.15
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (56 bp):
TTAATTATGAATATAAAATATTTTTAATACAATCATTATATATATTAAATATAGGG
Done.