Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 89 of 204
Found at i:27660860 original size:51 final size:50
Alignment explanation
Indices: 27660802--27660976 Score: 199
Period size: 51 Copynumber: 3.5 Consensus size: 50
27660792 TCAGTTCACA
*
27660802 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGGTACACG
* * * * * * * *
27660853 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCCGGTACACG
* * * *
27660904 TAGTAGTCTGCACATAGTACTACACATGCGACC-TATCATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGGTACACG
27660954 TAGTAGCCTGCACATAGTACTAC
1 TAGTAGCCTGCACATAGTACTAC
27660977 GCACATGACC
Statistics
Matches: 100, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 30 0.30
51 66 0.66
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGGTACACG
Found at i:27664348 original size:50 final size:49
Alignment explanation
Indices: 27664244--27664428 Score: 262
Period size: 50 Copynumber: 3.7 Consensus size: 49
27664234 CATGCCAAAT
** * *
27664244 CCATGTCACAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCAATG
1 CCATGTC-CAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAACG
* **
27664295 CCATGTCTCAGACATGGTTTTACGGGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTC-CAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
27664345 CCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCC-AGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
27664395 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 CCATGT-CCAGACATGGTCTTACATGGGACCTCT
27664429 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.01
50 93 0.77
51 27 0.22
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (49 bp):
CCATGTCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
Found at i:27668507 original size:29 final size:29
Alignment explanation
Indices: 27668466--27668693 Score: 300
Period size: 29 Copynumber: 7.9 Consensus size: 29
27668456 TGTGTTAAAC
* *
27668466 GATGGTCGTAACCATCCATTTTCATA-TT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
** * *
27668494 CGATGGTCGAAACCATCCCTTTTCATTAATC
1 -GATGGTCGTCACCATCCCTTTTCA-TAGTT
* *
27668525 AATGGTCGTCACCATCCCTTTTTATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *
27668554 GATGGTCATCACTATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
27668583 GATGGTC-TCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
27668611 GATGGTCGTCACCATCCCTTTTTATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *
27668640 GATGGTCATCACTATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
27668669 GATGGTC-TCACCATCCCTTTTCATA
1 GATGGTCGTCACCATCCCTTTTCATA
27668694 ATCGATAGCC
Statistics
Matches: 177, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
28 44 0.25
29 110 0.62
30 22 0.12
31 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATAGTT
Found at i:27668609 original size:57 final size:58
Alignment explanation
Indices: 27668466--27668693 Score: 293
Period size: 57 Copynumber: 3.9 Consensus size: 58
27668456 TGTGTTAAAC
* * * * *
27668466 GATGGTCGTAACCATCCATTTTCATA-TTCGATGGTCGA-AACCATCCCTTTTCATTAATC
1 GATGGTCGTCACCATCCCTTTTCATAGTT-GATGGTC-ATCACCATCCCTTTTCA-TAGTT
* * *
27668525 AATGGTCGTCACCATCCCTTTTTATAGTTGATGGTCATCACTATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTT
* *
27668583 GATGGTC-TCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTTATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTT
* *
27668640 GATGGTCATCACTATCCCTTTTCATAGTTGATGGTC-TCACCATCCCTTTTCATA
1 GATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATA
27668694 ATCGATAGCC
Statistics
Matches: 151, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
57 70 0.46
58 37 0.25
59 42 0.28
60 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (58 bp):
GATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTT
Found at i:27668633 original size:86 final size:86
Alignment explanation
Indices: 27668479--27668696 Score: 348
Period size: 86 Copynumber: 2.5 Consensus size: 86
27668469 GGTCGTAACC
* **
27668479 ATCCATTTTCATA-TTCGATGGTCGAAACCATCCCTTTTCATTAATCAATGGTCGTCACCATCCC
1 ATCCCTTTTCATAGTT-GATGGTC-TCACCATCCCTTTTCA-TAATCAATGGTCGTCACCATCCC
27668543 TTTTTATAGTTGATGGTCATCACT
63 TTTTTATAGTTGATGGTCATCACT
* **
27668567 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTT
1 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATCAATGGTCGTCACCATCCCTTT
27668632 TTATAGTTGATGGTCATCACT
66 TTATAGTTGATGGTCATCACT
27668653 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATC
1 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATC
27668697 GATAGCCGAA
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
86 86 0.71
87 14 0.12
88 19 0.16
89 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (86 bp):
ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATCAATGGTCGTCACCATCCCTTT
TTATAGTTGATGGTCATCACT
Found at i:27668712 original size:57 final size:56
Alignment explanation
Indices: 27668538--27668725 Score: 225
Period size: 57 Copynumber: 3.3 Consensus size: 56
27668528 GGTCGTCACC
* * * *
27668538 ATCCCTTTTTATAGTTGATGGTCATCACTATCCCTTTTCATAGTTGATGGTCTCACC
1 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTTGATGGTC-AACT
* *
27668595 ATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTTATAGTTGATGGTCATCACT
1 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCA--ACT
* * * *
27668653 ATCCCTTTTCATAGTTGATGGTC-TCACCATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTTGATGGTC-AA-CT
*
27668710 ATCCTTTTTCATAGTT
1 ATCCCTTTTCATAGTT
27668726 TGACAGCCAA
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
56 1 0.01
57 88 0.77
58 26 0.23
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (56 bp):
ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCAACT
Found at i:27668724 original size:86 final size:86
Alignment explanation
Indices: 27668479--27668725 Score: 311
Period size: 86 Copynumber: 2.8 Consensus size: 86
27668469 GGTCGTAACC
* ** * * * *
27668479 ATCCATTTTCATA-TTCGATGGTCGAAACCATCCCTTTTCATTAATCAATGGTCGTCACCATCCC
1 ATCCCTTTTCATAGTT-GATGGTC-TCACCATCCCTTTTCA-TAATCGATAGCCGTAACCATCCC
27668543 TTTTTATAGTTGATGGTCATCACT
63 TTTTTATAGTTGATGGTCATCACT
* * * * *
27668567 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTT
1 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATCGATAGCCGTAACCATCCCTTT
27668632 TTATAGTTGATGGTCATCACT
66 TTATAGTTGATGGTCATCACT
*
27668653 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATCGATAGCCG-AAGCTAT-CCTT
1 ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATCGATAGCCGTAA-CCATCCCTT
27668716 TTTCATAGTT
65 TTT-ATAGTT
27668726 TGACAGCCAA
Statistics
Matches: 144, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
85 8 0.06
86 101 0.70
87 14 0.10
88 19 0.13
89 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (86 bp):
ATCCCTTTTCATAGTTGATGGTCTCACCATCCCTTTTCATAATCGATAGCCGTAACCATCCCTTT
TTATAGTTGATGGTCATCACT
Found at i:27677122 original size:13 final size:13
Alignment explanation
Indices: 27677104--27677139 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
27677094 CGTGTGTGAC
27677104 ACATGGCCATTCG
1 ACATGGCCATTCG
27677117 ACATGGCCATTCG
1 ACATGGCCATTCG
*
27677130 ACATAGCCAT
1 ACATGGCCAT
27677140 GTGTCCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (13 bp):
ACATGGCCATTCG
Found at i:27678685 original size:13 final size:13
Alignment explanation
Indices: 27678669--27678693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27678659 ATTCGAGAGA
27678669 TTTTGGAGAGAAT
1 TTTTGGAGAGAAT
27678682 TTTTGGAGAGAA
1 TTTTGGAGAGAA
27678694 AAGGTTTAGA
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (13 bp):
TTTTGGAGAGAAT
Found at i:27681097 original size:17 final size:17
Alignment explanation
Indices: 27681072--27681104 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27681062 TGTATACGGT
*
27681072 ATTGTTTGTTTGTATTA
1 ATTGATTGTTTGTATTA
27681089 ATTGATTGTTTGTATT
1 ATTGATTGTTTGTATT
27681105 CATTAGTGTA
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:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (17 bp):
ATTGATTGTTTGTATTA
Found at i:27687180 original size:10 final size:11
Alignment explanation
Indices: 27687165--27687193 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
27687155 ACCAAAAATG
27687165 TGAATTGAAT-
1 TGAATTGAATA
27687175 TGAATTGAATA
1 TGAATTGAATA
27687186 TGAATTGA
1 TGAATTGA
27687194 TGTTAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:27690194 original size:20 final size:20
Alignment explanation
Indices: 27690157--27690196 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27690147 AGAAACTGAT
*
27690157 ACTTCTGAAAGATTTTTGAA
1 ACTTCTGAAAGATATTTGAA
27690177 ACTTCTGATAA-ATATTTGAA
1 ACTTCTGA-AAGATATTTGAA
27690197 GCATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (20 bp):
ACTTCTGAAAGATATTTGAA
Found at i:27698444 original size:16 final size:17
Alignment explanation
Indices: 27698423--27698456 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
27698413 AATATTAGGG
27698423 GCAAAAGTAT-AATTTT
1 GCAAAAGTATGAATTTT
27698439 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
27698456 G
1 G
27698457 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:27702343 original size:25 final size:25
Alignment explanation
Indices: 27702299--27702346 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27702289 ACGAATTTTC
*
27702299 TCAAAATTTTATCGGGGTAAAATCA
1 TCAAAATTTTATCGGAGTAAAATCA
27702324 TCAAAATTTTA-CAGGAGTAAAAT
1 TCAAAATTTTATC-GGAGTAAAAT
27702347 TGGGATGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTATCGGAGTAAAATCA
Found at i:27705177 original size:114 final size:114
Alignment explanation
Indices: 27705047--27705376 Score: 518
Period size: 114 Copynumber: 2.9 Consensus size: 114
27705037 CAATCATAGT
*
27705047 CATATCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACATTCATGTATTGTGTTCTGC
1 CATATCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACATTCATGTATTGTGTTTTGC
* *
27705112 CATTCCAGTTTCATCTTACTAGAGGCTACACTATGAACATTCCTACAGC
66 CATTCCAGTTTCATCTTACTAGAGGCTACACCATGAACATTCATACAGC
* * *
27705161 CATATCATATCATGCCAAGGGTCTTAACCACATGGTCTTATACACATTCATGTATAT-TGTTTTT
1 CATATCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACATTCATGTAT-TGTGTTTTG
* *
27705225 TCATTCTAGTTTCATCTTACTAGAGGCTACACCATGAACATTCATACAGC
65 CCATTCCAGTTTCATCTTACTAGAGGCTACACCATGAACATTCATACAGC
* * * *
27705275 CATATCATATCATGTCATGGGTATTAACCACATGGTCTTACACATATTCATGTATCGTGTTTTGC
1 CATATCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACATTCATGTATTGTGTTTTGC
* *
27705340 CATTCCAGTTTTAGCTTACTAGAGGCTACACCATGAA
66 CATTCCAGTTTCATCTTACTAGAGGCTACACCATGAA
27705377 TGGTTCCAAT
Statistics
Matches: 195, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
114 194 0.99
115 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (114 bp):
CATATCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACATTCATGTATTGTGTTTTGC
CATTCCAGTTTCATCTTACTAGAGGCTACACCATGAACATTCATACAGC
Found at i:27708523 original size:11 final size:11
Alignment explanation
Indices: 27708509--27708539 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
27708499 ATGATGTTGA
27708509 TGATATTTTGG
1 TGATATTTTGG
27708520 TGATATTTTGG
1 TGATATTTTGG
27708531 TGATTATTT
1 TGA-TATTT
27708540 ATTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (11 bp):
TGATATTTTGG
Found at i:27708607 original size:23 final size:23
Alignment explanation
Indices: 27708565--27708608 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27708555 TAAATATTAT
*
27708565 TTTATTAATATTTTGCTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
27708588 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
27708609 AAAATGATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:27717551 original size:39 final size:39
Alignment explanation
Indices: 27717508--27717591 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 39
27717498 CATGTTTCTA
* ** *
27717508 AGTATTACGAAATATTCTTGAATGTTATGTGATTATATG
1 AGTATTACGAAATATGCTTGAACATTATGTAATTATATG
* * *
27717547 AGTATTGCGATATGTGCTTGAACATTATGTAATTATATG
1 AGTATTACGAAATATGCTTGAACATTATGTAATTATATG
27717586 AGTATT
1 AGTATT
27717592 GTGATACATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (39 bp):
AGTATTACGAAATATGCTTGAACATTATGTAATTATATG
Found at i:27717621 original size:39 final size:39
Alignment explanation
Indices: 27717528--27717624 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 39
27717518 AATATTCTTG
** *
27717528 AATGTTATGTGATTATATGAGTATTGCGATATGTGCTTG
1 AATGTTATGTGATTATATGAGTATTGCGATACATGCTTA
** * * *
27717567 AACATTATGTAATTATATGAGTATTGTGATACATGGTTA
1 AATGTTATGTGATTATATGAGTATTGCGATACATGCTTA
*
27717606 AATGTTTTGTGATTATATG
1 AATGTTATGTGATTATATG
27717625 TGTAATATGA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (39 bp):
AATGTTATGTGATTATATGAGTATTGCGATACATGCTTA
Found at i:27723619 original size:40 final size:40
Alignment explanation
Indices: 27723582--27723767 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
27723572 GCTACTCGTT
* *
27723582 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
27723622 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
27723662 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
27723702 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
27723743 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
27723768 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:27728278 original size:218 final size:218
Alignment explanation
Indices: 27727913--27728423 Score: 670
Period size: 218 Copynumber: 2.3 Consensus size: 218
27727903 CTTCAACCTA
* * * *
27727913 CTCCACTGCAACCT-AAGGGAGATAAGATTACCGGCTTCAATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGCAACTTCAA-GGAGATAGGATTACTGGCTTCAATCTGATCCACTACTGCTTAGGGAG
* * *
27727977 ATAAGATCAT-CCATCCTCGATATGCCCCACTATTACTTAGGAAGATAAGTTTCGTAATTCTTCG
65 ATAAGATC-TGTCATCCTCGATATGCCCCACTACTACTTAGGAAGATAAGTTTCGTAATTCTTCA
* * * *
27728041 GCCTCCTCCGCTGCAACTTCAGGGAGATAAGACTTGATACAAACTACTCTACTGCAACTTCAGAG
129 GCCTACTCCACTGCAACTTCAGGGAGATAAGACCTAATACAAACTACTCTACTGCAACTTCAGAG
*
27728106 AGATAAGATCTTTTATTTTAATCCG
194 AGAAAAGATCTTTTATTTTAATCCG
* * *
27728131 CTCCAATGCAACTTCAAGGAGATAGGATTATTGGCTTCAATCTGATCCACTACTGCTCAGGGAGA
1 CTCCACTGCAACTTCAAGGAGATAGGATTACTGGCTTCAATCTGATCCACTACTGCTTAGGGAGA
* * * *
27728196 TAAGATCTGTCATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGATTT-GTAATTCTTCAG
66 TAAGATCTGTCATCCTCGATATGCCCCACTACTACTTAGGAAGATAAG-TTTCGTAATTCTTCAG
* * * * * * * *
27728260 TCTACTCCATTTCAACTTCAGGGAGATAAGACCTAATGCGATCTATTCTACTGTAACTTCAGAGA
130 CCTACTCCACTGCAACTTCAGGGAGATAAGACCTAATACAAACTACTCTACTGCAACTTCAGAGA
*
27728325 GAAAAGATCTTTTATTTTAATTCG
195 GAAAAGATCTTTTATTTTAATCCG
** *
27728349 CTCCACTTAAACTTCAAGGAGATAGGATTACTGGCTTCAATCT-ACTCTACTACTGCTTAGGGAG
1 CTCCACTGCAACTTCAAGGAGATAGGATTACTGGCTTCAATCTGA-TCCACTACTGCTTAGGGAG
*
27728413 ATACGATCTGT
65 ATAAGATCTGT
27728424 AATTTCATTA
Statistics
Matches: 254, Mismatches: 35, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
217 2 0.01
218 247 0.97
219 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (218 bp):
CTCCACTGCAACTTCAAGGAGATAGGATTACTGGCTTCAATCTGATCCACTACTGCTTAGGGAGA
TAAGATCTGTCATCCTCGATATGCCCCACTACTACTTAGGAAGATAAGTTTCGTAATTCTTCAGC
CTACTCCACTGCAACTTCAGGGAGATAAGACCTAATACAAACTACTCTACTGCAACTTCAGAGAG
AAAAGATCTTTTATTTTAATCCG
Found at i:27736336 original size:21 final size:21
Alignment explanation
Indices: 27736297--27736336 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27736287 ATTGCCCTAA
* *
27736297 ATTTCTCTTCAATCCATTTCC
1 ATTTCTCCTCAAACCATTTCC
*
27736318 ATTTCTCCTCAAACTATTT
1 ATTTCTCCTCAAACCATTT
27736337 TGGCAATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTCTCCTCAAACCATTTCC
Found at i:27745770 original size:27 final size:26
Alignment explanation
Indices: 27745751--27746057 Score: 319
Period size: 27 Copynumber: 11.4 Consensus size: 26
27745741 GGGTATAACA
*
27745751 GTCATTTTACCCTATGGGGGTATTTC
1 GTCATTCTACCCTATGGGGGTATTTC
*
27745777 GATCATTCTACCCTATGGGGGTATTTT
1 G-TCATTCTACCCTATGGGGGTATTTC
*
27745804 GATCATTCTACCCCATGGGGGTATTTC
1 G-TCATTCTACCCTATGGGGGTATTTC
27745831 AGTCATTCTACCCTATGGGGGTATTTC
1 -GTCATTCTACCCTATGGGGGTATTTC
*
27745858 GGTCATTCTACCCTATGGGTGTATTTC
1 -GTCATTCTACCCTATGGGGGTATTTC
* *
27745885 GATCATTCTACCCTATTGGAGTATTTC
1 G-TCATTCTACCCTATGGGGGTATTTC
*
27745912 GGTCATTCTACCCTATAGGGGTATTTC
1 -GTCATTCTACCCTATGGGGGTATTTC
*
27745939 GATCATTCTACCCTAT-GGGGTATTTTG
1 G-TCATTCTACCCTATGGGGGTA-TTTC
* * * * *
27745966 GTTATTTTAACTTATGGGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTA-TTTC
* * *
27745993 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTA-TTTC
* * * *
27746020 GTTATTTTATCCTATAGGGGTATTTC
1 GTCATTCTACCCTATGGGGGTATTTC
*
27746046 GGTCATTTTACC
1 -GTCATTCTACC
27746058 TAGTTTGAGG
Statistics
Matches: 246, Mismatches: 27, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
26 22 0.09
27 222 0.90
28 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (26 bp):
GTCATTCTACCCTATGGGGGTATTTC
Found at i:27745798 original size:54 final size:54
Alignment explanation
Indices: 27745751--27746057 Score: 375
Period size: 54 Copynumber: 5.7 Consensus size: 54
27745741 GGGTATAACA
* *
27745751 GTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCG
* *
27745805 ATCATTCTACCCCATGGGGGTATTTC-AGTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCGA-TCATTCTACCCTATGGGGGTATTTCG
* * *
27745859 GTCATTCTACCCTATGGGTGTATTTCGATCATTCTACCCTATTGGAGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCG
* *
27745913 GTCATTCTACCCTATAGGGGTATTTCGATCATTCTACCCTAT-GGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCG
* * * * * * * * *
27745966 GTTATTTTAACTTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCG
* * * * * *
27746020 GTTATTTTATCCTATAGGGGTATTTCGGTCATTTTACC
1 GTCATTCTACCCTATGGGGGTATTTCGATCATTCTACC
27746058 TAGTTTGAGG
Statistics
Matches: 224, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 44 0.20
54 179 0.80
55 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (54 bp):
GTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCG
Found at i:27745864 original size:81 final size:81
Alignment explanation
Indices: 27745740--27746044 Score: 369
Period size: 81 Copynumber: 3.8 Consensus size: 81
27745730 TCATCTCCTA
** *
27745740 GGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTTG
1 GGGGTATTTCAGTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTTG
*
27745805 ATCATTCTACCCCATG
66 ATCATTCTACCCTATG
* * *
27745821 GGGGTATTTCAGTCATTCTACCCTATGGGGGTATTTCGGTCATTCTACCCTATGGGTGTATTTCG
1 GGGGTATTTCAGTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTTG
*
27745886 ATCATTCTACCCTATT
66 ATCATTCTACCCTATG
* * *
27745902 GGAGTATTTCGGTCATTCTACCCTATAGGGGTATTTCGATCATTCTACCCTAT-GGGGTATTTTG
1 GGGGTATTTCAGTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTTG
* * * * *
27745966 GTTATTTTAACTTATG
66 ATCATTCTACCCTATG
** * * * * * * * *
27745982 GGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTTGGTTATTTTATCCTATAGGGGTATTT
1 GGGGTATTTCAGTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTT
27746045 CGGTCATTTT
Statistics
Matches: 193, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 62 0.32
81 131 0.68
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (81 bp):
GGGGTATTTCAGTCATTCTACCCTATGGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTTG
ATCATTCTACCCTATG
Found at i:27747511 original size:56 final size:50
Alignment explanation
Indices: 27747488--27747782 Score: 304
Period size: 50 Copynumber: 5.9 Consensus size: 50
27747478 CATTGACATT
27747488 ATGAGAGGTCCCATGTAAGACCATGTCTA-GGACATGGCATTGGCATCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTC-AGGGACATGGCATTGGCATCGAG
** * *
27747538 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCAGGGACATGGCATTGGCATCGAG
* * ** *
27747588 ATGAGAGGTCCTATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCAGGGACATGGCATTGGCATCGAG
* * * * * *
27747638 ATGAGAGGTCCCATGTAATACCATGTCTGGGACATGGCGTTAGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCAGGGACATGGCATTGGCATCGAG
** * * * * * *
27747688 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCTAT
1 ATGAGAGGTCCCATGTAAGACCATGTCAGGGACATGGCATTGGCATCGAG
** * * * * *
27747738 ATGAGAACTCTCATGTAAGACCATATCTGGGATATGACATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCAGGGACATGGCATTGGCA
27747783 GTACAAGAAA
Statistics
Matches: 215, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
50 215 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCAGGGACATGGCATTGGCATCGAG
Found at i:27747527 original size:50 final size:48
Alignment explanation
Indices: 27747488--27747828 Score: 297
Period size: 50 Copynumber: 6.9 Consensus size: 48
27747478 CATTGACATT
* * *
27747488 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-TTTGCA-CCAG
* *
27747538 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-TTTGCACC-AG
*
27747588 ATGAGAGGTCCTATGTAAGACCATGTCTGGGACATGG-TGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCT-TT-GCACC-AG
* *
27747638 ATGAGAGGTCCCATGTAATACCATGTCTGGGACATGGCGTTAGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-TTTGCACC-AG
** * ** *
27747688 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCTAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-TTTGCACC-AG
** * * * * * ** *
27747738 ATGAGAACTCTCATGTAAGACCATATCTGGGATATGACATTGGCAGTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-TTTGCACCAG
* * ** * *
27747787 AAGAAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTTTG
27747829 GCATGTTATA
Statistics
Matches: 244, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
48 4 0.02
49 31 0.13
50 207 0.85
51 1 0.00
52 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (48 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTTTGCACCAG
Found at i:27747621 original size:100 final size:100
Alignment explanation
Indices: 27747488--27747769 Score: 393
Period size: 100 Copynumber: 2.8 Consensus size: 100
27747478 CATTGACATT
* *
27747488 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * *
27747553 TAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
66 TAAGACCATGTCTGGGACATGGCGTTAGCACCAAG
* **
27747588 ATGAGAGGTCCTATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
*
27747653 TAATACCATGTCTGGGACATGGCGTTAGCACCAAG
66 TAAGACCATGTCTGGGACATGGCGTTAGCACCAAG
** * * * * ** *
27747688 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGAACTCTCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
*
27747753 TAAGACCATATCTGGGA
66 TAAGACCATGTCTGGGA
27747770 TATGACATTG
Statistics
Matches: 159, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 159 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (100 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
TAAGACCATGTCTGGGACATGGCGTTAGCACCAAG
Found at i:27747671 original size:150 final size:150
Alignment explanation
Indices: 27747488--27747769 Score: 395
Period size: 150 Copynumber: 1.9 Consensus size: 150
27747478 CATTGACATT
* * * *
27747488 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTAGCACCAAGATGAGAGGTCCCACG
* * * * ** *
27747553 TAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTC-CTATGTAAGACCATGTCTG
66 TAAGACCATGTCTGGGACATGACATGGGCACCGAGATGAGAACTCTC-ATGTAAGACCATATCTG
27747617 GGACATGGTGTTGGCACCGAG
130 GGACATGGTGTTGGCACCGAG
* * * *
27747638 ATGAGAGGTCCCATGTAATACCATGTCTGGGACATGGCGTTAGCACCAAGATGAGAGGTCCCCCG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTAGCACCAAGATGAGAGGTCCCACG
* *
27747703 TAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGAACTCTCATGTAAGACCATATCTGG
66 TAAGACCATGTCTGGGACATGACATGGGCACCGAGATGAGAACTCTCATGTAAGACCATATCTGG
27747768 GA
131 GA
27747770 TATGACATTG
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
150 113 0.99
151 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (150 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTAGCACCAAGATGAGAGGTCCCACG
TAAGACCATGTCTGGGACATGACATGGGCACCGAGATGAGAACTCTCATGTAAGACCATATCTGG
GACATGGTGTTGGCACCGAG
Found at i:27747816 original size:49 final size:50
Alignment explanation
Indices: 27747440--27747821 Score: 201
Period size: 50 Copynumber: 7.5 Consensus size: 50
27747430 GGTAAAGAGA
* * * * **
27747440 TCCCATGTAAGACCATGTCAGGGACATGTCATTGGCATCATTGACATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCA-C-CT-ACA--A-GAGAAC
* * * * * * * **
27747496 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
* * * * * * * **
27747546 TCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
* *** * * * * **
27747596 TCCTATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
* * * ** * * * **
27747646 TCCCATGTAATACCATGTCTGGGACATGGCGTTAGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
** * *
27747696 TCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
* * * * *
27747746 TCTCATGTAAGACCATATCTGGGATATGACATTGGCA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
*
27747794 ATCCCATGTAAGACTATGTCTGGGACAT
1 -TCCCATGTAAGACCATGTCTGGGACAT
27747822 AGCTTTGGCA
Statistics
Matches: 281, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
48 3 0.01
49 28 0.10
50 214 0.76
53 2 0.01
56 34 0.12
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCTACAAGAGAAC
Found at i:27755749 original size:31 final size:32
Alignment explanation
Indices: 27755693--27755755 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
27755683 AAATTACAAT
27755693 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
27755725 AGTAATTGAATCCTAAT-AAAACTCTTTAAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
27755756 TTATCTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (32 bp):
AGTAATTGAATCCTAATAAAAACTCTTTAAAA
Found at i:27760849 original size:12 final size:12
Alignment explanation
Indices: 27760826--27760858 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27760816 CAATTTTGGG
27760826 AAAAATAA-AAT
1 AAAAATAATAAT
27760837 AAAAATAATAAT
1 AAAAATAATAAT
*
27760849 AACAATAATA
1 AAAAATAATA
27760859 GGAAAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:27760923 original size:20 final size:19
Alignment explanation
Indices: 27760896--27760942 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
27760886 GTAGGCAACT
27760896 TTTTTTTTGCGCTTTTTGC
1 TTTTTTTTGCGCTTTTTGC
*
27760915 TTCTTTTTTGCGCTTTTTTC
1 TT-TTTTTTGCGCTTTTTGC
27760935 TTTTTTTT
1 TTTTTTTT
27760943 AAAGAATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.00, C:0.15, G:0.11, T:0.74
Consensus pattern (19 bp):
TTTTTTTTGCGCTTTTTGC
Found at i:27761550 original size:31 final size:32
Alignment explanation
Indices: 27761491--27761555 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
27761481 GGCAAATTAC
27761491 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
27761523 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
27761554 AA
1 AA
27761556 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:27781437 original size:18 final size:17
Alignment explanation
Indices: 27781410--27781450 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
27781400 AAGTTTTTTT
*
27781410 GAAAACAATAATAGAAAA
1 GAAAATAATAATA-AAAA
*
27781428 TAAAATAATAATAAAAA
1 GAAAATAATAATAAAAA
27781445 GAAAAT
1 GAAAAT
27781451 TATTATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (17 bp):
GAAAATAATAATAAAAA
Found at i:27783443 original size:26 final size:28
Alignment explanation
Indices: 27783400--27783454 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
27783390 TAGTTAAAAC
*
27783400 TCTTCTAAAAGAAAACTC-AAGAGAAAT
1 TCTTCTAAAAGAAAACTCAAAAAGAAAT
*
27783427 TCTTC-AAAAGAATACTCAAAAAGAAAT
1 TCTTCTAAAAGAAAACTCAAAAAGAAAT
27783454 T
1 T
27783455 TAATAACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (28 bp):
TCTTCTAAAAGAAAACTCAAAAAGAAAT
Found at i:27785170 original size:18 final size:17
Alignment explanation
Indices: 27785147--27785191 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
27785137 CATTACTTTT
*
27785147 AAAAAATATTTTTAGGA
1 AAAAAATATTTTTAAGA
*
27785164 CAAAAAATACTTTTAAGA
1 -AAAAAATATTTTTAAGA
*
27785182 TAAAAATATT
1 AAAAAATATT
27785192 ACTAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (17 bp):
AAAAAATATTTTTAAGA
Found at i:27785381 original size:35 final size:35
Alignment explanation
Indices: 27785335--27785406 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
27785325 AACTTTTGAC
27785335 GTTAAAAATTTGCAACGTGTTTCCCTTCAATTTCG
1 GTTAAAAATTTGCAACGTGTTTCCCTTCAATTTCG
27785370 GTTAAAAATTTGCAACGTGTTTCCCTTCAATTTCG
1 GTTAAAAATTTGCAACGTGTTTCCCTTCAATTTCG
27785405 GT
1 GT
27785407 CCAAATAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (35 bp):
GTTAAAAATTTGCAACGTGTTTCCCTTCAATTTCG
Found at i:27790377 original size:21 final size:21
Alignment explanation
Indices: 27790351--27790395 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
27790341 TCACTCAAAA
27790351 GTATGTATTTCTTAGAAATAT
1 GTATGTATTTCTTAGAAATAT
27790372 GTATGTATTTCTTAGAAATAT
1 GTATGTATTTCTTAGAAATAT
27790393 GTA
1 GTA
27790396 CAACTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (21 bp):
GTATGTATTTCTTAGAAATAT
Found at i:27796994 original size:63 final size:61
Alignment explanation
Indices: 27796916--27797060 Score: 164
Period size: 62 Copynumber: 2.3 Consensus size: 61
27796906 ATTAGAAATT
* * * * * *
27796916 ATGAAAATTTTCAAAAATTTGAGGGGGTCTAATTAAATTTTTTTTTAAAATTTCAAGGGAGAA
1 ATGAAAATTTCCAAAAATTT-AGGGGGCCTAATTAAA-ATTTTCTAAAAATTTCAAGGGAAAA
* *
27796979 ATGAAAATTTCCAAAAATTATTGGGGGCCTAATTAAAATTTTCTAAAAATTTCAAGTGAAAA
1 ATGAAAATTTCCAAAAATT-TAGGGGGCCTAATTAAAATTTTCTAAAAATTTCAAGGGAAAA
* * *
27797041 ATCATAATTTCCTAAAATTT
1 ATGAAAATTTCCAAAAATTT
27797061 TGAAGGGTCC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
61 1 0.01
62 36 0.51
63 32 0.46
64 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (61 bp):
ATGAAAATTTCCAAAAATTTAGGGGGCCTAATTAAAATTTTCTAAAAATTTCAAGGGAAAA
Found at i:27798840 original size:22 final size:24
Alignment explanation
Indices: 27798812--27798856 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
27798802 TTAACCAGTC
27798812 TATTGGTACCT-AAT-TTTTTTTA
1 TATTGGTACCTAAATATTTTTTTA
*
27798834 TATTGGTACTTAAATATTTTTTT
1 TATTGGTACCTAAATATTTTTTT
27798857 GGTCACAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 3 0.15
24 7 0.35
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.60
Consensus pattern (24 bp):
TATTGGTACCTAAATATTTTTTTA
Found at i:27803110 original size:9 final size:9
Alignment explanation
Indices: 27803090--27803165 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
27803080 ATGCCTTTTA
*
27803090 AATTAACCG
1 AATTACCCG
*
27803099 AATTACCTG
1 AATTACCCG
*
27803108 AATTAACCG
1 AATTACCCG
27803117 AATTACCCG
1 AATTACCCG
*
27803126 AATTACCCA
1 AATTACCCG
*
27803135 AATTATCCG
1 AATTACCCG
*
27803144 AATTACTCG
1 AATTACCCG
27803153 AATTACCCG
1 AATTACCCG
27803162 AATT
1 AATT
27803166 GAATCACTAG
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTACCCG
Found at i:27809278 original size:20 final size:21
Alignment explanation
Indices: 27809255--27809303 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
27809245 GAGCTCAAAC
* *
27809255 GAGCTGAGTTAA-GCTCATGT
1 GAGCTGAATTAACACTCATGT
*
27809275 GAGCTGAATTAACACTTATGT
1 GAGCTGAATTAACACTCATGT
27809296 GAGCTGAA
1 GAGCTGAA
27809304 CCAATCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (21 bp):
GAGCTGAATTAACACTCATGT
Found at i:27816511 original size:29 final size:29
Alignment explanation
Indices: 27816440--27816649 Score: 206
Period size: 29 Copynumber: 7.2 Consensus size: 29
27816430 GTATGCTAAA
* * * *
27816440 CGATGGTCGAAACCATCCATTTTCTTTAAT
1 CGATGGTTGAAACCATCCCTTTTC-ATATT
27816470 CGATGGTTGAAACCATCCCTTTTCATATT
1 CGATGGTTGAAACCATCCCTTTTCATATT
*
27816499 CGAAGGTTGAAACCATCCCTTTTCATATT
1 CGATGGTTGAAACCATCCCTTTTCATATT
* ** ** *
27816528 CTATGGCCGTCACCATCCCTTTTTATATT
1 CGATGGTTGAAACCATCCCTTTTCATATT
* **
27816557 TGATGGTCT-TCACCATCCCTTTTCATATT
1 CGATGGT-TGAAACCATCCCTTTTCATATT
* *
27816586 CAATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTTGAAACCATCCCTTTTCATATT
** * *
27816615 CGATGGTTGTCACCATTCCTTTTCATTAAT
1 CGATGGTTGAAACCATCCCTTTTCA-TATT
27816645 CGATG
1 CGATG
27816650 CTCGTTGATA
Statistics
Matches: 149, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
29 119 0.80
30 30 0.20
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (29 bp):
CGATGGTTGAAACCATCCCTTTTCATATT
Found at i:27835636 original size:20 final size:20
Alignment explanation
Indices: 27835611--27835672 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
27835601 TTGTACGGGA
27835611 TTTGCACTTCAGTGTCTCTG
1 TTTGCACTTCAGTGTCTCTG
* * *
27835631 TTTGCACTTCGGTGCCTCTA
1 TTTGCACTTCAGTGTCTCTG
* * * *
27835651 TATACACTTCAATGTCCCTG
1 TTTGCACTTCAGTGTCTCTG
27835671 TT
1 TT
27835673 CACACTACGG
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (20 bp):
TTTGCACTTCAGTGTCTCTG
Found at i:27835725 original size:20 final size:21
Alignment explanation
Indices: 27835681--27835725 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
27835671 TTCACACTAC
**
27835681 GGTGCCCCTGTTTGCACATTT
1 GGTGCCCCTGTCAGCACATTT
27835702 -GTGCCCCTGTCAGCAC-TTT
1 GGTGCCCCTGTCAGCACATTT
27835721 GGTGC
1 GGTGC
27835726 TTCTGTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.09, C:0.31, G:0.27, T:0.33
Consensus pattern (21 bp):
GGTGCCCCTGTCAGCACATTT
Found at i:27837283 original size:38 final size:38
Alignment explanation
Indices: 27837232--27837307 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
27837222 ACACGGCCGT
*
27837232 GTGACCCTTGTTTTCTAATTTTTGCATGTTTTTCCTAA
1 GTGACCCTTGTTTTCCAATTTTTGCATGTTTTTCCTAA
*
27837270 GTGACCCTTGTTTTCCAATTTTTGTATGTTTTTCCTAA
1 GTGACCCTTGTTTTCCAATTTTTGCATGTTTTTCCTAA
27837308 ACTTTTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (38 bp):
GTGACCCTTGTTTTCCAATTTTTGCATGTTTTTCCTAA
Found at i:27837969 original size:25 final size:25
Alignment explanation
Indices: 27837941--27837988 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
27837931 CATTAAGTGT
27837941 TTGCATCTTTTAATTATAATATGAA
1 TTGCATCTTTTAATTATAATATGAA
*
27837966 TTGCATCTTTTAATTATGATATG
1 TTGCATCTTTTAATTATAATATG
27837989 CATAATGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (25 bp):
TTGCATCTTTTAATTATAATATGAA
Found at i:27838123 original size:51 final size:50
Alignment explanation
Indices: 27837999--27838133 Score: 157
Period size: 50 Copynumber: 2.7 Consensus size: 50
27837989 CATAATGTGT
* * * *
27837999 TTTGCAT-TT-AATGAAGTCATGAATTATGAAACTCTTATGGTAGTTAAG
1 TTTGCATCTTAAATGAAGTCATGCATTATGTAACTCTCATGATAGTTAAG
* * * * *
27838047 ATTGCATCATAAATTATGACATGCATTATGTAACTCTCATGATAGTTAATG
1 TTTGCATCTTAAATGAAGTCATGCATTATGTAACTCTCATGATAGTTAA-G
*
27838098 TTTGCATCTTAAATGAAGTCATGCATTAAGTAACTC
1 TTTGCATCTTAAATGAAGTCATGCATTATGTAACTC
27838134 ATTTGTTCAT
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
48 6 0.09
49 1 0.01
50 31 0.45
51 31 0.45
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (50 bp):
TTTGCATCTTAAATGAAGTCATGCATTATGTAACTCTCATGATAGTTAAG
Found at i:27839592 original size:25 final size:25
Alignment explanation
Indices: 27839564--27839614 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
27839554 TTGCTTCTAA
27839564 CTGACTGTTGGAAGTGTTCCTTATT
1 CTGACTGTTGGAAGTGTTCCTTATT
27839589 CTGACTGTTGGAAGTGTTCCTTATT
1 CTGACTGTTGGAAGTGTTCCTTATT
27839614 C
1 C
27839615 AGGTCCTAAC
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:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (25 bp):
CTGACTGTTGGAAGTGTTCCTTATT
Found at i:27840345 original size:18 final size:18
Alignment explanation
Indices: 27840312--27840346 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27840302 AAGAAATGAG
*
27840312 AGAAAAAGAAATTGAAAA
1 AGAAAAAGAAAGTGAAAA
*
27840330 AGAAAAAGAGAGTGAAA
1 AGAAAAAGAAAGTGAAA
27840347 GAAAGGAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.09
Consensus pattern (18 bp):
AGAAAAAGAAAGTGAAAA
Found at i:27840355 original size:27 final size:26
Alignment explanation
Indices: 27840290--27840355 Score: 60
Period size: 28 Copynumber: 2.4 Consensus size: 26
27840280 AAAAGAATTT
* *
27840290 AAGAGAAGAAAAAAGAAATGAGAGAAA
1 AAGA-AAGGAAAAAGAAAAGAGAGAAA
* **
27840317 AAGAAATTGAAAAAGAAAAAGAGAGTGA
1 AAGAAA-GGAAAAAG-AAAAGAGAGAAA
27840345 AAGAAAGGAAA
1 AAGAAAGGAAA
27840356 GAGAGATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 2 0.06
27 14 0.45
28 15 0.48
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (26 bp):
AAGAAAGGAAAAAGAAAAGAGAGAAA
Found at i:27842802 original size:22 final size:24
Alignment explanation
Indices: 27842777--27842821 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
27842767 CCATTAACCA
27842777 TTCAACTA-A-ATACCATTACAAG
1 TTCAACTATACATACCATTACAAG
* *
27842799 TTCACCTATACATGCCATTACAA
1 TTCAACTATACATACCATTACAA
27842822 CCTTGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (24 bp):
TTCAACTATACATACCATTACAAG
Found at i:27859057 original size:51 final size:50
Alignment explanation
Indices: 27858943--27859068 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 50
27858933 TTTTGCGTTT
* * * *
27858943 AATGAATTCATGAATTATGAAACTCTCATGTTAGTTAAGTTTGCATCATA
1 AATGAAGTCATGCATTATGTAACTCTCATGATAGTTAAGTTTGCATCATA
* * * *
27858993 AATTATGACATGCATTATGTAACTCTCATGATAGTTAATGTTTGCATCTTA
1 AATGAAGTCATGCATTATGTAACTCTCATGATAGTTAA-GTTTGCATCATA
*
27859044 AATGAAGTCATGCATTAAGTAACTC
1 AATGAAGTCATGCATTATGTAACTC
27859069 ATTTGTTCAT
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 31 0.49
51 32 0.51
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (50 bp):
AATGAAGTCATGCATTATGTAACTCTCATGATAGTTAAGTTTGCATCATA
Found at i:27860623 original size:20 final size:20
Alignment explanation
Indices: 27860598--27860637 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27860588 AAATGCCTTT
27860598 AATGTCAAAACTTTTCAAGC
1 AATGTCAAAACTTTTCAAGC
27860618 AATGTCAAAACTTTTCAAGC
1 AATGTCAAAACTTTTCAAGC
27860638 GATTTTGGTA
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:0.20, G:0.10, T:0.30
Consensus pattern (20 bp):
AATGTCAAAACTTTTCAAGC
Found at i:27869238 original size:4 final size:4
Alignment explanation
Indices: 27869221--27869264 Score: 70
Period size: 4 Copynumber: 10.8 Consensus size: 4
27869211 CTAATCTTTG
*
27869221 ATTT ATTG ATTT ATTT ATTT ATTT ATCTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATT
27869265 CCTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:27869253 original size:17 final size:16
Alignment explanation
Indices: 27869221--27869264 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
27869211 CTAATCTTTG
*
27869221 ATTTATTGATTTATTT
1 ATTTATTTATTTATTT
27869237 ATTTATTTATCTTATTT
1 ATTTATTTAT-TTATTT
27869254 ATTTATTTATT
1 ATTTATTTATT
27869265 CCTTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTTATTTATTTATTT
Found at i:27869271 original size:17 final size:17
Alignment explanation
Indices: 27869232--27869274 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
27869222 TTTATTGATT
*
27869232 TATTTATTTATTTATCT
1 TATTTATTTATTTATCC
27869249 TATTTATTTATTTATTCC
1 TATTTATTTATTTA-TCC
27869267 T-TTTATTT
1 TATTTATTT
27869275 GACTTGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTATTTATTTATCC
Found at i:27869272 original size:21 final size:21
Alignment explanation
Indices: 27869229--27869274 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
27869219 TGATTTATTG
*
27869229 ATTTATTTATTTATTTATCTT
1 ATTTATTTATTTATTCATCTT
* *
27869250 ATTTATTTATTTATTCCTTTT
1 ATTTATTTATTTATTCATCTT
27869271 ATTT
1 ATTT
27869275 GACTTGGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTATTTATTTATTCATCTT
Found at i:27871050 original size:9 final size:9
Alignment explanation
Indices: 27871036--27871061 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27871026 CCAAGTGTTA
27871036 AAAGGTAAG
1 AAAGGTAAG
27871045 AAAGGTAAG
1 AAAGGTAAG
27871054 AAAGGTAA
1 AAAGGTAA
27871062 TAAAACATTA
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:0.00, G:0.31, T:0.12
Consensus pattern (9 bp):
AAAGGTAAG
Found at i:27892709 original size:19 final size:19
Alignment explanation
Indices: 27892681--27892722 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27892671 TGAGAGCTAA
*
27892681 GAGAGTTGAGAGAGAGGAT
1 GAGAGATGAGAGAGAGGAT
* *
27892700 GAGAGATGAGAGGGATGAT
1 GAGAGATGAGAGAGAGGAT
27892719 GAGA
1 GAGA
27892723 TGAGGGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.48, T:0.14
Consensus pattern (19 bp):
GAGAGATGAGAGAGAGGAT
Found at i:27892712 original size:15 final size:16
Alignment explanation
Indices: 27892687--27892739 Score: 69
Period size: 15 Copynumber: 3.5 Consensus size: 16
27892677 CTAAGAGAGT
27892687 TGAGA-GAGAGGATGA
1 TGAGATGAGAGGATGA
27892702 -GAGATGAGAGGGATGA
1 TGAGATGAGA-GGATGA
27892718 TGAGATGAG-GGATGA
1 TGAGATGAGAGGATGA
27892733 TG-GATGA
1 TGAGATGA
27892740 TGGATAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.26
15 12 0.34
16 6 0.17
17 8 0.23
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.17
Consensus pattern (16 bp):
TGAGATGAGAGGATGA
Found at i:27894390 original size:50 final size:50
Alignment explanation
Indices: 27894327--27894430 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 50
27894317 TTATGATATC
* * * *
27894327 GTGCGTTTCAAATTATGTGTTAAGTGTCTTGTTCCCAATCGTGAGTCTAT
1 GTGCGTTTAAAATTATGTGTTAAGTGCCGTGTTCCCAATCGTGAGTCTAA
* *
27894377 GTGCGTTTAAAATTATGTGTTAAGTGCCGTGTTCTCAATTGTGAGTCTAA
1 GTGCGTTTAAAATTATGTGTTAAGTGCCGTGTTCCCAATCGTGAGTCTAA
27894427 GTGC
1 GTGC
27894431 TATCATTAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (50 bp):
GTGCGTTTAAAATTATGTGTTAAGTGCCGTGTTCCCAATCGTGAGTCTAA
Found at i:27897141 original size:8 final size:8
Alignment explanation
Indices: 27897130--27897157 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
27897120 TTTTATCATT
27897130 TTTTACCA
1 TTTTACCA
27897138 TTTTACCA
1 TTTTACCA
27897146 TTTTACCA
1 TTTTACCA
27897154 TTTT
1 TTTT
27897158 GCCCTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTACCA
Found at i:27899349 original size:25 final size:24
Alignment explanation
Indices: 27899300--27899352 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
27899290 GTCATTAGGG
* *
27899300 TTACTGATTTCAACTCTTATGAGC
1 TTACTGATCTCAACTCGTATGAGC
*
27899324 TTACTGATACTCAGCTCGTATGAGC
1 TTACTGAT-CTCAACTCGTATGAGC
27899349 TTAC
1 TTAC
27899353 CGTTATTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (24 bp):
TTACTGATCTCAACTCGTATGAGC
Found at i:27899362 original size:25 final size:25
Alignment explanation
Indices: 27899308--27899397 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
27899298 GGTTACTGAT
* * * *
27899308 TTCAACTCTTATGAGCTTACTGATA
1 TTCAGCTCGTATGAGCTTACCGTTA
*
27899333 CTCAGCTCGTATGAGCTTACCGTTA
1 TTCAGCTCGTATGAGCTTACCGTTA
* *
27899358 TTCAGCTCAG-AGGAGCTTACCATTA
1 TTCAGCTC-GTATGAGCTTACCGTTA
* *
27899383 -ACAGCTCGAATGAGC
1 TTCAGCTCGTATGAGC
27899398 ATACATGTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.02
24 11 0.21
25 40 0.75
26 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (25 bp):
TTCAGCTCGTATGAGCTTACCGTTA
Found at i:27910645 original size:17 final size:17
Alignment explanation
Indices: 27910623--27910681 Score: 102
Period size: 16 Copynumber: 3.5 Consensus size: 17
27910613 TAGCTTCTTC
27910623 TTTTTTCACGAAAATTTT
1 TTTTTTCACG-AAATTTT
27910641 TTTTTTCACG-AATTTT
1 TTTTTTCACGAAATTTT
27910657 TTTTTTCACGAAATTTT
1 TTTTTTCACGAAATTTT
27910674 TTTTTTCA
1 TTTTTTCA
27910682 ACTTGATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 16 0.40
17 14 0.35
18 10 0.25
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTTTCACGAAATTTT
Found at i:27913623 original size:16 final size:14
Alignment explanation
Indices: 27913594--27913634 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
27913584 AACTAGCTTC
27913594 TTTTTTTCACAATT
1 TTTTTTTCACAATT
*
27913608 TTTTTTTCACGAAAT
1 TTTTTTTCAC-AATT
27913623 TTTTTTTCACAA
1 TTTTTTTCACAA
27913635 CTTGTTATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:27915221 original size:13 final size:13
Alignment explanation
Indices: 27915203--27915228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27915193 CGTGTATGAC
27915203 ACATGGCCATGTG
1 ACATGGCCATGTG
27915216 ACATGGCCATGTG
1 ACATGGCCATGTG
27915229 TCCCACGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
ACATGGCCATGTG
Found at i:27918669 original size:22 final size:22
Alignment explanation
Indices: 27918641--27918706 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
27918631 AAGGTGGAAG
*
27918641 TTATGTGGTAGCTTATCTG-TGA
1 TTATGTGGTAGCTTATC-GATAA
*
27918663 TTATGTGGTCG-TTATCGATAA
1 TTATGTGGTAGCTTATCGATAA
* * *
27918684 TTATGTGGTGGCTTGTCCATAA
1 TTATGTGGTAGCTTATCGATAA
27918706 T
1 T
27918707 GTGTTATCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 17 0.46
22 19 0.51
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.44
Consensus pattern (22 bp):
TTATGTGGTAGCTTATCGATAA
Found at i:27918738 original size:48 final size:48
Alignment explanation
Indices: 27918658--27918750 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
27918648 GTAGCTTATC
* * *
27918658 TGTGATTATGTGGTCGTTATCGATAATTATGTGGTGGCTTGTCCATAA
1 TGTGATTATCTGGTCGTTATCGACAATTATGTGCTGGCTTGTCCATAA
* *
27918706 TGTG-TTATCTGGTCGTTTATCGGCATTTATGTGCTGGCTTGTCCA
1 TGTGATTATCTGGTCG-TTATCGACAATTATGTGCTGGCTTGTCCA
27918751 CATATGGTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 10 0.26
48 29 0.74
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43
Consensus pattern (48 bp):
TGTGATTATCTGGTCGTTATCGACAATTATGTGCTGGCTTGTCCATAA
Found at i:27920657 original size:23 final size:23
Alignment explanation
Indices: 27920630--27920722 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 23
27920620 CAAAAGAGGT
27920630 TAATCAAAATACACCA-AACAGGC
1 TAATCAAAATACACCACAA-AGGC
* * *
27920653 TAATCAGAGTACAGCACAAAGGC
1 TAATCAAAATACACCACAAAGGC
* *** *
27920676 TAATCAGAATGTGCCACAAAGTC
1 TAATCAAAATACACCACAAAGGC
*
27920699 TAATCAAAATACGCCACAAAGGC
1 TAATCAAAATACACCACAAAGGC
27920722 T
1 T
27920723 CTATTTCGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 54 0.96
24 2 0.04
ACGTcount: A:0.45, C:0.24, G:0.15, T:0.16
Consensus pattern (23 bp):
TAATCAAAATACACCACAAAGGC
Found at i:27923041 original size:20 final size:21
Alignment explanation
Indices: 27923006--27923044 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27922996 CAGCTCGTTG
27923006 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
27923027 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
27923045 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:27923448 original size:13 final size:13
Alignment explanation
Indices: 27923430--27923455 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27923420 TGTGTCCTAA
27923430 TATGAATTAAATT
1 TATGAATTAAATT
27923443 TATGAATTAAATT
1 TATGAATTAAATT
27923456 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:27925258 original size:39 final size:39
Alignment explanation
Indices: 27925215--27925552 Score: 430
Period size: 39 Copynumber: 8.6 Consensus size: 39
27925205 TCTATAAACA
* * * *
27925215 TGATTATGTGTGTATTGTGACATATGCTTGAATTTTATG
1 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
*
27925254 TGATTATATGAGTATTATGATATATGCTTGAATGTTAT-
1 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
27925292 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
1 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
* *
27925331 AGATTATATGAGTATTGTGATATATGCTTGAATGTTAAG
1 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
* *
27925370 TGATTATATGTGTATTGGTGATATATGCCT-ACATGTTATG
1 TGATTATATGAGTATT-GTGATATATGCTTGA-ATGTTATG
*
27925410 TTATTATATGAGTATTGTGATATATGCTTGAATGTTATG
1 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
* * *
27925449 TGATTATATGTGTATTAGTGATATATGCCTAAATGTTATG
1 TGATTATATGAGTATT-GTGATATATGCTTGAATGTTATG
* * * *
27925489 TGATTCTATGTA-TATTGTGATATATGCTTAAATGTTCTA
1 TGATTATATG-AGTATTGTGATATATGCTTGAATGTTATG
* * * *
27925528 CGATTATATGTGTAATGCGATATAT
1 TGATTATATGAGTATTGTGATATAT
27925553 ACTTAAAAGT
Statistics
Matches: 263, Mismatches: 29, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
38 37 0.14
39 158 0.60
40 68 0.26
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (39 bp):
TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
Found at i:27925423 original size:79 final size:78
Alignment explanation
Indices: 27925215--27925552 Score: 441
Period size: 79 Copynumber: 4.3 Consensus size: 78
27925205 TCTATAAACA
* * * * *
27925215 TGATTATGTGTGTATTGTGACATATGCTTGAATTTTATGTGATTATATGAGTATTATGATATATG
1 TGATTATATGTGTATTGTGATATATGCCTGAATGTTATGTGATTATATGAGTATTGTGATATATG
*
27925280 CTTGAATGTT-AT
66 CTTGAATGTTAAG
* * *
27925292 TGATTATATGAGTATTGTGATATATGCTTGAATGTTATGAGATTATATGAGTATTGTGATATATG
1 TGATTATATGTGTATTGTGATATATGCCTGAATGTTATGTGATTATATGAGTATTGTGATATATG
27925357 CTTGAATGTTAAG
66 CTTGAATGTTAAG
*
27925370 TGATTATATGTGTATTGGTGATATATGCCT-ACATGTTATGTTATTATATGAGTATTGTGATATA
1 TGATTATATGTGTATT-GTGATATATGCCTGA-ATGTTATGTGATTATATGAGTATTGTGATATA
*
27925434 TGCTTGAATGTTATG
64 TGCTTGAATGTTAAG
* *
27925449 TGATTATATGTGTATTAGTGATATATGCCTAAATGTTATGTGATTCTATGTA-TATTGTGATATA
1 TGATTATATGTGTATT-GTGATATATGCCTGAATGTTATGTGATTATATG-AGTATTGTGATATA
* *
27925513 TGCTTAAATGTTCTA-
64 TGCTTGAATGTT-AAG
* * *
27925528 CGATTATATGTGTAATGCGATATAT
1 TGATTATATGTGTATTGTGATATAT
27925553 ACTTAAAAGT
Statistics
Matches: 234, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
77 69 0.29
78 25 0.11
79 138 0.59
80 2 0.01
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (78 bp):
TGATTATATGTGTATTGTGATATATGCCTGAATGTTATGTGATTATATGAGTATTGTGATATATG
CTTGAATGTTAAG
Found at i:27925534 original size:118 final size:116
Alignment explanation
Indices: 27925215--27925552 Score: 444
Period size: 118 Copynumber: 2.9 Consensus size: 116
27925205 TCTATAAACA
* * * *
27925215 TGATTATGTGTGTATTGTGACATATGCTTGAATTTTATGTGATTATATG-AGTATTATGATATAT
1 TGATTATATGTGTATTGTGATATATGCTTGAATGTTATGTGATTATATGTA-TATTGTGATATAT
*
27925279 GCTTGAATGTTATTGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
65 GCTTAAATGTTATTGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
* * * *
27925331 AGATTATATGAGTATTGTGATATATGCTTGAATGTTAAGTGATTATATGTGTATTGGTGATATAT
1 TGATTATATGTGTATTGTGATATATGCTTGAATGTTATGTGATTATATGTATATT-GTGATATAT
* * *
27925396 GCCTACATGTTATGTTATTATATGAGTATTGTGATATATGCTTGAATGTTATG
65 GCTTAAATGTTAT-TGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
* * *
27925449 TGATTATATGTGTATTAGTGATATATGCCTAAATGTTATGTGATTCTATGTATATTGTGATATAT
1 TGATTATATGTGTATT-GTGATATATGCTTGAATGTTATGTGATTATATGTATATTGTGATATAT
* * * * *
27925514 GCTTAAATGTTCTACGATTATATGTGTAATGCGATATAT
65 GCTTAAATGTTAT-TGATTATATGAGTATTGTGATATAT
27925553 ACTTAAAAGT
Statistics
Matches: 190, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
116 47 0.25
117 18 0.09
118 91 0.48
119 34 0.18
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (116 bp):
TGATTATATGTGTATTGTGATATATGCTTGAATGTTATGTGATTATATGTATATTGTGATATATG
CTTAAATGTTATTGATTATATGAGTATTGTGATATATGCTTGAATGTTATG
Found at i:27928990 original size:49 final size:49
Alignment explanation
Indices: 27928871--27929054 Score: 233
Period size: 49 Copynumber: 3.7 Consensus size: 49
27928861 CAAAACTCCA
* * *
27928871 TTTGTGGACAAGCCACCACTGATTTGCAGAGAAACTACCACTGATAACAC
1 TTTGTGGACAAGCCACCACTGATATGCAGATATACTACCACTGA-AACAC
* * *
27928921 TTTGTGGACAAGCCACCACTGATATGCAAATATACTGCCACTGAAGCAC
1 TTTGTGGACAAGCCACCACTGATATGCAGATATACTACCACTGAAACAC
** *
27928970 TTTAAGGACAAGCCACCACTGATATGCAGATCTACTACCACTGAAACAC
1 TTTGTGGACAAGCCACCACTGATATGCAGATATACTACCACTGAAACAC
** * * *
27929019 TTTGTGGGTAAGCCAGCACTGATATGTAGATCTACT
1 TTTGTGGACAAGCCACCACTGATATGCAGATATACT
27929055 GCCCACTTAC
Statistics
Matches: 116, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 77 0.66
50 39 0.34
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (49 bp):
TTTGTGGACAAGCCACCACTGATATGCAGATATACTACCACTGAAACAC
Found at i:27934632 original size:50 final size:50
Alignment explanation
Indices: 27934564--27934749 Score: 173
Period size: 50 Copynumber: 3.7 Consensus size: 50
27934554 TTATGAGAGG
* * *
27934564 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * *
27934614 TCCCCCGTATA-ACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTA-AGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * * * * * *
27934664 TCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTACAGGA-AATA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAA-C
* * *
27934713 TCCCATGTAAGACCATGTCTGGGAAATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
27934750 TGTTATTATA
Statistics
Matches: 113, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
48 3 0.03
49 38 0.34
50 71 0.63
51 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
Found at i:27942958 original size:6 final size:6
Alignment explanation
Indices: 27942947--27942973 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27942937 GTCAAAACCA
27942947 TTCCTT TTCCTT TTCCTT TTCCTT TTC
1 TTCCTT TTCCTT TTCCTT TTCCTT TTC
27942974 GTAGATGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCCTT
Found at i:27948438 original size:19 final size:18
Alignment explanation
Indices: 27948403--27948439 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
27948393 TGATATATAT
27948403 GTTAAATTAAATAAAAAG
1 GTTAAATTAAATAAAAAG
27948421 GTTAATATTATAATAAAAA
1 GTTAA-ATTA-AATAAAAA
27948440 CAAAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
GTTAAATTAAATAAAAAG
Found at i:27952673 original size:20 final size:22
Alignment explanation
Indices: 27952635--27952674 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
27952625 AATACAAGTA
27952635 TTTTCATTATGTTTGAGTTAAG
1 TTTTCATTATGTTTGAGTTAAG
*
27952657 TTTTC-TTA-GTTTTAGTTA
1 TTTTCATTATGTTTGAGTTA
27952675 TATTCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.20, C:0.05, G:0.15, T:0.60
Consensus pattern (22 bp):
TTTTCATTATGTTTGAGTTAAG
Found at i:27956326 original size:33 final size:33
Alignment explanation
Indices: 27956284--27956557 Score: 188
Period size: 33 Copynumber: 7.5 Consensus size: 33
27956274 ATCAGTGGAT
*
27956284 TCAGCACTTAGCAACCACCAATGAGTCGGAGAA
1 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
* * *
27956317 TCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGA
1 TCAGCACTTAGCAACCAC---CA-A--TGAG-T-CGG-GGAA
*
27956359 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
* *
27956392 TCAGCACTTAGCAATCCCCTTCACATTTAAGATACGGTGGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-GGAA
* *
27956434 TCAACACTTAGCAACCACCAATGACTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
* *
27956467 TCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAA
1 TCAGCACTTAGCAACCAC---CA-A--TGAG-T-CGG-GGAA
* *
27956509 TCAGAACTTAGCAACCACCAATGAATCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
27956542 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
27956558 CCCTTTATAT
Statistics
Matches: 190, Mismatches: 24, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
33 73 0.38
34 12 0.06
35 3 0.02
36 12 0.06
37 3 0.02
38 3 0.02
39 13 0.07
40 3 0.02
41 12 0.06
42 56 0.29
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
Found at i:27956415 original size:75 final size:75
Alignment explanation
Indices: 27956278--27956559 Score: 476
Period size: 75 Copynumber: 3.8 Consensus size: 75
27956268 TCCATTATCA
* * *
27956278 GTGGATTCAGCACTTAGCAACCACCAATGAGTCGGAGAATCAGCACTTAGCAACCCCTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
27956343 TTAAGATACG
66 TTAAGATACG
* *
27956353 GTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAATCCCC-TTCACA
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCTTTCACA
27956417 TTTAAGATACG
65 TTTAAGATACG
* *
27956428 GTGGAATCAACACTTAGCAACCACCAATGACTCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
27956493 TTAAGATACG
66 TTAAGATACG
*
27956503 GTGGAATCAGAACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
27956560 CTTTATATTC
Statistics
Matches: 195, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
74 4 0.02
75 187 0.96
76 4 0.02
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (75 bp):
GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
TTAAGATACG
Found at i:27956447 original size:42 final size:41
Alignment explanation
Indices: 27956388--27956524 Score: 141
Period size: 42 Copynumber: 3.5 Consensus size: 41
27956378 AATGATTCGG
*
27956388 GGAATCAGCACTTAGCAATCCCCTTCACATTTAAGATACGGT
1 GGAATCAACACTTAGCAA-CCCCTTCACATTTAAGATACGGT
*
27956430 GGAATCAACACTTAGCAACCAC--CA-A--T--GACT-CGG-
1 GGAATCAACACTTAGCAACCCCTTCACATTTAAGA-TACGGT
*
27956463 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAACACTTAGCAACCCC-TTCACATTTAAGATACGGT
27956505 GGAATCAGA-ACTTAGCAACC
1 GGAATCA-ACACTTAGCAACC
27956525 ACCAATGAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
33 20 0.26
34 5 0.06
35 1 0.01
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
40 1 0.01
41 8 0.10
42 35 0.45
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (41 bp):
GGAATCAACACTTAGCAACCCCTTCACATTTAAGATACGGT
Found at i:27957696 original size:3 final size:3
Alignment explanation
Indices: 27957688--27957713 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27957678 TCATAAAAAT
27957688 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
27957714 GTTTTCCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:27963794 original size:27 final size:27
Alignment explanation
Indices: 27963758--27963809 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
27963748 CCAATGAGTC
*
27963758 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGAACTTAGCAACCCCTCG
27963785 GGGGAATCAGAACTTAGCAACCCCT
1 GGGGAATCAGAACTTAGCAACCCCT
27963810 TTCACATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (27 bp):
GGGGAATCAGAACTTAGCAACCCCTCG
Found at i:27963846 original size:42 final size:42
Alignment explanation
Indices: 27963787--27963923 Score: 184
Period size: 42 Copynumber: 3.5 Consensus size: 42
27963777 ACCCCTCGGG
*
27963787 GGAATCAGAACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
* *
27963829 GGAATCAGCACTTAGCAACCAC---CA-A--TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
27963862 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
27963904 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
27963924 ACAATGAATC
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 21 0.26
34 3 0.04
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 3 0.04
42 40 0.49
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
Found at i:27963961 original size:75 final size:75
Alignment explanation
Indices: 27963786--27963957 Score: 310
Period size: 75 Copynumber: 2.3 Consensus size: 75
27963776 AACCCCTCGG
*
27963786 GGGAATCAGAACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCAC
* *
27963851 CAATGAGTCG
66 CAATGAATCA
27963861 GGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA-
1 GGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCAC
27963925 CAATGAATCA
66 CAATGAATCA
27963935 GGGAATCAGCACTTAGCAACCCC
1 GGGAATCAGCACTTAGCAACCCC
27963958 CTTTATATTC
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 31 0.33
75 63 0.67
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (75 bp):
GGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCAC
CAATGAATCA
Found at i:27964120 original size:21 final size:21
Alignment explanation
Indices: 27964080--27964120 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27964070 TATTCTATGT
*
27964080 TCAAATAAATCTAAACATATA
1 TCAAATAAATCTAAAAATATA
27964101 TCAAATAATATC-AAAAATAT
1 TCAAATAA-ATCTAAAAATAT
27964121 GCATTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (21 bp):
TCAAATAAATCTAAAAATATA
Found at i:27965085 original size:3 final size:3
Alignment explanation
Indices: 27965077--27965102 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27965067 TCATAAAAAT
27965077 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
27965103 TCCCTCGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:27966373 original size:215 final size:215
Alignment explanation
Indices: 27966002--27966432 Score: 862
Period size: 215 Copynumber: 2.0 Consensus size: 215
27965992 ATTACATGTA
27966002 AGTTTCAAGTAAATCATGGCATATACATAATAAGCATTTAGGCTTTCTATCTCATCCATCCCATA
1 AGTTTCAAGTAAATCATGGCATATACATAATAAGCATTTAGGCTTTCTATCTCATCCATCCCATA
27966067 TATATATCCATTAAACACTCTTATCATTTAAATCCACATAGTTAGTAGAAGATAAATAAACATAA
66 TATATATCCATTAAACACTCTTATCATTTAAATCCACATAGTTAGTAGAAGATAAATAAACATAA
27966132 CATCTATGGAACATATCATATATTAGGAAATAAATTCCATGCATATTTCATCCATCACATAATAA
131 CATCTATGGAACATATCATATATTAGGAAATAAATTCCATGCATATTTCATCCATCACATAATAA
27966197 ATTCTCATCATTTTCATTTC
196 ATTCTCATCATTTTCATTTC
27966217 AGTTTCAAGTAAATCATGGCATATACATAATAAGCATTTAGGCTTTCTATCTCATCCATCCCATA
1 AGTTTCAAGTAAATCATGGCATATACATAATAAGCATTTAGGCTTTCTATCTCATCCATCCCATA
27966282 TATATATCCATTAAACACTCTTATCATTTAAATCCACATAGTTAGTAGAAGATAAATAAACATAA
66 TATATATCCATTAAACACTCTTATCATTTAAATCCACATAGTTAGTAGAAGATAAATAAACATAA
27966347 CATCTATGGAACATATCATATATTAGGAAATAAATTCCATGCATATTTCATCCATCACATAATAA
131 CATCTATGGAACATATCATATATTAGGAAATAAATTCCATGCATATTTCATCCATCACATAATAA
27966412 ATTCTCATCATTTTCATTTC
196 ATTCTCATCATTTTCATTTC
27966432 A
1 A
27966433 TATATGCATA
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 216 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (215 bp):
AGTTTCAAGTAAATCATGGCATATACATAATAAGCATTTAGGCTTTCTATCTCATCCATCCCATA
TATATATCCATTAAACACTCTTATCATTTAAATCCACATAGTTAGTAGAAGATAAATAAACATAA
CATCTATGGAACATATCATATATTAGGAAATAAATTCCATGCATATTTCATCCATCACATAATAA
ATTCTCATCATTTTCATTTC
Found at i:27970534 original size:23 final size:23
Alignment explanation
Indices: 27970505--27970554 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
27970495 TACAGTAGTA
*
27970505 CAGATAAACTGCTAATAAATATG
1 CAGATAAACTGCCAATAAATATG
27970528 CAGATAAACTGCCAATAAATATG
1 CAGATAAACTGCCAATAAATATG
27970551 CAGA
1 CAGA
27970555 CAAGCAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (23 bp):
CAGATAAACTGCCAATAAATATG
Found at i:27970566 original size:23 final size:23
Alignment explanation
Indices: 27970518--27970566 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27970508 ATAAACTGCT
* *
27970518 AATAAATATGCAGATAAACTGCC
1 AATAAATATGCAGACAAACAGCC
* *
27970541 AATAAATATGCAGACAAGCAGTC
1 AATAAATATGCAGACAAACAGCC
27970564 AAT
1 AAT
27970567 TTCGTGGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (23 bp):
AATAAATATGCAGACAAACAGCC
Found at i:27973378 original size:25 final size:24
Alignment explanation
Indices: 27973321--27973393 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
27973311 CTTCATTCAA
* *
27973321 ACGTCCCATAAAGGACTTTC--AT
1 ACGTCCCATAAAGGGCTCTCATAT
* *
27973343 ACATCCGATAAAGGGGCTCTCATAT
1 ACGTCCCATAAA-GGGCTCTCATAT
*
27973368 ACGTCCCATAAAGGGCACTCATAT
1 ACGTCCCATAAAGGGCTCTCATAT
27973392 AC
1 AC
27973394 TGGCACCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 10 0.24
23 6 0.15
24 13 0.32
25 12 0.29
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.23
Consensus pattern (24 bp):
ACGTCCCATAAAGGGCTCTCATAT
Found at i:27985633 original size:19 final size:20
Alignment explanation
Indices: 27985586--27985646 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
27985576 GAAAATCATT
*
27985586 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
* *
27985606 TTGAAATCATTTTGACTTG-
1 TTAAAATCATTTTAACTTGA
**
27985625 TTAAAATCATTTGCACTTGA
1 TTAAAATCATTTTAACTTGA
27985645 TT
1 TT
27985647 TTAAAATTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:27988728 original size:22 final size:22
Alignment explanation
Indices: 27988703--27988763 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
27988693 TGATAATGAA
**
27988703 ATTTTAATATAATTGTA-AAAAT
1 ATTTTAAT-TAATCATATAAAAT
*
27988725 ATTTTAATTAATCATATTAAAT
1 ATTTTAATTAATCATATAAAAT
27988747 ATTTTAATTAATCATAT
1 ATTTTAATTAATCATAT
27988764 TTTAAAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 6 0.17
22 29 0.83
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTTAATTAATCATATAAAAT
Found at i:27988764 original size:22 final size:22
Alignment explanation
Indices: 27988721--27988764 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27988711 ATAATTGTAA
27988721 AAATATTTTAATTAATCATATT
1 AAATATTTTAATTAATCATATT
27988743 AAATATTTTAATTAATCATATT
1 AAATATTTTAATTAATCATATT
27988765 TTAAAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTTTAATTAATCATATT
Found at i:27990490 original size:4 final size:4
Alignment explanation
Indices: 27990481--27990572 Score: 184
Period size: 4 Copynumber: 23.0 Consensus size: 4
27990471 GGATCCCTTA
27990481 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
27990529 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
27990573 CATGCATGTC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 88 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:27997403 original size:36 final size:36
Alignment explanation
Indices: 27997363--27997436 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
27997353 ATAGAGTTAA
27997363 TATGAAAATATAATAAAGTTCGATTAAGAAATTGGT
1 TATGAAAATATAATAAAGTTCGATTAAGAAATTGGT
*
27997399 TATGAGAATATAATAAAGTTCGATTAAGAAATTGGT
1 TATGAAAATATAATAAAGTTCGATTAAGAAATTGGT
27997435 TA
1 TA
27997437 ATTAAAGTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.34
Consensus pattern (36 bp):
TATGAAAATATAATAAAGTTCGATTAAGAAATTGGT
Found at i:28001666 original size:21 final size:20
Alignment explanation
Indices: 28001622--28001671 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
28001612 AAAAGAATCG
*
28001622 GAAAAGAAAAAAATAAGTAA
1 GAAAAGAAAAAAATAAGAAA
28001642 -AAAAGAAGAAACAATAA-AAA
1 GAAAAGAA-AAA-AATAAGAAA
28001662 GAAAAGAAAA
1 GAAAAGAAAA
28001672 GAAAGAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.27
20 7 0.27
21 12 0.46
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (20 bp):
GAAAAGAAAAAAATAAGAAA
Found at i:28001668 original size:18 final size:19
Alignment explanation
Indices: 28001623--28001670 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
28001613 AAAGAATCGG
*
28001623 AAAAGAAAA-AAATAAGTA
1 AAAAGAAAAGAAACAAGTA
*
28001641 AAAA-AGAAGAAACAA-TA
1 AAAAGAAAAGAAACAAGTA
28001658 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
28001671 AGAAAGAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAGAAACAAGTA
Found at i:28002881 original size:28 final size:29
Alignment explanation
Indices: 28002845--28002920 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
28002835 CGGTGATTAT
28002845 AATTTCAGGTACTATGTACCGATG-TTAC
1 AATTTCAGGTACTATGTACCGATGTTTAC
* * * * * *
28002873 AATTCCAGGCACTCTGTGCCGGTGTTTAT
1 AATTTCAGGTACTATGTACCGATGTTTAC
*
28002902 AGTTTCAGGTACTATGTAC
1 AATTTCAGGTACTATGTAC
28002921 TGGTGGTGGA
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (29 bp):
AATTTCAGGTACTATGTACCGATGTTTAC
Found at i:28002925 original size:29 final size:28
Alignment explanation
Indices: 28002834--28002925 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 28
28002824 ACACTAGTTG
28002834 CCGGTGATTATAATTTCAGGTACTATGTA
1 CCGGTG-TTATAATTTCAGGTACTATGTA
* * * * * *
28002863 CCGATGTTACAATTCCAGGCACTCTGTG
1 CCGGTGTTATAATTTCAGGTACTATGTA
*
28002891 CCGGTGTTTATAGTTTCAGGTACTATGTA
1 CCGGTG-TTATAATTTCAGGTACTATGTA
*
28002920 CTGGTG
1 CCGGTG
28002926 GTGGATGCCA
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
28 22 0.46
29 26 0.54
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (28 bp):
CCGGTGTTATAATTTCAGGTACTATGTA
Found at i:28006157 original size:27 final size:27
Alignment explanation
Indices: 28006073--28006157 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
28006063 AGTTTCAATG
* * * * *
28006073 GACTATCCCATGTTTATTGTCCCAACA
1 GACTACCCCGTGTTTACTGTCCCGATA
** ** * *
28006100 GACTACGTCGTGTTTACTGTCTTGGTG
1 GACTACCCCGTGTTTACTGTCCCGATA
28006127 GACTACCCCGTGTTTACTGTCCCGATA
1 GACTACCCCGTGTTTACTGTCCCGATA
28006154 GACT
1 GACT
28006158 TTATTGGTCT
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (27 bp):
GACTACCCCGTGTTTACTGTCCCGATA
Found at i:28008079 original size:30 final size:30
Alignment explanation
Indices: 28008045--28008106 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28008035 CTTAACAAGA
28008045 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
28008075 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
28008105 AA
1 AA
28008107 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:28009812 original size:20 final size:20
Alignment explanation
Indices: 28009789--28009830 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28009779 TACAAACTAG
28009789 TTAAACCAACTAAAAACCGA
1 TTAAACCAACTAAAAACCGA
*
28009809 TTAAACCGACTAAAAACCGA
1 TTAAACCAACTAAAAACCGA
28009829 TT
1 TT
28009831 GAATTGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (20 bp):
TTAAACCAACTAAAAACCGA
Found at i:28010346 original size:24 final size:25
Alignment explanation
Indices: 28010319--28010388 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
28010309 ATTTTAAAAT
*
28010319 TTTAAAATATAATAATA-AATGATA
1 TTTAAAATATAATAATATAATAATA
*
28010343 TTT-AAATA-ATTTAATATAATAATA
1 TTTAAAATATA-ATAATATAATAATA
* *
28010367 TCTAAAATATCAATAATCTAAT
1 TTTAAAATAT-AATAATATAAT
28010389 TTTTATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 1 0.03
23 10 0.28
24 11 0.31
25 5 0.14
26 8 0.22
27 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (25 bp):
TTTAAAATATAATAATATAATAATA
Found at i:28012702 original size:41 final size:41
Alignment explanation
Indices: 28012652--28012732 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
28012642 ATATTTTATT
*
28012652 TTATGTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
*
28012693 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTC
28012733 TCAATTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
Found at i:28016558 original size:41 final size:41
Alignment explanation
Indices: 28016511--28016593 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
28016501 ATATTTTATT
*
28016511 TTATCTTTTAGTAGTTTACTAAAAAAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTACTAAAAAAAGGAAATTATTTTCC
* ** *
28016552 TTATCTTTTAGTAGTTTATTTGAATAAGGAAATTATTTTCC
1 TTATCTTTTAGTAGTTTACTAAAAAAAGGAAATTATTTTCC
28016593 T
1 T
28016594 AATTAGGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTACTAAAAAAAGGAAATTATTTTCC
Found at i:28032156 original size:33 final size:33
Alignment explanation
Indices: 28032114--28032179 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28032104 AGGAGTTTGT
28032114 TTTCCTATTGGAATAGACTTCTACAATTTAACG
1 TTTCCTATTGGAATAGACTTCTACAATTTAACG
28032147 TTTCCTATTGGAATAGACTTCTACAATTTAACG
1 TTTCCTATTGGAATAGACTTCTACAATTTAACG
28032180 AGGGTTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (33 bp):
TTTCCTATTGGAATAGACTTCTACAATTTAACG
Found at i:28034930 original size:40 final size:40
Alignment explanation
Indices: 28034884--28034964 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
28034874 TGGTCAAATA
28034884 TCAATTTAGGTAGTTAGTAAAAATATAAATTAAATAAGGG
1 TCAATTTAGGTAGTTAGTAAAAATATAAATTAAATAAGGG
28034924 TCAATTTAGGTAGTTAGTAAAAATATAAATTAAATAAGGG
1 TCAATTTAGGTAGTTAGTAAAAATATAAATTAAATAAGGG
28034964 T
1 T
28034965 GCATTTGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.17, T:0.33
Consensus pattern (40 bp):
TCAATTTAGGTAGTTAGTAAAAATATAAATTAAATAAGGG
Found at i:28035373 original size:20 final size:20
Alignment explanation
Indices: 28035348--28035388 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28035338 TTACTATTAC
28035348 AATTTT-ATTTTAACAATAAT
1 AATTTTAATTTTAA-AATAAT
*
28035368 AATTTTAATTTTTAAATAAT
1 AATTTTAATTTTAAAATAAT
28035388 A
1 A
28035389 TTCTTAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTTAATTTTAAAATAAT
Found at i:28035501 original size:23 final size:23
Alignment explanation
Indices: 28035474--28035522 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28035464 ATAAGAAATG
28035474 TTTT-ATGATATAAAATATGAATA
1 TTTTAATGATAT-AAATATGAATA
* *
28035497 TTTTAATTATATAAATATGAGTA
1 TTTTAATGATATAAATATGAATA
28035520 TTT
1 TTT
28035523 GTTTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
TTTTAATGATATAAATATGAATA
Found at i:28037021 original size:9 final size:10
Alignment explanation
Indices: 28036976--28037022 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
28036966 TAACATGTTA
*
28036976 AATTTTAATT
1 AATTTTGATT
*
28036986 AATTTTACATT
1 AATTTT-GATT
28036997 AAATTTTGATT
1 -AATTTTGATT
28037008 AATTTTGA-T
1 AATTTTGATT
28037017 AATTTT
1 AATTTT
28037023 CGACAGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 7 0.21
10 14 0.42
11 6 0.18
12 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (10 bp):
AATTTTGATT
Found at i:28039631 original size:50 final size:51
Alignment explanation
Indices: 28039558--28039682 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 51
28039548 ACATATGAAT
* *
28039558 AGAGTTTGCCTTAGGTCGCAAGACTGGTTT-GTTAAATAGAA-ACAATAGAC
1 AGAGTCTGCCTTAGGTCGCAAGACTGGTTTGGTTAAATAGAAGACAAGA-AC
* * *
28039608 AGGGTCTGCCTTAGGTCGTAAGACTGGTTTGGTTAAATAGAAGACACGAAC
1 AGAGTCTGCCTTAGGTCGCAAGACTGGTTTGGTTAAATAGAAGACAAGAAC
* *
28039659 AGAGTCTACCTTAGGTCACAAGAC
1 AGAGTCTGCCTTAGGTCGCAAGAC
28039683 CGATTCGGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 27 0.42
51 33 0.52
52 4 0.06
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (51 bp):
AGAGTCTGCCTTAGGTCGCAAGACTGGTTTGGTTAAATAGAAGACAAGAAC
Found at i:28040591 original size:26 final size:26
Alignment explanation
Indices: 28040528--28040596 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
28040518 GACTATATCA
* **
28040528 TTGACTAGCGAACCC-AGTTTGCAAC
1 TTGACTGGCGAACCCTAGTTCACAAC
*
28040553 TTGACTGGTGAACCCTAGTTCACAAC
1 TTGACTGGCGAACCCTAGTTCACAAC
*
28040579 TT-ACTTGGCGAACACTAG
1 TTGAC-TGGCGAACCCTAG
28040597 CTTCCCAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (26 bp):
TTGACTGGCGAACCCTAGTTCACAAC
Found at i:28042304 original size:22 final size:24
Alignment explanation
Indices: 28042270--28042313 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
28042260 TGTTTTGGTA
28042270 AAAAACTCGTTTATTAA-GTTTGG
1 AAAAACTCGTTTATTAATGTTTGG
28042293 AAAAACTC-TTTATTAATGTTT
1 AAAAACTCGTTTATTAATGTTT
28042314 AACAGAACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (24 bp):
AAAAACTCGTTTATTAATGTTTGG
Found at i:28042598 original size:32 final size:32
Alignment explanation
Indices: 28042558--28042621 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28042548 CATTAAGTTA
28042558 AAATAAAAGCAAATATAAGCAACAGTAGTTGT
1 AAATAAAAGCAAATATAAGCAACAGTAGTTGT
28042590 AAATAAAAGCAAATATAAGCAACAGTAGTTGT
1 AAATAAAAGCAAATATAAGCAACAGTAGTTGT
28042622 GTGGCCACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (32 bp):
AAATAAAAGCAAATATAAGCAACAGTAGTTGT
Found at i:28043262 original size:27 final size:27
Alignment explanation
Indices: 28043232--28043585 Score: 168
Period size: 27 Copynumber: 12.9 Consensus size: 27
28043222 TATAACAATT
28043232 ATTTTACCCTTCGGGGGTATTTCAGTC
1 ATTTTACCCTTCGGGGGTATTTCAGTC
* *
28043259 ATTTTACCCTAT-GAGGGTAGTTT-GGTC
1 ATTTTACCCT-TCGGGGGTA-TTTCAGTC
* ** *
28043286 ATTTT-GCCTTATAGGGGTAATTCAGTC
1 ATTTTACCCTT-CGGGGGTATTTCAGTC
* *
28043313 ATTTTAACCTAT-GGGAGTATTTC-GATC
1 ATTTTACCCT-TCGGGGGTATTTCAG-TC
* * * *
28043340 ATTCTACCCTACGGAGGTATTT-TGATC
1 ATTTTACCCTTCGGGGGTATTTCAG-TC
** * *
28043367 ATTTTACCCTTCAAGGGTTTTTCAATC
1 ATTTTACCCTTCGGGGGTATTTCAGTC
* ** *
28043394 CTTTTAGTCTTC-GGGGTATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCAGTC
* * ** * *
28043420 ATTTTAACCTTTGAAGGTATTT-TGATT
1 ATTTTACCCTTCGGGGGTATTTCAG-TC
* *
28043447 ATTTTACCCTTTGAGGGTATTTCAGTC
1 ATTTTACCCTTCGGGGGTATTTCAGTC
* * *
28043474 ATTTTACCCTTTGAGGGTATTTC-GATT
1 ATTTTACCCTTCGGGGGTATTTCAG-TC
* *
28043501 ATTTTACCCTTCGAGGGTAATTCGATATTTCGGTT
1 ATTTTACCCTTCG-GGG------G-TATTTCAGTC
*
28043536 ATTTTACCCTTCGGGGGTATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCAGTC
* * *
28043563 ATTTTACCTTTTGAGGGTATTTC
1 ATTTTACCCTTCGGGGGTATTTC
28043586 GAGAGCTCTT
Statistics
Matches: 253, Mismatches: 50, Indels: 48
0.72 0.14 0.14
Matches are distributed among these distances:
25 1 0.00
26 26 0.10
27 188 0.74
28 11 0.04
29 1 0.00
34 4 0.02
35 21 0.08
36 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCAGTC
Done.