Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003061.1 Hibiscus syriacus cultivar Beakdansim tig00006379_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 150185
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8084 original size:14 final size:15
Alignment explanation
Indices: 8067--8099 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
8057 TATTATTTTC
8067 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
8081 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
8096 AAAT
1 AAAT
8100 AAAATAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:11359 original size:2 final size:2
Alignment explanation
Indices: 11352--11381 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11342 TTTATACTCG
11352 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
11382 CTCAACGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12647 original size:19 final size:19
Alignment explanation
Indices: 12625--12663 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12615 CATATGATAT
12625 AAATAAATACATAACACAA
1 AAATAAATACATAACACAA
** *
12644 AAATATGTACATAATACAA
1 AAATAAATACATAACACAA
12663 A
1 A
12664 TGAATATTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.13, G:0.03, T:0.21
Consensus pattern (19 bp):
AAATAAATACATAACACAA
Found at i:14317 original size:3 final size:3
Alignment explanation
Indices: 14303--14349 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
14293 CAAAATGTAT
*
14303 TAA TAA -AA TAA TAA TAA TAA TAA TAC TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14349 T
1 T
14350 TAAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:14359 original size:26 final size:26
Alignment explanation
Indices: 14304--14359 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
14294 AAAATGTATT
**
14304 AATAAAATAATAATAATAATAATACT
1 AATAAAATAATAATAATAATAATAAA
*
14330 AATATAATAATAATAATAATTAA-AAA
1 AATAAAATAATAATAATAA-TAATAAA
14356 AATA
1 AATA
14360 GAAAAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AATAAAATAATAATAATAATAATAAA
Found at i:14746 original size:134 final size:132
Alignment explanation
Indices: 14507--14956 Score: 487
Period size: 134 Copynumber: 3.4 Consensus size: 132
14497 GTTGGTTGTT
* * * * * *
14507 GGGGACGACACTGCTCATACATGATGAAGAGTTCTGGTCATATTTAGGAATAGTGATAACTCGGT
1 GGGGATGACACTGCTCATACGTGATGAAGAATTCTGGCCATCTTTAGGAAGAGTGATAACTC-GT
*
14572 TCCTACGCGATGAGGACAGCTGGTTATCTAGGGGTGACACGGCTCCTACGCGATAAGGAGATCTG
65 TCCTACGCGATGAGGAC-GCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATAAGGAGATCTG
14637 GTC-
129 GTCA
*
14640 GGGGATGACACTGCTCATACGTGATGAAGAATTCTTGGCCATCTTTAGGAAGGGTGATAACTCGA
1 GGGGATGACACTGCTCATACGTGATGAAGAATTC-TGGCCATCTTTAGGAAGAGTGATAACTCG-
* * * * *
14705 CTCTTACGCGATGAGGACGTCTGGTTATCTAGGGGTGACACGGATCCTACGTGATGAGGAGGTCT
64 TTCCTACGCGATGAGGACG-CTGGTTATCTAGGGGTGACACGGCTCCTACGTGATAAGGAGATCT
14770 GGTCA
128 GGTCA
* * * * * *
14775 GGGGATGACACAGTTCCTACGTGATG-AGGATAGCTGGCCATCTTTAGG-AGTTA-TGATAATTA
1 GGGGATGACACTGCTCATACGTGATGAAGAAT-TCTGGCCATCTTTAGGAAG--AGTGATAACT-
* * * * * * * *
14837 TGTTCCTACGTGATGAGGATGACTGGTTATCTATGGTTGAAATGGCTCCTACGTGATGAA-GATA
62 CGTTCCTACGCGATGAGGACG-CTGGTTATCTAGGGGTGACACGGCTCCTACGTGAT-AAGGAGA
*
14901 TCTGGTCG
125 TCTGGTCA
* * *
14909 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGCCATCTTTAGG
1 GGGGATGACACTGCTCATACGTGATGAAGAATTCTGGCCATCTTTAGG
14957 GATATTGGTT
Statistics
Matches: 265, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
133 35 0.13
134 201 0.76
135 29 0.11
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (132 bp):
GGGGATGACACTGCTCATACGTGATGAAGAATTCTGGCCATCTTTAGGAAGAGTGATAACTCGTT
CCTACGCGATGAGGACGCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATAAGGAGATCTGGT
CA
Found at i:14762 original size:43 final size:40
Alignment explanation
Indices: 14709--14804 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 40
14699 ACTCGACTCT
* *
14709 TACGCGATGAGGACGTCTGGTTATCTAGGGG-TGACACGGATCC
1 TACGTGATGAGGACGTCTGG---TC-AGGGGATGACACAGATCC
* *
14752 TACGTGATGAGGAGGTCTGGTCAGGGGATGACACAGTTCC
1 TACGTGATGAGGACGTCTGGTCAGGGGATGACACAGATCC
14792 TACGTGATGAGGA
1 TACGTGATGAGGA
14805 TAGCTGGCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 5 0.10
40 25 0.52
43 18 0.38
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (40 bp):
TACGTGATGAGGACGTCTGGTCAGGGGATGACACAGATCC
Found at i:15034 original size:28 final size:29
Alignment explanation
Indices: 14964--15051 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 29
14954 AGGGATATTG
** * *
14964 GTTTCAAGTTAAACCAACTCAAAGGTGAT
1 GTTTCAAGAAAAACAAACTCAAAGATGAT
*
14993 GTTTCAA-AATAAACAAACTCAAAGAT-TT
1 GTTTCAAGAA-AAACAAACTCAAAGATGAT
* *
15021 GTTTCAAGAAAAACAAGCTCAAAGATAAT
1 GTTTCAAGAAAAACAAACTCAAAGATGAT
15050 GT
1 GT
15052 GTTTCAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
28 23 0.47
29 26 0.53
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (29 bp):
GTTTCAAGAAAAACAAACTCAAAGATGAT
Found at i:15143 original size:63 final size:64
Alignment explanation
Indices: 15058--15243 Score: 200
Period size: 67 Copynumber: 2.9 Consensus size: 64
15048 ATGTGTTTCA
* * *
15058 AAAGC-AACTGTCTCGAAAGAGACAAAATTCGTTTCAAGAGAAACGA-CTCAAAGATAACATT-G
1 AAAGCAAACTGTCTC-AAAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATAACATTCC
* * * **
15120 AAAGCAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAAC-ATTCTCAAAGATTGATGT
1 AAAGCAAACTGTCTCAA-AGAGACAAAATTTG-TTTCAAGGGAAACGA-TCTCAAAGA-TAACAT
15184 TCC
62 TCC
* *
15187 ATAGCAAACTGTCTCAAATGAGACAAAATTTGTATCAAGGGAAACGATCTCAAAGAT
1 AAAGCAAACTGTCTCAAA-GAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
15244 GTTTGTGTTG
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
62 7 0.07
63 22 0.21
64 11 0.11
65 9 0.09
66 24 0.23
67 30 0.29
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (64 bp):
AAAGCAAACTGTCTCAAAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATAACATTCC
Found at i:15767 original size:65 final size:67
Alignment explanation
Indices: 15698--15838 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 67
15688 TGGAAATGAT
* * * *
15698 CTCAAAGATGGGTATTT-TCAAAAGAAATTGTCTCGAGAGATAA-AATTTTGTTT-TAAAGAAAA
1 CTCAAAGAT-GGTATTTCTCAAAAGAAATTGTCTCAAGAGACAATAATTTTATTTCCAAAG-AAA
15760 CA-A
64 CAGA
** * * *
15763 CTCAAAGATTTTTTTTCTCCAAATAAATTGTCTCAAGAGACAATAATTTTATTTCCAAAGAAACA
1 CTCAAAGATGGTATTTCTCAAAAGAAATTGTCTCAAGAGACAATAATTTTATTTCCAAAGAAACA
15828 GA
66 GA
15830 CTCAAAGAT
1 CTCAAAGAT
15839 TTTTTTTATT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
64 4 0.06
65 31 0.49
66 14 0.22
67 14 0.22
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (67 bp):
CTCAAAGATGGTATTTCTCAAAAGAAATTGTCTCAAGAGACAATAATTTTATTTCCAAAGAAACA
GA
Found at i:15836 original size:67 final size:65
Alignment explanation
Indices: 15610--15845 Score: 212
Period size: 67 Copynumber: 3.6 Consensus size: 65
15600 TCAAAGATGG
* * * *
15610 TTTTATTTCAATAGAAACAAACTCAATGATTTTATGTTTCCAAATAAATTGCCTCAAGGGAGACA
1 TTTTATTTCAATAGAAACAGACTCAAAGATTTT-TTTTTCCAAATAAATTGTCTCAA--GAGACA
15675 AAA
63 AAA
* * * ** * * * * *
15678 -TTTGTTTCAATGGAAA-TGATCTCAAAGATGGGTATTTTCAAAAGAAATTGTCTCGAGAGATAA
1 TTTTATTTCAATAGAAACAGA-CTCAAAGAT-TTTTTTTTCCAAATAAATTGTCTCAAGAGACAA
15741 AA
64 AA
* *
15743 TTTTGTTTTAA-AGAAAACA-ACTCAAAGATTTTTTTTCTCCAAATAAATTGTCTCAAGAGACAA
1 TTTTATTTCAATAG-AAACAGACTCAAAGATTTTTTTT-TCCAAATAAATTGTCTCAAGAGACAA
15806 TAA
64 -AA
15809 TTTTATTTCCAA-AGAAACAGACTCAAAGATTTTTTTT
1 TTTTATTT-CAATAGAAACAGACTCAAAGATTTTTTTT
15846 ATTTCAAAAG
Statistics
Matches: 133, Mismatches: 26, Indels: 19
0.75 0.15 0.11
Matches are distributed among these distances:
64 4 0.03
65 40 0.30
66 28 0.21
67 60 0.45
68 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (65 bp):
TTTTATTTCAATAGAAACAGACTCAAAGATTTTTTTTTCCAAATAAATTGTCTCAAGAGACAAAA
Found at i:15869 original size:32 final size:33
Alignment explanation
Indices: 15809--15870 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
15799 GAGACAATAA
*
15809 TTTTATTTCCAAAGAAACAGACTCAAAGATTTT
1 TTTTATTTCAAAAGAAACAGACTCAAAGATTTT
15842 TTTTATTTCAAAAGAAAC-GACTCAAAGAT
1 TTTTATTTCAAAAGAAACAGACTCAAAGAT
15871 GATGGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (33 bp):
TTTTATTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:16381 original size:4 final size:4
Alignment explanation
Indices: 16372--16441 Score: 99
Period size: 4 Copynumber: 18.0 Consensus size: 4
16362 TTTATGTATC
* * *
16372 ATGT ATGT ATGT ATG- -TGT ATAT ATGT ATGT ATGT ATAT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
16418 ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT
16442 CTTTTCTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
4 56 0.97
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:17491 original size:4 final size:4
Alignment explanation
Indices: 17482--18003 Score: 1012
Period size: 4 Copynumber: 131.0 Consensus size: 4
17472 TATTGTACAC
17482 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17530 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17578 GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17624 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17672 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17720 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17768 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
17816 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GCAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17864 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17912 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17960 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
18004 ATATTGGGTA
Statistics
Matches: 514, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 512 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:24034 original size:22 final size:22
Alignment explanation
Indices: 24004--24047 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
23994 AGAGGAAGCT
*
24004 TGGCTTGGCAGCT-GAAACGTTG
1 TGGCATGGCAGCTGGAAA-GTTG
*
24026 TGGCATGGCGGCTGGAAAGTTG
1 TGGCATGGCAGCTGGAAAGTTG
24048 AAGAGGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.18, C:0.16, G:0.41, T:0.25
Consensus pattern (22 bp):
TGGCATGGCAGCTGGAAAGTTG
Found at i:24285 original size:3 final size:3
Alignment explanation
Indices: 24273--24349 Score: 122
Period size: 3 Copynumber: 26.3 Consensus size: 3
24263 CAAAATGTAT
* *
24273 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA T-A TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24319 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
24350 TAAAAAAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:28994 original size:110 final size:110
Alignment explanation
Indices: 28848--29051 Score: 345
Period size: 110 Copynumber: 1.9 Consensus size: 110
28838 TGGGAAATTA
28848 TTTGTTGACAATCAGACGCCCCTTCGTCGTAAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAATCAGACGCCCCTTCGTCGTAAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCC
**
28913 TTCGTTATGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTG
66 TTCACTATGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTG
* * *
28958 TTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCC
1 TTTGTTGACAATCAGACGCCCCTTCGTCGTAAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCC
* *
29023 TTCACTGTGAAGTTGAAATTGGCTCTGAA
66 TTCACTATGAAGTTGAAATTGACTCTGAA
29052 ATTGGGAAGC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (110 bp):
TTTGTTGACAATCAGACGCCCCTTCGTCGTAAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCC
TTCACTATGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTG
Found at i:33100 original size:27 final size:27
Alignment explanation
Indices: 33033--33110 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 27
33023 TTGTAAAAAT
* * *
33033 AAAAATAAACATGAGAA-AATAATAATA
1 AAAAATAAATAT-ATAATAATATTAATA
*
33060 AAAAAT-ATTAATATAATAATATTAATA
1 AAAAATAAAT-ATATAATAATATTAATA
33087 AAAAATAAATATATATATATATAT
1 AAAAATAAATATATA-ATA-ATAT
33111 AACAATGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.10
27 28 0.68
28 5 0.12
29 4 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAAATAAATATATAATAATATTAATA
Found at i:33543 original size:32 final size:32
Alignment explanation
Indices: 33469--33552 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 32
33459 GTCCTACTTG
* *
33469 GACTCAAATGC-TTCGGTTTTAGTGTTTCAATAG
1 GACTCAAATACGTT-GG-TTTAGTGTTTCAATAA
*
33502 GACTC-AATACGTTGGTTTAGTGTTTTAATAA
1 GACTCAAATACGTTGGTTTAGTGTTTCAATAA
*
33533 GACTCAAATACGTTGATTTA
1 GACTCAAATACGTTGGTTTA
33553 TTTTTTGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
31 19 0.42
32 19 0.42
33 7 0.16
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (32 bp):
GACTCAAATACGTTGGTTTAGTGTTTCAATAA
Found at i:33627 original size:23 final size:22
Alignment explanation
Indices: 33596--33649 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
33586 TGTGGGGCCT
* **
33596 ATAAAAATAATAACAAAATATTA
1 ATAATAATAATAAATAAATAT-A
33619 ATAATAATAATAAATAAATATA
1 ATAATAATAATAAATAAATATA
33641 AT-ATAATAA
1 ATAATAATAA
33650 AATATTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 7 0.25
22 3 0.11
23 18 0.64
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAATAATAATAAATAAATATA
Found at i:38067 original size:17 final size:18
Alignment explanation
Indices: 38036--38069 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38026 TTTTGTAGAA
38036 ATAACTATAAATACAATC
1 ATAACTATAAATACAATC
*
38054 ATAA-TATAATTACAAT
1 ATAACTATAAATACAAT
38070 TAATTAGTAT
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAACTATAAATACAATC
Found at i:41349 original size:11 final size:11
Alignment explanation
Indices: 41333--41358 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41323 AAATTAATTT
41333 AAATAAAATAA
1 AAATAAAATAA
41344 AAATAAAATAA
1 AAATAAAATAA
41355 AAAT
1 AAAT
41359 GATTATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:42578 original size:23 final size:24
Alignment explanation
Indices: 42542--42604 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 24
42532 CCACTATATA
42542 ATATATATATTATAATATAATATGT
1 ATATATATATTATAATATAA-ATGT
42567 ATATAT-TA-TATAATATAAATGT
1 ATATATATATTATAATATAAATGT
*
42589 AACATATATACTTATA
1 -ATATATATA-TTATA
42605 CAATACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 4 0.12
23 15 0.45
24 4 0.12
25 6 0.18
26 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (24 bp):
ATATATATATTATAATATAAATGT
Found at i:42634 original size:25 final size:27
Alignment explanation
Indices: 42566--42634 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 27
42556 ATATAATATG
*
42566 TATAT-ATTATATAATATAAATGTAACA
1 TATATAATTATATAATACAAA-GTAACA
* *
42593 TATATACTTATACAATACAAA-TAA-A
1 TATATAATTATATAATACAAAGTAACA
*
42618 TATATAATCATATAATA
1 TATATAATTATATAATA
42635 TTTATACTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 15 0.43
26 3 0.09
27 5 0.14
28 12 0.34
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (27 bp):
TATATAATTATATAATACAAAGTAACA
Found at i:49756 original size:21 final size:21
Alignment explanation
Indices: 49732--49772 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49722 TTGAAATGTT
* *
49732 GTTGCTTTTTCTACTTCTCTC
1 GTTGCTCTATCTACTTCTCTC
*
49753 GTTGCTCTATCTGCTTCTCT
1 GTTGCTCTATCTACTTCTCT
49773 GCTCCATAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.29, G:0.12, T:0.54
Consensus pattern (21 bp):
GTTGCTCTATCTACTTCTCTC
Found at i:52100 original size:42 final size:43
Alignment explanation
Indices: 51985--52140 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 43
51975 AAACAAGCGT
* * * * * *
51985 CACTAAAGTACGAGTCTTTAGTGACATTTTTAAACACAAACAC
1 CACTAAAGTATGAGTGTATAGAGGCATTTGTAAACACAAACAC
* **
52028 CACTAAAGTATGAGTTTATAGAGGCATTTGTAAACACAAATGC
1 CACTAAAGTATGAGTGTATAGAGGCATTTGTAAACACAAACAC
* * * *
52071 CACT-AAGTACT-AGTGTATAGCGGCGTTTGTATA-A-AAACGC
1 CACTAAAGTA-TGAGTGTATAGAGGCATTTGTAAACACAAACAC
** *
52111 CACTAAAGTATGAGCCTATAGCGGCATTTG
1 CACTAAAGTATGAGTGTATAGAGGCATTTG
52141 CATAAAAACG
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
40 10 0.11
41 21 0.22
42 23 0.24
43 40 0.43
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (43 bp):
CACTAAAGTATGAGTGTATAGAGGCATTTGTAAACACAAACAC
Found at i:52132 original size:41 final size:41
Alignment explanation
Indices: 51962--52239 Score: 245
Period size: 41 Copynumber: 6.7 Consensus size: 41
51952 ATGTAAAATT
* * * *
51962 GCGGCGTTTGTAAAAACAAGCGTCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAA-AA-CGCCACTAAAGTATGAGTCTATA
* * * * * * *
52005 GTGACATTTTTAAACACAAACACCACTAAAGTATGAGTTTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTATGAGTCTATA
* * * * *
52048 GAGGCATTTGTAAACACAAATGCCACT-AAGTACT-AGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTA-TGAGTCTATA
*
52090 GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGCCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATA
* * * *
52131 GCGGCATTTGCATAAAAACGTCACTAAAGTATGAATCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATA
* * * *
52172 GCGACGTTTGCATAAAAATGCCATTAAAGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATA
*
52213 GCGTCGTTTGTATAAAAACGCCACTAA
1 GCGGCGTTTGTATAAAAACGCCACTAA
52240 CGTACTAGTC
Statistics
Matches: 194, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
40 10 0.05
41 106 0.55
42 23 0.12
43 51 0.26
44 3 0.02
45 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATA
Found at i:54082 original size:13 final size:13
Alignment explanation
Indices: 54064--54093 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54054 TTTAATTTTC
54064 GATTTGTATGTTT
1 GATTTGTATGTTT
54077 GATTTGTATGTTT
1 GATTTGTATGTTT
54090 -ATTT
1 GATTT
54094 AAATTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (13 bp):
GATTTGTATGTTT
Found at i:62324 original size:8 final size:8
Alignment explanation
Indices: 62311--62433 Score: 106
Period size: 8 Copynumber: 14.6 Consensus size: 8
62301 CTTGAAGAAG
*
62311 AAAAATTA
1 AAAAATGA
62319 AAAAATG-
1 AAAAATGA
62326 AAAAATGA
1 AAAAATGA
**
62334 AAAAGAAAA
1 AAAA-ATGA
62343 AAAAATGA
1 AAAAATGA
* *
62351 GAAAGA-GC
1 -AAAAATGA
*
62359 AAAAAGGA
1 AAAAATGA
62367 AAAAATGA
1 AAAAATGA
62375 AAAAATGA
1 AAAAATGA
62383 AAAAATGAA
1 AAAAATG-A
62392 AAAAATGA
1 AAAAATGA
62400 AAAAATGGAA
1 AAAAAT-G-A
62410 GAAGAAATGAA
1 -AA-AAATG-A
62421 AAAAATGA
1 AAAAATGA
62429 AAAAA
1 AAAAA
62434 AAGAAGAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
7 11 0.11
8 49 0.51
9 24 0.25
10 3 0.03
11 5 0.05
12 4 0.04
ACGTcount: A:0.74, C:0.01, G:0.15, T:0.10
Consensus pattern (8 bp):
AAAAATGA
Found at i:62348 original size:17 final size:16
Alignment explanation
Indices: 62326--62446 Score: 71
Period size: 17 Copynumber: 7.0 Consensus size: 16
62316 TTAAAAAATG
62326 AAAAATGAAAAAGAAAA
1 AAAAATGAAAAA-AAAA
* * **
62343 AAAAATGAGAAAGAGC
1 AAAAATGAAAAAAAAA
* **
62359 AAAAAGGAAAAAATGA
1 AAAAATGAAAAAAAAA
*
62375 AAAAATGAAAAAATGAA
1 AAAAATGAAAAAA-AAA
62392 AAAAATGAAAAAATGGAAGA
1 AAAAATGAAAAAA---AA-A
*
62412 AGAAATGAAAAAAATGAA
1 AAAAATGAAAAAAA--AA
*
62430 AAAAAAGAAGAAAAAAA
1 AAAAATGAA-AAAAAAA
62447 GAACATAAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
16 24 0.30
17 28 0.35
18 8 0.10
19 7 0.09
20 13 0.16
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.07
Consensus pattern (16 bp):
AAAAATGAAAAAAAAA
Found at i:63844 original size:55 final size:56
Alignment explanation
Indices: 63778--64148 Score: 353
Period size: 55 Copynumber: 6.8 Consensus size: 56
63768 GAAGCAAATC
* * * *
63778 AAGATTGTTCGAGTTC-TATACTCGCTGAAAGAATAAGGAGCGGACCCGTTTTCAG
1 AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGCTG
* ** * * * *
63833 AAGATTGTTCGAGTTC-TATACTCCCTGAAAAAATAGGGAAAGAACTCGTTTTCAG
1 AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGCTG
* * * * * *
63888 AAGATTGTTCGTGTTC-TATACTCCCTAAAAAGAATAGGTAGCGGGCTCATTTGCTG
1 AAGATTGTTCGAGTTCTTATACTCCCT-GAAAGAATAGGGAGCGGACCCGTTTGCTG
* * **
63944 AATATTGTTTGAG-TCTTATACTCCCTGAAAGAATAGGGAG-TAACCCGTTTGCTG
1 AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGCTG
* * **
63998 AAGATTGTTCGAG-TCTTATACTCCCTAAAAGAATAGGGAGTGGAAACGTTTGCTG
1 AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGCTG
* * * ** ** * *
64053 AAAATTGTTC-ATTTCTTATACTCCCTGAACGAATAGGGAGAAGAAACATTTGTTG
1 AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGCTG
* *
64108 AAGATTATTAGAG-TCTTATACTCCCTGAAAGAATAGGGAGC
1 AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGC
64149 AGACTCGCCA
Statistics
Matches: 262, Mismatches: 49, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
54 47 0.18
55 175 0.67
56 40 0.15
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (56 bp):
AAGATTGTTCGAGTTCTTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTTGCTG
Found at i:66928 original size:12 final size:13
Alignment explanation
Indices: 66902--66933 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
66892 TGGTTTAATT
66902 TTTGATTTGTATG
1 TTTGATTTGTATG
66915 TTTGATTT-TATG
1 TTTGATTTGTATG
66927 TTT-ATTT
1 TTTGATTT
66934 AAATTTAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.21
12 7 0.37
13 8 0.42
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (13 bp):
TTTGATTTGTATG
Found at i:68047 original size:81 final size:81
Alignment explanation
Indices: 67956--68236 Score: 298
Period size: 82 Copynumber: 3.4 Consensus size: 81
67946 CGTTTTGACA
* * * * * * *
67956 TAAAGAACTACTTTATTGCGGTGTTTGTTGAAAAAAACCATTATAGATGAACCCATTGTGACGCT
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAAACCACTATAGATGAACCCATTGCGACGTT
* *
68021 TGTATAAAAACGCCAC
66 TGTATAAAAACGACGC
* ** *
68037 TAAAGTACTACTCTGTTGTGATGTTTGTTG-AAAAAACGTCACTATAGATTAACCCTATTGCGAC
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAAAC--CACTATAGATGAACCC-ATTGCGAC
* *
68101 GTTTGTATAAAAATGATGC
63 GTTTGTATAAAAACGACGC
* * * * * *
68120 TAAAGTACTAC-ATGTTGCAGCGTTTGTTGAAAAAATGCCACTATAGATGATCCTATTGCGGCGT
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAA-ACCACTATAGATGAACCCATTGCGACGT
68184 TTGTATAAAAAC-ATCGC
65 TTGTATAAAAACGA-CGC
*
68201 TAAAGTACTTCTCTGTTGCGGCGTTTGTTGAAAAAA
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAA
68237 CACTGTTAAA
Statistics
Matches: 165, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
80 8 0.05
81 57 0.35
82 62 0.38
83 37 0.22
84 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (81 bp):
TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAAACCACTATAGATGAACCCATTGCGACGTT
TGTATAAAAACGACGC
Found at i:68113 original size:42 final size:42
Alignment explanation
Indices: 67997--68113 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
67987 AAAAAACCAT
* *
67997 TATAGATGAACCC-ATTGTGACGCTTGTAT-AAAAACGCCAC
1 TATAGATTAACCCTATTGTGACGTTTGTATAAAAAACGCCAC
* * * * * *
68037 TAAAGTACT-ACTCTGTTGTGATGTTTGT-TGAAAAAACGTCAC
1 TATAG-ATTAACCCTATTGTGACGTTTGTAT-AAAAAACGCCAC
*
68079 TATAGATTAACCCTATTGCGACGTTTGTATAAAAA
1 TATAGATTAACCCTATTGTGACGTTTGTATAAAAA
68114 TGATGCTAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
40 8 0.14
41 14 0.25
42 34 0.60
43 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (42 bp):
TATAGATTAACCCTATTGTGACGTTTGTATAAAAAACGCCAC
Found at i:69087 original size:51 final size:49
Alignment explanation
Indices: 69023--69139 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 49
69013 AATTATTAAA
* * *
69023 ATATTTAA-AATATATTTAATAATATTTATAATAATATAAAAT-TATTTTT
1 ATATTTAATAATATATTCAATAATA-TTATAATAAAATAAAATATA-TATT
* * *
69072 ATATTATAATAATATACTCAATTATATTATAATAAAATAACATATCATATT
1 ATATT-TAATAATATATTCAATAATATTATAATAAAATAAAATAT-ATATT
69123 ATATTTTAATAATATAT
1 ATA-TTTAATAATATAT
69140 AAAAATTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
49 5 0.09
50 18 0.32
51 30 0.54
52 3 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (49 bp):
ATATTTAATAATATATTCAATAATATTATAATAAAATAAAATATATATT
Found at i:69098 original size:23 final size:25
Alignment explanation
Indices: 69070--69138 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 25
69060 AAAATTATTT
69070 TTATATTATAATAATATAC-TCA-A
1 TTATATTATAATAATATACATCATA
*
69093 TTATATTATAATAAAATAACATATCATA
1 TTATATTATAATAATAT-AC--ATCATA
*
69121 TTATATTTTAATAATATA
1 TTATATTATAATAATATA
69139 TAAAAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 16 0.42
24 2 0.05
27 4 0.11
28 16 0.42
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (25 bp):
TTATATTATAATAATATACATCATA
Found at i:69132 original size:28 final size:28
Alignment explanation
Indices: 69070--69134 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
69060 AAAATTATTT
* * *
69070 TTATATTATAATAATATACTCAATTATA
1 TTATAATAAAATAACATACTCAATTATA
69098 TTATAATAAAATAACATA-TCATATTATA
1 TTATAATAAAATAACATACTCA-ATTATA
*
69126 TTTTAATAA
1 TTATAATAA
69135 TATATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (28 bp):
TTATAATAAAATAACATACTCAATTATA
Found at i:69190 original size:27 final size:25
Alignment explanation
Indices: 69160--69231 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 25
69150 AATTAAATTT
69160 ATATTATTTATTAATTTCAT-AGAAATA
1 ATATTATTTATT-ATTT-ATAAG-AATA
*
69187 ATATTATTAAATTATTTATAATGAATA
1 ATATTATT-TATTATTTATAA-GAATA
69214 ATATTATTTATGTATTTA
1 ATATTATTTAT-TATTTA
69232 ACATTGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 4 0.10
27 31 0.79
28 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (25 bp):
ATATTATTTATTATTTATAAGAATA
Found at i:69265 original size:22 final size:22
Alignment explanation
Indices: 69240--69315 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
69230 TAACATTGAT
69240 ATAATAATATTTTAATATTTTA
1 ATAATAATATTTTAATATTTTA
* * *
69262 ATAAAAATATTTAAAATATATTA
1 ATAATAATATTT-TAATATTTTA
* * *
69285 ATTAATACT-TTTTAA-AATATA
1 A-TAATAATATTTTAATATTTTA
69306 AT-ATAATATT
1 ATAATAATATT
69316 ATTACTTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 4 0.10
20 3 0.07
21 4 0.10
22 13 0.32
23 12 0.29
24 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATAATATTTTAATATTTTA
Found at i:69425 original size:17 final size:17
Alignment explanation
Indices: 69405--69461 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
69395 AAATTATAGA
*
69405 AATAATATTTTAATAAT
1 AATAATATTTAAATAAT
69422 AATAA-A--TAAATAAT
1 AATAATATTTAAATAAT
* *
69436 TATAATAGTTCAAA-AAT
1 AATAATA-TTTAAATAAT
69453 AATAATATT
1 AATAATATT
69462 ACGTTTTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
16 3 0.09
17 14 0.44
18 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AATAATATTTAAATAAT
Found at i:70303 original size:2 final size:2
Alignment explanation
Indices: 70296--70326 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
70286 AAAAATAAAT
70296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70327 TAAAAAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78385 original size:8 final size:8
Alignment explanation
Indices: 78374--78411 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
78364 CTCCTCGTTC
78374 TCTTCATT
1 TCTTCATT
78382 TCTTCATT
1 TCTTCATT
*
78390 TCTTCACT
1 TCTTCATT
78398 TCTTCATT
1 TCTTCATT
*
78406 CCTTCA
1 TCTTCA
78412 CATTTTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (8 bp):
TCTTCATT
Found at i:80977 original size:12 final size:12
Alignment explanation
Indices: 80960--80993 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
80950 GCGTAGTGAT
80960 GGTATGGGCAGA
1 GGTATGGGCAGA
80972 GGTATGGGCAGA
1 GGTATGGGCAGA
*
80984 GGCATGGGCA
1 GGTATGGGCA
80994 TAGTGGCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.50, T:0.15
Consensus pattern (12 bp):
GGTATGGGCAGA
Found at i:81566 original size:42 final size:42
Alignment explanation
Indices: 81467--81571 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
81457 CCAAAGGTCT
* *
81467 TATAGATGGCCCGAAGG-TCTTATCATCTTGCGCGAAAGACA
1 TATAGATGGCCCGAAGGATCTTAGCATCATGCGCGAAAGACA
* * * *
81508 TATAGATGACCTGAAGGAT-TTAAGCATCATGCTCGAAAGACT
1 TATAGATGGCCCGAAGGATCTT-AGCATCATGCGCGAAAGACA
81550 TACT-GATGGCCCGAAGGA-CTTA
1 TA-TAGATGGCCCGAAGGATCTTA
81572 CATGTCAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
41 18 0.35
42 33 0.63
43 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (42 bp):
TATAGATGGCCCGAAGGATCTTAGCATCATGCGCGAAAGACA
Found at i:81653 original size:39 final size:39
Alignment explanation
Indices: 81610--82440 Score: 997
Period size: 39 Copynumber: 21.3 Consensus size: 39
81600 TTAGTTTCTT
* * *
81610 ATAAAATCTTTTGTTTCGAGAGAAACTATCTCAAGCCAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
** * *
81649 ATAAAATCTTCTGTTTTAAGGGAAACTATTTGAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
81688 ACAAAATCTTCTGTTTCGAGGAAAACTATCTTAAGCGAT
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
81727 ACAAAATCATT-TATTTAGAGGGAAGCTATCTCAAGCGAG
1 ATAAAATC-TTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
81766 ATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
81805 ATAAAATCTTTTGTTTCGAGGGAAACTATCTTAAACGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
81844 ATAAAATCTT-TTTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * **
81882 ATAAAATCTTGTGTTTCTAGTAAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
81921 ATAAAATCTTCTATTTCAAGTGAAACTATCTCAATG-GAC
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAA-GCGAG
*
81960 ATAAAATCTTATGTTT-GAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
81998 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAACAAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
82037 ATAAAATCTTTTGTTTCAAGGGAGACCATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* ** **
82076 ATAAAATCTTTTGTTTCGAGTAAAACTATCTCAAAAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
82115 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGGCTTGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAA-GC--GAG
* *
82157 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCAAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* ** *
82196 ATAAAATCTTCTATTTCGAATGAAACTGTCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
82235 ATAAAATCTACCGTTTCGAGGGAAACTATCTCAAGCAAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
82274 ATAAAATCTTCTATTTCGAGTGAAACTGTCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
82313 ATAAAATCTACTGTTTCGAGGGATACTATCTCAAGAGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
82352 ATAAAATATTCTGTTTCGA-GGAAACTATCTCAAGCGAT
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
** * * *
82390 ACCAAATCCTCTGTTTCAAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
82429 GTAAAATCTTCT
1 ATAAAATCTTCT
82441 TTAAAACAAT
Statistics
Matches: 677, Mismatches: 105, Indels: 20
0.84 0.13 0.02
Matches are distributed among these distances:
37 1 0.00
38 99 0.15
39 535 0.79
40 3 0.00
41 2 0.00
42 37 0.05
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (39 bp):
ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
Found at i:81796 original size:22 final size:22
Alignment explanation
Indices: 81771--81837 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 22
81761 GCGAGATAAA
81771 ATCTTATGTTTCGAGGGAAACT
1 ATCTTATGTTTCGAGGGAAACT
* * **
81793 ATCTCAAG---CGAGATAAA--
1 ATCTTATGTTTCGAGGGAAACT
*
81810 ATCTTTTGTTTCGAGGGAAACT
1 ATCTTATGTTTCGAGGGAAACT
81832 ATCTTA
1 ATCTTA
81838 AACGAGATAA
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
17 5 0.17
19 7 0.23
20 7 0.23
22 11 0.37
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (22 bp):
ATCTTATGTTTCGAGGGAAACT
Found at i:81911 original size:116 final size:116
Alignment explanation
Indices: 81610--82438 Score: 980
Period size: 116 Copynumber: 7.1 Consensus size: 116
81600 TTAGTTTCTT
* * **
81610 ATAAAATCTTTTGTTTCGAGAGAAACTATCTCAAGCCAGATAAAATCTTCTGTTTTAAGGGAAAC
1 ATAAAATCTTTT-TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC
* * * * * *
81675 TATTTGAAGCGAGACAAAATCTTCTGTTTCGAGGAAAACTATCTTAAGCGAT
65 TATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * * *
81727 ACAAAATCATTTATTTAGAGGGAAGCTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGGAAAC
1 ATAAAATC-TTTTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC
* * *
81792 TATCTCAAGCGAGATAAAATCTTTTGTTTCGAGGGAAACTATCTTAAACGAG
65 TATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * **
81844 ATAAAATCTTTTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTGTGTTTCTAGTAAAACT
1 ATAAAATCTTTTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
* * * *
81909 ATCTCAAGCGAGATAAAATCTTCTATTTCAAGTGAAACTATCTCAATG-GAC
66 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAA-GCGAG
* *
81960 ATAAAATCTTATGTTT-GAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGGGAAAC
1 ATAAAATCTT-TTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC
* * * * * *
82024 TATCTCAAACAAGATAAAATCTTTTGTTTCAAGGGAGACCATCTCAAGCGAG
65 TATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
** ** *
82076 ATAAAATCTTTTGTTTCGAGTAAAACTATCTCAAAAGAGATAAAATCTTTTGTTTCGAGGGAAAC
1 ATAAAATCTTTT-TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC
* *
82141 TATCTCAAGGCTTGAGATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCAAG
65 TATCTCAA-GC--GAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* ** * * *
82196 ATAAAATCTTCTATTTCGAATGAAACTGTCTCAAGCGAGATAAAATCTACCGTTTCGAGGGAAAC
1 ATAAAATCTT-TTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC
* * * *
82261 TATCTCAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTGTCTCAAGCGAG
65 TATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * * *
82313 ATAAAATCTACTGTTTCGAGGGATACTATCTCAAGAGAGATAAAATATTCTGTTTCGA-GGAAAC
1 ATAAAATCT-TTTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC
* ** * * *
82377 TATCTCAAGCGATACCAAATCCTCTGTTTCAAGTGAAACTATCTCAAGCGAG
65 TATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
82429 GTAAAATCTT
1 ATAAAATCTT
82439 CTTTAAAACA
Statistics
Matches: 611, Mismatches: 90, Indels: 24
0.84 0.12 0.03
Matches are distributed among these distances:
115 2 0.00
116 260 0.43
117 243 0.40
118 4 0.01
119 2 0.00
120 99 0.16
121 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (116 bp):
ATAAAATCTTTTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACT
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
Found at i:82515 original size:37 final size:38
Alignment explanation
Indices: 82464--82571 Score: 96
Period size: 36 Copynumber: 2.8 Consensus size: 38
82454 GAGTGAAATG
* *
82464 AAATGTCTTCTTTTAAGTAAAAACTGTCTCAAACGAGAC
1 AAAT-TCTTGTTTTAAGTAAAAACTGTCTCAAACGAAAC
* * **
82503 AAA-TCTTGTTTTAAG-AAAAA-TAATCTGAAGTGAAAC
1 AAATTCTTGTTTTAAGTAAAAACT-GTCTCAAACGAAAC
*
82539 AAATCTTCTTGTTTAAAGTAAAAACTGTCTCAA
1 AAA--TTCTTGTTTTAAGTAAAAACTGTCTCAA
82572 GATAGACATA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
35 1 0.02
36 17 0.31
37 11 0.20
39 14 0.26
40 10 0.19
41 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (38 bp):
AAATTCTTGTTTTAAGTAAAAACTGTCTCAAACGAAAC
Found at i:82638 original size:36 final size:38
Alignment explanation
Indices: 82560--82638 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
82550 TTTAAAGTAA
* * **
82560 AAACTGTCTCAAGATAGACATAATCTTTTGTTTCAAGGG
1 AAACTGTCTCAAGAGAGACATAA-CATTTGTTTCAAAAG
82599 AAACTGTCTCAAGAGAGACA-AA-ATTTGTTTCAAAAG
1 AAACTGTCTCAAGAGAGACATAACATTTGTTTCAAAAG
82635 AAAC
1 AAAC
82639 AAACTCAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 15 0.42
38 2 0.06
39 19 0.53
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (38 bp):
AAACTGTCTCAAGAGAGACATAACATTTGTTTCAAAAG
Found at i:82718 original size:37 final size:36
Alignment explanation
Indices: 82651--82722 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
82641 ACTCAGGCTT
*
82651 TTGTTTTGAGAGAAACTGTCTCAAAAGAGACAAAAC
1 TTGTTTTGAGAAAAACTGTCTCAAAAGAGACAAAAC
* *
82687 TTGTTTTGAGTAAAAATTGTCTCAAATGAGACAAAA
1 TTGTTTTGAG-AAAAACTGTCTCAAAAGAGACAAAA
82723 TTCATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (36 bp):
TTGTTTTGAGAAAAACTGTCTCAAAAGAGACAAAAC
Found at i:82896 original size:42 final size:42
Alignment explanation
Indices: 82824--82917 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
82814 TGGATGACCC
* *
82824 GAAGGACTTA-TCATCTTGCTCGAAAGACTTA-TAGATAGCCT
1 GAAGGACTTACGCATCATGCTCGAAAGACTTACTA-ATAGCCT
*
82865 GAAGGACTTACGCATCATGCTCGAAAGACTTACTAATGGCCT
1 GAAGGACTTACGCATCATGCTCGAAAGACTTACTAATAGCCT
82907 GAAGGACTTAC
1 GAAGGACTTAC
82918 TCATTAAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
41 10 0.21
42 36 0.75
43 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
GAAGGACTTACGCATCATGCTCGAAAGACTTACTAATAGCCT
Found at i:83063 original size:43 final size:43
Alignment explanation
Indices: 82957--83173 Score: 337
Period size: 43 Copynumber: 5.1 Consensus size: 43
82947 AGTTTCTTAG
*
82957 TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCTAG-
1 TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
* *
82999 TTTTCATCAAGGAACCCCTACATATAACGTTGGTCCCTCAAGC
1 TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
* * * *
83042 TTATCATCAAGAAACCCCTACATATCACGTTGGTCCTTCTAGT
1 TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
*
83085 TTATCATCAAGGAACCCCTACATATCACATTGGTCCCTCAAGC
1 TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
* *
83128 TTATCATCAAGGAACCCCTACATATCATGTTGGTACCTCAAGC
1 TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
83171 TTA
1 TTA
83174 ATTTCTTATA
Statistics
Matches: 157, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
42 39 0.25
43 118 0.75
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (43 bp):
TTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
Found at i:83111 original size:21 final size:21
Alignment explanation
Indices: 83086--83155 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
83076 CCTTCTAGTT
83086 TATCATCAAGGAACCCCTACA
1 TATCATCAAGGAACCCCTACA
* * * *
83107 TATCA-CATTGG-TCCCTCAAGCT
1 TATCATCA-AGGAACCC-CTA-CA
83129 TATCATCAAGGAACCCCTACA
1 TATCATCAAGGAACCCCTACA
83150 TATCAT
1 TATCAT
83156 GTTGGTACCT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 5 0.14
21 16 0.44
22 10 0.28
23 5 0.14
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (21 bp):
TATCATCAAGGAACCCCTACA
Found at i:85208 original size:1 final size:1
Alignment explanation
Indices: 85204--85266 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
85194 TCTTTTTTCC
* * ** * * * *
85204 TTTTTTGTTTTTTTTTTTTTTATTTTTTCCTTTTTTTTCTTTTTCTTATTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
85267 GTTATATATT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.03, C:0.08, G:0.02, T:0.87
Consensus pattern (1 bp):
T
Found at i:85208 original size:8 final size:7
Alignment explanation
Indices: 85191--85266 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
85181 TTCGTCACTC
85191 TTTTCTT
1 TTTTCTT
85198 TTTTCCTT
1 TTTT-CTT
*
85206 TTTTGTTT
1 TTTT-CTT
*
85214 TTTTTTT
1 TTTTCTT
*
85221 TTTTATT
1 TTTTCTT
85228 TTTTCCTT
1 TTTT-CTT
*
85236 TTTTTTCT
1 TTTTCT-T
85244 TTTTC-T
1 TTTTCTT
*
85250 TATT-TT
1 TTTTCTT
85256 TTTTCTT
1 TTTTCTT
85263 TTTT
1 TTTT
85267 GTTATATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
6 8 0.14
7 24 0.43
8 24 0.43
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:85240 original size:26 final size:27
Alignment explanation
Indices: 85211--85266 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
85201 TCCTTTTTTG
85211 TTTTTTT-TTTTT-TTA-TTTTTTCCT
1 TTTTTTTCTTTTTCTTATTTTTTTCCT
*
85235 TTTTTTTCTTTTTCTTATTTTTTTTCT
1 TTTTTTTCTTTTTCTTATTTTTTTCCT
85262 TTTTT
1 TTTTT
85267 GTTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.25
25 5 0.18
26 3 0.11
27 13 0.46
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.88
Consensus pattern (27 bp):
TTTTTTTCTTTTTCTTATTTTTTTCCT
Found at i:85242 original size:47 final size:49
Alignment explanation
Indices: 85191--85285 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 49
85181 TTCGTCACTC
*
85191 TTTTCTTTTTTCCTT-TTTTGTTTT-TTTTTT-TT-T-TATTTTTTCCTTTT
1 TTTTC-TTTTT-CTTATTTT-TTTTCTTTTTTGTTATATATTTTCTCCTTTT
85238 TTTTCTTTTTCTTATTTTTTTTCTTTTTTGTTATATATTTTCTCCTTT
1 TTTTCTTTTTCTTATTTTTTTTCTTTTTTGTTATATATTTTCTCCTTT
85286 CTCTTTGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
45 7 0.17
46 15 0.36
47 7 0.17
48 1 0.02
49 12 0.29
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (49 bp):
TTTTCTTTTTCTTATTTTTTTTCTTTTTTGTTATATATTTTCTCCTTTT
Found at i:85255 original size:16 final size:14
Alignment explanation
Indices: 85191--85259 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 14
85181 TTCGTCACTC
* *
85191 TTTTCTTTTTTCCT
1 TTTTTTTTTTTTCT
85205 TTTTTGTTTTTTT-T
1 TTTTT-TTTTTTTCT
85219 TTTTTTATTTTTTCCT
1 TTTTTT-TTTTTT-CT
85235 TTTTTTTCTTTTTCT
1 TTTTTTT-TTTTTCT
85250 TATTTTTTTT
1 T-TTTTTTTT
85260 CTTTTTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
13 1 0.02
14 16 0.34
15 12 0.26
16 18 0.38
ACGTcount: A:0.03, C:0.10, G:0.01, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTTCT
Found at i:85264 original size:23 final size:23
Alignment explanation
Indices: 85189--85264 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
85179 CTTTCGTCAC
*
85189 TCTTTTCTTTTTTCCTT-TTTTGTT
1 TCTTTTC-TTTTT-CTTATTTTTTT
85213 T-TTTT-TTTTT-TTATTTTTTCCTT
1 TCTTTTCTTTTTCTTA-TTTTT--TT
*
85236 TTTTTTCTTTTTCTTATTTTTTT
1 TCTTTTCTTTTTCTTATTTTTTT
85259 TCTTTT
1 TCTTTT
85265 TTGTTATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
19 2 0.05
21 9 0.21
23 14 0.33
24 5 0.12
25 10 0.23
26 3 0.07
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (23 bp):
TCTTTTCTTTTTCTTATTTTTTT
Found at i:85278 original size:19 final size:19
Alignment explanation
Indices: 85238--85280 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
85228 TTTTCCTTTT
* *
85238 TTTTC-TTTTTCTTATTTT
1 TTTTCTTTTTTCTTATATA
*
85256 TTTTCTTTTTTGTTATATA
1 TTTTCTTTTTTCTTATATA
85275 TTTTCT
1 TTTTCT
85281 CCTTTCTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTTTCTTATATA
Found at i:88243 original size:18 final size:18
Alignment explanation
Indices: 88201--88244 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
88191 AAAAATCGGG
88201 TGATTTTAATAAAATATT
1 TGATTTTAATAAAATATT
*
88219 TTATTTTAATAAAAT-TT
1 TGATTTTAATAAAATATT
88236 TGAGTTTTA
1 TGA-TTTTA
88245 GGGCCTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TGATTTTAATAAAATATT
Found at i:100887 original size:33 final size:33
Alignment explanation
Indices: 100845--100908 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
100835 AAAGTATGAC
100845 GATTATGAGAGATCCAAATTACCATCTTCCAAT
1 GATTATGAGAGATCCAAATTACCATCTTCCAAT
100878 GATTATGAGAGATCCAAATTACCATCTTCCA
1 GATTATGAGAGATCCAAATTACCATCTTCCA
100909 CGTTAGTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (33 bp):
GATTATGAGAGATCCAAATTACCATCTTCCAAT
Found at i:101678 original size:20 final size:20
Alignment explanation
Indices: 101653--101700 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
101643 AAGAAAGGAT
101653 TATTGATAATGCTAGGAGAG
1 TATTGATAATGCTAGGAGAG
*
101673 TATTGATAATGCTGGGAGAG
1 TATTGATAATGCTAGGAGAG
*
101693 TATCGATA
1 TATTGATA
101701 TTGCCTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.31
Consensus pattern (20 bp):
TATTGATAATGCTAGGAGAG
Found at i:102973 original size:32 final size:32
Alignment explanation
Indices: 102906--102977 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
102896 GTCAATGTTG
* *
102906 CATTTAGATAATGCACAACAGATTTAGTATTA
1 CATTTAGATAATGCACAACAGATTCAGTATCA
* * *
102938 CATTTAGATAATTCACAATAG-TGTCAGTGTCA
1 CATTTAGATAATGCACAACAGAT-TCAGTATCA
102970 CATTTAGA
1 CATTTAGA
102978 GAATATACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (32 bp):
CATTTAGATAATGCACAACAGATTCAGTATCA
Found at i:114346 original size:40 final size:42
Alignment explanation
Indices: 114273--114356 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
114263 GGAAAAAAAA
*
114273 TATATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATATACACCAAAGTATTAATAAAATAGAA-AAGC
*
114315 TATATATATATATACACCAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
114355 TA
1 TA
114357 CCCTCTCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 12 0.31
41 7 0.18
42 20 0.51
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (42 bp):
TATATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
Found at i:114814 original size:18 final size:17
Alignment explanation
Indices: 114791--114833 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
114781 ATATATACAT
114791 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
114809 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
114826 ATAA-AATA
1 ATAATAATA
114834 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:115280 original size:36 final size:36
Alignment explanation
Indices: 115224--115324 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
115214 ATAGTAGAAC
115224 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
115261 TTTATCCTA-TTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
115294 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
115325 TAGGAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 13 0.22
34 19 0.32
36 19 0.32
37 8 0.14
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:116171 original size:105 final size:105
Alignment explanation
Indices: 115872--116532 Score: 872
Period size: 105 Copynumber: 6.3 Consensus size: 105
115862 CATTGTTCCA
* * * * * * *
115872 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-GGAATCGGGAAATTGTTTATTGATAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * * **
115936 CCAGCCGTCCCTTCGTTGTGTAGTTGAACTTGTGTTGTCTCA
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*** * * *
115978 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTAAATCT--GAAT--GAAATT-TTGTTGAGAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAGC
*
116038 AGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
116078 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAGC
*
116143 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
116183 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAGC
*
116248 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
116288 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGAGAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAGATTGGGAAGTTGTTGTTGACAAG
116352 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
116393 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGAGAAGTTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAGATTGGGAAGTTG-TTGTTGACAA
* * * *
116457 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
116499 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
116533 CGTGGATGGC
Statistics
Matches: 504, Mismatches: 40, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
100 77 0.15
102 9 0.02
104 6 0.01
105 304 0.60
106 83 0.16
107 4 0.01
109 21 0.04
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:116429 original size:315 final size:312
Alignment explanation
Indices: 115872--116532 Score: 963
Period size: 315 Copynumber: 2.1 Consensus size: 312
115862 CATTGTTCCA
*
115872 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTATTGATAAC
1 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTATTGACAAC
* * *
115937 CAGCCGTCCCTTCGTTGTGTAGTTGAACTTGTGTTGTCTCAAGTCCAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTTCGTTGTGAAG
* *
116002 TTGAAATTAAATCTGAATGAAATTTTGTTGAGAAGCAGCGGTCCCTTTGTCGTGAAGTTGAACTT
131 TTGAAATTAAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
116067 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAGATTGGGAAGTTG
196 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGAGAAGTTG
* *
116131 -TTGTTGACAAGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
260 TTTGTTGACAACCAGTC-GTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCG
* * * * *
116183 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAGATTGGGAAGTTG-TTGTTGACAA
1 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGA-ATCGGGAAATTGTTTATTGACAA
* * *
116246 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAA
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTTCGTTGTGAA
***
116311 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
130 GTTGAAATTAAATCTG-AA-TGA-AA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
*
116376 GAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
190 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
* **
116441 AGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
255 AGTTGTTTGTTGACAACCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCG
*
116499 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTCGTGAAGTTGAAAT
116533 CGTGGATGGC
Statistics
Matches: 311, Mismatches: 27, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
310 82 0.26
311 48 0.15
312 3 0.01
313 2 0.01
314 2 0.01
315 98 0.32
316 50 0.16
317 4 0.01
319 22 0.07
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (312 bp):
AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTATTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTAAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
TTGTTGACAACCAGTCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCG
Found at i:117268 original size:67 final size:68
Alignment explanation
Indices: 117122--117292 Score: 206
Period size: 68 Copynumber: 2.5 Consensus size: 68
117112 GGAAACGATC
* * *
117122 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
117187 TAAAT
64 TAAAT
** * * *
117192 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAAATT-T-TTTTAGGGGAAAT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAAC-AAAATTATGTTTTAAGGGAAAT
117255 AAAT
65 AAAT
*
117259 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
117293 ATAGACGAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
65 22 0.25
66 3 0.03
67 21 0.24
68 27 0.31
69 9 0.10
70 6 0.07
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (68 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATA
AAT
Found at i:117319 original size:36 final size:36
Alignment explanation
Indices: 117267--117647 Score: 338
Period size: 36 Copynumber: 11.0 Consensus size: 36
117257 ATTCAAAGAT
* *
117267 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
117303 TTTGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
117339 CTTAGTTCCAAAAGAAACTGTCTCAAG-GGGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
117375 TTTGTTTC-AGAGAAAACATAT-TC-------A-AATA
1 TTTGTTTCAAG-GGAAAC-TGTCTCAAGAGAGACAAAA
117403 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
117439 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
117475 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
117511 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
* * * *
117549 TTTATTTCAAGGGAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
117577 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC--AA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
117612 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
117648 CTCTTCTAGT
Statistics
Matches: 281, Mismatches: 38, Indels: 52
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.01
28 19 0.07
29 18 0.06
30 3 0.01
32 1 0.00
34 30 0.11
35 16 0.06
36 117 0.42
37 71 0.25
38 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:117364 original size:37 final size:36
Alignment explanation
Indices: 117279--117365 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
117269 TGTTTCAAGG
* * * * *
117279 GAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAAAGACAAAATTAGTTCCAAAA
*
117315 GAAACTGTCTCAAGAAAGATAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAAAGACAAAA-TTAGTTCCAAAA
117352 GAAACTGTCTCAAG
1 GAAACTGTCTCAAG
117366 GGGACGAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 21 0.48
37 23 0.52
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (36 bp):
GAAACTGTCTCAAGAAAGACAAAATTAGTTCCAAAA
Found at i:117414 original size:136 final size:136
Alignment explanation
Indices: 117216--117520 Score: 389
Period size: 136 Copynumber: 2.2 Consensus size: 136
117206 TTTCAAGAGT
* * * *
117216 AACTGTCTCAAGGGAGACAAAAATTT-TTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGG
1 AACTGTCTCAAGGG-GAC-AAAATTTGTTTCAGAGAAAACAAATTCAAAGATTTTGTTTCAAGGG
* * * *
117280 AAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTTAGT
64 AAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTA-T
117345 TCCAAAAGA
128 TCCAAAAGA
* * *
117354 AACTGTCTCAAGGGGACGAAATTTGTTTCAGAGAAAACATATTCAAATA-TTTGTTTCAAGGGAA
1 AACTGTCTCAAGGGGACAAAATTTGTTTCAGAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAA
* * * *
117418 ACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTC
66 ACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTATTCC
**
117483 AAGGGA
131 AAAAGA
*
117489 AACTGTCTCAAGAGAGACAAAATTTTGTTTCA
1 AACTGTCTCAAG-GGGACAAAA-TTTGTTTCA
117521 AGGGAAACTA
Statistics
Matches: 145, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
135 19 0.13
136 82 0.57
137 30 0.21
138 14 0.10
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (136 bp):
AACTGTCTCAAGGGGACAAAATTTGTTTCAGAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAA
ACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGACAAAACTTATTCC
AAAAGA
Found at i:117465 original size:172 final size:173
Alignment explanation
Indices: 117271--117647 Score: 485
Period size: 172 Copynumber: 2.2 Consensus size: 173
117261 AAAGATTTTG
* * * *
117271 TTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGATA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGACA
* * *
117336 AAACTTAGTTCCAAAAGAAACTGTCTCAAG-GGGACG-AAATTTGTTTC-AGAGAAAACATATTC
66 AAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAG-GAAAACATATTC
*
117398 AAAT-ATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
130 -AATGATTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AATTTA
* *
117443 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGACA
* * * ** * ** *
117508 AAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAGGGAAATGTTTTCA
66 AAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAGGAAAACATATTCA
* * *
117573 ATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATTTG
131 ATGATTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAATTTA
117616 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
117648 CTCTTCTAGT
Statistics
Matches: 178, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
172 83 0.47
173 45 0.25
174 20 0.11
175 30 0.17
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (173 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAAAGACA
AAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAGGAAAACATATTCA
ATGATTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAATTTA
Found at i:117602 original size:15 final size:15
Alignment explanation
Indices: 117584--117640 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
117574 TGTTTATGTT
117584 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
* *
117599 TCAAGGGAGACAATTTGTT
1 TCAA--GAGA-AA-CTGTC
*
117618 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
117633 TCAAGAGA
1 TCAAGAGA
117641 GACAAAACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 14 0.44
16 2 0.06
17 7 0.22
18 2 0.06
19 7 0.22
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:117643 original size:34 final size:34
Alignment explanation
Indices: 117580--117645 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
117570 TCAATGTTTA
*
117580 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAATT
*
117614 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
117646 AACTCTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (34 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAATT
Found at i:117697 original size:35 final size:35
Alignment explanation
Indices: 117404--117697 Score: 143
Period size: 36 Copynumber: 8.4 Consensus size: 35
117394 ATTCAAATAT
*
117404 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
* *
117440 TTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
* * *
117476 TTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
* *
117513 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC--AAATC
* * * * *
117550 TTATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TT
1 TTGTTTCAA-GAAAACTG-TCTCAAGAGAGACAAATC
*
117578 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAT-
1 T-TGTTTCAAGA-AAACTGTCTCAAGAGAGACAAATC
* *
117613 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATC
* * * *
117649 -T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATC
1 TTGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATC
*
117684 TTGTTTTAAGAAAA
1 TTGTTTCAAGAAAA
117698 ACAATCATGA
Statistics
Matches: 213, Mismatches: 24, Indels: 43
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.00
28 2 0.01
29 13 0.06
30 3 0.01
32 1 0.00
34 30 0.14
35 34 0.16
36 76 0.36
37 48 0.23
38 5 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (35 bp):
TTGTTTCAAGAAAACTGTCTCAAGAGAGACAAATC
Found at i:118155 original size:18 final size:18
Alignment explanation
Indices: 118128--118163 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
118118 TGTTGAATCC
*
118128 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
118146 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
118164 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:118623 original size:22 final size:22
Alignment explanation
Indices: 118598--118641 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
118588 CATTTTTGTT
118598 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAAT-GTTTGA
118620 CATTTGATGCTCAAATGTTTGA
1 CATTTGATGCTCAAATGTTTGA
118642 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (22 bp):
CATTTGATGCTCAAATGTTTGA
Found at i:119260 original size:17 final size:16
Alignment explanation
Indices: 119240--119311 Score: 63
Period size: 16 Copynumber: 4.3 Consensus size: 16
119230 TTTTTGTCCC
119240 TTTTTCTTTTTTTTTCT
1 TTTTTCTTTTTTTTT-T
119257 TTTTTCTTTTTGTTCTTT
1 TTTTTCTTTTT-TT-TTT
* *
119275 TTTTGCTTTTGTTTTT
1 TTTTTCTTTTTTTTTT
** * *
119291 TGCTTCTTTATTTTTC
1 TTTTTCTTTTTTTTTT
119307 TTTTT
1 TTTTT
119312 GCCCTTTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 16 0.37
17 13 0.30
18 12 0.28
19 2 0.05
ACGTcount: A:0.01, C:0.11, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:119272 original size:16 final size:16
Alignment explanation
Indices: 119229--119277 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
119219 TTTGCATATG
* *
119229 CTTTTTGTCCCTTTTT
1 CTTTTTGTTCTTTTTT
*
119245 CTTTTTTTTTCTTTTTT
1 C-TTTTTGTTCTTTTTT
119262 CTTTTTGTTCTTTTTT
1 CTTTTTGTTCTTTTTT
119278 TGCTTTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (16 bp):
CTTTTTGTTCTTTTTT
Found at i:119275 original size:25 final size:25
Alignment explanation
Indices: 119247--119311 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
119237 CCCTTTTTCT
119247 TTTTTTTTCTTTTTTCTTTTTG-TTC
1 TTTTTTTTCTTTTTT-TTTTTGCTTC
* *
119272 TTTTTTTGCTTTTGTTTTTTGCTTC
1 TTTTTTTTCTTTTTTTTTTTGCTTC
119297 TTTATTTTTCTTTTT
1 TTT-TTTTTCTTTTT
119312 GCCCTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.18
25 19 0.56
26 9 0.26
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (25 bp):
TTTTTTTTCTTTTTTTTTTTGCTTC
Found at i:119291 original size:16 final size:15
Alignment explanation
Indices: 119240--119291 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 15
119230 TTTTTGTCCC
*
119240 TTTTTCTTTTTTTTTCT
1 TTTTTC-TTTTGTTT-T
119257 TTTTTCTTTTTGTTCTT
1 TTTTTC-TTTTGTT-TT
119274 TTTTTGCTTTTGTTTT
1 TTTTT-CTTTTGTTTT
119290 TT
1 TT
119292 GCTTCTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.12
17 26 0.81
18 2 0.06
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTGTTTT
Found at i:119304 original size:13 final size:12
Alignment explanation
Indices: 119263--119304 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
119253 TTCTTTTTTC
119263 TTTTTG-TTCTT
1 TTTTTGCTTCTT
*
119274 TTTTTGCTTTTGT
1 TTTTTGCTTCT-T
119287 TTTTTGCTTCTT
1 TTTTTGCTTCTT
119299 TATTTT
1 T-TTTT
119305 TCTTTTTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 6 0.23
12 5 0.19
13 15 0.58
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.79
Consensus pattern (12 bp):
TTTTTGCTTCTT
Found at i:123833 original size:38 final size:40
Alignment explanation
Indices: 123764--123843 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
123754 GAAAAAAAAA
*
123764 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACACCAAAGTATTAATAAAATAGAA-AAGC
*
123804 TATATATATATACACCAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
123842 TA
1 TA
123844 CCCTCTCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
Found at i:124211 original size:2 final size:2
Alignment explanation
Indices: 124204--124240 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
124194 TATTAAAGAA
*
124204 AT AT AT AT AT AA 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 A
124241 ATAAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:124219 original size:10 final size:10
Alignment explanation
Indices: 124206--124292 Score: 60
Period size: 10 Copynumber: 9.0 Consensus size: 10
124196 TTAAAGAAAT
124206 ATATATATAA
1 ATATATATAA
*
124216 ATATATATAT
1 ATATATATAA
*
124226 ATATATATAT
1 ATATATATAA
124236 ATATA-ATAA
1 ATATATATAA
124245 A-ATATAGTAA
1 ATATATA-TAA
*
124255 A-AGA-ATGAGA
1 ATATATAT-A-A
124265 ATA-ATATAA
1 ATATATATAA
*
124274 A-ATATATAT
1 ATATATATAA
*
124283 ATACATATAA
1 ATATATATAA
124293 TAATAATAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
8 5 0.08
9 15 0.24
10 40 0.63
11 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (10 bp):
ATATATATAA
Found at i:124219 original size:12 final size:12
Alignment explanation
Indices: 124202--124243 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
124192 AATATTAAAG
124202 AAATATATATAT
1 AAATATATATAT
124214 AAATATATATAT
1 AAATATATATAT
*
124226 ATATATATATAT
1 AAATATATATAT
124238 ATAATA
1 A-AATA
124244 AAATATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 24 0.89
13 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATATATATAT
Found at i:124249 original size:12 final size:14
Alignment explanation
Indices: 124204--124250 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
124194 TATTAAAGAA
124204 ATATATATATAAAT
1 ATATATATATAAAT
*
124218 ATATATATATATAT
1 ATATATATATAAAT
124232 ATATATATAATAAA-
1 ATATATAT-ATAAAT
124246 ATATA
1 ATATA
124251 GTAAAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 26 0.87
15 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:124312 original size:18 final size:17
Alignment explanation
Indices: 124289--124331 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
124279 ATATATACAT
124289 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
124307 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
124324 ATAA-AATA
1 ATAATAATA
124332 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:124765 original size:37 final size:35
Alignment explanation
Indices: 124719--124822 Score: 158
Period size: 34 Copynumber: 2.9 Consensus size: 35
124709 ATAATAGTAT
*
124719 AATTCTATCCTATTTTTAAGAGTTTGAATCCTACCAA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTA--AA
124756 AATAT-TATCCTATTTTTAGGAGTTTGAATCCT-AA
1 AAT-TCTATCCTATTTTTAGGAGTTTGAATCCTAAA
124790 AATTCTATCCTATTTTTAGGAGTTTGAATCCTA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTA
124823 GTAGGACGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
33 1 0.02
34 32 0.51
37 29 0.46
38 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (35 bp):
AATTCTATCCTATTTTTAGGAGTTTGAATCCTAAA
Found at i:133379 original size:48 final size:48
Alignment explanation
Indices: 133316--133419 Score: 172
Period size: 48 Copynumber: 2.2 Consensus size: 48
133306 TCACAATTAT
*
133316 TTTCAATATTTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
1 TTTCAATTTTTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
* * *
133364 TTTCAATTTTTTATTATTCTTTCATTATTTATTTATTTATTTATTTAT
1 TTTCAATTTTTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
133412 TTTCAATT
1 TTTCAATT
133420 CATTTATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (48 bp):
TTTCAATTTTTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
Found at i:133429 original size:4 final size:4
Alignment explanation
Indices: 133340--133413 Score: 66
Period size: 4 Copynumber: 18.5 Consensus size: 4
133330 TATTCTTGCA
*
133340 TTAT TTAT TTAT GTAT TTAT TTAGT TTCAAT TT-T TTA- TTAT TCT-T
1 TTAT TTAT TTAT TTAT TTAT TTA-T TT--AT TTAT TTAT TTAT T-TAT
*
133385 TCA- TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
133414 TCAATTCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
3 8 0.14
4 42 0.72
5 4 0.07
6 3 0.05
7 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:136234 original size:42 final size:41
Alignment explanation
Indices: 136172--136291 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 41
136162 TGAATATTAT
136172 TGATGTTGATTTTATTTAGACTTATTGAGACTTATTAGTGTTA
1 TGATGTT-A-TTTATTTAGACTTATTGAGACTTATTAGTGTTA
* * * *
136215 TGGTGTTATTTATTTTAGACTTATTGAGAATTAATGGTGTTA
1 TGATGTTATTTA-TTTAGACTTATTGAGACTTATTAGTGTTA
136257 TGATGTTATTTAATTTAGACTTATTGAGACTTATT
1 TGATGTTATTT-ATTTAGACTTATTGAGACTTATT
136292 TGATAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.06
42 57 0.84
43 7 0.10
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (41 bp):
TGATGTTATTTATTTAGACTTATTGAGACTTATTAGTGTTA
Found at i:142442 original size:2 final size:2
Alignment explanation
Indices: 142435--142464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
142425 GTGAAAAGAA
142435 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
142465 GGGGTTAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.