Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007863.1 Hibiscus syriacus cultivar Beakdansim tig00110234_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: 1653362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1068420 original size:58 final size:58
Alignment explanation
Indices: 1068356--1068489 Score: 178
Period size: 58 Copynumber: 2.3 Consensus size: 58
1068346 TTCGATTTCT
* *** * * *
1068356 TTTAATTTCTGTCATTTACATTTTTGCTCTTTAGTTTATGCTATTTATATTTATGCCC
1 TTTAATTTCTGTTATTTACATTTCCACCCTTTAATTTATGCTATTTACATTTATGCCC
* * *
1068414 TTTAATTTATGTTATTTACATTTCCACCCTTTAATTTCTGCTATTTACATTTTTGCCC
1 TTTAATTTCTGTTATTTACATTTCCACCCTTTAATTTATGCTATTTACATTTATGCCC
1068472 TTTAATTTCTGTTATTTA
1 TTTAATTTCTGTTATTTA
1068490 TACTTCTACC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.57
Consensus pattern (58 bp):
TTTAATTTCTGTTATTTACATTTCCACCCTTTAATTTATGCTATTTACATTTATGCCC
Found at i:1068536 original size:45 final size:46
Alignment explanation
Indices: 1068486--1068629 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 46
1068476 ATTTCTGTTA
1068486 TTTATACTTCTA-CCTTATATTTTTAATTCATTTCGATTTACTTTC
1 TTTATACTTCTATCCTTATATTTTTAATTCATTTCGATTTACTTTC
* * * * * * * *
1068531 TTTATATTTGTTATTTGCTTCTAATTTT-GTTCATTTTCAATTTTCTTT-
1 TTTATACTT-CTA--TCCTTATATTTTTAATTCA-TTTCGATTTACTTTC
* *
1068579 TATTTTAACTTC-ATCCTTATATTTTTAATTCATTTCGATTTACTTCC
1 T-TTAT-ACTTCTATCCTTATATTTTTAATTCATTTCGATTTACTTTC
1068626 TTTA
1 TTTA
1068630 CATTTGTTAT
Statistics
Matches: 71, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
45 8 0.11
46 25 0.35
47 5 0.07
48 6 0.08
49 24 0.34
50 3 0.04
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.60
Consensus pattern (46 bp):
TTTATACTTCTATCCTTATATTTTTAATTCATTTCGATTTACTTTC
Found at i:1068583 original size:95 final size:95
Alignment explanation
Indices: 1068477--1068672 Score: 315
Period size: 95 Copynumber: 2.1 Consensus size: 95
1068467 TGCCCTTTAA
* * *
1068477 TTTCTGTTA-TTTATACTTC-TACCTTATATTTTTAATTCATTTCGATTTACTTTCTTTATATTT
1 TTTCTTTTATTTTA-ACTTCAT-CCTTATATTTTTAATTCATTTCGATTTACTTCCTTTACATTT
1068540 GTTATTTGCTTCTAATTTTGTTCATTTTCAAT
64 GTTATTTGCTTCTAATTTTGTTCATTTTCAAT
1068572 TTTCTTTTATTTTAACTTCATCCTTATATTTTTAATTCATTTCGATTTACTTCCTTTACATTTGT
1 TTTCTTTTATTTTAACTTCATCCTTATATTTTTAATTCATTTCGATTTACTTCCTTTACATTTGT
* *
1068637 TATTTGTTTTTAATTTTGTTCATTTTCAAT
66 TATTTGCTTCTAATTTTGTTCATTTTCAAT
1068667 TTTCTT
1 TTTCTT
1068673 CAACTTGGTC
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
95 89 0.95
96 5 0.05
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (95 bp):
TTTCTTTTATTTTAACTTCATCCTTATATTTTTAATTCATTTCGATTTACTTCCTTTACATTTGT
TATTTGCTTCTAATTTTGTTCATTTTCAAT
Found at i:1069029 original size:12 final size:13
Alignment explanation
Indices: 1069014--1069070 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
1069004 TTAAAATATA
1069014 TATTATAT-TTAT
1 TATTATATATTAT
*
1069026 TATTATATACTA-
1 TATTATATATTAT
*
1069038 TAGTATGATTATTAT
1 TATTAT-A-TATTAT
1069053 TATTAT-TATTAT
1 TATTATATATTAT
1069065 TATTAT
1 TATTAT
1069071 TAATACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 25 0.68
13 3 0.08
14 4 0.11
15 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:1069030 original size:3 final size:3
Alignment explanation
Indices: 1069022--1069072 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1069012 TATATTATAT
* * *
1069022 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1069067 TTA TTA
1 TTA TTA
1069073 ATACAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1076968 original size:12 final size:12
Alignment explanation
Indices: 1076951--1077007 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
1076941 AAGCAATGAT
1076951 AATAAAGAAAAA
1 AATAAAGAAAAA
1076963 AATAAAG--AAA
1 AATAAAGAAAAA
* **
1076973 AA-AAACAATGA
1 AATAAAGAAAAA
*
1076984 AAGAAAGAAAAA
1 AATAAAGAAAAA
1076996 AATAAAGAAAAA
1 AATAAAGAAAAA
1077008 GGGGCGAGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
9 3 0.09
10 5 0.14
11 3 0.09
12 24 0.69
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.07
Consensus pattern (12 bp):
AATAAAGAAAAA
Found at i:1076996 original size:33 final size:34
Alignment explanation
Indices: 1076924--1077007 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
1076914 AAAAAGAGGG
* *
1076924 AAAAAATAAA-AAAATTAAAGCAATGATAATAAAGA
1 AAAAAATAAAGAAAA--AAAACAATGATAAGAAAGA
1076959 AAAAAATAAAGAAAAAAAACAATGA-AAGAAAGA
1 AAAAAATAAAGAAAAAAAACAATGATAAGAAAGA
1076992 AAAAAATAAAGAAAAA
1 AAAAAATAAAGAAAAA
1077008 GGGGCGAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 23 0.50
34 9 0.20
35 10 0.22
36 4 0.09
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.11
Consensus pattern (34 bp):
AAAAAATAAAGAAAAAAAACAATGATAAGAAAGA
Found at i:1078139 original size:33 final size:32
Alignment explanation
Indices: 1078009--1078175 Score: 237
Period size: 32 Copynumber: 5.2 Consensus size: 32
1077999 AAGCAATAAA
* *
1078009 GGGCATC-TTGGAAGATTCAACATCACATATTG
1 GGGCATCTTTGG-AGATTCAACATCAAATGTTG
*
1078041 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
1078073 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
1078105 GGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* ** *
1078138 GGGCATCTTTGGAGATTCAATATTGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
1078170 GGGCAT
1 GGGCAT
1078176 TCAATATCCT
Statistics
Matches: 125, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
32 91 0.73
33 34 0.27
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:1078317 original size:34 final size:34
Alignment explanation
Indices: 1078274--1078372 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
1078264 TTTTTCTTAA
* * *
1078274 AAAAAAAATTTTGTGTCACTTGAGATAATTTCTC
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
1078308 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
* *
1078342 AAAACAAATTCTGTCTCGCTTGAGACAATTT
1 AAAACAAATTTTGTCTCACTTGAGACAATTT
1078373 TTCTCTGAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (34 bp):
AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
Found at i:1078693 original size:76 final size:74
Alignment explanation
Indices: 1078538--1078693 Score: 177
Period size: 76 Copynumber: 2.1 Consensus size: 74
1078528 TGTTTCATTT
* * * * * *
1078538 GAAACAAAGTTGTCTCACTTGTGACTGTTTTACTTGAAAGAAGACATTTAATTTGACTCAAGATT
1 GAAACAAAGTTGTCTCACTGGAGACTGTTTTACTTAAAACAAGACATTTAATTTCACTCAAGATA
**
1078603 GTTTTTCTC
66 GTTTCCCTC
* * * * *
1078612 AAAACAAGATTTGTCTCGCTGGAGACATGTTTTATTTAAAACAAGACATTTTATTTCACTCAAGA
1 GAAACAA-AGTTGTCTCACTGGAGAC-TGTTTTACTTAAAACAAGACATTTAATTTCACTCAAGA
1078677 TAGTTTCCCTC
64 TAGTTTCCCTC
1078688 GAAACA
1 GAAACA
1078694 GAAAAATTTT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
74 6 0.09
75 14 0.21
76 46 0.70
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (74 bp):
GAAACAAAGTTGTCTCACTGGAGACTGTTTTACTTAAAACAAGACATTTAATTTCACTCAAGATA
GTTTCCCTC
Found at i:1078744 original size:36 final size:36
Alignment explanation
Indices: 1078697--1078873 Score: 264
Period size: 36 Copynumber: 4.9 Consensus size: 36
1078687 CGAAACAGAA
1078697 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * *
1078733 AAATTTTGTCTCCCTTGACACAATTTCTCTCGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
*
1078769 AAATTTTGTCTCCCTTGAGACAGTTTCACTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * *
1078805 AAATTTTGTCTCCTTTAAGACGGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
1078841 AAATTTTGTCTCCCTTGAGACAATCTCCCTTGA
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
1078874 GACAGTTTCC
Statistics
Matches: 124, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:1078748 original size:21 final size:21
Alignment explanation
Indices: 1078722--1078786 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1078712 TGAGACAGTT
1078722 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1078743 TCCCTTGACAC-AA--TT-TC
1 TCCCTTGAAACAAATTTTGTC
*
1078760 T--CTCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
1078779 TCCCTTGA
1 TCCCTTGA
1078787 GACAGTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 6 0.18
16 2 0.06
17 3 0.09
18 4 0.12
19 3 0.09
20 2 0.06
21 14 0.41
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1078869 original size:15 final size:15
Alignment explanation
Indices: 1078849--1078893 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1078839 ACAAATTTTG
1078849 TCTCCCTTGAGACAA
1 TCTCCCTTGAGACAA
*
1078864 TCTCCCTTGAGACAG
1 TCTCCCTTGAGACAA
* *
1078879 TTTCCCTTGAAACAA
1 TCTCCCTTGAGACAA
1078894 ATTTTGTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (15 bp):
TCTCCCTTGAGACAA
Found at i:1078882 original size:51 final size:51
Alignment explanation
Indices: 1078813--1078911 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
1078803 ACAAATTTTG
* *
1078813 TCTCCTTTAAGACGGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
1 TCTCCCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
*
1078864 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 TCTCCCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1078912 TAGTTTCTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (51 bp):
TCTCCCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
Found at i:1078904 original size:36 final size:36
Alignment explanation
Indices: 1078864--1078944 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
1078854 CTTGAGACAA
*
1078864 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTCGAAACAAATTTTG
* *
1078900 TCTCCCTTGAGATAGTTTCTCTCGAAACAAATTTTG
1 TCTCCCTTGAGACAGTTTCCCTCGAAACAAATTTTG
1078936 TCTCCCTTG
1 TCTCCCTTG
1078945 GAACACATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (36 bp):
TCTCCCTTGAGACAGTTTCCCTCGAAACAAATTTTG
Found at i:1078907 original size:21 final size:21
Alignment explanation
Indices: 1078881--1078966 Score: 67
Period size: 21 Copynumber: 4.4 Consensus size: 21
1078871 TGAGACAGTT
1078881 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* * *
1078902 TCCCTTG--AGATA-GTT-TC
1 TCCCTTGAAACAAATTTTGTC
*
1078919 T--CTCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
1078938 TCCCTTGGAACACATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1078959 TCTCTTGA
1 TCCCTTGA
1078967 GGCAGTTTCC
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
15 3 0.06
17 6 0.13
18 4 0.09
19 6 0.13
21 28 0.60
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1079041 original size:36 final size:36
Alignment explanation
Indices: 1078938--1079085 Score: 161
Period size: 36 Copynumber: 4.0 Consensus size: 36
1078928 AAATTTTGTC
* * **
1078938 TCCCTTGGAACACATTTTGTCTCTCTTGAGGCAGTT
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
* * *
1078974 TCCATTAAAACAAATTTTGTCTCTCTTGAGATGGTT
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
* *
1079010 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAATT
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
* * *
1079046 TCACTTGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
1 TCCCTTGAAAC--AA-ATTTTGTCTCTCTTGAGATAGTT
1079085 T
1 T
1079086 TGCTCGAAAC
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
36 70 0.75
38 2 0.02
39 21 0.23
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
Found at i:1079095 original size:39 final size:39
Alignment explanation
Indices: 1079023--1079105 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
1079013 CTTGAAACAA
* *
1079023 ATTTTGTCTCCCTTGAGATAATTTCACTTGAAACAAAAG
1 ATTTTATCTCCCTTGAGATAATTTCACTCGAAACAAAAG
* * ** * *
1079062 ATTTTATCTCGCTTGAGATAGTTTTGCTCGAAACATAAT
1 ATTTTATCTCCCTTGAGATAATTTCACTCGAAACAAAAG
1079101 ATTTT
1 ATTTT
1079106 TATAAACTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (39 bp):
ATTTTATCTCCCTTGAGATAATTTCACTCGAAACAAAAG
Found at i:1079188 original size:43 final size:43
Alignment explanation
Indices: 1079127--1079231 Score: 165
Period size: 43 Copynumber: 2.4 Consensus size: 43
1079117 CCTAATTTTC
*
1079127 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
** *
1079170 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCGTCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
*
1079213 AGGGGTTCCTTGATGAAAA
1 AGGGGTTTCTTGATGAAAA
1079232 ATTTGATGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (43 bp):
AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
Found at i:1079639 original size:90 final size:90
Alignment explanation
Indices: 1079300--1079879 Score: 939
Period size: 90 Copynumber: 6.4 Consensus size: 90
1079290 AGAAACTGAG
*
1079300 CTTGATTTTTAAGTCCTTCGGGCCATTCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
1079365 TAAGAAACTGAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
* * * * *
1079390 CTT-AATTTTAAGTCATTCGGGTCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATT
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
1079454 TAAGAAACTGAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
1079479 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
*
1079544 CTAAGAAACTGAGCCTTCAGGGGTTT
65 CTAAGAAACTGAGCCTTCGGGGGTTT
* * * *
1079570 CTTGATTTTTAAGTCCTTTGGGCCATCCGTAAGACCTTCAGTGCAGGATATTTTCAAATGAGATT
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
*
1079635 TAAGAAACTGAGCCTTTGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
*
1079660 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1079725 CTAAGAAACTGAGCCTTCGGGGGTTT
65 CTAAGAAACTGAGCCTTCGGGGGTTT
* * *
1079751 CTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATT
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
*
1079816 TAAGAAACTAAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
* * *
1079841 CTTGATTTTTTAAGTCCTTCAGG-CAACTATAAGACCTTC
1 CTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
1079880 GAGCAAAATG
Statistics
Matches: 453, Mismatches: 33, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
89 83 0.18
90 186 0.41
91 184 0.41
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (90 bp):
CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
TAAGAAACTGAGCCTTCGGGGGTTT
Found at i:1079671 original size:181 final size:181
Alignment explanation
Indices: 1079300--1079879 Score: 1013
Period size: 181 Copynumber: 3.2 Consensus size: 181
1079290 AGAAACTGAG
*
1079300 CTTGA-TTTTTAAGTCCTTCGGGCCATTCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
* * *
1079364 CTAAGAAACTGAGCCTTCGGGGGTTTCTT-AATTTTAAGTCATTCGGGTCATCCGTAAGACCTTC
66 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
1079428 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
131 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
1079479 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
* *
1079544 CTAAGAAACTGAGCCTTCAGGGGTTTCTTGATTTTTAAGTCCTTTGGGCCATCCGTAAGACCTTC
66 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
* *
1079609 AGTGCAGGATATTTTCAAATGAGATTTAAGAAACTGAGCCTTTGGGGGTTT
131 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
*
1079660 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1079725 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
66 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
* *
1079790 AGTGCAAGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCGGGGGTTT
131 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
* * *
1079841 CTTGATTTTTTAAGTCCTTCAGG-CAACTATAAGACCTTC
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
1079880 GAGCAAAATG
Statistics
Matches: 380, Mismatches: 19, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
179 5 0.01
180 99 0.26
181 276 0.73
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (181 bp):
CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
Found at i:1086705 original size:54 final size:54
Alignment explanation
Indices: 1086444--1086716 Score: 343
Period size: 54 Copynumber: 5.0 Consensus size: 54
1086434 TATGTATTGC
* * *
1086444 ATTTACCGTATTGGCACTATATGTGCAACCTAATAAATTCATAATTACTTTATGA
1 ATTT-CCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
* *
1086499 ATTTCCGTATTGGAACTATGTGTGCAACCTAAGAAATTCATAATTACTTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
1086553 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
* * * * * * *
1086607 ATTTCCATATTGGAACTATGTGTG-TACCTCATGTAATTCATAATGAGTTTGTGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCT-AAGAAATTCATAATTAGTTTATGA
* * * * * *
1086661 ATTACCGTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATGAGCTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTA-AGAAATTCATAATTAGTTTATGA
1086715 AT
1 AT
1086717 GATAGTATCG
Statistics
Matches: 193, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
53 4 0.02
54 181 0.94
55 8 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (54 bp):
ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
Found at i:1087528 original size:26 final size:26
Alignment explanation
Indices: 1087498--1087550 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1087488 AATGTATACG
1087498 GGAAATGGGTGTTACAAGAGATATGA
1 GGAAATGGGTGTTACAAGAGATATGA
1087524 GGAAATGGGTGTTACAAGAGATATGA
1 GGAAATGGGTGTTACAAGAGATATGA
1087550 G
1 G
1087551 AGAGCAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.36, T:0.23
Consensus pattern (26 bp):
GGAAATGGGTGTTACAAGAGATATGA
Found at i:1091611 original size:23 final size:22
Alignment explanation
Indices: 1091581--1091629 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
1091571 TTTATATTCG
*
1091581 GAAAAAATAGAGATAAAAGAGAA
1 GAAAAAATAGA-AAAAAAGAGAA
1091604 GAAAAAATAGAAAAAAAGAGAA
1 GAAAAAATAGAAAAAAAGAGAA
1091626 -AAAA
1 GAAAA
1091630 CAACAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 10 0.40
23 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (22 bp):
GAAAAAATAGAAAAAAAGAGAA
Found at i:1091655 original size:16 final size:15
Alignment explanation
Indices: 1091593--1091669 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
1091583 AAAAATAGAG
*
1091593 ATAAAAGAGAAGAAAAA
1 ATAAAA-AGAA-AAGAA
* *
1091610 ATAGAAA-AAAAGAG
1 ATAAAAAGAAAAGAA
*
1091624 A-AAAAACAACAA-AA
1 ATAAAAAGAA-AAGAA
1091638 ATAAAAAGGAAAAGAA
1 ATAAAAA-GAAAAGAA
1091654 ATAAAAAGAAAAGAA
1 ATAAAAAGAAAAGAA
1091669 A
1 A
1091670 AAAGATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 4 0.08
14 8 0.16
15 20 0.41
16 12 0.24
17 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (15 bp):
ATAAAAAGAAAAGAA
Found at i:1091659 original size:22 final size:21
Alignment explanation
Indices: 1091582--1091685 Score: 61
Period size: 22 Copynumber: 4.8 Consensus size: 21
1091572 TTATATTCGG
* * *
1091582 AAAAAATAGAGATAAAAGAGAA
1 AAAAAATAAAAATAAAA-AGGA
* *
1091604 GAAAAAATAGAAAA-AAAGAGAA
1 -AAAAAATA-AAAATAAAAAGGA
*
1091626 AAAACAACAAAAATAAAAAGGA
1 AAAA-AATAAAAATAAAAAGGA
*
1091648 AAAGAAATAAAAA-GAAAA-GA
1 AAA-AAATAAAAATAAAAAGGA
1091668 AAAAAGATAATAAATAAA
1 AAAAA-ATAA-AAATAAA
1091686 GTACTTCAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.03
20 9 0.14
21 15 0.23
22 25 0.38
23 12 0.18
24 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.08
Consensus pattern (21 bp):
AAAAAATAAAAATAAAAAGGA
Found at i:1091670 original size:10 final size:9
Alignment explanation
Indices: 1091602--1091670 Score: 50
Period size: 10 Copynumber: 7.2 Consensus size: 9
1091592 GATAAAAGAG
1091602 AAGAAAAAA
1 AAGAAAAAA
*
1091611 TAGAAAAAA
1 AAGAAAAAA
1091620 AGAGAAAAAA
1 A-AGAAAAAA
*
1091630 CAACAAAAATA
1 -AAGAAAAA-A
**
1091641 AA-AAGGAA
1 AAGAAAAAA
1091649 AAGAAATAAA
1 AAGAAA-AAA
1091659 AAGAAAAGAA
1 AAGAAAA-AA
1091669 AA
1 AA
1091671 AAGATAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
8 3 0.06
9 14 0.30
10 28 0.60
11 2 0.04
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1094060 original size:9 final size:9
Alignment explanation
Indices: 1094046--1094080 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1094036 TCTGCAAACA
1094046 TATCATTAT
1 TATCATTAT
1094055 TATCATTAT
1 TATCATTAT
* *
1094064 TAACATTCT
1 TATCATTAT
1094073 TATCATTA
1 TATCATTA
1094081 ATTCATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (9 bp):
TATCATTAT
Found at i:1096618 original size:259 final size:259
Alignment explanation
Indices: 1096153--1097223 Score: 1445
Period size: 259 Copynumber: 4.1 Consensus size: 259
1096143 CATTAAGTTG
* * * * * * *
1096153 TTTTGA-AAAATGAGAAAGTGATTTCTAAATTTTATCTTTTTAATAATTTT-AGAAAATGAAA-T
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTC-ATTTAAT-GTTTTCAGAAAATGAAATT
* * * *
1096215 CTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTAATTCCAAAATTGGTAAG
64 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAG
* * * *
1096280 TCCTTAAGG-CTATCAATAAG-CATTTCGAGCATGTTGATTAAATCATTCGGGTCATCTGTCAGT
129 TCCTTCAGGTC-ATCAGTAAGTC-TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGT
* * *
1096343 CTTTCGAACAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGGGCATGATGTTTTCACAT
192 CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACAT
1096408 GAT
257 GAT
* *
1096411 TTTTGAGAAAATGAGAAGGAGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAACTTT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
*
1096476 TGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
66 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
*
1096541 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCCATCTGTCAGTCTTT
131 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * * * * * *
1096606 CGAGCAAGATGATAAGTCCTTCAGACCATCTGTAAAACCATCAGACATGATTTTTTCACATGAT
196 CGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
* **
1096670 TTTCGAGAAAATGAGAAGGCGATTTCCAAAACTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
* * * * * * *
1096735 TGAAACGTAAAAAAGTGATTTCCAGAGTTTTTTACCTAGTAAACTATTTCCAAAATTGGTATGTC
66 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
* * * *
1096800 CTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCC-TCAGGTCATCTGTCAGTCTTT
131 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * *
1096864 CGAGCAAAGATGATAAGTCCTTAGGGCCATCTGTAAGACCTTCAAGCAGGATGTTTCCACATGAT
196 CGAGC-AAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
* * *
1096929 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGCTTCTCATTTAATTTTTTCAAAAAATGAAATTTT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
* **
1096994 TGAAAAGTAAGAAAGCGATTTCCAGAGTTTCTTACCCAGTAGCCTATTTCCAAAATTGGTAAGTC
66 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
* * *
1097059 CTTTAGGTCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTT
131 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * * * * * * * *
1097124 TGAGCAAGATGTTGAGTCATTCGAG-TAGTCTATAAGACCTTCGGGCAGGATATTTTCACATGAT
196 CGAGCAAGATGATAAGTCCTTCGGGCCA-TCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
* *
1097188 TTTCGATAAAATGAGAAGGCGATTTCCAAAGTTTCT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCT
1097224 TACCCAGTAA
Statistics
Matches: 722, Mismatches: 83, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
257 4 0.01
258 48 0.07
259 645 0.89
260 25 0.03
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (259 bp):
TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
CGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
Found at i:1096638 original size:41 final size:42
Alignment explanation
Indices: 1096535--1096640 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
1096525 CCAAAATTGG
* * *
1096535 TAAGTCCTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGAT
* * *
1096577 TAAATCCTTCGGGCCATCTGTCAGTCTTTCGAGCAAGATGA-
1 TAAGTCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGAT
*
1096618 TAAGTCCTTCAGACCATCTGTAA
1 TAAGTCCTTCAGGCCATCTGTAA
1096641 AACCATCAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 19 0.35
42 35 0.65
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGAT
Found at i:1096895 original size:42 final size:42
Alignment explanation
Indices: 1096797--1096900 Score: 115
Period size: 41 Copynumber: 2.5 Consensus size: 42
1096787 AAATTGGTAT
* *
1096797 GTCCTTCGGGCCAT-TAGTAAGTCTTTCGAGCATGATGATTAA
1 GTCCTTAGGGCCATCT-GTAAGTCTTTCGAGCAAGATGATTAA
* * * *
1096839 ATCCTCA-GGTCATCTGTCAGTCTTTCGAGCAAAGATGA-TAA
1 GTCCTTAGGGCCATCTGTAAGTCTTTCGAGC-AAGATGATTAA
1096880 GTCCTTAGGGCCATCTGTAAG
1 GTCCTTAGGGCCATCTGTAAG
1096901 ACCTTCAAGC
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
41 27 0.55
42 22 0.45
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
GTCCTTAGGGCCATCTGTAAGTCTTTCGAGCAAGATGATTAA
Found at i:1097380 original size:198 final size:198
Alignment explanation
Indices: 1097003--1097416 Score: 580
Period size: 198 Copynumber: 2.1 Consensus size: 198
1096993 TTGAAAAGTA
* * ** * *
1097003 AGAAAGCGATTTCCAGAGTTTCTTACCCAGTAGCCTATTTCCAAAATTGGTAAGTCCTTTAGGTC
1 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
* * *
1097068 ATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
* *
1097133 TGTTGAGTCATTCGAGTAGTCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGATAAA
131 TGTTGAGTCATTCGAGTAGTCTACAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGAGAAA
1097198 ATG
196 ATG
*
1097201 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTTAGTCATTCAGG-C
1 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
* * * * *
1097265 TATCAGTTAGTCTTTTGAGCATGATGATTAAATTCTTCGGGTCATCTATCAGTCTTTCGAGTAAG
66 -ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * * * * *
1097330 ATGTTGAGTCATTCGGGTCA-TCTACAAGACTTTTGGGCATGATGTTTTCACATGATTTTTGAGA
130 ATGTTGAGTCATTCGAGT-AGTCTACAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGAGA
1097394 AAATG
194 AAATG
*
1097399 AGAAGGTGATTTCCAAAG
1 AGAAGGCGATTTCCAAAG
1097417 CTTATCATTT
Statistics
Matches: 190, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
197 1 0.01
198 188 0.99
199 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (198 bp):
AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
TGTTGAGTCATTCGAGTAGTCTACAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGAGAAA
ATG
Found at i:1097611 original size:716 final size:714
Alignment explanation
Indices: 1096485--1097937 Score: 2006
Period size: 716 Copynumber: 2.0 Consensus size: 714
1096475 TTGAAAAGTA
* *
1096485 AGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCTTCAGGTC
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
*
1096550 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCCATCTGTCAGTCTTTCGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCCATCTATCAGTCTTTCGAGCAAGA
* ** *
1096615 TGATAAGTCCTTCAGACCATCTGTAAAACCATCAGACATGATTTTTTCACATGATTTTCGAGAAA
131 TGATAAGTCATTCAGACCATCTACAAAACCATCAGACATGATGTTTTCACATGATTTTCGAGAAA
* *
1096680 ATGAGAAGGCGATTTCCAAAACTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAACGTAA
196 ATGAGAAGGCGATTTCCAAAACTTATCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAA
* * * * *
1096745 AAAAGTGATTTCCAGAGTTTTTTACCTAGTAAACTATTTCCAAAATTGGTATGTCCTTCGGGCCA
261 AAAAGTGATTTCCAGAGTTTCTTACCTAGTAAAATATTTCCAAAATTAGTAAGTCATTCGGGCCA
1096810 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTCAGGTCATCTGTCAGTCTTTCGAGCAAAGAT
326 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTCAGGTCATCTGTCAGTCTTTCGAGCAAAGAT
* * * * *
1096875 GATAAGTCCTTAGGGCCATCTGTAAGACCTTCAAGCAGGATGTTTCCACATGATTTTTGAGAAAA
391 GATAAGTCATTAGGGCCATCTATAAGACATTCAAGCAGGATGTTTCCACATGACTTTCGAGAAAA
*
1096940 TGAGAAGGCGATTTCCAAAGCTTCTCATTTAAT-TTTTTCAAAAAATGAAATTTTTGAAAAGTAA
456 TGAGAAAGCGATTTCCAAAGCTTCTCATTTAATGTTTTT-AAAAAATGAAATTTTTGAAAAGTAA
* * * *
1097004 GAAAGCGATTTCCAGAGTTTCTTACCCAGTAGCCTATTTCCAAAATTGGTAAGTCCTTTAGGTCA
520 GAAAGCGATTTCCAAAATTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGT-CTTTAGGGCA
* * *
1097069 TT-AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT-AAGTCTTTTGAGCAAG
584 TTCAGTAAGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAA-TCTTTCGAGCAAG
* * * * *
1097132 ATGTTGAGTCATTCGAGTAGTCTATAAGA-CCTTCGGGCAGGATATTTTCACATGATTTTCGATA
648 ATGATAAGTCATTCGAGTAATCTATAAGATCCTT-GAGCAGGATATTTTCACATGATTTT--AAA
1097196 AAATG
710 AAATG
* *
1097201 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTTAGTCATTCAGG-C
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
* * * * *
1097265 TATCAGTTAGTCTTTTGAGCATGATGATTAAATTCTTCGGGTCATCTATCAGTCTTTCGAGTAAG
66 -ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCCATCTATCAGTCTTTCGAGCAAG
* * * ** * ** ** * *
1097330 ATGTTGAGTCATTCGGGTCATCTACAAGACTTTTGGGCATGATGTTTTCACATGATTTTTGAGAA
130 ATGATAAGTCATTCAGACCATCTACAAAACCATCAGACATGATGTTTTCACATGATTTTCGAGAA
* * *
1097395 AATGAGAAGGTGATTTCCAAAGCTTATCATTTAATGTTTTCAGAAAATGAATTTTTTGAAAAGTA
195 AATGAGAAGGCGATTTCCAAAACTTATCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTA
* **
1097460 AGAAAGTGATTTCCA-ATGTTTCTTA-CTCAGTAAAATATTTTGAAAATTAGTAAGTCATTCGGG
260 AAAAAGTGATTTCCAGA-GTTTCTTACCT-AGTAAAATATTTCCAAAATTAGTAAGTCATTCGGG
* * * * *
1097523 CCATTAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGGGTTATCTGTTAGTCTTTCGAGC-A
323 CCATTAGTAAGTCTTTCGAGCATGATGATTAAATC-CTCAGGTCATCTGTCAGTCTTTCGAGCAA
* * ** * ** *
1097587 AGATGTTAAGTCATTCA-TGCCATCTATAAGACATTCGGGCATGATGTTTTTACATTACTTTCGA
387 AGATGATAAGTCATT-AGGGCCATCTATAAGACATTCAAGCAGGATGTTTCCACATGACTTTCGA
* *
1097651 GAAAATGAGAAAGCGATTTCCAAATCTTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAA
451 GAAAATGAGAAAGCGATTTCCAAAGCTTCTCATTTAATGTTTTTAAAAAATGAAATTTTTGAAAA
* *
1097716 GTAAGAAAGCGATTTCCAAAATTTCTTACCCAGTAGACTATTTCCAAAATTTGTAAGTCTTTTGG
516 GTAAGAAAGCGATTTCCAAAATTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCTTTAGG
* * **
1097781 GCCTTCAGTAAGCCTTTCAAGCATGATGATTAAGTCCTTTTGGTCATCTGTCAATCTTTCGAGCA
581 GCATTCAGTAAGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAATCTTTCGAGCA
* * *
1097846 AGATGATAAGTCATTCGGGTAATCTATAAGATCCTTGAGCATGATGTTTTCACATGATTTTAAAA
646 AGATGATAAGTCATTCGAGTAATCTATAAGATCCTTGAGCAGGATATTTTCACATGATTTTAAAA
1097911 AATG
711 AATG
*
1097915 AGAAAGTGATTTCCAAAGTTTCT
1 AGAAAGCGATTTCCAAAGTTTCT
1097938 CGCTTAGTGT
Statistics
Matches: 645, Mismatches: 83, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
714 28 0.04
715 13 0.02
716 569 0.88
717 35 0.05
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (714 bp):
AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCCATCTATCAGTCTTTCGAGCAAGA
TGATAAGTCATTCAGACCATCTACAAAACCATCAGACATGATGTTTTCACATGATTTTCGAGAAA
ATGAGAAGGCGATTTCCAAAACTTATCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAA
AAAAGTGATTTCCAGAGTTTCTTACCTAGTAAAATATTTCCAAAATTAGTAAGTCATTCGGGCCA
TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTCAGGTCATCTGTCAGTCTTTCGAGCAAAGAT
GATAAGTCATTAGGGCCATCTATAAGACATTCAAGCAGGATGTTTCCACATGACTTTCGAGAAAA
TGAGAAAGCGATTTCCAAAGCTTCTCATTTAATGTTTTTAAAAAATGAAATTTTTGAAAAGTAAG
AAAGCGATTTCCAAAATTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCTTTAGGGCATT
CAGTAAGCCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATG
ATAAGTCATTCGAGTAATCTATAAGATCCTTGAGCAGGATATTTTCACATGATTTTAAAAAATG
Found at i:1097615 original size:457 final size:457
Alignment explanation
Indices: 1096746--1097674 Score: 1247
Period size: 457 Copynumber: 2.0 Consensus size: 457
1096736 GAAACGTAAA
* * * * * *
1096746 AAAGTGATTTCCAGAGTTTTTTACCTAGTAAACTATTTCCAAAATTGGTATGTCCTTCGGGCCAT
1 AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTATGTCATTCAGGCCAT
* *
1096811 TAGTAAGTCTTTCGAGCATGATGATTAAATCCTCAGGTCATCTGTCAGTCTTTCGAGCAAAGATG
66 CAGTAAGTCTTTCGAGCATGATGATTAAATCCTCAGGTCATCTATCAGTCTTTCGAGCAAAGATG
* **
1096876 ATAAGTCCTTAGGGCCATCTGTAAGACCTTCAAGCAGGATGTTTCCACATGATTTTTGAGAAAAT
131 ATAAGTCATTAGGGCCATCTACAAGACCTTCAAGCAGGATGTTTCCACATGATTTTTGAGAAAAT
* *
1096941 GAGAAGGCGATTTCCAAAGCTTCTCATTTAATTTTTTCAAAAAATGAAATTTTTGAAAAGTAAGA
196 GAGAAGGCGATTTCCAAAGCTTATCATTTAATGTTTTCAAAAAATGAAATTTTTGAAAAGTAAGA
*** * * * *
1097006 AAGCGATTTCCAGAGTTTCTTACCCAGTAGCCTATTTCCAAAATTGGTAAGTCCTTTAGGTCATT
261 AAGCGATTTCCAGAGTTTCTTACCCAGTAAAATATTTCCAAAATTAGTAAGTCATTCAGGCCATT
*
1097071 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGT
326 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGT
* * * * *
1097136 TGAGTCATTCGAGTAGTCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGATAAAATG
391 TAAGTCATTCGAGCAGTCTATAAGACATTCGGGCAGGATATTTTCACATGACTTTCGAGAAAATG
1097201 AG
456 AG
* *
1097203 AAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT-TAGTCATTCAGGCTA
1 AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAT-GTCATTCAGGCCA
* * * * *
1097267 TCAGTTAGTCTTTTGAGCATGATGATTAAATTCTTCGGGTCATCTATCAGTCTTTCGAG-TAAGA
65 TCAGTAAGTCTTTCGAGCATGATGATTAAA-TCCTCAGGTCATCTATCAGTCTTTCGAGCAAAGA
* * * * * *** * *
1097331 TGTTGAGTCATTCGGGTCATCTACAAGACTTTTGGGCATGATGTTTTCACATGATTTTTGAGAAA
129 TGATAAGTCATTAGGGCCATCTACAAGACCTTCAAGCAGGATGTTTCCACATGATTTTTGAGAAA
* * *
1097396 ATGAGAAGGTGATTTCCAAAGCTTATCATTTAATGTTTTCAGAAAATGAATTTTTTGAAAAGTAA
194 ATGAGAAGGCGATTTCCAAAGCTTATCATTTAATGTTTTCAAAAAATGAAATTTTTGAAAAGTAA
* * ** *
1097461 GAAAGTGATTTCCA-ATGTTTCTTACTCAGTAAAATATTTTGAAAATTAGTAAGTCATTCGGGCC
259 GAAAGCGATTTCCAGA-GTTTCTTACCCAGTAAAATATTTCCAAAATTAGTAAGTCATTCAGGCC
* * * *
1097525 ATTAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGGGTTATCTGTTAGTCTTTCGAGCAAGA
323 ATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* * * *
1097590 TGTTAAGTCATTC-ATGCCA-TCTATAAGACATTCGGGCATGATGTTTTTACATTACTTTCGAGA
388 TGTTAAGTCATTCGA-G-CAGTCTATAAGACATTCGGGCAGGATATTTTCACATGACTTTCGAGA
1097653 AAATGAG
451 AAATGAG
1097660 AAAGCGATTTCCAAA
1 AAAGCGATTTCCAAA
1097675 TCTTCTCATT
Statistics
Matches: 407, Mismatches: 60, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
456 3 0.01
457 378 0.93
458 26 0.06
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (457 bp):
AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTATGTCATTCAGGCCAT
CAGTAAGTCTTTCGAGCATGATGATTAAATCCTCAGGTCATCTATCAGTCTTTCGAGCAAAGATG
ATAAGTCATTAGGGCCATCTACAAGACCTTCAAGCAGGATGTTTCCACATGATTTTTGAGAAAAT
GAGAAGGCGATTTCCAAAGCTTATCATTTAATGTTTTCAAAAAATGAAATTTTTGAAAAGTAAGA
AAGCGATTTCCAGAGTTTCTTACCCAGTAAAATATTTCCAAAATTAGTAAGTCATTCAGGCCATT
AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGT
TAAGTCATTCGAGCAGTCTATAAGACATTCGGGCAGGATATTTTCACATGACTTTCGAGAAAATG
AG
Found at i:1097671 original size:259 final size:255
Alignment explanation
Indices: 1097201--1098091 Score: 1055
Period size: 259 Copynumber: 3.5 Consensus size: 255
1097191 CGATAAAATG
* * * *
1097201 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTTAGTCATTCAGGCT
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCC
* * * * *
1097266 ATCAGTTAGTCTTTTGAGCATGATGATTAAATTCTTCGGGTCATCTATCAGTCTTTCGAGTAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGATTAAA-TCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGA
* * *
1097331 TGTTGAGTCATTCGGGTCATCTACAAGACTTTTGGGCATGATGTTTTCACATGATTTTTGAGAAA
130 TGTTAAGTCATTCGGGTCATCTATAAGAC-ATTGGGCATGATGTTTTCACATGA--TTTGAGAAA
* * *
1097396 ATGAGAAGGTGATTTCCAAAGCTTATCATTTAATGTTTTCAGAAAATGAATTTTTTGAAAAGTA
192 ATGAGAAAGTGATTTCCAAAGCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
* * * * ** *
1097460 AGAAAGTGATTTCCAATGTTTCTTACTCAGTAAAATATTTTGAAAATTAGTAAGTCATTCGGGCC
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCC
* * * *
1097525 ATTAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGGGTTATCTGTTAGTCTTTCGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTT-GGGTCATCTGTCAGTCTTTCGAGCAAGA
** * * *
1097590 TGTTAAGTCATTCATGCCATCTATAAGACATTCGGGCATGATGTTTTTACATTACTTTCGAGAAA
130 TGTTAAGTCATTCGGGTCATCTATAAGACATT-GGGCATGATGTTTTCACATGA-TTT-GAGAAA
* * *
1097655 ATGAGAAAGCGATTTCCAAATCTTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTA
192 ATGAGAAAGTGATTTCCAAAGCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
* * * * *
1097719 AGAAAGCGATTTCCAAAATTTCTTACCCAGTAGACTATTTCCAAAATTTGTAAGTCTTTTGGGCC
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCC
* * * * * *
1097784 TTCAGTAAGCCTTTCAAGCATGATGATTAAGTCCTTTTGGTCATCTGTCAATCTTTCGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTTGGGTCATCTGTCAGTCTTTCGAGCAAGA
* * * * * *
1097849 TGATAAGTCATTCGGGTAATCTATAAGATCCTTGAGCATGATGTTTTCACATGATTTTAAAAAAT
130 TGTTAAGTCATTCGGGTCATCTATAAGA-CATTGGGCATGATGTTTTCACATGATTTGAGAAAAT
* ** * * *
1097914 GAGAAAGTGATTTCCAAAGTTTCTCGCTTAGTGTTTTTAAAAAATTAATTTTTTGAAAAGTA
194 GAGAAAGTGATTTCCAAAGCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
* * * * * * *
1097976 AGAAAGCAATTTTCAAAGTTTCTTACCTAGTAAATTATTTCCGAAATTGGTACGTACA-TCGGAC
1 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGT-CATTCGGGC
* * * *
1098040 CATCAGTAAGTCTTTCGAGTATGATGATTGAATCATTTGGATTATCTGTCAG
65 CATCAGTAAGTCTTTCGAGCATGATGATTAAATC-TTTGGGTCATCTGTCAG
1098092 CCTCATTTGA
Statistics
Matches: 529, Mismatches: 96, Indels: 16
0.83 0.15 0.02
Matches are distributed among these distances:
256 1 0.00
257 149 0.28
258 13 0.02
259 359 0.68
260 7 0.01
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (255 bp):
AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCC
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGAT
GTTAAGTCATTCGGGTCATCTATAAGACATTGGGCATGATGTTTTCACATGATTTGAGAAAATGA
GAAAGTGATTTCCAAAGCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
Found at i:1098223 original size:3 final size:3
Alignment explanation
Indices: 1098215--1098289 Score: 80
Period size: 3 Copynumber: 24.7 Consensus size: 3
1098205 TTTTTCTGGG
* * * *
1098215 TTA TTA TTAA TTT TTA ATA TTA ATA TTA TTG TTA TTA TTA TTA TT-
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1098260 TAAA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1098290 TATGTTTTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.02
3 54 0.92
4 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1099254 original size:22 final size:22
Alignment explanation
Indices: 1099226--1099268 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1099216 AGTTTATTTA
1099226 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTT-CTTTTC
*
1099248 AAGTTTTTTCCTTTTTCTTTT
1 AAGTTTTCTCCTTTTTCTTTT
1099269 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTCTTTTC
Found at i:1102269 original size:19 final size:18
Alignment explanation
Indices: 1102215--1102257 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1102205 TCTTCTTATT
*
1102215 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATTGCTTTTA
1102234 TTTATTTAATTGCTTTTA
1 TTTATTTAATTGCTTTTA
1102252 -TTATTT
1 TTTATTT
1102258 TTAATATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTGCTTTTA
Found at i:1102878 original size:29 final size:29
Alignment explanation
Indices: 1102845--1102959 Score: 176
Period size: 29 Copynumber: 4.0 Consensus size: 29
1102835 TTCAATTTCT
*
1102845 TTTAATTTATGTTATTTACATTTATGCCC
1 TTTAATTTATGTTATTTACATTTCTGCCC
* *
1102874 TTTAATTTATGATATTTATATTTCTGCCC
1 TTTAATTTATGTTATTTACATTTCTGCCC
* * *
1102903 TTTAATTTCTATTATTTACATTTCTACCC
1 TTTAATTTATGTTATTTACATTTCTGCCC
1102932 TTTAATTTATGTTATTTACATTTCTGCC
1 TTTAATTTATGTTATTTACATTTCTGCC
1102960 TTACATTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTAATTTATGTTATTTACATTTCTGCCC
Found at i:1102881 original size:14 final size:14
Alignment explanation
Indices: 1102845--1102910 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
1102835 TTCAATTTCT
**
1102845 TTTAATTTATGTTA
1 TTTAATTTATGCCA
*
1102859 TTTACATTTATGCCC
1 TTTA-ATTTATGCCA
**
1102874 TTTAATTTATGATA
1 TTTAATTTATGCCA
* *
1102888 TTTATATTTCTGCCC
1 TTTA-ATTTATGCCA
1102903 TTTAATTT
1 TTTAATTT
1102911 CTATTATTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 19 0.47
15 21 0.52
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTAATTTATGCCA
Found at i:1103063 original size:95 final size:96
Alignment explanation
Indices: 1102946--1103132 Score: 313
Period size: 95 Copynumber: 2.0 Consensus size: 96
1102936 ATTTATGTTA
* * *
1102946 TTTACATTTCTGCCTTACATTTTTAATTCATTTCGTTTTACTTCCTTTATATTTGTTATTTGTTT
1 TTTACATTTCAGCCTTACATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
*
1103011 CTAATTTTGTTCATTTTCAATTTTCTTTTAT
66 CTAATTTTCTTCATTTTCAATTTTCTTTTAT
*
1103042 TTTA-ATTTCAGCCTTATATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
1 TTTACATTTCAGCCTTACATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
*
1103106 TTAATTTTCTTCATTTTCAATTTTCTT
66 CTAATTTTCTTCATTTTCAATTTTCTT
1103133 CATTTTCAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
95 81 0.95
96 4 0.05
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (96 bp):
TTTACATTTCAGCCTTACATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
CTAATTTTCTTCATTTTCAATTTTCTTTTAT
Found at i:1103127 original size:16 final size:16
Alignment explanation
Indices: 1103103--1103148 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
1103093 TTGTTATTTG
*
1103103 TTTTTAATTTTCTTCA
1 TTTTCAATTTTCTTCA
1103119 TTTTCAATTTTCTTCA
1 TTTTCAATTTTCTTCA
1103135 TTTTCAATTTTCTT
1 TTTTCAATTTTCTT
1103149 TAACTTGGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTCTTCA
Found at i:1103475 original size:13 final size:13
Alignment explanation
Indices: 1103457--1103481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1103447 TTATCTTCTG
1103457 TTTTATTTTATTA
1 TTTTATTTTATTA
1103470 TTTTATTTTATT
1 TTTTATTTTATT
1103482 TTACTTTAAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:1105900 original size:2 final size:2
Alignment explanation
Indices: 1105893--1105925 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1105883 TTAAACATTT
1105893 TA 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 TA T
1105926 TTCTAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1111339 original size:85 final size:85
Alignment explanation
Indices: 1111218--1111522 Score: 475
Period size: 85 Copynumber: 3.6 Consensus size: 85
1111208 CAGGAATGTA
* * *
1111218 TATCTGTCAACCAAGACCTTCGATTTCGATTACACTCAGCTCAAAGGCACATCAAATTTGCAGCA
1 TATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCA
1111283 TAGCTCAAGGCGAGAAGGGT
66 TAGCTCAAGGCGAGAAGGGT
* * *
1111303 TATTTGTCAACAAAGACCTTCGAGTTCGATTACACTCACCTCAAAGGCATATCAAATTTACAGCA
1 TATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCA
* *
1111368 TAACTCAAGGCAAGAAGGGT
66 TAGCTCAAGGCGAGAAGGGT
* * * *
1111388 TATCTGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCTCGAAGGCATATCAAATTCACAGCA
1 TATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCA
* * *
1111453 TAGCTCAAGTCGAAAAGGGG
66 TAGCTCAAGGCGAGAAGGGT
1111473 TATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAT
1 TATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAT
1111523 GTGAGAAGGC
Statistics
Matches: 197, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 197 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (85 bp):
TATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCA
TAGCTCAAGGCGAGAAGGGT
Found at i:1111561 original size:145 final size:145
Alignment explanation
Indices: 1111388--1111667 Score: 463
Period size: 145 Copynumber: 1.9 Consensus size: 145
1111378 CAAGAAGGGT
* *
1111388 TATCTGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCTCGAAGGCATATCAAATTCACAGCA
1 TATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAATTCACAGCA
* * *
1111453 TAGCTC-AAGTCGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAA
66 TAACGCAAAG-CGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAA
1111517 AGGCATGTGAGAAGGC
130 AGGCATGTGAGAAGGC
* *
1111533 TATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAATTTACATCA
1 TATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAATTCACAGCA
* *
1111598 TAACGCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAA
66 TAACGCAAAGCGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAA
1111663 GGCAT
131 GGCAT
1111668 ATCAAATTTG
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
145 122 0.98
146 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (145 bp):
TATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAATTCACAGCA
TAACGCAAAGCGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAA
GGCATGTGAGAAGGC
Found at i:1111676 original size:85 final size:85
Alignment explanation
Indices: 1111525--1111862 Score: 482
Period size: 85 Copynumber: 4.0 Consensus size: 85
1111515 AAAGGCATGT
* *
1111525 GAGAA-GGCTATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAA
1 GAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAA
* *
1111589 TTTACATCATAACGCAAAGC
66 TTTACAGCATAACTCAAAGC
* *
1111609 GAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCATATCAAA
1 GAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAA
* * * *
1111674 TTTGCAGCATAGCTTAAGGC
66 TTTACAGCATAACTCAAAGC
* * *
1111694 AAGAAGGGCGATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGAATATCAAA
1 GAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAA
1111759 TTTACAGCATAACTC-AAGAC
66 TTTACAGCATAACTCAAAG-C
* * *
1111779 GAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATCAAA
1 GAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAA
* * *
1111844 TTTGCAGGATAGCTCAAAG
66 TTTACAGCATAACTCAAAG
1111863 GCTTTTCAAG
Statistics
Matches: 223, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
84 7 0.03
85 213 0.96
86 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (85 bp):
GAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAA
TTTACAGCATAACTCAAAGC
Found at i:1111710 original size:230 final size:230
Alignment explanation
Indices: 1111307--1111749 Score: 710
Period size: 230 Copynumber: 1.9 Consensus size: 230
1111297 AAGGGTTATT
*
1111307 TGTCAACAAAGACCTTCGAGTTCGATTACACTCACCTCAAAGGCATATCAAATTTACAGCATAAC
1 TGTCAACAAAGACCTTCGAGTTCGATTACAATCACCTCAAAGGCATATCAAATTTACAGCATAAC
* * * * * *
1111372 TCAAGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCTCGAAGGCA
66 GCAAAGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
*
1111437 TATCAAATTCACAGCATAGCTCAAGTCGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGA
131 TATCAAATTCACAGCATAGCTCAAGGCGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGA
1111502 TTACACTCAGCTCAAAGGCATGTGAGAAGGCTATC
196 TTACACTCAGCTCAAAGGCATGTGAGAAGGCTATC
* * * *
1111537 TGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAATTTACATCATAAC
1 TGTCAACAAAGACCTTCGAGTTCGATTACAATCACCTCAAAGGCATATCAAATTTACAGCATAAC
*
1111602 GCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
66 GCAAAGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
** *
1111667 TATCAAATTTGCAGCATAGCTTAAGGC-AAGAAGGGCG-ATCTGTCAACCAAGACCTTCGAGTTC
131 TATCAAATTCACAGCATAGCTCAAGGCGAA-AAGGG-GTATCTGTCAACCAAGACCTTCGAGTTC
1111730 GATTACACTCAGCTCAAAGG
194 GATTACACTCAGCTCAAAGG
1111750 AATATCAAAT
Statistics
Matches: 195, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
229 2 0.01
230 192 0.98
231 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (230 bp):
TGTCAACAAAGACCTTCGAGTTCGATTACAATCACCTCAAAGGCATATCAAATTTACAGCATAAC
GCAAAGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
TATCAAATTCACAGCATAGCTCAAGGCGAAAAGGGGTATCTGTCAACCAAGACCTTCGAGTTCGA
TTACACTCAGCTCAAAGGCATGTGAGAAGGCTATC
Found at i:1111794 original size:315 final size:315
Alignment explanation
Indices: 1111218--1111837 Score: 990
Period size: 315 Copynumber: 2.0 Consensus size: 315
1111208 CAGGAATGTA
* *
1111218 TATCTGTCAACCAAGACCTTCGATTTCGATTACACTCAGCTCAAAGGCACATCAAATTTGCAGCA
1 TATCTGTCAACCAAGACCTTCGATTTCGATTACAATCAGCTCAAAGGCACATCAAATTTACAGCA
* * * * *
1111283 TAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAGACCTTCGAGTTCGATTACACTCACCTCAAA
66 TAACGCAAAGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAACTCAAA
**
1111348 GGCATATCAAATTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGT
131 GGCATATCAAATTTACAGCATAACTCAAGGCAAGAAGGGCGATCTGTCAACCAAGACCTTCGAGT
* * * * * *
1111413 TTGATTACATTCAGCTCGAAGGCATATCAAATTCACAGCATAGCTCAAGTCGAAAAGGGGTATCT
196 TCGATTACACTCAGCTCAAAGGAATATCAAATTCACAGCATAACTCAAGACGAAAAGGGGTATCT
1111478 GTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATGTGAGAAGGC
261 GTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATGTGAGAAGGC
* *
1111533 TATCTGTCAACCAAGACCTTCGAGTTT-GATTACAATCAGCTCAAAGGCATATCAAATTTACATC
1 TATCTGTCAACCAAGACCTTCGA-TTTCGATTACAATCAGCTCAAAGGCACATCAAATTTACAGC
*
1111597 ATAACGCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAACTCAA
65 ATAACGCAAAGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAACTCAA
* * *
1111662 AGGCATATCAAATTTGCAGCATAGCTTAAGGCAAGAAGGGCGATCTGTCAACCAAGACCTTCGAG
130 AGGCATATCAAATTTACAGCATAACTCAAGGCAAGAAGGGCGATCTGTCAACCAAGACCTTCGAG
* * *
1111727 TTCGATTACACTCAGCTCAAAGGAATATCAAATTTACAGCATAACTCAAGACGAGAAGGGTTATC
195 TTCGATTACACTCAGCTCAAAGGAATATCAAATTCACAGCATAACTCAAGACGAAAAGGGGTATC
* *
1111792 TGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCAT
260 TGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAT
1111838 ATCAAATTTG
Statistics
Matches: 278, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
315 275 0.99
316 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (315 bp):
TATCTGTCAACCAAGACCTTCGATTTCGATTACAATCAGCTCAAAGGCACATCAAATTTACAGCA
TAACGCAAAGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAACTCAAA
GGCATATCAAATTTACAGCATAACTCAAGGCAAGAAGGGCGATCTGTCAACCAAGACCTTCGAGT
TCGATTACACTCAGCTCAAAGGAATATCAAATTCACAGCATAACTCAAGACGAAAAGGGGTATCT
GTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATGTGAGAAGGC
Found at i:1111821 original size:170 final size:169
Alignment explanation
Indices: 1111526--1111857 Score: 549
Period size: 170 Copynumber: 2.0 Consensus size: 169
1111516 AAGGCATGTG
* * *
1111526 AGAAGGCTATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCAAAGGCATATCAAATT
1 AGAAGGCGATCTGTCAACCAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGAATATCAAATT
*
1111591 TACATCATAACGCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCA
66 TACAGCATAACGCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCA
1111656 ACTCAAAGGCATATCAAATTTGCAGCATAGCTTAAGGCA
131 ACTCAAAGGCATATCAAATTTGCAGCATAGCTTAAGGCA
*
1111695 AGAAGGGCGATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGAATATCAAAT
1 AGAA-GGCGATCTGTCAACCAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGAATATCAAAT
* * *
1111760 TTACAGCATAACTC-AAGACGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACATT
65 TTACAGCATAACGCAAAG-CGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACT
* *
1111824 CAGCTCAAAGGCATATCAAATTTGCAGGATAGCT
129 CAACTCAAAGGCATATCAAATTTGCAGCATAGCT
1111858 CAAAGGCTTT
Statistics
Matches: 151, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
169 7 0.05
170 144 0.95
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (169 bp):
AGAAGGCGATCTGTCAACCAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGAATATCAAATT
TACAGCATAACGCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCA
ACTCAAAGGCATATCAAATTTGCAGCATAGCTTAAGGCA
Found at i:1113716 original size:2 final size:2
Alignment explanation
Indices: 1113709--1113733 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1113699 TCTTAAACAT
1113709 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 T
1113734 TAATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1113875 original size:15 final size:16
Alignment explanation
Indices: 1113857--1113886 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1113847 GTTTTTTTGT
1113857 TTATTTTTT-ATTTAG
1 TTATTTTTTAATTTAG
1113872 TTATTTTTTAATTTA
1 TTATTTTTTAATTTA
1113887 ATTTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTTTTTAATTTAG
Found at i:1113888 original size:5 final size:5
Alignment explanation
Indices: 1113878--1113905 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1113868 TTAGTTATTT
1113878 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1113906 TTTTCATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:1117105 original size:16 final size:16
Alignment explanation
Indices: 1117081--1117111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1117071 ACTCGACATG
1117081 TTATCAACCTGACCTA
1 TTATCAACCTGACCTA
*
1117097 TTATGAACCTGACCT
1 TTATCAACCTGACCT
1117112 GTAATTGACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (16 bp):
TTATCAACCTGACCTA
Found at i:1118213 original size:2 final size:2
Alignment explanation
Indices: 1118097--1118194 Score: 93
Period size: 2 Copynumber: 51.5 Consensus size: 2
1118087 ATGTTTAATG
1118097 AT AT AT AT AT AT A- 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 AT AT AT AT
* * * *
1118138 AT AT AT AC AC AC AT -T AT AT -T AT AT AT ACT A- AC ACT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
1118178 AT AT -T AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1118195 CTTTGTTATA
Statistics
Matches: 84, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
1 7 0.08
2 74 0.88
3 3 0.04
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1118546 original size:12 final size:12
Alignment explanation
Indices: 1118529--1118561 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1118519 AAGGATATTA
1118529 GTCTTTAATCTG
1 GTCTTTAATCTG
1118541 GTCTTTAATCTG
1 GTCTTTAATCTG
1118553 GTCTTTAAT
1 GTCTTTAAT
1118562 TATGATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (12 bp):
GTCTTTAATCTG
Found at i:1118598 original size:20 final size:21
Alignment explanation
Indices: 1118560--1118601 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1118550 CTGGTCTTTA
*
1118560 ATTATGATATACATGCATCAT
1 ATTATCATATACATGCATCAT
*
1118581 ATTATCATA-ACATTCATCAT
1 ATTATCATATACATGCATCAT
1118601 A
1 A
1118602 AATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTATCATATACATGCATCAT
Found at i:1125819 original size:2 final size:2
Alignment explanation
Indices: 1125812--1125846 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1125802 GGAAATATTC
1125812 TA TA 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 TA TA T
1125847 GTTGGATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1132028 original size:21 final size:24
Alignment explanation
Indices: 1132001--1132058 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 24
1131991 AATGGGGCAT
*
1132001 CAGTATCGATACTGCT-ACCCT-G
1 CAGTATCGATACTACTCACCCTGG
*
1132023 -AGTATCAATACTACTCACCCTGG
1 CAGTATCGATACTACTCACCCTGG
1132046 CAGTATCGATACT
1 CAGTATCGATACT
1132059 CCCATATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 13 0.43
22 5 0.17
23 1 0.03
24 11 0.37
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (24 bp):
CAGTATCGATACTACTCACCCTGG
Found at i:1135733 original size:43 final size:43
Alignment explanation
Indices: 1135671--1135757 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
1135661 TATGAGCTTG
*
1135671 TAGGATAATGTGATGTCATACCCTTCATGATCTTTACATTCAT
1 TAGGATAATGTGATATCATACCCTTCATGATCTTTACATTCAT
*
1135714 TAGGATAATTTGATATCATACCCTTCATGATCTTTACATTCAT
1 TAGGATAATGTGATATCATACCCTTCATGATCTTTACATTCAT
1135757 T
1 T
1135758 CGATAAAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (43 bp):
TAGGATAATGTGATATCATACCCTTCATGATCTTTACATTCAT
Found at i:1136811 original size:16 final size:18
Alignment explanation
Indices: 1136790--1136825 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
1136780 TTGGATTAGC
1136790 TTTAAAT-TTCTT-AATT
1 TTTAAATATTCTTGAATT
1136806 TTTAAATATTCTTGAATT
1 TTTAAATATTCTTGAATT
1136824 TT
1 TT
1136826 ATCTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTAAATATTCTTGAATT
Found at i:1141443 original size:13 final size:13
Alignment explanation
Indices: 1141425--1141452 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1141415 ATTACAGATG
1141425 TGCATATGAAGAC
1 TGCATATGAAGAC
1141438 TGCATATGAAGAC
1 TGCATATGAAGAC
1141451 TG
1 TG
1141453 TTCAATCATG
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:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (13 bp):
TGCATATGAAGAC
Found at i:1141772 original size:7 final size:7
Alignment explanation
Indices: 1141760--1141787 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1141750 TTCTCTGATT
1141760 GTTTCTG
1 GTTTCTG
1141767 GTTTCTG
1 GTTTCTG
1141774 GTTTCTG
1 GTTTCTG
1141781 GTTTCTG
1 GTTTCTG
1141788 TAAGTTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.29, T:0.57
Consensus pattern (7 bp):
GTTTCTG
Found at i:1150133 original size:6 final size:6
Alignment explanation
Indices: 1150122--1150160 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1150112 GTTGCAGTGG
*
1150122 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGGAGA TGG
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGG
1150161 CATAAGTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (6 bp):
TGGTGA
Found at i:1150187 original size:33 final size:33
Alignment explanation
Indices: 1150142--1150259 Score: 168
Period size: 33 Copynumber: 3.6 Consensus size: 33
1150132 GATGGTGATG
*
1150142 GTGATGGTGATGGAGATGGCATAAGTGATGTAA
1 GTGATGGAGATGGAGATGGCATAAGTGATGTAA
*
1150175 GTGATGGAGATGGAGATGGCATAAGTGATGTAG
1 GTGATGGAGATGGAGATGGCATAAGTGATGTAA
* *
1150208 GTGATGGAGATGGAGATGACGGT-AGTGATGT-A
1 GTGATGGAGATGGAGATGGC-ATAAGTGATGTAA
1150240 GATGATGGAGATGGAGATGG
1 G-TGATGGAGATGGAGATGG
1150260 TGGTAGTGAT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.43, T:0.25
Consensus pattern (33 bp):
GTGATGGAGATGGAGATGGCATAAGTGATGTAA
Found at i:1152187 original size:23 final size:24
Alignment explanation
Indices: 1152161--1152207 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1152151 ACCAACATGG
1152161 CCTTGT-GGGCTGGAAAAACAGAA
1 CCTTGTAGGGCTGGAAAAACAGAA
1152184 CCTTGTAGGGCTGGAAAAACAGAA
1 CCTTGTAGGGCTGGAAAAACAGAA
1152208 TCCTGCGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.36, C:0.17, G:0.30, T:0.17
Consensus pattern (24 bp):
CCTTGTAGGGCTGGAAAAACAGAA
Found at i:1152218 original size:24 final size:24
Alignment explanation
Indices: 1152167--1152220 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1152157 ATGGCCTTGT
*
1152167 GGGCTGGAAAAACAGAACCTTGTA
1 GGGCTGGAAAAACAGAACCTTGCA
*
1152191 GGGCTGGAAAAACAGAATCC-TGCG
1 GGGCTGGAAAAACAGAA-CCTTGCA
1152215 GGGCTG
1 GGGCTG
1152221 TTATCAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.31, C:0.19, G:0.35, T:0.15
Consensus pattern (24 bp):
GGGCTGGAAAAACAGAACCTTGCA
Found at i:1157555 original size:6 final size:6
Alignment explanation
Indices: 1157544--1157570 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1157534 CACTAAACTC
1157544 TCCTCT TCCTCT TCCTCT TCCTCT TCC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCC
1157571 CCATATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTCT
Found at i:1158248 original size:13 final size:13
Alignment explanation
Indices: 1158230--1158262 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1158220 TTAATAATTC
1158230 TAATTTATTTTAT
1 TAATTTATTTTAT
1158243 TAATTTATTTTAT
1 TAATTTATTTTAT
*
1158256 TATTTTA
1 TAATTTA
1158263 ATAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TAATTTATTTTAT
Found at i:1165741 original size:16 final size:16
Alignment explanation
Indices: 1165703--1165745 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1165693 TAAAAGTAGC
* *
1165703 CTAAACCAAAATCAAT
1 CTAAACCGAAAGCAAT
**
1165719 CCGAACCGAAAGCAAT
1 CTAAACCGAAAGCAAT
1165735 CTAAACCGAAA
1 CTAAACCGAAA
1165746 ATCTATATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.28, G:0.09, T:0.12
Consensus pattern (16 bp):
CTAAACCGAAAGCAAT
Found at i:1166095 original size:16 final size:16
Alignment explanation
Indices: 1166074--1166106 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1166064 TAATAAATAA
1166074 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1166090 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1166106 A
1 A
1166107 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1166233 original size:90 final size:92
Alignment explanation
Indices: 1166080--1166272 Score: 336
Period size: 90 Copynumber: 2.1 Consensus size: 92
1166070 ATAAACGAAC
* ***
1166080 ATAAACGAACACGAACATAAACGAACAAATTTTTTTTTGTTTATGTTCGTTCATTAAGGAATATA
1 ATAAACGAACACGAACATAAACCAACAAAAAATTTTTTGTTTATGTTCGTTCATTAAGGAATATA
1166145 GTTTGTTCATGTTCATTCATTTAAATG
66 GTTTGTTCATGTTCATTCATTTAAATG
1166172 ATAAACGAACACGAACAT-AACCAA-AAAAAATTTTTTGTTTATGTTCGTTCATTAAGGAATATA
1 ATAAACGAACACGAACATAAACCAACAAAAAATTTTTTGTTTATGTTCGTTCATTAAGGAATATA
1166235 GTTTGTTCATGTTCATTCATTTAAATG
66 GTTTGTTCATGTTCATTCATTTAAATG
1166262 ATAAACGAACA
1 ATAAACGAACA
1166273 TAAACGAACA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 74 0.76
91 5 0.05
92 18 0.19
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (92 bp):
ATAAACGAACACGAACATAAACCAACAAAAAATTTTTTGTTTATGTTCGTTCATTAAGGAATATA
GTTTGTTCATGTTCATTCATTTAAATG
Found at i:1166277 original size:10 final size:10
Alignment explanation
Indices: 1166262--1166319 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
1166252 CATTTAAATG
1166262 ATAAACGAAC
1 ATAAACGAAC
1166272 ATAAACGAAC
1 ATAAACGAAC
*
1166282 ACAAACGAAC
1 ATAAACGAAC
*
1166292 --GAAC-ATA-
1 ATAAACGA-AC
*
1166299 ATAAATGAAC
1 ATAAACGAAC
1166309 ATAAACGAAC
1 ATAAACGAAC
1166319 A
1 A
1166320 ACACAAACAC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.03
8 4 0.11
9 3 0.08
10 30 0.79
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1166314 original size:27 final size:26
Alignment explanation
Indices: 1166272--1166322 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1166262 ATAAACGAAC
1166272 ATAAACGAACACAAACGAACGAACATA
1 ATAAACGAACACAAACGAAC-AACATA
* *
1166299 ATAAATGAACATAAACGAACAACA
1 ATAAACGAACACAAACGAACAACA
1166323 CAAACACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.61, C:0.20, G:0.10, T:0.10
Consensus pattern (26 bp):
ATAAACGAACACAAACGAACAACATA
Found at i:1167753 original size:32 final size:32
Alignment explanation
Indices: 1167712--1167775 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1167702 TCTCAATATC
*
1167712 AATCATTTATAAAGTTCTTACAAAGTCTTCAT
1 AATCATTTATAAAGTTCTTACAAAGTATTCAT
1167744 AATCATTTATAAAGTTCTTACAAAGTATTCAT
1 AATCATTTATAAAGTTCTTACAAAGTATTCAT
1167776 TAACAAGCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (32 bp):
AATCATTTATAAAGTTCTTACAAAGTATTCAT
Found at i:1167825 original size:21 final size:21
Alignment explanation
Indices: 1167801--1167841 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1167791 ATAGAGCTAA
1167801 ACATTTCATATCATTATTATC
1 ACATTTCATATCATTATTATC
* *
1167822 ACATTTTATCTCATTATTAT
1 ACATTTCATATCATTATTAT
1167842 TATTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (21 bp):
ACATTTCATATCATTATTATC
Found at i:1167842 original size:3 final size:3
Alignment explanation
Indices: 1167834--1167865 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1167824 ATTTTATCTC
1167834 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1167866 CAATTATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1169865 original size:23 final size:22
Alignment explanation
Indices: 1169837--1169883 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1169827 AAAACTCTCC
1169837 TTCTTATCTCCAATAAAACCAAA
1 TTCTTA-CTCCAATAAAACCAAA
* * *
1169860 TTCTTACTCGATTAAACCCAAA
1 TTCTTACTCCAATAAAACCAAA
1169882 TT
1 TT
1169884 TAAACTGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (22 bp):
TTCTTACTCCAATAAAACCAAA
Found at i:1180663 original size:42 final size:42
Alignment explanation
Indices: 1180585--1180805 Score: 156
Period size: 42 Copynumber: 5.4 Consensus size: 42
1180575 TTTGTTGTAA
* * *
1180585 AAACGCTGCAATAGAGTTG-ACATATAGCGGCGTTTTTACAAC
1 AAACGCCGCAATAGAGTGGTAAAT-TAGCGGCGTTTTTACAAC
* ** * *
1180627 AAACGCCGCAATAGGGTGGTTTATT-GCGGTGTTTTT-TAAC
1 AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTTTACAAC
* * *
1180667 AAATGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTTTACAAC
* *
1180709 AAACGCCGTAATAGA-T--TAACATATAGTGGCG-TTTTAGCCAA-
1 AAACGCCGCAATAGAGTGGTAA-AT-TAGCGGCGTTTTTA--CAAC
* * * *
1180750 AAA-GCCGTAATAGA-TCAGTAAATTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAGT-GGTAAATTAGCGGCGTTTTTACAAC
*
1180791 AAACGCCGTAATAGA
1 AAACGCCGCAATAGA
1180806 TTACACATAT
Statistics
Matches: 143, Mismatches: 23, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
39 3 0.02
40 44 0.31
41 40 0.28
42 51 0.36
43 5 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTTTACAAC
Found at i:1180806 original size:42 final size:40
Alignment explanation
Indices: 1180665--1180806 Score: 164
Period size: 42 Copynumber: 3.5 Consensus size: 40
1180655 GTGTTTTTTA
* *
1180665 ACAAATGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACC
1 ACAAACGCCGTAATAGA-T-GTAAATTAGCGGCGTTTATACC
*
1180707 ACAAACGCCGTAATAGAT-TAACATATAGTGGCGTTT-TAGCC
1 ACAAACGCCGTAATAGATGTAA-AT-TAGCGGCGTTTATA-CC
*
1180748 A-AAAAGCCGTAATAGATCAGTAAATTAGCGGCGTTTATACC
1 ACAAACGCCGTAATAGAT--GTAAATTAGCGGCGTTTATACC
1180789 ACAAACGCCGTAATAGAT
1 ACAAACGCCGTAATAGAT
1180807 TACACATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
39 3 0.03
40 19 0.22
41 27 0.31
42 34 0.40
43 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (40 bp):
ACAAACGCCGTAATAGATGTAAATTAGCGGCGTTTATACC
Found at i:1180827 original size:42 final size:41
Alignment explanation
Indices: 1180699--1180867 Score: 173
Period size: 42 Copynumber: 4.1 Consensus size: 41
1180689 ATTAGCGGCG
*
1180699 TTTATACCACAAACGCCGTAATAGATTA-ACATATAGTGGCG
1 TTTATACCA-AAACGCCGTAATAGATTACACATATAGTGGCA
* * * * * *
1180740 TTT-TAGCCAAAAAGCCGTAATAGATCAGTAAAT-TAGCGGCG
1 TTTATA-CCAAAACGCCGTAATAGATTA-CACATATAGTGGCA
*
1180781 TTTATACCACAAACGCCGTAATAGATTACACATATAGTGACA
1 TTTATACCA-AAACGCCGTAATAGATTACACATATAGTGGCA
* * *
1180823 TTTATTCTTAAAACGCCGCAATAGATTACACATATAGTGGCA
1 TTTATAC-CAAAACGCCGTAATAGATTACACATATAGTGGCA
1180865 TTT
1 TTT
1180868 TGAATGCAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
40 18 0.17
41 22 0.21
42 65 0.61
43 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (41 bp):
TTTATACCAAAACGCCGTAATAGATTACACATATAGTGGCA
Found at i:1180879 original size:42 final size:42
Alignment explanation
Indices: 1180790--1180889 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
1180780 GTTTATACCA
* ** *
1180790 CAAACGCCGTAATAGATTACACATATAGTGACATTTATTCTT
1 CAAACGCCGCAATAGATTACACATATAGTGACATTTATAATG
* *
1180832 AAAACGCCGCAATAGATTACACATATAGTGGCATTT-TGAATG
1 CAAACGCCGCAATAGATTACACATATAGTGACATTTAT-AATG
*
1180874 CAAACGCCGCTATAGA
1 CAAACGCCGCAATAGA
1180890 CTCACCTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (42 bp):
CAAACGCCGCAATAGATTACACATATAGTGACATTTATAATG
Found at i:1184097 original size:14 final size:15
Alignment explanation
Indices: 1184056--1184100 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
1184046 AATTACTGAA
1184056 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
1184071 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
1184086 -CTGGAAAATGAATT
1 ACTGGAAAATGAATT
1184100 A
1 A
1184101 AATTTCTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:1184122 original size:14 final size:14
Alignment explanation
Indices: 1184103--1184133 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1184093 ATGAATTAAA
1184103 TTTCTGAAAAATGT
1 TTTCTGAAAAATGT
*
1184117 TTTCTGAAAGATGT
1 TTTCTGAAAAATGT
1184131 TTT
1 TTT
1184134 ACGTTCTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (14 bp):
TTTCTGAAAAATGT
Found at i:1184330 original size:49 final size:50
Alignment explanation
Indices: 1184233--1184331 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
1184223 TACAAATATT
*
1184233 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
1184283 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
1184332 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:1184469 original size:23 final size:23
Alignment explanation
Indices: 1184420--1184482 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1184410 GTGTTATATT
* **
1184420 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
1184443 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1184466 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1184483 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1184510 original size:19 final size:20
Alignment explanation
Indices: 1184458--1184515 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1184448 TTAAATATCT
1184458 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1184477 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
*
1184498 TTATTAAATATATAATTT
1 TTATTAAATATATTATTT
1184516 TTTTATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 8 0.26
20 11 0.35
21 6 0.19
22 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1184529 original size:27 final size:28
Alignment explanation
Indices: 1184466--1184566 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 28
1184456 CTTTATTAAA
1184466 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAATAATATTAT
** *
1184495 -TCATTATTAAATATAT-AATTTTTTTAT
1 AT-ATTATTAAATATATAAATAATATTAT
*
1184522 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATAT-ATAA-ATAATAT-TAT
1184551 ATATTATTATAATATA
1 ATATTATTA-AATATA
1184567 ATTGATTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
26 2 0.04
27 18 0.32
28 13 0.23
29 18 0.32
30 4 0.07
31 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATTATTAAATATATAAATAATATTAT
Found at i:1184593 original size:17 final size:17
Alignment explanation
Indices: 1184549--1184606 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
1184539 ATATAATATC
1184549 TTATATTATTATAATATAA
1 TTATATTATTATAA-AT-A
1184568 TTGATTATT-TTATATAATA
1 TT-A-TATTATTATA-AATA
1184587 TTATATTATTATAAATA
1 TTATATTATTATAAATA
1184604 TTA
1 TTA
1184607 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 11 0.31
18 6 0.17
19 5 0.14
20 8 0.23
21 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATATTATTATAAATA
Found at i:1184858 original size:42 final size:41
Alignment explanation
Indices: 1184800--1184914 Score: 167
Period size: 42 Copynumber: 2.8 Consensus size: 41
1184790 ATGAATTACA
* * *
1184800 TTTCGGAAAACCAATTACGTTAAACAAATACGGGAAAACAT
1 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
*
1184841 TTTCTGGAAAACGAATTACGTGAAACAAACACGGGAAAATAT
1 TTTC-GGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
*
1184883 TTTCCAGAAAACGAATTACGTGAAACAAACAC
1 TTT-CGGAAAACGAATTACGTGAAACAAACAC
1184915 AAGAATTCGG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 4 0.06
42 62 0.93
43 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (41 bp):
TTTCGGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
Found at i:1189251 original size:21 final size:22
Alignment explanation
Indices: 1189222--1189267 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1189212 AACTTAAACT
1189222 TGAAAAATAAAA-AA-AATGAAA
1 TGAAAAATAAAATAACAAT-AAA
*
1189243 TGAAGAATAAAATAACAATAAA
1 TGAAAAATAAAATAACAATAAA
1189265 TGA
1 TGA
1189268 TACACCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 8 0.36
23 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (22 bp):
TGAAAAATAAAATAACAATAAA
Found at i:1191997 original size:210 final size:210
Alignment explanation
Indices: 1191571--1192204 Score: 1106
Period size: 210 Copynumber: 3.0 Consensus size: 210
1191561 GTTGTGAAGT
* * * *
1191571 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAATTTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
1191636 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTGTTGA
*
1191701 CAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
129 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1191766 GAAGTTGAAATTGGCTC
194 GAAGTTGAAATTGGCTC
1191783 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
1191848 TGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
*
1191913 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
1191978 AGTTGAAATTGACTC
196 AGTTGAAATTGGCTC
* *
1191993 TGAATCTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGCTGTC
1 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1192058 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
* * *
1192123 ACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGA
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
1192188 AGTTGAAATTGGCTC
196 AGTTGAAATTGGCTC
1192203 TG
1 TG
1192205 GGTAAAACCT
Statistics
Matches: 403, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
210 293 0.73
211 99 0.25
212 11 0.03
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (210 bp):
TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTC
Found at i:1192095 original size:315 final size:310
Alignment explanation
Indices: 1191486--1192205 Score: 1193
Period size: 315 Copynumber: 2.3 Consensus size: 310
1191476 CTGGGACTGG
* * *
1191486 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCC
1 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCC
*
1191551 AATATCCTTCGTTGTGAAGTTGAAATT-G----GGAAATTGTTTATTGACAACCAGCGGTCCCTT
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAAAATGTTTATTGACAACCAGCGGTCCCTT
* *
1191611 CGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCT
130 CGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACT
* *
1191676 CTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTG
195 CTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGCTG
1191741 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
260 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
*
1191792 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
* *
1191857 ATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGT
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-----GA-AAATGTTTATTGACAACCAGCGGT
1191922 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
125 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
*
1191987 TGACTCTG-AATCTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
190 TGACTCTGAAAT-TGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTT
1192050 GCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
254 GCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
* *
1192107 GAAATGTTTGTTGACAACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1192172 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
1192206 GTAAAACCTG
Statistics
Matches: 386, Mismatches: 16, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
305 82 0.21
306 5 0.01
310 2 0.01
315 198 0.51
316 99 0.26
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (310 bp):
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAAAATGTTTATTGACAACCAGCGGTCCCTTC
GTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTC
TGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGCTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
Found at i:1193058 original size:1 final size:1
Alignment explanation
Indices: 1193048--1193099 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
1193038 CGTTATTCTC
* * * * *
1193048 TTTTTGTTTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1193100 CAACTTAGGA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:1193062 original size:9 final size:9
Alignment explanation
Indices: 1193048--1193096 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
1193038 CGTTATTCTC
1193048 TTTTTGTTT
1 TTTTTGTTT
1193057 TTTTTGTTT
1 TTTTTGTTT
*
1193066 TTTGT-TTT
1 TTTTTGTTT
1193074 TTTTTGTTT
1 TTTTTGTTT
1193083 TTTTT-TCTT
1 TTTTTGT-TT
1193092 TTTTT
1 TTTTT
1193097 TTTCAACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 8 0.22
9 28 0.78
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:1193067 original size:10 final size:10
Alignment explanation
Indices: 1193048--1193098 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
1193038 CGTTATTCTC
*
1193048 TTTTTGTTTTT
1 TTTTT-TTTTG
1193059 TTTGTTTTTTG
1 TTT-TTTTTTG
1193070 TTTTTTTTTG
1 TTTTTTTTTG
*
1193080 TTTTTTTTTC
1 TTTTTTTTTG
1193090 TTTTTTTTT
1 TTTTTTTTT
1193099 TCAACTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 25 0.68
11 10 0.27
12 2 0.05
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1193069 original size:16 final size:16
Alignment explanation
Indices: 1193048--1193099 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
1193038 CGTTATTCTC
1193048 TTTTTGTTTTTTTTGT
1 TTTTTGTTTTTTTTGT
1193064 TTTTTGTTTTTTTTTGT
1 TTTTTG-TTTTTTTTGT
1193081 TTTTT-TTTCTTTTT-T
1 TTTTTGTTT-TTTTTGT
1193096 TTTT
1 TTTT
1193100 CAACTTAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 15 0.44
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (16 bp):
TTTTTGTTTTTTTTGT
Found at i:1193078 original size:26 final size:24
Alignment explanation
Indices: 1193048--1193099 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
1193038 CGTTATTCTC
*
1193048 TTTTTGTTTTTTTTGTTTTTTGTTTT
1 TTTTTGTTTTTTTT-TCTTTT-TTTT
1193074 TTTTTGTTTTTTTTTCTTTTTTTT
1 TTTTTGTTTTTTTTTCTTTTTTTT
1193098 TT
1 TT
1193100 CAACTTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.24
25 5 0.20
26 14 0.56
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (24 bp):
TTTTTGTTTTTTTTTCTTTTTTTT
Found at i:1207985 original size:24 final size:24
Alignment explanation
Indices: 1207958--1208023 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
1207948 GACTTGCTAC
1207958 AACAATGAACATCCTATTTGCATG
1 AACAATGAACATCCTATTTGCATG
1207982 AACAATGAACATCCTATTTGCATG
1 AACAATGAACATCCTATTTGCATG
1208006 AACAATGAACATCC-ATTT
1 AACAATGAACATCCTATTT
1208024 ATGTTCCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 4 0.10
24 38 0.90
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (24 bp):
AACAATGAACATCCTATTTGCATG
Found at i:1209133 original size:31 final size:29
Alignment explanation
Indices: 1209098--1209164 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1209088 AACGGTTTAT
* * *
1209098 TAACAACTATTAACGTCGAGTGATTATTTTG
1 TAACAAC-AATAACGT-GAGTAATCATTTTG
*
1209129 TAACAAACAATAACGTTAGTAATCATTTTG
1 TAAC-AACAATAACGTGAGTAATCATTTTG
1209159 TAACAA
1 TAACAA
1209165 ATGATAACGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 15 0.48
31 11 0.35
32 3 0.10
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (29 bp):
TAACAACAATAACGTGAGTAATCATTTTG
Found at i:1212213 original size:3 final size:3
Alignment explanation
Indices: 1212205--1212269 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1212195 TAATTTGTAT
1212205 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1212253 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
1212270 TGTAATTGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1212730 original size:35 final size:35
Alignment explanation
Indices: 1212686--1212798 Score: 142
Period size: 35 Copynumber: 3.2 Consensus size: 35
1212676 AAAACAATTC
*
1212686 TCAATTTCATTCTAAACCACAAATTTC-AAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTTCTAAAATAAT
1212721 TCAATTTCATTCTAAACCCTAAA-TTCTAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTTCTAAAATAAT
* *
1212756 TCAATTACATTCTAAAACCCAAA-TTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTTCTAAAATAAT
*
1212791 TTAATTTC
1 TCAATTTC
1212799 TGTCTTTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
34 4 0.06
35 60 0.86
36 6 0.09
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCAAATTTCTAAAATAAT
Found at i:1213863 original size:35 final size:34
Alignment explanation
Indices: 1213815--1213926 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
1213805 ATTTCTCCTT
*
1213815 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTGGGGTTTAGAATG
* *
1213850 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTGGGGTTTAGAATG
* * *
1213885 AAATTGAATTACTTTGAAATTTGGGATTTATAATG
1 AAATTGAATTATTTTG-AATTTGGGGTTTAGAATG
1213920 AAATTGA
1 AAATTGA
1213927 GGAATGTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
34 1 0.01
35 66 0.99
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGAATTTGGGGTTTAGAATG
Found at i:1216135 original size:13 final size:13
Alignment explanation
Indices: 1216081--1216143 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
1216071 TTAAAATTAA
1216081 ATATATAAATATT
1 ATATATAAATATT
* *
1216094 ATATATATATTTT
1 ATATATAAATATT
* *
1216107 A-ATTTAAAT-TAA
1 ATATATAAATAT-T
1216119 ATATATAAATATT
1 ATATATAAATATT
*
1216132 ATATATATATAT
1 ATATATAAATAT
1216144 ATTTTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 1 0.03
12 7 0.18
13 30 0.77
14 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATAAATATT
Found at i:1216152 original size:42 final size:41
Alignment explanation
Indices: 1216074--1216184 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 41
1216064 ATATATATTA
1216074 AAATTAAATATATAA-A-TAT-TATATATATATTTTAATTT
1 AAATTAAATATATAATATTATATATATATATATTTTAATTT
1216112 AAATTAAATATATAAATATTATATATATATATATTTTAATTT
1 AAATTAAATATAT-AATATTATATATATATATATTTTAATTT
*
1216154 AAATTAAATTTATTAATATTATATATATATA
1 AAATTAAATATA-TAATATTATATATATATA
1216185 ATAATTATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
38 13 0.19
39 2 0.03
40 1 0.01
41 3 0.04
42 47 0.70
43 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (41 bp):
AAATTAAATATATAATATTATATATATATATATTTTAATTT
Found at i:1216190 original size:38 final size:38
Alignment explanation
Indices: 1216061--1216190 Score: 165
Period size: 38 Copynumber: 3.4 Consensus size: 38
1216051 TCGGGCCGGG
*
1216061 TATATAT-AT-ATTAAAATTAAATATATAAATATTATA
1 TATATATAATAATTTAAATTAAATATATAAATATTATA
**
1216097 TATATATTTTAATTTAAATTAAATATATAAATATTATA
1 TATATATAATAATTTAAATTAAATATATAAATATTATA
* *
1216135 TATATATATATTTTAATTTAAATTAAATTTATTAATATTATA
1 TATATATA-A---TAATTTAAATTAAATATATAAATATTATA
1216177 TATATATAATAATT
1 TATATATAATAATT
1216191 ATTTTTAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
36 7 0.09
37 1 0.01
38 38 0.46
41 1 0.01
42 35 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATAATAATTTAAATTAAATATATAAATATTATA
Found at i:1216705 original size:114 final size:112
Alignment explanation
Indices: 1216473--1216687 Score: 274
Period size: 114 Copynumber: 1.9 Consensus size: 112
1216463 AAAGGGCCCC
* * * *
1216473 AAAAAAGTATATATATAGTGGCGTTTTTTCAATAAACGCCACTATAGATGGATCTATTGCGACGT
1 AAAAAAGTATACATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACGT
* * * *
1216538 TTTTTTAAAAAAACTCCACTATTATTGTGCAGGCCTAAAAAAAGCCCAA
66 TTTTTTAAAAAAACGCCACTATTAGTGTGC--GCCCAAAAAAAGACCAA
*
1216587 AAAAAAGTATACATATAGTGGCGTTTTTCCAATAAACACTACTATAGATGGACCTATTGCGACGT
1 AAAAAAGTATACATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACG-
* * *
1216652 TTTTTTTCAAAAGACGCTACTATT-GT-TGC-CCCAAAA
65 TTTTTTTAAAAAAACGCCACTATTAGTGTGCGCCCAAAA
1216688 TCGAATATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
110 6 0.07
113 3 0.03
114 60 0.67
115 20 0.22
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (112 bp):
AAAAAAGTATACATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACGT
TTTTTTAAAAAAACGCCACTATTAGTGTGCGCCCAAAAAAAGACCAA
Found at i:1218313 original size:4 final size:4
Alignment explanation
Indices: 1218304--1218333 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1218294 ACCATAAAAT
1218304 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1218334 TATTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1220687 original size:3 final size:3
Alignment explanation
Indices: 1220679--1220736 Score: 66
Period size: 3 Copynumber: 18.7 Consensus size: 3
1220669 TATTTTATTT
1220679 ATA ATA ATA ATA AGTA ATA ATA ATAA ATA ATA ATA ATA A-A TATGA A-A
1 ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA ATA ATA -AT-A ATA
1220726 ATA ATA ATA AT
1 ATA ATA ATA AT
1220737 TAAAACTCGG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 3 0.06
3 38 0.78
4 7 0.14
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1220698 original size:13 final size:13
Alignment explanation
Indices: 1220679--1220736 Score: 77
Period size: 13 Copynumber: 4.6 Consensus size: 13
1220669 TATTTTATTT
1220679 ATAATAATAATAA
1 ATAATAATAATAA
*
1220692 GTAATAATAATAA
1 ATAATAATAATAA
1220705 ATAATAATAATAA
1 ATAATAATAATAA
1220718 AT-ATGAA-AAT-A
1 ATAAT-AATAATAA
1220729 ATAATAAT
1 ATAATAAT
1220737 TAAAACTCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 5 0.12
12 7 0.17
13 28 0.70
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:1220700 original size:16 final size:16
Alignment explanation
Indices: 1220679--1220735 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
1220669 TATTTTATTT
1220679 ATAATAAT-AATAAGTA
1 ATAATAATAAATAA-TA
1220695 ATAATAATAAATAATA
1 ATAATAATAAATAATA
*
1220711 ATAATAA-ATATGAA-A
1 ATAATAATAAAT-AATA
1220726 ATAATAATAA
1 ATAATAATAA
1220736 TTAAAACTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 11 0.31
16 20 0.56
17 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:1221137 original size:134 final size:134
Alignment explanation
Indices: 1220892--1221596 Score: 844
Period size: 134 Copynumber: 5.3 Consensus size: 134
1220882 TTTCTTCAGG
* * * * * *
1220892 GGGAAAATCAGATCTGGGGA-TGTTGATTCATTCCATTATACCTCAAGGAAAATTGAATTGAGGC
1 GGGAAAATCAGATCTGGGGACT-TTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGC
** * * * * * *** *
1220956 AGACTAATTCCATTGTTAC-CAAGGAAATATCAAATCTTAAAAAAGATGGACT-TGCTCTATTTT
65 AGACTTGTTCCACTGTTACTCATGG-AATATCAAATCTTGAAAGAGATGGA-TATGTTCCGCTTC
1221019 TTCTTGA
128 TTCTTGA
* *** * *
1221026 GGGAAAATCAGATCTGGGGACGTTGATTCATTCTGTTATTCCTCAGGGAAGATTGAATCAAGGCA
1 GGGAAAATCAGATCTGGGGACTTTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
* * * *
1221091 GACTTGTTCCATTGTTACTCATGGAATATCAAATCTTAAAAGAGATGAATATGTTCCGCTTCTTA
66 GACTTGTTCCACTGTTACTCATGGAATATCAAATCTTGAAAGAGATGGATATGTTCCGCTTCTTC
1221156 TTGA
131 TTGA
* * * *
1221160 GGGAAAATCATATCTGAGGAATTTGATTTATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
1 GGGAAAATCAGATCTGGGGACTTTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
* ** * *
1221225 GACTTGTTCCACTGTTACTCATGGAATATCAAATCTTGAAAGAGATGGATCTGTTATGCTTATTT
66 GACTTGTTCCACTGTTACTCATGGAATATCAAATCTTGAAAGAGATGGATATGTTCCGCTTCTTC
1221290 TTGA
131 TTGA
1221294 GGGAAAATCAGATCTGGGGACTTTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
1 GGGAAAATCAGATCTGGGGACTTTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
* * * * * *
1221359 GACTTGTTTCGA-TGTTACTTAGGGAATATCAAATCTTGAAAGGGATCGATCTGTTCCGCTTCTT
66 GACTTG-TTCCACTGTTACTCATGGAATATCAAATCTTGAAAGAGATGGATATGTTCCGCTTCTT
1221423 CTTGA
130 CTTGA
* * * * * *
1221428 GGGAAAATAATATATGGGGACTTTGATTCATTCCACTGTTACTCAAGGAAAATTGAATCGAGGCA
1 GGGAAAATCAGATCTGGGGACTTTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
* * *
1221493 TACTTATTCAACTGTTACTCA-GTGAATATCAAATCTTGAAAGAGATGGATATGTTCCGCTTCTT
66 GACTTGTTCCACTGTTACTCATG-GAATATCAAATCTTGAAAGAGATGGATATGTTCCGCTTCTT
1221557 CTTGA
130 CTTGA
* * *
1221562 GGTAAAGTTAGATCTGGGGACTTTGATTCATTCCA
1 GGGAAAATCAGATCTGGGGACTTTGATTCATTCCA
1221597 TTTTTACTTA
Statistics
Matches: 497, Mismatches: 68, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
133 6 0.01
134 483 0.97
135 8 0.02
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (134 bp):
GGGAAAATCAGATCTGGGGACTTTGATTCATTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCA
GACTTGTTCCACTGTTACTCATGGAATATCAAATCTTGAAAGAGATGGATATGTTCCGCTTCTTC
TTGA
Found at i:1222892 original size:8 final size:8
Alignment explanation
Indices: 1222881--1222991 Score: 91
Period size: 8 Copynumber: 13.2 Consensus size: 8
1222871 TTATTCTCTC
1222881 TTTCTTTT
1 TTTCTTTT
1222889 TTTCTTTT
1 TTTCTTTT
1222897 CTTTCTTTTT
1 -TTTC-TTTT
*
1222907 TTTCATTT
1 TTTCTTTT
1222915 TTTCATTTCATT
1 TTTC--TT--TT
*
1222927 TTTCTTTA
1 TTTCTTTT
1222935 TTTCTTTAT
1 TTTCTTT-T
1222944 TTTC-TTT
1 TTTCTTTT
*
1222951 TAT-TTTT
1 TTTCTTTT
*
1222958 TTCCTTTT
1 TTTCTTTT
*
1222966 TTCCTTTT
1 TTTCTTTT
*
1222974 TTCCTTTT
1 TTTCTTTT
1222982 TTTCTTTT
1 TTTCTTTT
1222990 TT
1 TT
1222992 CATTTTTCAT
Statistics
Matches: 86, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
7 7 0.08
8 54 0.63
9 12 0.14
10 7 0.08
12 6 0.07
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1222931 original size:38 final size:36
Alignment explanation
Indices: 1222887--1222996 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 36
1222877 TCTCTTTCTT
1222887 TTTTTCTTTTCTTTCTTTTTTTTCATTTTTTCATTT-CA
1 TTTTTC-TTT-TTTCTTTTTTTTC-TTTTTTCATTTCCA
* ** *
1222925 TTTTTCTTTATTTCTTTATTTTCTTTTATTTTTTTCCT
1 TTTTTCTTT-TTTCTTTTTTTTCTTTT-TTCATTTCCA
*
1222963 TTTTTCCTTTTTTCCTTTTTTTCTTTTTTCATTT
1 TTTTT-CTTTTTTCTTTTTTTTCTTTTTTCATTT
1222997 TTCATTCTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
36 4 0.07
37 25 0.42
38 27 0.45
39 4 0.07
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.78
Consensus pattern (36 bp):
TTTTTCTTTTTTCTTTTTTTTCTTTTTTCATTTCCA
Found at i:1222965 original size:7 final size:8
Alignment explanation
Indices: 1222954--1222998 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
1222944 TTTCTTTTAT
1222954 TTTTTTCC
1 TTTTTTCC
1222962 TTTTTTCC
1 TTTTTTCC
1222970 TTTTTTCC
1 TTTTTTCC
*
1222978 TTTTTTTC
1 TTTTTTCC
*
1222986 TTTTTTCA
1 TTTTTTCC
1222994 TTTTT
1 TTTTT
1222999 CATTCTTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:1222990 original size:9 final size:9
Alignment explanation
Indices: 1222881--1222991 Score: 77
Period size: 9 Copynumber: 12.1 Consensus size: 9
1222871 TTATTCTCTC
1222881 TTTC-TTTT
1 TTTCTTTTT
*
1222889 TTTCTTTTC
1 TTTCTTTTT
1222898 TTTCTTTTT
1 TTTCTTTTT
*
1222907 TTTC-ATTT
1 TTTCTTTTT
1222915 TTTCATTTCATT
1 TTTC-TTT--TT
*
1222927 TTTC-TTTA
1 TTTCTTTTT
*
1222935 TTTCTTTAT
1 TTTCTTTTT
1222944 TTTCTTTTAT
1 TTTCTTTT-T
*
1222954 TTTTTTCCTTT
1 TTTCTT--TTT
*
1222965 TTTC-CTTT
1 TTTCTTTTT
*
1222973 TTTCCTTTT
1 TTTCTTTTT
1222982 TTTCTTTTT
1 TTTCTTTTT
1222991 T
1 T
1222992 CATTTTTCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
8 23 0.29
9 36 0.45
10 9 0.11
11 4 0.05
12 8 0.10
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1222993 original size:69 final size:69
Alignment explanation
Indices: 1222870--1222999 Score: 165
Period size: 69 Copynumber: 1.9 Consensus size: 69
1222860 CCCTCTTTTG
* * * *
1222870 TTTATTCTCTCTTTCTTTTTTTCTTTTCTTTCTTTTTTTTCATTTTTTCATTTCATTTTTCTTTA
1 TTTATTCTCTCTTTATTTTTTTCCTTTCTTTCCTTTTTTCCATTTTTTCATTTCATTTTTCTTTA
1222935 TTTC
66 TTTC
* * *
1222939 TTTATTTTCT-TTTATTTTTTTCCTTT-TTTCCTTTTTTCCTTTTTTTCTTTTTTCATTTTTC
1 TTTATTCTCTCTTTATTTTTTTCCTTTCTTTCCTTTTTTCCATTTTTTC--ATTTCATTTTTC
1223000 ATTCTTTAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 18 0.35
68 14 0.27
69 20 0.38
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (69 bp):
TTTATTCTCTCTTTATTTTTTTCCTTTCTTTCCTTTTTTCCATTTTTTCATTTCATTTTTCTTTA
TTTC
Found at i:1224394 original size:16 final size:16
Alignment explanation
Indices: 1224369--1224399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1224359 ATGATACTCA
*
1224369 AACAATGATCAAAATG
1 AACAAAGATCAAAATG
1224385 AACAAAGATCAAAAT
1 AACAAAGATCAAAAT
1224400 AGCCGCAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16
Consensus pattern (16 bp):
AACAAAGATCAAAATG
Found at i:1225533 original size:3 final size:3
Alignment explanation
Indices: 1225512--1225569 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
1225502 CCTGCATCAA
* *
1225512 AAT ATT AAT AA- ATT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
1225557 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
1225570 TTTTTAAGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 45 0.92
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1225774 original size:39 final size:39
Alignment explanation
Indices: 1225720--1225821 Score: 179
Period size: 39 Copynumber: 2.6 Consensus size: 39
1225710 GGATTGAACA
*
1225720 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGCCG
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGACG
*
1225759 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGACG
1225798 AGTTCTTCTCATTATGAAC-TCTTC
1 AGTTCTTCTCATTATGAACTTCTTC
1225822 ACTAAAAATG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
38 5 0.08
39 56 0.92
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.47
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGACG
Done.