Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 102 of 168
Found at i:30028695 original size:43 final size:44
Alignment explanation
Indices: 30028639--30028827 Score: 120
Period size: 44 Copynumber: 4.3 Consensus size: 44
30028629 TGAAATCTTT
*
30028639 AATCTATTCCACTGCTGCCCAGGGAGATAGAAT-TACTGGCTTC
1 AATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTC
* ** * * * ***
30028682 AATATACTCCACTGCAACCTCAGTGAGGTAAAATCTACCATCTTC
1 AATCTACTCCACTGCTGCC-CAGGGAGATAGAATCTACTGGCTTC
* * * ** *
30028727 GATCTGCTCCACTACTGCTTAGGGAGATA-AGATCTGTAAT--CTTC
1 AATCTACTCCACTGCTGCCCAGGGAGATAGA-ATC--TACTGGCTTC
* *
30028771 AATCTATTCCACTGTTGCCCAGGGA-AGTAGAAT-TACTGGCTTC
1 AATCTACTCCACTGCTGCCCAGGGAGA-TAGAATCTACTGGCTTC
*
30028814 AATGTACTCCACTG
1 AATCTACTCCACTG
30028828 TAACCACAGG
Statistics
Matches: 105, Mismatches: 32, Indels: 18
0.68 0.21 0.12
Matches are distributed among these distances:
41 3 0.03
43 33 0.31
44 47 0.45
45 20 0.19
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTC
Found at i:30028782 original size:44 final size:44
Alignment explanation
Indices: 30028596--30028783 Score: 103
Period size: 44 Copynumber: 4.3 Consensus size: 44
30028586 GCCATCTTTG
* * * * * *
30028596 ATCTGCTCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTTA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCA
* * * * *
30028640 ATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTAAT--CTTCA
* * ** * * * *** *
30028683 ATATACTCCACTGCAACCTCAGTGAGGTAAAATCTACCATCTTCG
1 ATCTACTCCACTAC-TGCTCAGGGAGATAAGATCTGTAATCTTCA
* *
30028728 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCA
*
30028772 ATCTATTCCACT
1 ATCTACTCCACT
30028784 GTTGCCCAGG
Statistics
Matches: 99, Mismatches: 39, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 19 0.19
44 58 0.59
45 17 0.17
46 1 0.01
47 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCA
Found at i:30030258 original size:8 final size:7
Alignment explanation
Indices: 30030214--30030255 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
30030204 TTAGCCTCTC
30030214 CATTTTT
1 CATTTTT
30030221 -ACTTTTT
1 CA-TTTTT
30030228 CATTTTT
1 CATTTTT
30030235 CA-TTTT
1 CATTTTT
30030241 CATCTTTT
1 CAT-TTTT
30030249 CATTTTT
1 CATTTTT
30030256 TCACATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:30031221 original size:20 final size:20
Alignment explanation
Indices: 30031196--30031236 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
30031186 GGTTTGGCAG
*
30031196 AAAAAATC-TGAAGGAATGAA
1 AAAAAATCGT-AAAGAATGAA
30031216 AAAAAATCGTAAAGAATGAA
1 AAAAAATCGTAAAGAATGAA
30031236 A
1 A
30031237 GAACATTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.05, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAAATCGTAAAGAATGAA
Found at i:30034116 original size:41 final size:40
Alignment explanation
Indices: 30034056--30034201 Score: 129
Period size: 41 Copynumber: 3.6 Consensus size: 40
30034046 TGATTCGATA
30034056 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTATAGTCCGAAAT-TAT
* * * *
30034097 CACCGGCATTAAGCATGCTAGACGTAAAGTCTG-AATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATT-A-T
* *
30034138 CACCGGCATTAAGCCTGCTAGGCAC-ATAG-CCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGAC-CTATAGTCC-GAAAT-TAT
**
30034179 CACCGGCATCCAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
30034202 AATAAGTCTG
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
39 1 0.01
40 5 0.06
41 72 0.85
42 6 0.07
43 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATTAT
Found at i:30034209 original size:82 final size:82
Alignment explanation
Indices: 30034056--30034211 Score: 185
Period size: 82 Copynumber: 1.9 Consensus size: 82
30034046 TGATTCGATA
* * *
30034056 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTAAGCATGCTAGACG
1 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCATGCTAGACA
30034121 TAAAGTCTGAATTAATT
66 TAAAGTCTGAATTAATT
* * * *
30034138 CACCGGCATTA-AGCCTGCTAGGCAC-ATAG-CCTGAATTATATCACCGGCATCCAGCCTGCTAG
1 CACCGGC-TTATAGCCTGCTAGAC-CTATAGTCC-GAAATATATCACCGGCATCAAGCATGCTAG
30034200 ACA-ATAAGTCTG
63 ACATA-AAGTCTG
30034212 GTTTACATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
81 3 0.05
82 56 0.89
83 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (82 bp):
CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCATGCTAGACA
TAAAGTCTGAATTAATT
Found at i:30038243 original size:34 final size:34
Alignment explanation
Indices: 30038166--30038249 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
30038156 AAATAAAATG
* *
30038166 AAAATATAAAAAATATGTATATGTATATACATTT
1 AAAATATAAAAAATATGAATATGTATATACATAT
* **
30038200 ACAGCATAAAAGAA-ATGAATATGTATATATC-TAT
1 AAAATATAAAA-AATATGAATATGTATATA-CATAT
*
30038234 AAAATATAAAATATAT
1 AAAATATAAAAAATAT
30038250 AAAAGCTAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
33 1 0.03
34 34 0.89
35 3 0.08
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (34 bp):
AAAATATAAAAAATATGAATATGTATATACATAT
Found at i:30038472 original size:2 final size:2
Alignment explanation
Indices: 30038467--30038492 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30038457 GTTATAAAAA
30038467 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30038493 CTTATAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30048602 original size:6 final size:6
Alignment explanation
Indices: 30048586--30048632 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
30048576 ACAATGTTGG
* *
30048586 AAATGA TAATGA CAATGA AAATGA AAATGA AAATGA AAATGA AAATG
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATG
30048633 GAAGGTGCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.19
Consensus pattern (6 bp):
AAATGA
Found at i:30054986 original size:12 final size:12
Alignment explanation
Indices: 30054963--30055005 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
30054953 GCAAATGGAT
*
30054963 CATTTCTCATTTT
1 CATTT-TCATTTC
*
30054976 CTTTTTCATTTC
1 CATTTTCATTTC
30054988 CATTTTCATTTC
1 CATTTTCATTTC
30055000 CATTTT
1 CATTTT
30055006 TGAGAAACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (12 bp):
CATTTTCATTTC
Found at i:30054993 original size:18 final size:19
Alignment explanation
Indices: 30054962--30055004 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
30054952 TGCAAATGGA
*
30054962 TCATTTCTCATTTTCTTTT
1 TCATTTCTCATTTTCATTT
30054981 TCATTTC-CATTTTCATTT
1 TCATTTCTCATTTTCATTT
*
30054999 CCATTT
1 TCATTT
30055005 TTGAGAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (19 bp):
TCATTTCTCATTTTCATTT
Found at i:30065525 original size:31 final size:31
Alignment explanation
Indices: 30065486--30065583 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
30065476 AATAGCCACT
*
30065486 CGCCCGTGTAGTATGCCTGTGTGGGCCTACA
1 CGCCCGTGTAGCATGCCTGTGTGGGCCTACA
** * *
30065517 CGTTCGTGTAACATGTCC-GTGTGGGCCCACA
1 CGCCCGTGTAGCATG-CCTGTGTGGGCCTACA
*
30065548 CGCCCATGTAGCATG-CTCGTGTGGGCCTACA
1 CGCCCGTGTAGCATGCCT-GTGTGGGCCTACA
*
30065579 TGCCC
1 CGCCC
30065584 AATTTGGCCT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
31 50 0.94
32 2 0.04
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.24
Consensus pattern (31 bp):
CGCCCGTGTAGCATGCCTGTGTGGGCCTACA
Found at i:30070575 original size:116 final size:116
Alignment explanation
Indices: 30070455--30070668 Score: 331
Period size: 116 Copynumber: 1.8 Consensus size: 116
30070445 TTGCAATAGG
* * *
30070455 TATCGATACCACAT-AACATGTATCAATACTTGTGACTTAAATGAAGTATTTTTAAAACACCAAA
1 TATCGATACCACATGAA-AGGTATCAATACATGTAACTTAAATGAAGTATTTTTAAAACACCAAA
30070519 ACTAAAAACAGTATCGGTACCCACCCAAGGGTATCGATACTTTTTGGAAAAA
65 ACTAAAAACAGTATCGGTACCCACCCAAGGGTATCGATACTTTTTGGAAAAA
* ** *
30070571 TATCGATACCACATGAAAGGTATCGATACATGTAACTTAAATGAAGTATTTTTAAAACACTGAAG
1 TATCGATACCACATGAAAGGTATCAATACATGTAACTTAAATGAAGTATTTTTAAAACACCAAAA
* *
30070636 CTAAAAATAGTATCGGTACCCAGCCAAGGGTAT
66 CTAAAAACAGTATCGGTACCCACCCAAGGGTAT
30070669 TGATGTAACA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
116 86 0.98
117 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (116 bp):
TATCGATACCACATGAAAGGTATCAATACATGTAACTTAAATGAAGTATTTTTAAAACACCAAAA
CTAAAAACAGTATCGGTACCCACCCAAGGGTATCGATACTTTTTGGAAAAA
Found at i:30077965 original size:18 final size:18
Alignment explanation
Indices: 30077944--30078008 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
30077934 TTTAATAAAA
30077944 TTAATAAATTTTATTATT
1 TTAATAAATTTTATTATT
* *
30077962 TTAATAAATTATT-TAATA
1 TTAATAAATT-TTATTATT
30077980 TT-AT-AATTTTATT-TT
1 TTAATAAATTTTATTATT
*
30077995 GATAATAAATTTTA
1 -TTAATAAATTTTA
30078009 ACAATAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
15 3 0.08
16 6 0.16
17 4 0.11
18 22 0.59
19 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTAATAAATTTTATTATT
Found at i:30077970 original size:26 final size:27
Alignment explanation
Indices: 30077926--30077990 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 27
30077916 CATATTTAGT
*
30077926 TATT-TAAATTTAATAAAATTAATAAA
1 TATTATAATTTTAATAAAATTAATAAA
* * * *
30077952 TTTTATTATTTTAAT-AAATTATTTAA
1 TATTATAATTTTAATAAAATTAATAAA
30077978 TATTATAATTTTA
1 TATTATAATTTTA
30077991 TTTTGATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTATAATTTTAATAAAATTAATAAA
Found at i:30077989 original size:34 final size:34
Alignment explanation
Indices: 30077950--30078056 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 34
30077940 AAAATTAATA
30077950 AATTTTATTATTTTAATAAATTATTTAATATTAT
1 AATTTTATTATTTTAATAAATTATTTAATATTAT
* * *
30077984 AATTTTATT-TTGATAATAAA-T-TTTAACAATAAT
1 AATTTTATTATT-TTAATAAATTATTTAA-TATTAT
*
30078017 AATTTTA-AATTTTAATAATATTTATATTAATA-TAT
1 AATTTTATTATTTTAATAA-A-TTAT-TTAATATTAT
30078052 AATTT
1 AATTT
30078057 ATAAATATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
32 11 0.19
33 17 0.29
34 16 0.28
35 8 0.14
36 2 0.03
37 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
AATTTTATTATTTTAATAAATTATTTAATATTAT
Found at i:30078046 original size:22 final size:22
Alignment explanation
Indices: 30077944--30078046 Score: 60
Period size: 22 Copynumber: 4.9 Consensus size: 22
30077934 TTTAATAAAA
30077944 TTAATAA-ATTT-TATT--ATT
1 TTAATAATATTTATATTAAATT
30077962 TTAATAAATTATTTAATATTATAATT
1 TTAAT-AA-TATTT-ATATTA-AATT
* *
30077988 TT-AT--T-TTGATAATAAATT
1 TTAATAATATTTATATTAAATT
* * * *
30078006 TTAACAATAATAATTTTAAATT
1 TTAATAATATTTATATTAAATT
30078028 TTAATAATATTTATATTAA
1 TTAATAATATTTATATTAA
30078047 TATATAATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 20
0.67 0.12 0.22
Matches are distributed among these distances:
18 11 0.18
19 8 0.13
20 2 0.03
21 6 0.10
22 24 0.39
23 4 0.06
25 2 0.03
26 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
TTAATAATATTTATATTAAATT
Found at i:30078048 original size:15 final size:17
Alignment explanation
Indices: 30078028--30078059 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30078018 ATTTTAAATT
30078028 TTAATA-AT-ATTTATA
1 TTAATATATAATTTATA
30078043 TTAATATATAATTTATA
1 TTAATATATAATTTATA
30078060 AATATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATATAATTTATA
Found at i:30078064 original size:27 final size:25
Alignment explanation
Indices: 30078033--30078084 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
30078023 AAATTTTAAT
*
30078033 AATATTTATATTAATATATAATTTATA
1 AATATTTA-A-TAATAAATAATTTATA
*
30078060 AATATTTAATAATAAATATTTTATA
1 AATATTTAATAATAAATAATTTATA
30078085 GTACAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 1 0.04
27 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATTTAATAATAAATAATTTATA
Found at i:30078079 original size:35 final size:33
Alignment explanation
Indices: 30077963--30078079 Score: 103
Period size: 35 Copynumber: 3.3 Consensus size: 33
30077953 TTTATTATTT
*
30077963 TAATAAATTATTTAATATTATAATTTT--ATTTTGA
1 TAATAAA-TA-TTAATA-TATAATTTTAAATTTTAA
* *
30077997 TAATAAATTTTAACAATAATAATTTTAAATTTTAA
1 TAATAAATATTAA-TAT-ATAATTTTAAATTTTAA
*
30078032 TAATATTTATATTAATATATAATTTATAAATATTTAA
1 TAATA--AATATTAATATATAATTT-TAAAT-TTTAA
30078069 TAATAAATATT
1 TAATAAATATT
30078080 TTATAGTACA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
32 5 0.07
33 10 0.15
34 7 0.10
35 23 0.34
36 7 0.10
37 16 0.24
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (33 bp):
TAATAAATATTAATATATAATTTTAAATTTTAA
Found at i:30079304 original size:37 final size:37
Alignment explanation
Indices: 30079234--30079304 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
30079224 ACTCCAGTAC
*
30079234 CTAGACTCAACAGTTCGACACGATCTGAAACTGGTAA
1 CTAGACTCAACAGTTCGACACAATCTGAAACTGGTAA
* *
30079271 CTAGACTCAACAGTTCGACACAATTTGACACTGG
1 CTAGACTCAACAGTTCGACACAATCTGAAACTGG
30079305 ACATAGATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (37 bp):
CTAGACTCAACAGTTCGACACAATCTGAAACTGGTAA
Found at i:30079690 original size:20 final size:20
Alignment explanation
Indices: 30079667--30079718 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
30079657 TAGAAGTGAG
30079667 GTAGAAGATGAAGAGATCAA
1 GTAGAAGATGAAGAGATCAA
30079687 GTAGAAGATGAAGAGATCAA
1 GTAGAAGATGAAGAGATCAA
* *
30079707 TTAGAAAATGAA
1 GTAGAAGATGAA
30079719 ATAGATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.52, C:0.04, G:0.27, T:0.17
Consensus pattern (20 bp):
GTAGAAGATGAAGAGATCAA
Found at i:30082637 original size:36 final size:36
Alignment explanation
Indices: 30082588--30082705 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
30082578 ATTCCAACCA
**
30082588 AAACACATTAGATGCTCATAAGAGCTAATCCATCTG
1 AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
* **
30082624 AAACACACCAGATGCTCATAAGAGCTAATCTATCCA
1 AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
* * *
30082660 AAACACACCA-ATGGCTCCA-AAAAGCTAGTCCAACTG
1 AAACACACCAGAT-GCT-CATAAGAGCTAATCCATCTG
30082696 AAACACACCA
1 AAACACACCA
30082706 AAACAGGGAG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 2 0.03
36 65 0.94
37 2 0.03
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (36 bp):
AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
Found at i:30088362 original size:13 final size:13
Alignment explanation
Indices: 30088310--30088494 Score: 65
Period size: 13 Copynumber: 14.2 Consensus size: 13
30088300 CATATCTATC
*
30088310 CATATAAACATTT
1 CATATAATCATTT
*
30088323 CATATAA-CACTT
1 CATATAATCATTT
30088335 CATATAATCGA-TT
1 CATATAATC-ATTT
*
30088348 CATATAATTATTT
1 CATATAATCATTT
* * **
30088361 CATTTAGTTGTTT
1 CATATAATCATTT
* *
30088374 CTGTATAACTGA-TT
1 C-ATATAA-TCATTT
* *
30088388 CATATAACCATTA
1 CATATAATCATTT
*
30088401 CGTAT-ATCTATTT
1 CATATAATC-ATTT
*
30088414 CTATATAATCAATT
1 C-ATATAATCATTT
* *
30088428 CTTATATTCATTT
1 CATATAATCATTT
* *
30088441 CACA-AAACAATTT
1 CATATAATC-ATTT
* * *
30088454 CGTATAACCAATT
1 CATATAATCATTT
*
30088467 CATATAACCATTT
1 CATATAATCATTT
** *
30088480 TGTATAACCATTT
1 CATATAATCATTT
30088493 CA
1 CA
30088495 AAGTATTAAC
Statistics
Matches: 125, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
12 17 0.14
13 87 0.70
14 17 0.14
15 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:30090837 original size:13 final size:13
Alignment explanation
Indices: 30090819--30090843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30090809 CTGTTAATAA
30090819 TTTTTTAATTTGT
1 TTTTTTAATTTGT
30090832 TTTTTTAATTTG
1 TTTTTTAATTTG
30090844 GATTTTGACA
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTAATTTGT
Found at i:30094754 original size:1 final size:1
Alignment explanation
Indices: 30094748--30094772 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
30094738 TTCTAAATCC
30094748 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
30094773 TCTCTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30099533 original size:2 final size:2
Alignment explanation
Indices: 30099526--30099566 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30099516 TCTAATCTCC
30099526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30099567 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30099681 original size:2 final size:2
Alignment explanation
Indices: 30099674--30099714 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30099664 NNNTATCTAC
30099674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30099715 GGAGCATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30107810 original size:31 final size:31
Alignment explanation
Indices: 30107775--30107833 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
30107765 TTGGTCATTA
30107775 AACTATTCGAAAGTTTTCATTTAAGCCACTG
1 AACTATTCGAAAGTTTTCATTTAAGCCACTG
* *
30107806 AACTATTTGAAAGTTTTTATTTAAGCCA
1 AACTATTCGAAAGTTTTCATTTAAGCCA
30107834 TTGGATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (31 bp):
AACTATTCGAAAGTTTTCATTTAAGCCACTG
Found at i:30110037 original size:6 final size:6
Alignment explanation
Indices: 30110007--30110036 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30109997 ATAGAAACAA
*
30110007 GAATAT GAATAT GAATAT GAATAT AAATAT
1 GAATAT GAATAT GAATAT GAATAT GAATAT
30110037 ACAAATTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (6 bp):
GAATAT
Found at i:30113069 original size:15 final size:15
Alignment explanation
Indices: 30113046--30113082 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
30113036 TTAAATTTTT
30113046 TATAAAATTTTAAAA
1 TATAAAATTTTAAAA
*
30113061 TATATAATTTTAAAA
1 TATAAAATTTTAAAA
*
30113076 TTTAAAA
1 TATAAAA
30113083 AGCCAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAATTTTAAAA
Found at i:30113184 original size:19 final size:20
Alignment explanation
Indices: 30113150--30113194 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
30113140 TACCTTAATA
**
30113150 TTTAAATACCTTTTTAGGTTT
1 TTTAAATA-CTTTTTACATTT
30113171 TTTAAATA-TTTTTACATTT
1 TTTAAATACTTTTTACATTT
30113190 TTTAA
1 TTTAA
30113195 TAGTATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAAATACTTTTTACATTT
Found at i:30122115 original size:21 final size:21
Alignment explanation
Indices: 30122091--30122130 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30122081 GATTATATTT
30122091 ATATATTT-TAAATATTATAAA
1 ATATATTTAT-AATATTATAAA
30122112 ATATATTTATAATATTATA
1 ATATATTTATAATATTATA
30122131 GATCTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATTTATAATATTATAAA
Found at i:30131331 original size:32 final size:30
Alignment explanation
Indices: 30131289--30131355 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 30
30131279 AGCAAACAAA
*
30131289 ATAATTAAATATAAATAAATACATATTTATAT
1 ATAATAAAATATAAATAAA-ACA-ATTTATAT
*
30131321 ATAATAAAATATAAATAGAACAATTTATAT
1 ATAATAAAATATAAATAAAACAATTTATAT
30131351 ATAAT
1 ATAAT
30131356 TTGTCAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 13 0.39
31 3 0.09
32 17 0.52
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (30 bp):
ATAATAAAATATAAATAAAACAATTTATAT
Found at i:30136082 original size:26 final size:25
Alignment explanation
Indices: 30136040--30136108 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 25
30136030 CCCGATATAT
30136040 GGCTCTTCGGAGCTTCCCAATTAAA
1 GGCTCTTCGGAGCTTCCCAATTAAA
* * *
30136065 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCG-GAGCTTCCCAATTAAA
*
30136091 GGCTCTCCGGAGCTTCCC
1 GGCTCTTCGGAGCTTCCC
30136109 GATATGGCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCAATTAAA
Found at i:30136163 original size:73 final size:73
Alignment explanation
Indices: 30136076--30136215 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
30136066 GCTCTTTGTG
* * *
30136076 AGCTTCCTAATTAATGGCTCTCCGGAGCTTCCCGATA-TGGCTCGCTTGAACTTCCTGATATATG
1 AGCTTCCTAATTAATGGCTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCTGA-ATATG
30136140 GCTATCCGA
65 GCTATCCGA
* ** * *
30136149 AGCTTCTTAATTAATGGCTCTTTAGAGCTACCCGTTATTGGCTCGCATGAGCTTCCTGAATATGG
1 AGCTTCCTAATTAATGGCTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCTGAATATGG
30136214 CT
66 CT
30136216 CTTATAAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 39 0.67
74 19 0.33
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (73 bp):
AGCTTCCTAATTAATGGCTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCTGAATATGG
CTATCCGA
Found at i:30136252 original size:25 final size:25
Alignment explanation
Indices: 30136219--30136285 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
30136209 TATGGCTCTT
* * *
30136219 ATAAGCTTCCTGTTATACATCCCGG
1 ATAAGCTTCCCGTTATACAACCCGA
*
30136244 ATAAGCTTCCCGTTATACAACTCGA
1 ATAAGCTTCCCGTTATACAACCCGA
30136269 ATAAGCTTCCCGTTATA
1 ATAAGCTTCCCGTTATA
30136286 TGGCTCGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (25 bp):
ATAAGCTTCCCGTTATACAACCCGA
Found at i:30136292 original size:25 final size:25
Alignment explanation
Indices: 30136174--30136293 Score: 82
Period size: 25 Copynumber: 4.9 Consensus size: 25
30136164 GGCTCTTTAG
* * *
30136174 AGCTACCCGTTAT-TGGCTCGCATG
1 AGCTTCCCGTTATATGGCTCGAATA
* * **
30136198 AGCTTCCTG-AATATGGCTCTTATA
1 AGCTTCCCGTTATATGGCTCGAATA
* *** * *
30136222 AGCTTCCTGTTATACATCCCGGATA
1 AGCTTCCCGTTATATGGCTCGAATA
***
30136247 AGCTTCCCGTTATACAACTCGAATA
1 AGCTTCCCGTTATATGGCTCGAATA
30136272 AGCTTCCCGTTATATGGCTCGA
1 AGCTTCCCGTTATATGGCTCGA
30136294 GAGAGAGCTT
Statistics
Matches: 74, Mismatches: 20, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
23 2 0.03
24 24 0.32
25 48 0.65
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGAATA
Found at i:30141409 original size:85 final size:84
Alignment explanation
Indices: 30141299--30141485 Score: 277
Period size: 85 Copynumber: 2.2 Consensus size: 84
30141289 TACATCTTTT
* * * * * *
30141299 TTTGGAAACAAAAGAATATCGAATAAAATCTTTTTAGACGACGGGAATAAATC-CTGAAACAGAT
1 TTTGGAAACAAAAAAAAATCAAATAAAATCTTGTTAAACGACGAGAATAAATCTC-GAAACAGAT
30141363 TTTATTTAATTTTAATTCTAA
65 TTTATTTAA-TTTAATTCTAA
* *
30141384 TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCTCGAAACAGATT
1 TTTGGAAACAAAAAAAAATCAAATAAAATCTTGTTAAACGACGAGAATAAATCTCGAAACAGATT
30141449 TTATTTAATTTAATTCTAA
66 TTATTTAATTTAATTCTAA
30141468 TTTGGAAACAAAAAAAAA
1 TTTGGAAACAAAAAAAAA
30141486 AAACAAAACA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
84 28 0.30
85 64 0.69
86 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (84 bp):
TTTGGAAACAAAAAAAAATCAAATAAAATCTTGTTAAACGACGAGAATAAATCTCGAAACAGATT
TTATTTAATTTAATTCTAA
Found at i:30141645 original size:182 final size:179
Alignment explanation
Indices: 30141320--30141649 Score: 427
Period size: 182 Copynumber: 1.8 Consensus size: 179
30141310 AAGAATATCG
* * *
30141320 AATAAAATCTTTTTAGACGACGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTAAT
1 AATAAAATCTTGTTAAACGACGAGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTAAT
*
30141385 TTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCTCGAAACAGATTT
66 TTGGAAACAAAATAAAATCAAATAAAATCTCGTTAAACGGCGAGAATAAATCTCGAAACAGATTT
30141450 TATTTAATTTAATTCTAATTTGGAAACAAAAAAAAAAAACAAAACAAAACAA
131 TA-TT-ATTTAATT-TAATTTGGAAACAAAAAAAAAAAACAAAACAAAACAA
30141502 AATAAAATCTTGTTAAACGACGAGAATAAATCGC-GAAACAGATTTTATTTAATTTTAATTTCTC
1 AATAAAATCTTGTTAAACGACGAGAATAAATC-CTGAAACAGATTTTATTTAATTTTAA-TTCT-
* * * * * * *
30141566 ATTTTTGGAAATAAAATCAAAATTAGAATAAAATC-CGTTGAACGGTGGGGATAAAT-TCCGAAA
63 A-ATTTGGAAACAAAAT-AAAATCA-AATAAAATCTCGTTAAACGGCGAGAATAAATCT-CGAAA
*
30141629 TAGATTTTA-T-TTTAATTTAAT
124 CAGATTTTATTATTTAATTTAAT
30141650 ACTCGTTTTT
Statistics
Matches: 129, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
181 4 0.03
182 60 0.47
183 5 0.04
184 2 0.02
185 14 0.11
186 35 0.27
187 9 0.07
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (179 bp):
AATAAAATCTTGTTAAACGACGAGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTAAT
TTGGAAACAAAATAAAATCAAATAAAATCTCGTTAAACGGCGAGAATAAATCTCGAAACAGATTT
TATTATTTAATTTAATTTGGAAACAAAAAAAAAAAACAAAACAAAACAA
Found at i:30141786 original size:87 final size:87
Alignment explanation
Indices: 30141525--30141914 Score: 382
Period size: 88 Copynumber: 4.4 Consensus size: 87
30141515 TAAACGACGA
* *
30141525 GAATAAATCGCGAAAC-AGATTTTATTTAATTTTAATTTCTCATTTTTGGAAATAAAATCAAAAT
1 GAATAAATC-CGAAACGA-ATTTTATTTACTTTTAATTTCCCA--TTTGGAAATAAAATCAAAAT
* *
30141589 -TAGAATAAAATCCGTTGAACGGTGG
62 ATAGAATAAAATCCATTGAACGGCGG
* * * * ***
30141614 GGATAAATTCCGAAA-TAGATTTTATTTTA-ATTTAATACTCGTTTTTGGAAATAAAATCAAAAT
1 GAATAAA-TCCGAAACGA-ATTTTA-TTTACTTTTAAT-TTCCCATTTGGAAATAAAATCAAAAT
*
30141677 TTAGAATAAAAT-CATTGAACGGCGG
62 ATAGAATAAAATCCATTGAACGGCGG
*
30141702 GAATAAATCCTGAAACGAATTTTATTTACCTTTAATTTCCCATTTGGAAAT-AAAT-AAAATAAT
1 GAATAAATCC-GAAACGAATTTTATTTACTTTTAATTTCCCATTTGGAAATAAAATCAAAAT-AT
* *
30141765 GGAATAAAATCCATTGAACGGCGA
64 AGAATAAAATCCATTGAACGGCGG
* * *
30141789 GAATAAATCCGGAAACGGATTTTATTTACTTTTAATTTTCCATTTGGAAAT-AAATAAAAATAAT
1 GAATAAATCC-GAAACGAATTTTATTTACTTTTAATTTCCCATTTGGAAATAAAATCAAAAT-AT
* * * *
30141853 GGAATAAAATTCGTTGAACGGAGG
64 AGAATAAAATCCATTGAACGGCGG
* * *
30141877 AAATAAATCCCGAAAAGGATTTTATTTACTTTTAATTT
1 GAATAAAT-CCGAAACGAATTTTATTTACTTTTAATTT
30141915 GGAAACAAAA
Statistics
Matches: 261, Mismatches: 28, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
85 5 0.02
86 14 0.05
87 81 0.31
88 114 0.44
89 39 0.15
90 8 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (87 bp):
GAATAAATCCGAAACGAATTTTATTTACTTTTAATTTCCCATTTGGAAATAAAATCAAAATATAG
AATAAAATCCATTGAACGGCGG
Found at i:30141812 original size:175 final size:175
Alignment explanation
Indices: 30141525--30141914 Score: 418
Period size: 175 Copynumber: 2.2 Consensus size: 175
30141515 TAAACGACGA
* *
30141525 GAATAAATCGCGAAAC-AGATTTTATTTAATTTTAATTTCTCATTTTTGGAAATAAAATCAAAAT
1 GAATAAATC-CGAAACGA-ATTTTATTTACTTTTAATTTCCCA-TTTTGGAAATAAAATCAAAAT
* * * * *
30141589 TAGAATAAAATCCGTTGAACGGTGGGGATAAATTCCGAAATAGATTTTATTTTA-ATTTAATACT
63 TAGAATAAAATCCATTGAACGGCGAGAATAAATTCCGAAACAGATTTTA-TTTACATTTAATACT
** * * *
30141653 CGTTTTTGGAAATAAAATCAAAAT-TTAGAATAAAA-TCATTGAACGGCGG
127 C-CATTTGGAAAT-AAATAAAAATAATAGAATAAAATTCATTGAACGGAGG
*
30141702 GAATAAATCCTGAAACGAATTTTATTTACCTTTAATTTCCCA-TTTGGAAAT-AAAT-AAAATAA
1 GAATAAATCC-GAAACGAATTTTATTTACTTTTAATTTCCCATTTTGGAAATAAAATCAAAAT--
* * * **
30141764 TGGAATAAAATCCATTGAACGGCGAGAATAAA-TCCGGAAACGGATTTTATTTACTTTTAATTTT
63 TAGAATAAAATCCATTGAACGGCGAGAATAAATTCC-GAAACAGATTTTATTTACATTTAATACT
* *
30141828 CCATTTGGAAATAAATAAAAATAATGGAATAAAATTCGTTGAACGGAGG
127 CCATTTGGAAATAAATAAAAATAATAGAATAAAATTCATTGAACGGAGG
* * *
30141877 AAATAAATCCCGAAAAGGATTTTATTTACTTTTAATTT
1 GAATAAAT-CCGAAACGAATTTTATTTACTTTTAATTT
30141915 GGAAACAAAA
Statistics
Matches: 180, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
173 14 0.08
174 29 0.16
175 98 0.54
176 3 0.02
177 35 0.19
178 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (175 bp):
GAATAAATCCGAAACGAATTTTATTTACTTTTAATTTCCCATTTTGGAAATAAAATCAAAATTAG
AATAAAATCCATTGAACGGCGAGAATAAATTCCGAAACAGATTTTATTTACATTTAATACTCCAT
TTGGAAATAAATAAAAATAATAGAATAAAATTCATTGAACGGAGG
Found at i:30147174 original size:21 final size:21
Alignment explanation
Indices: 30147145--30147184 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30147135 ATAAGTAGCT
30147145 TTGTAATGGTTGAAATATGAC
1 TTGTAATGGTTGAAATATGAC
* *
30147166 TTGTTATGGTTGAATTATG
1 TTGTAATGGTTGAAATATG
30147185 GTAGATAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (21 bp):
TTGTAATGGTTGAAATATGAC
Found at i:30153374 original size:31 final size:31
Alignment explanation
Indices: 30153339--30153440 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
30153329 GGTTGTAATA
* *
30153339 GTAAATTAGTGAGCTGTTTAGAGTTGTGATC
1 GTAAATTAGTGAGCTATTTAGAGTTGCGATC
* *
30153370 GTAAATCAGTGAGCTATTTGGAGTTGCGATC
1 GTAAATTAGTGAGCTATTTAGAGTTGCGATC
* *** * *
30153401 GTAAATAAACAAGCTTTTTGGAGTTGCGATC
1 GTAAATTAGTGAGCTATTTAGAGTTGCGATC
30153432 GTAAATTAG
1 GTAAATTAG
30153441 CTAACTTAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.34
Consensus pattern (31 bp):
GTAAATTAGTGAGCTATTTAGAGTTGCGATC
Found at i:30153509 original size:94 final size:94
Alignment explanation
Indices: 30153392--30153688 Score: 384
Period size: 94 Copynumber: 3.2 Consensus size: 94
30153382 GCTATTTGGA
* * *
30153392 GTTGCGATCGTAAATAAACAAGCTTTTTGGAGTTGCGATCGTAAATTAGCTAACTTAGAAGAAAT
1 GTTGTGATCGTAAATCAACAAGCTTTTTGGAGTTGCGATCGTAAATCAGCTAACTTAGAAGAAAT
* *
30153457 TGTTCATGATCGTAAATTAATAAATTTAG
66 TGTTCATGATCGTAAATAAATGAATTTAG
* * *
30153486 GTTGTGATCGTAAATCAGCAAGCTATTTAGAGTTGCGATCGTAAATCAGCTAACTTAGAAGAAAT
1 GTTGTGATCGTAAATCAACAAGCTTTTTGGAGTTGCGATCGTAAATCAGCTAACTTAGAAGAAAT
* * * *
30153551 TGTTCATGATTGTAAATCAGTGAACTTAG
66 TGTTCATGATCGTAAATAAATGAATTTAG
* * * *
30153580 GTTGTGATCGTAAATCAATAAG-TTGTTTGGAGTTGCAATCGAAAATCA-ATCAACTTAGAAGAA
1 GTTGTGATCGTAAATCAACAAGCTT-TTTGGAGTTGCGATCGTAAATCAGCT-AACTTAGAAG-A
*
30153643 AATT-TTCATGATCGTAAATAAATGCATTTAG
63 AATTGTTCATGATCGTAAATAAATGAATTTAG
*
30153674 GTTGTGGTCGTAAAT
1 GTTGTGATCGTAAAT
30153689 TAGCGAGCCT
Statistics
Matches: 176, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
93 2 0.01
94 169 0.96
95 5 0.03
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (94 bp):
GTTGTGATCGTAAATCAACAAGCTTTTTGGAGTTGCGATCGTAAATCAGCTAACTTAGAAGAAAT
TGTTCATGATCGTAAATAAATGAATTTAG
Found at i:30153527 original size:31 final size:31
Alignment explanation
Indices: 30153350--30153535 Score: 114
Period size: 31 Copynumber: 6.0 Consensus size: 31
30153340 TAAATTAGTG
* * **
30153350 AGCTGTTTAGAGTTGTGATCGTAAATCAGTG
1 AGCTATTTAGAGTTGCGATCGTAAATCAGCA
* * *
30153381 AGCTATTTGGAGTTGCGATCGTAAATAAACA
1 AGCTATTTAGAGTTGCGATCGTAAATCAGCA
* * *
30153412 AGCTTTTTGGAGTTGCGATCGTAAATTAGCTA
1 AGCTATTTAGAGTTGCGATCGTAAATCAGC-A
** * * **
30153444 A-CT-TAGAAGAAATTGTTCATGATCGTAAATTAATA
1 AGCTAT-TTAG-AGTTG--C--GATCGTAAATCAGCA
*
30153479 A---ATTTAG-GTTGTGATCGTAAATCAGCA
1 AGCTATTTAGAGTTGCGATCGTAAATCAGCA
30153506 AGCTATTTAGAGTTGCGATCGTAAATCAGC
1 AGCTATTTAGAGTTGCGATCGTAAATCAGC
30153536 TAACTTAGAA
Statistics
Matches: 119, Mismatches: 24, Indels: 24
0.71 0.14 0.14
Matches are distributed among these distances:
27 13 0.11
30 7 0.06
31 75 0.63
32 6 0.05
33 2 0.02
34 2 0.02
35 2 0.02
36 12 0.10
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (31 bp):
AGCTATTTAGAGTTGCGATCGTAAATCAGCA
Found at i:30153866 original size:103 final size:103
Alignment explanation
Indices: 30153683--30153894 Score: 280
Period size: 103 Copynumber: 2.1 Consensus size: 103
30153673 GGTTGTGGTC
* * * * * * * * *
30153683 GTAAATTAGCGAGCCTTAATAATATCAGTCGTGATCATAAATTAGCGAGTTGTTTGGAGTTGTGA
1 GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCATAAATCAGCGAGCTATTTAGAGTTGCGA
*
30153748 TCGTAAATTAACTAACTCAGAAAAAAATATTCATGATA
66 TCGTAAATCAACTAACTCAGAAAAAAATATTCATGATA
* *
30153786 GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCTTAAATCATCGAGCTATTTAGAGTTGCGA
1 GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCATAAATCAGCGAGCTATTTAGAGTTGCGA
* * * *
30153851 TTGTAAATCATCTAACTCAGAAAAAAATGTTCATGATG
66 TCGTAAATCAACTAACTCAGAAAAAAATATTCATGATA
30153889 GTAAAT
1 GTAAAT
30153895 TAATAAACTT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (103 bp):
GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCATAAATCAGCGAGCTATTTAGAGTTGCGA
TCGTAAATCAACTAACTCAGAAAAAAATATTCATGATA
Found at i:30158907 original size:18 final size:18
Alignment explanation
Indices: 30158884--30158918 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
30158874 TGAAAAAGTT
30158884 AGAAAAATTTATTAATTA
1 AGAAAAATTTATTAATTA
30158902 AGAAAAATTTATTAATT
1 AGAAAAATTTATTAATT
30158919 GATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AGAAAAATTTATTAATTA
Found at i:30159476 original size:8 final size:8
Alignment explanation
Indices: 30159453--30159493 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
30159443 AATAAATAAG
30159453 TATTATAT
1 TATTATAT
30159461 TAATTATAT
1 T-ATTATAT
*
30159470 TATTATAA
1 TATTATAT
30159478 TATTATAT
1 TATTATAT
30159486 TATTATAT
1 TATTATAT
30159494 ATGTAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:30159574 original size:13 final size:13
Alignment explanation
Indices: 30159552--30159585 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
30159542 ACAGAGAAGG
*
30159552 AGAAAGGAAAGAA
1 AGAAAAGAAAGAA
30159565 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
30159578 AGAAAAGA
1 AGAAAAGA
30159586 GAATTTTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:30160310 original size:13 final size:14
Alignment explanation
Indices: 30160292--30160324 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
30160282 AATTAAAGTG
30160292 GAATATATAT-TAT
1 GAATATATATGTAT
30160305 GAATATATATGTAT
1 GAATATATATGTAT
*
30160319 AAATAT
1 GAATAT
30160325 GAAATTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (14 bp):
GAATATATATGTAT
Found at i:30160481 original size:25 final size:25
Alignment explanation
Indices: 30160452--30160535 Score: 132
Period size: 25 Copynumber: 3.4 Consensus size: 25
30160442 TTAGCGCGCG
*
30160452 CTCTGATTATTAGCACGTTGGTGCT
1 CTCTGATTATTAGCACGTTAGTGCT
*
30160477 CTCTGATTATTAGTACGTTAGTGCT
1 CTCTGATTATTAGCACGTTAGTGCT
* *
30160502 CTCTGATTACTAGCACGTCAGTGCT
1 CTCTGATTATTAGCACGTTAGTGCT
30160527 CTCTGATTA
1 CTCTGATTA
30160536 GCACATCTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (25 bp):
CTCTGATTATTAGCACGTTAGTGCT
Found at i:30160547 original size:22 final size:23
Alignment explanation
Indices: 30160472--30160575 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 23
30160462 TAGCACGTTG
* * *
30160472 GTGCTCTCTGATTATTAGTACGTTA
1 GTGCTCTCTGA-TA-TAGCACATCA
*
30160497 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGA-TA-TAGCACATCA
*
30160522 GTGCTCTCTGAT-TAGCACATCT
1 GTGCTCTCTGATATAGCACATCA
*
30160544 GTGCTCTCTG-TATAGCACTTCA
1 GTGCTCTCTGATATAGCACATCA
30160566 GTGCTCTCTG
1 GTGCTCTCTG
30160576 TTCATTAGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.01
22 36 0.51
24 1 0.01
25 33 0.46
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (23 bp):
GTGCTCTCTGATATAGCACATCA
Found at i:30160583 original size:47 final size:48
Alignment explanation
Indices: 30160452--30160583 Score: 130
Period size: 50 Copynumber: 2.8 Consensus size: 48
30160442 TTAGCGCGCG
* ** * *
30160452 CTCTGATTATTAGCACGTTGGTGCTCTCTGATTATTAGTACGTTAGTGCT
1 CTCTGA-TACTAGCACGTCAGTGCTCTCTG-TTATTAGCACATTAGTGCT
30160502 CTCTGATTACTAGCACGTCAGTGCTCTCTG--ATTAGCACATCT-GTGCT
1 CTCTGA-TACTAGCACGTCAGTGCTCTCTGTTATTAGCACAT-TAGTGCT
*
30160549 CTCTG-TA-TAGCACTTCAGTGCTCTCTGTTCATTAG
1 CTCTGATACTAGCACGTCAGTGCTCTCTGTT-ATTAG
30160584 TGCATAATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
44 19 0.26
45 2 0.03
47 23 0.32
48 1 0.01
50 27 0.38
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (48 bp):
CTCTGATACTAGCACGTCAGTGCTCTCTGTTATTAGCACATTAGTGCT
Found at i:30163970 original size:23 final size:24
Alignment explanation
Indices: 30163927--30163971 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30163917 TATTTATTTT
30163927 ATTTAATATTACTGATTATATAAA
1 ATTTAATATTACTGATTATATAAA
* *
30163951 ATTTAATTTTA-TTATTATATA
1 ATTTAATATTACTGATTATATA
30163972 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTAATATTACTGATTATATAAA
Found at i:30165969 original size:6 final size:7
Alignment explanation
Indices: 30165941--30165970 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
30165931 ACTAGAATAT
30165941 AATTTTA
1 AATTTTA
30165948 AATTTTA
1 AATTTTA
30165955 AATTTTA
1 AATTTTA
30165962 AA-TTTA
1 AATTTTA
30165968 AAT
1 AAT
30165971 ATTATCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTTA
Found at i:30179894 original size:49 final size:49
Alignment explanation
Indices: 30179841--30179934 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
30179831 TTGTTTGAAC
*
30179841 ATTTGTGTTTGATATGCAAAAAAATAGAGAAAGTTAAATTTATATAAAA
1 ATTTGTGTTTAATATGCAAAAAAATAGAGAAAGTTAAATTTATATAAAA
* *
30179890 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
1 ATTTGTGTTTAATATGCAAAAAAATAGAGAAAGTTAAATTTATAT
30179935 CTACTTCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (49 bp):
ATTTGTGTTTAATATGCAAAAAAATAGAGAAAGTTAAATTTATATAAAA
Found at i:30181338 original size:14 final size:16
Alignment explanation
Indices: 30181310--30181348 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
30181300 TGTACAAACG
30181310 AAATATTTATGTTTA-
1 AAATATTTATGTTTAT
*
30181325 AAAT-TTTATTTTTAT
1 AAATATTTATGTTTAT
30181340 AAATATTTA
1 AAATATTTA
30181349 AATTGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 8 0.38
16 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AAATATTTATGTTTAT
Found at i:30181493 original size:2 final size:2
Alignment explanation
Indices: 30181486--30181523 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30181476 TGGGAGCATG
30181486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30181524 AAGAATCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30186168 original size:20 final size:20
Alignment explanation
Indices: 30186143--30186180 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30186133 CGTAGTTGAT
30186143 GAAAAATTGAAAGTTTGAAC
1 GAAAAATTGAAAGTTTGAAC
*
30186163 GAAAAATTGAATGTTTGA
1 GAAAAATTGAAAGTTTGA
30186181 TTGAAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (20 bp):
GAAAAATTGAAAGTTTGAAC
Found at i:30186186 original size:20 final size:19
Alignment explanation
Indices: 30186138--30186187 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
30186128 GTTACCGTAG
30186138 TTGATGAAAAATTGAAAGT
1 TTGATGAAAAATTGAAAGT
* *
30186157 TTGAACGAAAAATTGAATGT
1 TTG-ATGAAAAATTGAAAGT
30186177 TTGATTGAAAA
1 TTGA-TGAAAA
30186188 CCTGAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (19 bp):
TTGATGAAAAATTGAAAGT
Found at i:30186317 original size:27 final size:27
Alignment explanation
Indices: 30186278--30186337 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
30186268 GGAATGACAG
30186278 AAATCTAAGGAATTAAGTTTGGGAATCA
1 AAAT-TAAGGAATTAAGTTTGGGAATCA
30186306 AAATTAAGGAATTAAGTTTGGGAATCA
1 AAATTAAGGAATTAAGTTTGGGAATCA
30186333 AAATT
1 AAATT
30186338 GAATTAGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (27 bp):
AAATTAAGGAATTAAGTTTGGGAATCA
Found at i:30198521 original size:19 final size:19
Alignment explanation
Indices: 30198492--30198535 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30198482 TTAATAAACG
30198492 ATATT-AAAATAAGAA-AAA
1 ATATTAAAAATAA-AATAAA
30198510 ATATTAAAAATAAAATAAA
1 ATATTAAAAATAAAATAAA
*
30198529 ATTTTAA
1 ATATTAA
30198536 TTGAGTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
ATATTAAAAATAAAATAAA
Found at i:30204111 original size:3 final size:3
Alignment explanation
Indices: 30204069--30204094 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30204059 TGAAAGTGAA
30204069 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
30204095 CGACGATGTA
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:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:30204450 original size:105 final size:105
Alignment explanation
Indices: 30204315--30204524 Score: 395
Period size: 105 Copynumber: 2.0 Consensus size: 105
30204305 TGCCATAAAG
*
30204315 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTTAAACTCGTG
1 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
30204380 ATTCG-GGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
66 ATT-GAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
30204420 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
1 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
30204485 ATTGAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
66 ATTGAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
30204525 GCAAATCTGA
Statistics
Matches: 103, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
104 1 0.01
105 102 0.99
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (105 bp):
CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
ATTGAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
Found at i:30212747 original size:30 final size:29
Alignment explanation
Indices: 30212713--30212770 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
30212703 AAAATTTATT
* *
30212713 TTATTTGAATATCAATTAAAGTTTAAATGC
1 TTATTTGAA-ACCAATTAAAGTATAAATGC
*
30212743 TTATTTGAAGCCAATTAAAGTATAAATG
1 TTATTTGAAACCAATTAAAGTATAAATG
30212771 TATAATTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (29 bp):
TTATTTGAAACCAATTAAAGTATAAATGC
Found at i:30218251 original size:28 final size:28
Alignment explanation
Indices: 30218220--30218275 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
30218210 TAATAATAAT
* *
30218220 AATATTCGTATTTATTATGTATCGTTTA
1 AATATTCGCATTTATTATGTACCGTTTA
30218248 AATATTCGCATTTATTATGTACCGTTTA
1 AATATTCGCATTTATTATGTACCGTTTA
30218276 TGTTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (28 bp):
AATATTCGCATTTATTATGTACCGTTTA
Found at i:30219509 original size:14 final size:14
Alignment explanation
Indices: 30219490--30219524 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
30219480 ATTTTATTTT
*
30219490 TTCTAATGATACTA
1 TTCTAACGATACTA
30219504 TTCTAACGATACTA
1 TTCTAACGATACTA
30219518 TTCTAAC
1 TTCTAAC
30219525 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:30220836 original size:62 final size:61
Alignment explanation
Indices: 30220748--30220915 Score: 264
Period size: 62 Copynumber: 2.7 Consensus size: 61
30220738 CAACATTACA
* * * *
30220748 ACATTAAAACACTAAAACTTGTAACAAAGTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTG-AACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
30220810 ACATTACAACATTAAAAATTAGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATT-GAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
30220872 ACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAAATT-GAACAAACTTTGTAATATAAATT
30220916 AGGTACATTG
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
62 98 0.99
63 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (61 bp):
ACATTACAACATTAAAAATTGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:30224177 original size:27 final size:27
Alignment explanation
Indices: 30224139--30224217 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
30224129 TATACTAGGT
30224139 GTGCCGCCTATCAGATAGGCACCACCA
1 GTGCCGCCTATCAGATAGGCACCACCA
* *** *
30224166 GTGCCGCCTATCATATAGGGGTCACTA
1 GTGCCGCCTATCAGATAGGCACCACCA
*
30224193 GTGCCGCCTATCGGATAGGCACCAC
1 GTGCCGCCTATCAGATAGGCACCAC
30224218 ACCCGCTTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (27 bp):
GTGCCGCCTATCAGATAGGCACCACCA
Found at i:30224308 original size:3 final size:3
Alignment explanation
Indices: 30224297--30224327 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
30224287 ACTACTAAAA
*
30224297 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30224328 TTTTAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30229910 original size:21 final size:21
Alignment explanation
Indices: 30229877--30229919 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30229867 TTTGGGTGGA
* * *
30229877 TCAGTTCTTACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTATGT
30229898 TCAGCTCTCACGAGCTTATGT
1 TCAGCTCTCACGAGCTTATGT
30229919 T
1 T
30229920 GGCGTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTATGT
Found at i:30242703 original size:28 final size:28
Alignment explanation
Indices: 30242671--30242767 Score: 149
Period size: 28 Copynumber: 3.5 Consensus size: 28
30242661 AATAAGTTCA
* * *
30242671 CACACTTAGTGCTTAATAATCAAACTCG
1 CACACTTAGTGCTTTACAATTAAACTCG
*
30242699 CACACTTAGTGCTTTACCATTAAACTCG
1 CACACTTAGTGCTTTACAATTAAACTCG
*
30242727 CACACTTAGTGCTTTACAATTAAACTCA
1 CACACTTAGTGCTTTACAATTAAACTCG
30242755 CACACTTAGTGCT
1 CACACTTAGTGCT
30242768 AATCTCATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (28 bp):
CACACTTAGTGCTTTACAATTAAACTCG
Found at i:30246299 original size:5 final size:5
Alignment explanation
Indices: 30246289--30246321 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
30246279 TCAACTAAAG
*
30246289 TTTTA TTTTA TTTTA TTTTA -TATA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
30246322 TATTGGCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:30247956 original size:14 final size:15
Alignment explanation
Indices: 30247937--30247966 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
30247927 ATTTTAATCA
30247937 TTAATTTA-ATTTTT
1 TTAATTTATATTTTT
30247951 TTAATTTATATTTTT
1 TTAATTTATATTTTT
30247966 T
1 T
30247967 GTCAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTAATTTATATTTTT
Found at i:30248126 original size:21 final size:21
Alignment explanation
Indices: 30248093--30248173 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
30248083 TTAAAAATTA
* *
30248093 AAAAAATATAAAAATTATTTT
1 AAAAATTAAAAAAATTATTTT
*
30248114 AAAAATT-AAAAAATATATATT
1 AAAAATTAAAAAAAT-TATTTT
*
30248135 AAAAAGTATAAAAAA-TATTTTT
1 AAAAATTA-AAAAAATTA-TTTT
*
30248157 AAAATTTAAAAAAATTA
1 AAAAATTAAAAAAATTA
30248174 ATTAAATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
22 11 0.23
23 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (21 bp):
AAAAATTAAAAAAATTATTTT
Found at i:30248625 original size:35 final size:35
Alignment explanation
Indices: 30248568--30248635 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
30248558 AAAGCCTACT
**
30248568 GAATCTTAACTCGATTAATATTAGTATAATTGTTA
1 GAATCTTAACTCGATTAATATTAACATAATTGTTA
* **
30248603 GAATCTTAACTTGATTGGTATTAACATAATTGT
1 GAATCTTAACTCGATTAATATTAACATAATTGT
30248636 CAGTACAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (35 bp):
GAATCTTAACTCGATTAATATTAACATAATTGTTA
Found at i:30257174 original size:37 final size:37
Alignment explanation
Indices: 30257124--30257205 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
30257114 TATTTCCTAG
* *
30257124 AATAAAATCTTTAAAAGATAATATAATATTAAATTAA
1 AATAAAATATTTAAAAGATAATATAATATTAAAATAA
* * *
30257161 AATAAAATATTTAAAGGATAATATTATTTTAAAATAA
1 AATAAAATATTTAAAAGATAATATAATATTAAAATAA
30257198 AATAAAAT
1 AATAAAAT
30257206 TTGAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (37 bp):
AATAAAATATTTAAAAGATAATATAATATTAAAATAA
Found at i:30257183 original size:19 final size:19
Alignment explanation
Indices: 30257124--30257205 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 19
30257114 TATTTCCTAG
*
30257124 AATAAAATCTTTAAAAGAT
1 AATAAAATATTTAAAAGAT
* ** *
30257143 AATATAATA-TTAAATTAA
1 AATAAAATATTTAAAAGAT
*
30257161 AATAAAATATTTAAAGGAT
1 AATAAAATATTTAAAAGAT
** * *
30257180 AATATTAT-TTTAAAATAA
1 AATAAAATATTTAAAAGAT
30257198 AATAAAAT
1 AATAAAAT
30257206 TTGAAAAAAA
Statistics
Matches: 46, Mismatches: 16, Indels: 3
0.71 0.25 0.05
Matches are distributed among these distances:
18 27 0.59
19 19 0.41
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (19 bp):
AATAAAATATTTAAAAGAT
Found at i:30257479 original size:21 final size:21
Alignment explanation
Indices: 30257416--30257479 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
30257406 ATCATATATA
* * *
30257416 TTACAATTTTTTATATATTTC
1 TTACAAATTTTTATATTTTTT
* *
30257437 TTA-ATAAATTTTA-ATTAATTT
1 TTACA-AATTTTTATATT-TTTT
30257458 TTACAAATTTTTATATTTTTT
1 TTACAAATTTTTATATTTTTT
30257479 T
1 T
30257480 ACCAGGTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTACAAATTTTTATATTTTTT
Found at i:30260515 original size:31 final size:31
Alignment explanation
Indices: 30260479--30260540 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
30260469 AGATAATTTT
30260479 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
30260510 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
30260541 TAATTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:30263361 original size:437 final size:437
Alignment explanation
Indices: 30262547--30263430 Score: 1581
Period size: 437 Copynumber: 2.0 Consensus size: 437
30262537 TAGCCCGTGT
*
30262547 GGCCCACACGGCCACACAATCTCCGTCACATGGCTATGTCTCACACACAGCCAGCCGCACGACCG
1 GGCCCACACGGCCACACAATCTCCGTCACATGGCTACGTCTCACACACAGCCAGCCGCACGACCG
* * *
30262612 ACCACACGCCCGTGTGGTGTCGACAGACCAAATTTTTAGCTTTCGTCGAACCTTATTTTCTCATG
66 ACCACACGCCCATGTGGCGTCGACAGACCAAATTTTTAGCTTTCGCCGAACCTTATTTTCTCATG
* *
30262677 TTTTAGGTATACACCTGGTACAGTTTTGATGTGAAAGTAATTCTGAGCCCTTCCAAACCTAAAAA
131 TTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATTCCGAGCCCTTCCAAACCTAAAAA
* * *
30262742 ACAGATACATTATGCAAATAACAGATAATAGATACAAAATCACATGATTAACATGCTCGTATATA
196 ACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGCTCGTATACA
*
30262807 GATATTGTACTTACTTATGCTGAATAGTCAGACATATATATCGATTTCCTACTCAGATCAGACTA
261 GATATTGTACTTACTTATGCTGAATAGTCAGACATATATATCGATTTCCTACTCAGATCAAACTA
* *
30262872 TTAGATTAACAGATTACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGGTAGGCGTACAG
326 TTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGATAGGCGTACAG
* *
30262937 TCGATCAGAATGACTTGTGCTACCCTAAAGAAATTTTTAGAATTTTG
391 TCGATCAGAATGACCTGTGCTACCCTAAACAAATTTTTAGAATTTTG
*
30262984 GGCCCACACGGCCACACAATCTCCGTCACATGGCTGCGTCTCACACACAGCCAGCCGCACGACCG
1 GGCCCACACGGCCACACAATCTCCGTCACATGGCTACGTCTCACACACAGCCAGCCGCACGACCG
* *
30263049 GCCACACGCTCATGTGGCGTCGACAGACCAAATTTTTAGCTTTCGCCGAACCTTATTTTCTCATG
66 ACCACACGCCCATGTGGCGTCGACAGACCAAATTTTTAGCTTTCGCCGAACCTTATTTTCTCATG
30263114 TTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATTCCGAGCCCTTCCAAACCTAAAAA
131 TTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATTCCGAGCCCTTCCAAACCTAAAAA
30263179 ACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGCTCGTATACA
196 ACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGCTCGTATACA
30263244 GATATTGTACTTACTTATGCTGAATAGTCAGACATATATATCTG-TTTCCTACTCAGATCAAACT
261 GATATTGTACTTACTTATGCTGAATAGTCAGACATATATATC-GATTTCCTACTCAGATCAAACT
*
30263308 ATTAGATTAATAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGATAGGCGTACA
325 ATTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGATAGGCGTACA
*
30263373 GTCGATCGGAATGACCTGTGCTACCCTAAACAAATTTTTAGAATTTTG
390 GTCGATCAGAATGACCTGTGCTACCCTAAACAAATTTTTAGAATTTTG
30263421 GGCCCACACG
1 GGCCCACACG
30263431 CCCAATCTGG
Statistics
Matches: 427, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
437 426 1.00
438 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (437 bp):
GGCCCACACGGCCACACAATCTCCGTCACATGGCTACGTCTCACACACAGCCAGCCGCACGACCG
ACCACACGCCCATGTGGCGTCGACAGACCAAATTTTTAGCTTTCGCCGAACCTTATTTTCTCATG
TTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATTCCGAGCCCTTCCAAACCTAAAAA
ACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGCTCGTATACA
GATATTGTACTTACTTATGCTGAATAGTCAGACATATATATCGATTTCCTACTCAGATCAAACTA
TTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGATAGGCGTACAG
TCGATCAGAATGACCTGTGCTACCCTAAACAAATTTTTAGAATTTTG
Found at i:30272088 original size:22 final size:22
Alignment explanation
Indices: 30272063--30272109 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
30272053 TATACTTTTA
* *
30272063 AATAATAACCTTATTATTATTG
1 AATAATAACCGTATTATCATTG
30272085 AATAATAACCGTATTATCATTG
1 AATAATAACCGTATTATCATTG
30272107 AAT
1 AAT
30272110 TGGGTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (22 bp):
AATAATAACCGTATTATCATTG
Found at i:30275927 original size:3 final size:3
Alignment explanation
Indices: 30275919--30275947 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30275909 CATGGCTGAA
30275919 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30275948 AATTTGTTTC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30276234 original size:9 final size:9
Alignment explanation
Indices: 30276220--30276250 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30276210 GTTAAACTAA
30276220 TCGAGTTAT
1 TCGAGTTAT
*
30276229 TCGAGTTAA
1 TCGAGTTAT
30276238 TCGAGTTAT
1 TCGAGTTAT
30276247 TCGA
1 TCGA
30276251 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:30276421 original size:32 final size:32
Alignment explanation
Indices: 30276385--30276446 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
30276375 TTTTACTTTT
*
30276385 CCCCCAAAACTTTTACTCTCCTCCCCTCCCAA
1 CCCCCAAAACTTTTACTCCCCTCCCCTCCCAA
30276417 CCCCCAAAACTTTTACTCCCCTCCCCTCCC
1 CCCCCAAAACTTTTACTCCCCTCCCCTCCC
30276447 CTCCCAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.56, G:0.00, T:0.24
Consensus pattern (32 bp):
CCCCCAAAACTTTTACTCCCCTCCCCTCCCAA
Found at i:30278573 original size:20 final size:20
Alignment explanation
Indices: 30278535--30278573 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30278525 TCTTTCTTTT
* **
30278535 TTCTTTTCTTTTTGGTTCTG
1 TTCTATTCTTTTTCCTTCTG
30278555 TTCTATTCTTTTTCCTTCT
1 TTCTATTCTTTTTCCTTCT
30278574 TCTTTTTCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (20 bp):
TTCTATTCTTTTTCCTTCTG
Found at i:30290610 original size:21 final size:21
Alignment explanation
Indices: 30290584--30290645 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
30290574 AAAACACGCC
* *
30290584 AACAGAAGCTCGTGAGTGCTA
1 AACAGAAGCTCATGAGAGCTA
*
30290605 AACAGAAGCTCATGAGAGTTA
1 AACAGAAGCTCATGAGAGCTA
* *
30290626 AACAGAAGGTCATTAGAGCT
1 AACAGAAGCTCATGAGAGCT
30290646 GATCCACCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCATGAGAGCTA
Found at i:30297233 original size:21 final size:22
Alignment explanation
Indices: 30297209--30297253 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
30297199 AGAAAAAGAG
30297209 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
30297230 AAATCAAGAAAGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
30297252 AA
1 AA
30297254 CAATTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:30300088 original size:34 final size:34
Alignment explanation
Indices: 30300045--30300222 Score: 221
Period size: 34 Copynumber: 5.2 Consensus size: 34
30300035 CAGGTCCAAA
* *
30300045 AAGAAATGATACATGAACAGGAGAGATTCCCTGC
1 AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
* * *
30300079 AAGAAATGATGTGTTAACAGGAGAGATTCCCCGC
1 AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
* *
30300113 AACAAAATAATGCGTGAACAGGAGAGATTCCCTGC
1 AA-GAAATGATGCGTGAACAGGAGAGATTCCCTGC
* *
30300148 AATAAATGATGTGTGAACAGGAGAGATTCCCTGC
1 AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
* * * *
30300182 AACAAAATAATGCGTGAACAGGAAATATTCCCTGC
1 AA-GAAATGATGCGTGAACAGGAGAGATTCCCTGC
30300217 AAGAAA
1 AAGAAA
30300223 AGACAAGTGA
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
34 65 0.53
35 58 0.47
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (34 bp):
AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
Found at i:30300140 original size:35 final size:34
Alignment explanation
Indices: 30300058--30300223 Score: 215
Period size: 35 Copynumber: 4.8 Consensus size: 34
30300048 AAATGATACA
* * *
30300058 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
* *
30300092 TTAACAGGAGAGATTCCCCGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAATGCG
* * *
30300127 TGAACAGGAGAGATTCCCTGCAATAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
30300161 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAATGCG
* *
30300196 TGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAGAGATTCCCTGCAA-AAAA
30300224 GACAAGTGAA
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
34 52 0.46
35 62 0.54
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
Found at i:30300233 original size:69 final size:69
Alignment explanation
Indices: 30300058--30300222 Score: 285
Period size: 69 Copynumber: 2.4 Consensus size: 69
30300048 AAATGATACA
*
30300058 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTTAACAGGAGAGATTCCCCGCAACAAAATAA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
30300123 TGCG
66 TGCG
* *
30300127 TGAACAGGAGAGATTCCCTGCAATAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
30300192 TGCG
66 TGCG
* *
30300196 TGAACAGGAAATATTCCCTGCAAGAAA
1 TGAACAGGAGAGATTCCCTGCAAGAAA
30300223 AGACAAGTGA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 90 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (69 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
TGCG
Found at i:30300442 original size:18 final size:18
Alignment explanation
Indices: 30300419--30300474 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
30300409 TTTCTCCAAA
30300419 AAGTTTCTCAAAACTTTT
1 AAGTTTCTCAAAACTTTT
*
30300437 AAGTTT-ACAAAA--TTT
1 AAGTTTCTCAAAACTTTT
30300452 -AGTTTCTCAAAACTTTT
1 AAGTTTCTCAAAACTTTT
30300469 AAGTTT
1 AAGTTT
30300475 ACAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
17 8 0.25
18 11 0.34
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (18 bp):
AAGTTTCTCAAAACTTTT
Found at i:30300456 original size:32 final size:32
Alignment explanation
Indices: 30300420--30300484 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
30300410 TTCTCCAAAA
30300420 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
1 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
30300452 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
1 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
30300484 A
1 A
30300485 ATTTTTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (32 bp):
AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
Found at i:30300479 original size:17 final size:17
Alignment explanation
Indices: 30300427--30300480 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
30300417 AAAAGTTTCT
30300427 CAAAACTTTTAAGTTTA
1 CAAAACTTTTAAGTTTA
*
30300444 CAAAA--TTT-AGTTTCT
1 CAAAACTTTTAAGTTT-A
30300459 CAAAACTTTTAAGTTTA
1 CAAAACTTTTAAGTTTA
30300476 CAAAA
1 CAAAA
30300481 TTTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
17 13 0.42
18 5 0.16
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (17 bp):
CAAAACTTTTAAGTTTA
Found at i:30300520 original size:13 final size:14
Alignment explanation
Indices: 30300502--30300536 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
30300492 AGTTTCCAAA
30300502 TTTTCAAAC-TAAG
1 TTTTCAAACTTAAG
30300515 TTTTCAAACTTAAG
1 TTTTCAAACTTAAG
30300529 TTTTCAAA
1 TTTTCAAA
30300537 TTACAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTTCAAACTTAAG
Found at i:30302842 original size:6 final size:6
Alignment explanation
Indices: 30302831--30302858 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30302821 TAAATAAGTA
30302831 AATATT AATATT AATATT AATATT AATA
1 AATATT AATATT AATATT AATATT AATA
30302859 GTAGAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:30303041 original size:3 final size:3
Alignment explanation
Indices: 30302973--30303023 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
30302963 AAATGGAAAT
* * * * *
30302973 ATA ATG ATA ATA ACA ATA ATA CTA ATA GTA ATA CTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30303021 ATA
1 ATA
30303024 TATTAGTTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:30305246 original size:13 final size:13
Alignment explanation
Indices: 30305228--30305257 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30305218 ACTAAGTTTA
30305228 AATTTTAGTACTC
1 AATTTTAGTACTC
*
30305241 AATTTTATTACTC
1 AATTTTAGTACTC
30305254 AATT
1 AATT
30305258 AGAATCTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTTTAGTACTC
Found at i:30307779 original size:29 final size:30
Alignment explanation
Indices: 30307747--30307835 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 30
30307737 TTGATTTAAT
*
30307747 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTATATACATGAAACTTTAATTTG
* * *
30307776 GTGCAATTATACACGTGAAACTCTAATTGTG
1 GTGCAATTATATACATGAAACTTTAATT-TG
* * * *
30307807 GTTCAAATCTATACTTGAAACTTTAATTT
1 GTGCAATTATATACATGAAACTTTAATTT
30307836 TGATTTAATC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 14 0.29
30 10 0.21
31 24 0.50
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (30 bp):
GTGCAATTATATACATGAAACTTTAATTTG
Found at i:30309325 original size:43 final size:43
Alignment explanation
Indices: 30309277--30309571 Score: 351
Period size: 43 Copynumber: 6.9 Consensus size: 43
30309267 TTATGTGGAA
* * * * *
30309277 AAACACCGCTATAGAACATGACATTTACCAGTGCTCTT-CCCAT
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCGCT-TTCCCCAC
*
30309320 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
* * *
30309363 AAACGCCGCTATAGAATATGACCTTTAGC-GCCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAG-CGCTTTCCCCAC
*
30309406 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
* * * * * * * *
30309449 AAACGCTGCTATAGAATATGACGTTTAGCTGCACTTTTCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
*
30309492 AAACACTGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
** * *
30309535 AAATGCCGCTAAATAACATGACCTTTAGCGGCGCTTT
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCGCTTT
30309572 TAATAAAAGT
Statistics
Matches: 217, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
42 3 0.01
43 213 0.98
44 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACACCGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
Found at i:30309572 original size:86 final size:86
Alignment explanation
Indices: 30309277--30309572 Score: 412
Period size: 86 Copynumber: 3.4 Consensus size: 86
30309267 TTATGTGGAA
* * * * * * * *
30309277 AAACACCGCTATAGAACATGACATTTACCAGTGCTCTTCCCATAAACACCGCTAAAGAACATGAC
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
30309342 CTTTAGCGGCGCTTTCCCCAC
66 CTTTAGCGGCGCTTTCCCCAC
* *
30309363 AAACGCCGCTATAGAATATGACCTTTAGCGCCGCTTTCCCCACAAACACCGCTAAAGAACATGAC
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
30309428 CTTTAGCGGCGCTTTCCCCAC
66 CTTTAGCGGCGCTTTCCCCAC
* * * * *
30309449 AAACGCTGCTATAGAATATGACGTTTAGCTGCACTTTTCCCACAAACACTGCTAAAGAACATGAC
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
*
30309514 CTTTAGCAGCGCTTTCCCCAC
66 CTTTAGCGGCGCTTTCCCCAC
* * * *
30309535 AAATGCCGCTAAATAACATGACCTTTAGCGGCGCTTTT
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTT
30309573 AATAAAAGTG
Statistics
Matches: 184, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 184 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTCCCCAC
Found at i:30309970 original size:21 final size:21
Alignment explanation
Indices: 30309944--30309988 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
30309934 CTTTGCTTTA
**
30309944 CTTCCCTCGTTGCTGCCTCTG
1 CTTCCCTCACTGCTGCCTCTG
30309965 CTTCCCTCACTGCTGCCTCTG
1 CTTCCCTCACTGCTGCCTCTG
30309986 CTT
1 CTT
30309989 TAAGCTGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.44, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTCCCTCACTGCTGCCTCTG
Found at i:30317299 original size:2 final size:2
Alignment explanation
Indices: 30317292--30317339 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
30317282 GAGGAGGAAA
* * *
30317292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30317334 AT AT AT
1 AT AT AT
30317340 GAATATTCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30317345 original size:8 final size:8
Alignment explanation
Indices: 30317293--30317345 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
30317283 AGGAGGAAAA
*
30317293 TATATATA
1 TATATATG
*
30317301 TATATATA
1 TATATATG
*
30317309 TATATATA
1 TATATATG
30317317 TATATATG
1 TATATATG
*
30317325 TATGTATG
1 TATATATG
30317333 TATATATG
1 TATATATG
*
30317341 AATAT
1 TATAT
30317346 TCAGTTAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (8 bp):
TATATATG
Found at i:30321232 original size:9 final size:9
Alignment explanation
Indices: 30321218--30321265 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
30321208 TAAGTATAAT
30321218 TAAGTTATG
1 TAAGTTATG
30321227 TAAGTTATG
1 TAAGTTATG
*
30321236 ATATATATTTATG
1 ---TA-AGTTATG
30321249 TAAGTTATG
1 TAAGTTATG
30321258 TAAGTTAT
1 TAAGTTAT
30321266 AAAATTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 23 0.70
10 2 0.06
12 2 0.06
13 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:30321970 original size:29 final size:30
Alignment explanation
Indices: 30321911--30321982 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
30321901 GATTTGGATT
*
30321911 TAAATTTTTAAAATAATATAATTTGAGTAA
1 TAAATTTTTAAAATAATATAATTTCAGTAA
30321941 TAAATTATTT-AAA-AATATAATATTCA-TAA
1 TAAATT-TTTAAAATAATATAAT-TTCAGTAA
*
30321970 T-TATTTTTAAAAT
1 TAAATTTTTAAAAT
30321983 TTATGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 3 0.08
28 6 0.17
29 12 0.33
30 12 0.33
31 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (30 bp):
TAAATTTTTAAAATAATATAATTTCAGTAA
Found at i:30322424 original size:2 final size:2
Alignment explanation
Indices: 30322417--30322450 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30322407 CTATTTAAAC
30322417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30322451 GCATCAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30327844 original size:110 final size:111
Alignment explanation
Indices: 30327644--30327871 Score: 300
Period size: 110 Copynumber: 2.0 Consensus size: 111
30327634 CAAATTATAC
* **
30327644 AATTACAAGTCATGCACATCATCTAAGATAGGTAATGTATCCAAGAATGGTTCAAAATATAATAT
1 AATTACAAGTCATGCACATCATCTAAGATAGGTAACGTA--CAAGAAAAGTTCAAAATATAATAT
*
30327709 TATCAAAGAAAGTTCAAAGAGGAAGTA-TCCAAAGTCCTAACAAAACCT
64 TACCAAAGAAAGTTCAAAGAGGAAGTACT-CAAAGTCCTAACAAAACCT
** *
30327757 AATTACAAGTCATGCGTATCATTTAAGATTA-GTAACGTA-AAGAAAAGTTCAAAATATAATATT
1 AATTACAAGTCATGCACATCATCTAAGA-TAGGTAACGTACAAGAAAAGTTCAAAATATAATATT
** * *
30327820 ACCATGGAAAGTTCAAAGATGAAGTACTCAAAGTTCTAACAAAACCT
65 ACCAAAGAAAGTTCAAAGAGGAAGTACTCAAAGTCCTAACAAAACCT
30327867 AATTA
1 AATTA
30327872 TACAAAGCCC
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
110 67 0.66
111 1 0.01
113 32 0.31
114 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (111 bp):
AATTACAAGTCATGCACATCATCTAAGATAGGTAACGTACAAGAAAAGTTCAAAATATAATATTA
CCAAAGAAAGTTCAAAGAGGAAGTACTCAAAGTCCTAACAAAACCT
Found at i:30344853 original size:15 final size:15
Alignment explanation
Indices: 30344833--30344861 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30344823 TGTTAAAAAA
30344833 TGGATAATTTTGTTG
1 TGGATAATTTTGTTG
30344848 TGGATAATTTTGTT
1 TGGATAATTTTGTT
30344862 ATAGATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (15 bp):
TGGATAATTTTGTTG
Found at i:30345043 original size:17 final size:18
Alignment explanation
Indices: 30345013--30345046 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30345003 TATTTAATCT
30345013 AATTCATTTAATATATTC
1 AATTCATTTAATATATTC
*
30345031 AATT-ATTTTATATATT
1 AATTCATTTAATATATT
30345047 AAATATTTAA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTCATTTAATATATTC
Found at i:30356144 original size:21 final size:18
Alignment explanation
Indices: 30356103--30356145 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 18
30356093 AATAAATTTT
*
30356103 TTTTATTATTTTAAATTA
1 TTTTATTATTTTAAATAA
30356121 TTTTATTAATTTTTACAATAA
1 TTTTATT-A-TTTTA-AATAA
30356142 TTTT
1 TTTT
30356146 GTAATTACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 5 0.24
21 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTATTTTAAATAA
Found at i:30359652 original size:13 final size:13
Alignment explanation
Indices: 30359636--30359663 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30359626 AAAACACGCT
30359636 AATAAAAAGTAAA
1 AATAAAAAGTAAA
30359649 AATAAAAAGTAAA
1 AATAAAAAGTAAA
30359662 AA
1 AA
30359664 AAACTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AATAAAAAGTAAA
Found at i:30359672 original size:16 final size:17
Alignment explanation
Indices: 30359646--30359687 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
30359636 AATAAAAAGT
30359646 AAAAA-TAAAA-AGTAAA
1 AAAAACTAAAATA-TAAA
30359662 AAAAACTAAAATATAAA
1 AAAAACTAAAATATAAA
30359679 AAAAACTAA
1 AAAAACTAA
30359688 TGGAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.21
17 18 0.75
18 1 0.04
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAAACTAAAATATAAA
Found at i:30365842 original size:28 final size:28
Alignment explanation
Indices: 30365809--30365907 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
30365799 TAATGAGATT
* * *
30365809 AGCACTAAGTGTGTGAGTTTAATTG-AA
1 AGCACTAAGTGTGCGAGTATAATGGTAA
30365836 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATGGTAA
* * ** *
30365865 AGCACTAAGTGTGCGAGTGTGATTATTA
1 AGCACTAAGTGTGCGAGTATAATGGTAA
30365893 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
30365908 TACTTATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 58 0.94
29 3 0.05
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATAATGGTAA
Found at i:30367987 original size:36 final size:39
Alignment explanation
Indices: 30367927--30368002 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 39
30367917 ATAAACATTA
* *
30367927 AAAAATTATTTTAAAAATTTAAAAATAAAA-ATAT-TTT
1 AAAAAGTATTTTAAAAATTAAAAAATAAAATATATATTT
30367964 AAAAAGTATTTT-AAAATTAAAAAATAAAATATATATTT
1 AAAAAGTATTTTAAAAATTAAAAAATAAAATATATATTT
30368002 A
1 A
30368003 TTATATTCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 16 0.46
37 15 0.43
38 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (39 bp):
AAAAAGTATTTTAAAAATTAAAAAATAAAATATATATTT
Found at i:30381455 original size:44 final size:45
Alignment explanation
Indices: 30381377--30381461 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
30381367 ATCATACTTG
30381377 ACCTGAATCTAACCCCACCCGACCTAACCGATTAGCACTAATTTA
1 ACCTGAATCTAACCCCACCCGACCTAACCGATTAGCACTAATTTA
* * *
30381422 ACCTGAATCTAGCCCC-GCCGACCTAGCTC-ATTAGCACTAA
1 ACCTGAATCTAACCCCACCCGACCTAAC-CGATTAGCACTAA
30381462 GGGCCAGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 20 0.56
45 16 0.44
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.21
Consensus pattern (45 bp):
ACCTGAATCTAACCCCACCCGACCTAACCGATTAGCACTAATTTA
Found at i:30381495 original size:13 final size:13
Alignment explanation
Indices: 30381477--30381542 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
30381467 AGTTCTTCAT
30381477 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
30381490 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
** *
30381503 TGCCGTGGAAAAG
1 TGCTTTTGAAAAG
* *
30381516 TGATTTTGAGAAG
1 TGCTTTTGAAAAG
30381529 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
30381542 T
1 T
30381543 TTGGTTTAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:30381765 original size:31 final size:29
Alignment explanation
Indices: 30381712--30381773 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
30381702 TTATAACTTG
*
30381712 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATAT-AAATATAAA
*
30381742 TTGTAAATATTTTTAAT-TAATAAATATTAA
1 TTGTAAATA-TTTTAATAT-ATAAATATAAA
30381772 TT
1 TT
30381774 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (29 bp):
TTGTAAATATTTTAATATATAAATATAAA
Found at i:30381789 original size:31 final size:33
Alignment explanation
Indices: 30381724--30381828 Score: 92
Period size: 33 Copynumber: 3.1 Consensus size: 33
30381714 GTTAATATTT
* *
30381724 TAATATATAAAATATAAATTGTAAATATTTTTAATTAA
1 TAATATATAAACTAT--ATTTTAAATA--TTTAATT-A
*
30381762 TAA-ATATTAA-T-TATTTATAAA-ATTTAATTA
1 TAATATATAAACTATATTT-TAAATATTTAATTA
*
30381792 TAATATATAAACTATATTTTAAATATTTAAATA
1 TAATATATAAACTATATTTTAAATATTTAATTA
30381825 TAAT
1 TAAT
30381829 CATTAAATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
30 4 0.07
31 13 0.22
32 5 0.09
33 21 0.36
34 4 0.07
35 1 0.02
36 1 0.02
37 6 0.10
38 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
TAATATATAAACTATATTTTAAATATTTAATTA
Done.