Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1214740 original size:16 final size:16
Alignment explanation
Indices: 1214697--1214740 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1214687 ACAGAGCTTC
*
1214697 TGAATCATTCAACATT
1 TGAATCATTCAGCATT
1214713 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
1214729 TGAATCATTCAG
1 TGAATCATTCAG
1214741 TGCTTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:1217965 original size:15 final size:15
Alignment explanation
Indices: 1217945--1217981 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1217935 TAGTCCTTCA
*
1217945 TGTATATGTGTATTT
1 TGTATATGTATATTT
1217960 TGTATATGTATATTT
1 TGTATATGTATATTT
1217975 TGTATAT
1 TGTATAT
1217982 TGTGACTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (15 bp):
TGTATATGTATATTT
Found at i:1218792 original size:25 final size:23
Alignment explanation
Indices: 1218759--1218810 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1218749 AATCACCAAA
*
1218759 TTTTCAAATAAAAGTCATAATTGTT
1 TTTTAAAATAAAA--CATAATTGTT
* *
1218784 TTTTAAAATAATACTTAATTGTT
1 TTTTAAAATAAAACATAATTGTT
1218807 TTTT
1 TTTT
1218811 TCAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
25 11 0.46
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (23 bp):
TTTTAAAATAAAACATAATTGTT
Found at i:1219954 original size:54 final size:54
Alignment explanation
Indices: 1219889--1220013 Score: 164
Period size: 53 Copynumber: 2.3 Consensus size: 54
1219879 CCTGAAAGAT
* * * *
1219889 GGTATCAATACCCTTGAAACATCGAATGCCAGATT-GGTATCGGTACCTTGAGGA
1 GGTATCGATACCCTTGAAACATCGAATGCCA-ATTCAGTATCGGTACCATGAGAA
* *
1219943 GGTATCGATACCCTTG-AACATCGAATGCTATTTCAGTATCGGTACCATGAGAA
1 GGTATCGATACCCTTGAAACATCGAATGCCAATTCAGTATCGGTACCATGAGAA
*
1219996 GGTATCGACACCCTTGAA
1 GGTATCGATACCCTTGAA
1220014 GGGAAGTATC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 2 0.03
53 44 0.71
54 16 0.26
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (54 bp):
GGTATCGATACCCTTGAAACATCGAATGCCAATTCAGTATCGGTACCATGAGAA
Found at i:1220597 original size:21 final size:21
Alignment explanation
Indices: 1220571--1220650 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 21
1220561 TTGAGGGTTT
1220571 TATGTGGTCA-TTCGGGACAAA
1 TATGTGG-CACTTCGGGACAAA
1220592 TATGTGGCACTTCGGTG-CAAA
1 TATGTGGCACTTCGG-GACAAA
** * *
1220613 CCTATGTGGTTCTTCGGGATAAT
1 --TATGTGGCACTTCGGGACAAA
1220636 TATGTGGCACTTCGG
1 TATGTGGCACTTCGG
1220651 TGCAAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 2 0.04
21 29 0.60
22 2 0.04
23 15 0.31
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (21 bp):
TATGTGGCACTTCGGGACAAA
Found at i:1220640 original size:44 final size:44
Alignment explanation
Indices: 1220571--1220656 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
1220561 TTGAGGGTTT
1220571 TATGTGGTCATTCGGGACAAATATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCATTCGGGACAAATATGTGGCACTTCGGTGCAAACC
* *
1220615 TATGTGGTTC-TTCGGGATAATTATGTGGCACTTCGGTGCAAA
1 TATGTGG-TCATTCGGGACAAATATGTGGCACTTCGGTGCAAA
1220657 TTATGAGCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (44 bp):
TATGTGGTCATTCGGGACAAATATGTGGCACTTCGGTGCAAACC
Found at i:1228346 original size:30 final size:32
Alignment explanation
Indices: 1228310--1228388 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 32
1228300 AATATCAAAC
*
1228310 TTTAAAAAACCCGACCCAAACCCG-A-TTTTT
1 TTTAAAAAATCCGACCCAAACCCGAATTTTTT
* * *
1228340 TTTAAAAAATCC-AACCGATCCCGAATTTTTT
1 TTTAAAAAATCCGACCCAAACCCGAATTTTTT
1228371 TTTAAAAAAATCCGACCC
1 TTT-AAAAAATCCGACCC
1228389 GAATACCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 8 0.20
30 12 0.30
31 8 0.20
32 9 0.22
33 3 0.08
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (32 bp):
TTTAAAAAATCCGACCCAAACCCGAATTTTTT
Found at i:1228507 original size:24 final size:24
Alignment explanation
Indices: 1228475--1228526 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1228465 TTATGAATGA
1228475 AATTTACTTTCCCTCCCTTGATGG
1 AATTTACTTTCCCTCCCTTGATGG
1228499 AATTTACTTTCCCTCCCTTGATGG
1 AATTTACTTTCCCTCCCTTGATGG
1228523 AATT
1 AATT
1228527 GTATTCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (24 bp):
AATTTACTTTCCCTCCCTTGATGG
Found at i:1230092 original size:34 final size:34
Alignment explanation
Indices: 1230049--1230140 Score: 175
Period size: 34 Copynumber: 2.7 Consensus size: 34
1230039 TGAAAGTATT
1230049 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGGA
1 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGGA
1230083 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGGA
1 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGGA
1230117 AAAATGGTTTTCAAAGTTTGGTAA
1 AAAATGGTTTTC-AAGTTTGGTAA
1230141 ATGTTTCTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 46 0.81
35 11 0.19
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (34 bp):
AAAATGGTTTTCAAGTTTGGTAACCAACTTTGGA
Found at i:1230165 original size:37 final size:36
Alignment explanation
Indices: 1230076--1230194 Score: 120
Period size: 37 Copynumber: 3.3 Consensus size: 36
1230066 TGGTAACCAA
****
1230076 CTTTGGAAAAATGGTTTTC-AAGTTTGGT-AA-CCAA
1 CTTT-GAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1230110 CTTTGGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTT-GAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
1230147 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1230184 -GTTGAAAAATG
1 CTTTGAAAAATG
1230195 ATAATGGGAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
34 19 0.26
35 10 0.14
36 18 0.24
37 27 0.36
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1234703 original size:34 final size:35
Alignment explanation
Indices: 1234648--1234740 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 35
1234638 TGAAAGTATT
1234648 AAAATGGTTTTC-AAGTTTGGTAA-CCAACTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTGA
****
1234681 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTGA
*
1234717 AAAATAGTTTTTCAAAGTTTGGTA
1 AAAAT-GGTTTTCAAAGTTTGGTA
1234741 GATGTTTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 12 0.24
34 9 0.18
35 2 0.04
36 12 0.24
37 16 0.31
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTGA
Found at i:1234738 original size:37 final size:36
Alignment explanation
Indices: 1234675--1234758 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 36
1234665 TGGTAACCAA
1234675 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
1234711 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1234748 -GTTGAAAAATG
1 CTTTGAAAAATG
1234759 ATAATGGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.02
36 20 0.45
37 23 0.52
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1235666 original size:27 final size:29
Alignment explanation
Indices: 1235612--1235668 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
1235602 ATTACTAGAT
1235612 TATTATATCAATATTAAATACATAAATAA
1 TATTATATCAATATTAAATACATAAATAA
1235641 TATTAT-TCAATATT-AATA-ATTAAATAA
1 TATTATATCAATATTAAATACA-TAAATAA
1235668 T
1 T
1235669 GTTTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 1 0.04
27 12 0.44
28 8 0.30
29 6 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (29 bp):
TATTATATCAATATTAAATACATAAATAA
Found at i:1235740 original size:26 final size:29
Alignment explanation
Indices: 1235711--1235807 Score: 74
Period size: 32 Copynumber: 3.2 Consensus size: 29
1235701 TTATTTATAC
*
1235711 TATATTATATTTTATTA-AA-ATAA-GAA
1 TATATTATATATTATTATAATATAATGAA
1235737 TATAATATCATATATTATTATAATATAATTGAA
1 TAT-AT-T-ATATATTATTATAATATAA-TGAA
* * *
1235770 TATATTATTATAATATTGAAAATATTAATTAA
1 TATATTA-TATATTATT-ATAATA-TAATGAA
1235802 TATATT
1 TATATT
1235808 TTAAATATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.05
27 2 0.04
28 1 0.02
29 10 0.18
30 3 0.05
31 13 0.23
32 16 0.28
33 9 0.16
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (29 bp):
TATATTATATATTATTATAATATAATGAA
Found at i:1235777 original size:20 final size:20
Alignment explanation
Indices: 1235752--1235796 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1235742 TATCATATAT
*
1235752 TATTATAAT-ATAATTGAATA
1 TATTATAATAAT-ATTGAAAA
*
1235772 TATTATTATAATATTGAAAA
1 TATTATAATAATATTGAAAA
1235792 TATTA
1 TATTA
1235797 ATTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TATTATAATAATATTGAAAA
Found at i:1235806 original size:21 final size:21
Alignment explanation
Indices: 1235748--1235816 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1235738 ATAATATCAT
* *
1235748 ATATTATTATAATATAATTGAAT
1 ATATTAAT-TAATAT-ATTGAAA
1235771 ATATT-ATT-ATAATATTGAAA
1 ATATTAATTAAT-ATATTGAAA
**
1235791 ATATTAATTAATATATTTTAA
1 ATATTAATTAATATATTGAAA
1235812 ATATT
1 ATATT
1235817 TTAATAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.33
21 18 0.46
22 3 0.08
23 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
ATATTAATTAATATATTGAAA
Found at i:1235828 original size:30 final size:33
Alignment explanation
Indices: 1235758--1235816 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1235748 ATATTATTAT
1235758 AATA-TAATTGAATATATTATTATAATATTGAA
1 AATATTAATTGAATATATTATTATAATATTGAA
1235790 AATATTAATT-AATATATT-TTA-AATATT
1 AATATTAATTGAATATATTATTATAATATT
1235817 TTAATAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 6 0.23
31 3 0.12
32 12 0.46
33 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (33 bp):
AATATTAATTGAATATATTATTATAATATTGAA
Found at i:1237424 original size:14 final size:15
Alignment explanation
Indices: 1237384--1237425 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1237374 TAAGATGCTC
*
1237384 ATTAATAATATTTGT
1 ATTAAAAATATTTGT
1237399 ATATATAAAATATTT-T
1 AT-TA-AAAATATTTGT
1237415 ATTAAAAATAT
1 ATTAAAAATAT
1237426 AAATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.29
15 4 0.17
16 5 0.21
17 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATTAAAAATATTTGT
Found at i:1238954 original size:2 final size:2
Alignment explanation
Indices: 1238947--1238976 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1238937 AACTCTTTTA
1238947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1238977 GTAGCAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1239108 original size:3 final size:3
Alignment explanation
Indices: 1239102--1239145 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1239092 AACAAAAATT
1239102 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1239146 TAAAGTCACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1240001 original size:16 final size:16
Alignment explanation
Indices: 1239982--1240014 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1239972 TCATTTTAGG
1239982 TTGTTTTC-AGTTCGGA
1 TTGTTTTCGA-TTCGGA
1239998 TTGTTTTCGATTCGGA
1 TTGTTTTCGATTCGGA
1240014 T
1 T
1240015 CGGGTATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (16 bp):
TTGTTTTCGATTCGGA
Found at i:1242972 original size:15 final size:15
Alignment explanation
Indices: 1242952--1242982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1242942 TTAATTTGAA
1242952 TATTTTATTATTATT
1 TATTTTATTATTATT
*
1242967 TATTTTATTTTTATT
1 TATTTTATTATTATT
1242982 T
1 T
1242983 TAATCGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTATTATTATT
Found at i:1242980 original size:21 final size:21
Alignment explanation
Indices: 1242954--1243005 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1242944 AATTTGAATA
**
1242954 TTTTATTATTATTTATTTTAT
1 TTTTATTATTATCGATTTTAT
1242975 TTTTATT-TTAATCGATTTTAT
1 TTTTATTATT-ATCGATTTTAT
1242996 TTTTA-TATTA
1 TTTTATTATTA
1243006 ATTTGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTATTATCGATTTTAT
Found at i:1243006 original size:21 final size:21
Alignment explanation
Indices: 1242968--1243007 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1242958 ATTATTATTT
*
1242968 ATTTTATTTTTATTTTAATCG
1 ATTTTATTTTTATATTAATCG
1242989 ATTTTATTTTTATATTAAT
1 ATTTTATTTTTATATTAAT
1243008 TTGAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTTATTTTTATATTAATCG
Found at i:1244174 original size:21 final size:21
Alignment explanation
Indices: 1244148--1244203 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1244138 CCCAAAATAG
1244148 GGAGTATCGGTACTACCTTTT
1 GGAGTATCGGTACTACCTTTT
1244169 GGAGTATCGGTACTACCTTTT
1 GGAGTATCGGTACTACCTTTT
*
1244190 GGAGTATCCGTACT
1 GGAGTATCGGTACT
1244204 TCTTTTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (21 bp):
GGAGTATCGGTACTACCTTTT
Found at i:1247873 original size:13 final size:13
Alignment explanation
Indices: 1247855--1247893 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1247845 TTTTTAGAAA
1247855 TTTCATATTTCAT
1 TTTCATATTTCAT
* *
1247868 TTTCATCTTTCAC
1 TTTCATATTTCAT
1247881 TTTCATA-TTCAT
1 TTTCATATTTCAT
1247893 T
1 T
1247894 ACATAACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:1247954 original size:19 final size:19
Alignment explanation
Indices: 1247927--1247996 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1247917 ATGAATTCAT
* * *
1247927 TTTCTGATTCAGAACTTAC
1 TTTCAGATTCATAACTTAA
1247946 TTTCAGATTCATAACTTAA
1 TTTCAGATTCATAACTTAA
* *
1247965 TTTCAGATTCATAGCTTAT
1 TTTCAGATTCATAACTTAA
*
1247984 TTTCAAATTCATA
1 TTTCAGATTCATA
1247997 GTCCAAGGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.44
Consensus pattern (19 bp):
TTTCAGATTCATAACTTAA
Found at i:1248361 original size:2 final size:2
Alignment explanation
Indices: 1248354--1248422 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
1248344 ATAACAAAGG
1248354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1248396 TA TA TA TA TA TA TA TA GA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1248423 CATGAACATC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1259938 original size:13 final size:13
Alignment explanation
Indices: 1259920--1259958 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1259910 TTTTTAGAAA
1259920 TTTCATATTTCAT
1 TTTCATATTTCAT
* *
1259933 TTTCATTTTTCAC
1 TTTCATATTTCAT
1259946 TTTCATA-TTCAT
1 TTTCATATTTCAT
1259958 T
1 T
1259959 ACATAACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:1260026 original size:19 final size:18
Alignment explanation
Indices: 1260004--1260061 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1259994 TCTGACTCAG
1260004 AACTTACTTTCAGATTCAT
1 AACTTA-TTTCAGATTCAT
*
1260023 AACTTAATTTTAGATTCAT
1 AACTT-ATTTCAGATTCAT
* *
1260042 AGCTTATTATCATATTCAT
1 AACTTATT-TCAGATTCAT
1260061 A
1 A
1260062 TCCCAATGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.09
19 29 0.88
20 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (18 bp):
AACTTATTTCAGATTCAT
Found at i:1260398 original size:2 final size:2
Alignment explanation
Indices: 1260391--1260416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1260381 TGGGTAGCTC
1260391 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
1260417 CATGAACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1265772 original size:21 final size:21
Alignment explanation
Indices: 1265739--1265778 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1265729 TTCTACGTGG
*
1265739 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
1265760 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
1265779 GGTACTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:1265786 original size:21 final size:21
Alignment explanation
Indices: 1265748--1265788 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1265738 GTCCTTCGGG
*
1265748 ACATATATGTAATCCTTTGGA
1 ACATATATGTAATACTTTGGA
**
1265769 ACATATATGTGGTACTTTGG
1 ACATATATGTAATACTTTGG
1265789 TACACCTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
ACATATATGTAATACTTTGGA
Found at i:1266177 original size:18 final size:18
Alignment explanation
Indices: 1266137--1266179 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1266127 TGACTAAGAG
* *
1266137 ATAATAATTAAAATAATG
1 ATAATAATTAAAAGAATA
* *
1266155 CTAATAATTATAAGAATA
1 ATAATAATTAAAAGAATA
1266173 ATAATAA
1 ATAATAA
1266180 GGACAATGAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (18 bp):
ATAATAATTAAAAGAATA
Found at i:1281149 original size:20 final size:20
Alignment explanation
Indices: 1281126--1281205 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 20
1281116 TTCGTGCAGA
1281126 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCC-TGAG
*
1281146 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC--TG-AG
* *
1281169 GGGAACCGATTCCCCCT-AG
1 GGGAATCGATACCCCCTGAG
1281188 GGGAATCGATACCCCCTG
1 GGGAATCGATACCCCCTG
1281206 GGGTTCTGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 17 0.33
20 15 0.29
21 3 0.06
22 1 0.02
23 15 0.29
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (20 bp):
GGGAATCGATACCCCCTGAG
Found at i:1281913 original size:12 final size:12
Alignment explanation
Indices: 1281881--1281906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1281871 ACACCGTCAA
1281881 CCAAATCCTCCT
1 CCAAATCCTCCT
1281893 CCAAATCCTCCT
1 CCAAATCCTCCT
1281905 CC
1 CC
1281907 TATTCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (12 bp):
CCAAATCCTCCT
Found at i:1285417 original size:21 final size:21
Alignment explanation
Indices: 1285384--1285433 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1285374 TTCTACGTGG
*
1285384 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
* *
1285405 TCCTTTGGAACATTTATGT-A
1 TCCTTCGGAACATATATGTAA
1285425 TCACTTCGG
1 TC-CTTCGG
1285434 TACACCTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:1285529 original size:21 final size:21
Alignment explanation
Indices: 1285503--1285563 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1285493 ATATATGTGA
1285503 TATGTGGTCCTTCGGGACATC
1 TATGTGGTCCTTCGGGACATC
* *
1285524 TATGTGGTCATTCGGGACATT
1 TATGTGGTCCTTCGGGACATC
* *
1285545 TATATGGTCCTTCAGGACA
1 TATGTGGTCCTTCGGGACA
1285564 AATTCATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATC
Found at i:1287548 original size:76 final size:77
Alignment explanation
Indices: 1287418--1287568 Score: 223
Period size: 76 Copynumber: 2.0 Consensus size: 77
1287408 TTAAATGTTA
* *
1287418 TTTCAATGGTGAAAGTCTATGTTATATACCACTATTGGAATTAAGTGATAATTTAACTAGTGTAA
1 TTTCAATGGTGAAAGTATATATTATATACCACTATTGGAATTAAGTGATAATTTAACTAGTGTAA
1287483 GT-TATGTTAAG
66 GTCTATGTTAAG
* * * * * *
1287494 TTTCATTGGTGTAAGTATATATTATATACCACTTTTGGAATTAAGTGATGATTTAGCTGGTGTAA
1 TTTCAATGGTGAAAGTATATATTATATACCACTATTGGAATTAAGTGATAATTTAACTAGTGTAA
1287559 GTCTATGTTA
66 GTCTATGTTA
1287569 TATAGCACTA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
76 59 0.89
77 7 0.11
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (77 bp):
TTTCAATGGTGAAAGTATATATTATATACCACTATTGGAATTAAGTGATAATTTAACTAGTGTAA
GTCTATGTTAAG
Found at i:1287560 original size:51 final size:51
Alignment explanation
Indices: 1287500--1287772 Score: 323
Period size: 51 Copynumber: 5.4 Consensus size: 51
1287490 TAAGTTTCAT
* * * *
1287500 TGGTGTAAGTATATATTATATACCACTTTTGGAATTAAGTGATGATTTAGC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* **
1287551 TGGTGTAAGTCTATGTTATATAGCACTACTGGAATTAAGTGATGATTTAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* * * * * *
1287602 TAGTGTAAGTCTATATTATATATCACTGCTGGAAGTAAGTGACGATTTAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* * *
1287653 TAGTGTAAGTCTATGTTATATATCACTGTTGGAATTAAGTGATGATTCAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* * * **
1287704 TGGTTTAAATCTATGTTATATTCCACTGTTGGAATTATA-TGATGATCGAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTA-AGTGATGATTTAAC
* *
1287755 TGGTGTAAATCCATGTTA
1 TGGTGTAAGTCTATGTTA
1287773 AGTTTCACTA
Statistics
Matches: 195, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
51 194 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (51 bp):
TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
Found at i:1287744 original size:26 final size:26
Alignment explanation
Indices: 1287664--1287744 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
1287654 AGTGTAAGTC
1287664 TATGTTATATAT-CACTGTTGGAATTA
1 TATGTTATAT-TCCACTGTTGGAATTA
* * * * *
1287690 -A-GTGATGATTCAACTGGTT-TAAATC
1 TATGTTAT-ATTCCACT-GTTGGAATTA
1287715 TATGTTATATTCCACTGTTGGAATTA
1 TATGTTATATTCCACTGTTGGAATTA
1287741 TATG
1 TATG
1287745 ATGATCGAAC
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
24 5 0.13
25 12 0.31
26 18 0.46
27 4 0.10
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (26 bp):
TATGTTATATTCCACTGTTGGAATTA
Found at i:1290146 original size:38 final size:37
Alignment explanation
Indices: 1290065--1290156 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 37
1290055 TTTGTTTTTC
* * *
1290065 TTTTTTTCTTTTTTTTTGTTTTTTTAAATAGTGCTACT
1 TTTTTTTCTTTTTTTCTCTTTTTTTAAACAGTGC-ACT
* *
1290103 ATTTTTTCCTGTTTTTCTCTTTTTTCTAAACAGTGC-CT
1 -TTTTTTTCTTTTTTTCTCTTTTTT-TAAACAGTGCACT
1290141 TTTTTTTCTTTTTTTC
1 TTTTTTTCTTTTTTTC
1290157 GTGGGTCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
37 14 0.31
38 2 0.04
39 20 0.44
40 9 0.20
ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68
Consensus pattern (37 bp):
TTTTTTTCTTTTTTTCTCTTTTTTTAAACAGTGCACT
Found at i:1292077 original size:20 final size:20
Alignment explanation
Indices: 1292052--1292114 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
1292042 ATTCTACCAC
*
1292052 ATGCAACTATATGCTCTTAA
1 ATGCAACTATATGCTCCTAA
1292072 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
1292092 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
1292112 ATG
1 ATG
1292115 GGCTCTTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:1294583 original size:15 final size:15
Alignment explanation
Indices: 1294563--1294592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1294553 TATGAGCTAT
1294563 GTGATAAGAAACTAC
1 GTGATAAGAAACTAC
*
1294578 GTGATAAGAAGCTAC
1 GTGATAAGAAACTAC
1294593 AAGCCTATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (15 bp):
GTGATAAGAAACTAC
Found at i:1295115 original size:9 final size:9
Alignment explanation
Indices: 1295066--1295116 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
1295056 ATAACTAAGA
1295066 GATAATAAT
1 GATAATAAT
*
1295075 GAAAATAAT
1 GATAATAAT
*
1295084 GCTAATAAT
1 GATAATAAT
*
1295093 GATAAGAAT
1 GATAATAAT
* *
1295102 AATAATAAG
1 GATAATAAT
1295111 GATAAT
1 GATAAT
1295117 GAAATGATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (9 bp):
GATAATAAT
Found at i:1296526 original size:77 final size:77
Alignment explanation
Indices: 1296424--1296571 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 77
1296414 TTAAATTTTA
* * *
1296424 TTTCAATGGTGTAAGTCTGTGTTATATACCACTATTAGAATTAAGTGATAATTTAACTAGTGTAA
1 TTTCAATGGTGTAAGTATATATTATATACCACTATTAGAATTAAGTGATAATTTAACTAGTGTAA
1296489 GTCTATATTAAG
66 GTCTATATTAAG
* * * * * * *
1296501 TTTCATTGGTGTAAGTATATATTATATACCACTGTTTGAATTAGGTGATGATTTAGCTGGTGTAA
1 TTTCAATGGTGTAAGTATATATTATATACCACTATTAGAATTAAGTGATAATTTAACTAGTGTAA
1296566 GTCTAT
66 GTCTAT
1296572 GTTATATAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 61 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (77 bp):
TTTCAATGGTGTAAGTATATATTATATACCACTATTAGAATTAAGTGATAATTTAACTAGTGTAA
GTCTATATTAAG
Found at i:1296586 original size:51 final size:51
Alignment explanation
Indices: 1296507--1296779 Score: 305
Period size: 51 Copynumber: 5.4 Consensus size: 51
1296497 TAAGTTTCAT
* * * * *
1296507 TGGTGTAAGTATATATTATATACCACTGTTTGAATTAGGTGATGATTTAGC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
** * *
1296558 TGGTGTAAGTCTATGTTATATAGAACTGTTGGAACTAAGTGATTATTTAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* * * * * *
1296609 TGGTGTAAGTCTATATTATATATCACTGCTAGAAGTAAATGATGATTTAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* * * *
1296660 TAGTGTAAGTCTATGTTATATATCACTATTGGAATTAAGTGATGATTTAAT
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
* * *
1296711 TGGTTTAAGACTATGTTATATACCGCTGTTGGAATTATA-TGATGATTTAAC
1 TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTA-AGTGATGATTTAAC
* * *
1296762 TAGTGTAAATCCATGTTA
1 TGGTGTAAGTCTATGTTA
1296780 AGTTTCACTA
Statistics
Matches: 184, Mismatches: 37, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
51 183 0.99
52 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (51 bp):
TGGTGTAAGTCTATGTTATATACCACTGTTGGAATTAAGTGATGATTTAAC
Found at i:1296692 original size:102 final size:102
Alignment explanation
Indices: 1296507--1296779 Score: 339
Period size: 102 Copynumber: 2.7 Consensus size: 102
1296497 TAAGTTTCAT
* * ** * *
1296507 TGGTGTAAGTATATATTATATACCACTGTTTGAATTAGGTGATGATTTAGCTGGTGTAAGTCTAT
1 TGGTGTAAGTCTATATTATATACCACTGTTAGAATTAAATGATGATTTAACTAGTGTAAGTCTAT
* *
1296572 GTTATATAGAACTGTTGGAACTAAGTGATTATTTAAC
66 GTTATATAGAACTATTGGAACTAAGTGATGATTTAAC
* * *
1296609 TGGTGTAAGTCTATATTATATATCACTGCTAGAAGTAAATGATGATTTAACTAGTGTAAGTCTAT
1 TGGTGTAAGTCTATATTATATACCACTGTTAGAATTAAATGATGATTTAACTAGTGTAAGTCTAT
** * *
1296674 GTTATATATCACTATTGGAATTAAGTGATGATTTAAT
66 GTTATATAGAACTATTGGAACTAAGTGATGATTTAAC
* * * * * * * *
1296711 TGGTTTAAGACTATGTTATATACCGCTGTTGGAATTATATGATGATTTAACTAGTGTAAATCCAT
1 TGGTGTAAGTCTATATTATATACCACTGTTAGAATTAAATGATGATTTAACTAGTGTAAGTCTAT
1296776 GTTA
66 GTTA
1296780 AGTTTCACTA
Statistics
Matches: 145, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
102 145 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (102 bp):
TGGTGTAAGTCTATATTATATACCACTGTTAGAATTAAATGATGATTTAACTAGTGTAAGTCTAT
GTTATATAGAACTATTGGAACTAAGTGATGATTTAAC
Found at i:1299725 original size:129 final size:130
Alignment explanation
Indices: 1299564--1299818 Score: 503
Period size: 129 Copynumber: 2.0 Consensus size: 130
1299554 TCATGGGAAG
1299564 TCAATAAAAAAATTAAGAAAATTCATTAATCATGTCATTTCCACTATCATGTATCCTAATTCAAA
1 TCAATAAAAAAATTAAGAAAATTCATTAATCATGTCATTTCCACTATCATGTATCCTAATTCAAA
1299629 TAAAAGTGTGATCAAGAACTCAAGTGACATTCAAAGAGACAGC-AAAATCGAATTTGTAAAGAAA
66 TAAAAGTGTGATCAAGAACTCAAGTGACATTCAAAGAGACAGCAAAAATCGAATTTGTAAAGAAA
1299693 TCAATAAAAAAATTAAGAAAATTCATTAATCATGTCATTTCCACTATCATGTATCCTAATTCAAA
1 TCAATAAAAAAATTAAGAAAATTCATTAATCATGTCATTTCCACTATCATGTATCCTAATTCAAA
1299758 TAAAAGTGTGATCAAGAACTCAAGTGACATTCAAAGAGACAGCAAAAATCGAATTTGTAAA
66 TAAAAGTGTGATCAAGAACTCAAGTGACATTCAAAGAGACAGCAAAAATCGAATTTGTAAA
1299819 TAGAAAATTC
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 108 0.86
130 17 0.14
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.27
Consensus pattern (130 bp):
TCAATAAAAAAATTAAGAAAATTCATTAATCATGTCATTTCCACTATCATGTATCCTAATTCAAA
TAAAAGTGTGATCAAGAACTCAAGTGACATTCAAAGAGACAGCAAAAATCGAATTTGTAAAGAAA
Found at i:1303878 original size:20 final size:20
Alignment explanation
Indices: 1303849--1303892 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1303839 TCAACCGCAC
*
1303849 CAAATCCTCTCAAAATATAT
1 CAAATCCTCTCAAAACATAT
* *
1303869 CAAATTCTCTCAAACCATAT
1 CAAATCCTCTCAAAACATAT
1303889 CAAA
1 CAAA
1303893 AACTAAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
CAAATCCTCTCAAAACATAT
Found at i:1305983 original size:3 final size:3
Alignment explanation
Indices: 1305975--1306022 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1305965 TATCTGCTCC
* * * * *
1305975 TGA TGA TGA TGA CGA CGA TGA TAA TGA TGA TGG TGA TTA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1306023 CAGTGAGGAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:1306861 original size:81 final size:82
Alignment explanation
Indices: 1306726--1306890 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 82
1306716 ATCCATAAAA
1306726 CGGTTATAGTCTTGATGGGTTTGCGAGCAAGCTGGTATGACATGAGAGCATAGATACTTCACAGC
1 CGGTTATAGTCTTGATGGGTTTGCGAGCAAGCTGGTATGACATGAGAGCATAGATACTTCACAGC
1306791 TTGAAAAAA-CCACAGT
66 TTGAAAAAACCCACAGT
1306807 CGGTTATAGTCTTGATGGGTTTGCGAGCAAGCTGGTATGACATGAGAGCATAGATACTTCACAGC
1 CGGTTATAGTCTTGATGGGTTTGCGAGCAAGCTGGTATGACATGAGAGCATAGATACTTCACAGC
1306872 TTGAAAAAACCCACAGT
66 TTGAAAAAACCCACAGT
1306889 CG
1 CG
1306891 CACCATCTGT
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 74 0.89
82 9 0.11
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (82 bp):
CGGTTATAGTCTTGATGGGTTTGCGAGCAAGCTGGTATGACATGAGAGCATAGATACTTCACAGC
TTGAAAAAACCCACAGT
Found at i:1321989 original size:21 final size:21
Alignment explanation
Indices: 1321964--1322070 Score: 160
Period size: 21 Copynumber: 5.1 Consensus size: 21
1321954 AATTTAAAAT
* *
1321964 GTGTATCGATGCACTACTACA
1 GTGTACCGATGCACTGCTACA
1321985 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
1322006 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
* * * *
1322027 ATGTATCAATGCACTGGTACA
1 GTGTACCGATGCACTGCTACA
1322048 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
1322069 GT
1 GT
1322071 AATTTCAGCC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:1322593 original size:23 final size:23
Alignment explanation
Indices: 1322567--1322649 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
1322557 CTCGTATAAA
* *
1322567 TGCACTGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
1322590 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
* * *
1322613 TACACCAAAGTGCCGCGTAGTAT
1 TGCACCGAAGTGCCGCGTAGAAT
1322636 TGCACC-ATAGTGCC
1 TGCACCGA-AGTGCC
1322650 ATATAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 1 0.02
23 50 0.98
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:1324382 original size:19 final size:19
Alignment explanation
Indices: 1324345--1324383 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1324335 ATGGGGATTT
*
1324345 AAAAATAATGAAAGTAATA
1 AAAAATAATGAAAGGAATA
1324364 AAAAATAAT-AAATGGAATA
1 AAAAATAATGAAA-GGAATA
1324383 A
1 A
1324384 TGAGATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (19 bp):
AAAAATAATGAAAGGAATA
Found at i:1325169 original size:114 final size:114
Alignment explanation
Indices: 1324969--1325196 Score: 456
Period size: 114 Copynumber: 2.0 Consensus size: 114
1324959 CAATATTAGA
1324969 CACAACTTAAACTTTGAGAGACAACTTTGAGACACAATCACAAAGTTGAATTAGGAAATCACTTA
1 CACAACTTAAACTTTGAGAGACAACTTTGAGACACAATCACAAAGTTGAATTAGGAAATCACTTA
1325034 GAAAATTCCTTTCAAATTCGTTCTTTCTGGTGATAGAGAAAGGTAAGAT
66 GAAAATTCCTTTCAAATTCGTTCTTTCTGGTGATAGAGAAAGGTAAGAT
1325083 CACAACTTAAACTTTGAGAGACAACTTTGAGACACAATCACAAAGTTGAATTAGGAAATCACTTA
1 CACAACTTAAACTTTGAGAGACAACTTTGAGACACAATCACAAAGTTGAATTAGGAAATCACTTA
1325148 GAAAATTCCTTTCAAATTCGTTCTTTCTGGTGATAGAGAAAGGTAAGAT
66 GAAAATTCCTTTCAAATTCGTTCTTTCTGGTGATAGAGAAAGGTAAGAT
1325197 TGTGTTCGAC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (114 bp):
CACAACTTAAACTTTGAGAGACAACTTTGAGACACAATCACAAAGTTGAATTAGGAAATCACTTA
GAAAATTCCTTTCAAATTCGTTCTTTCTGGTGATAGAGAAAGGTAAGAT
Found at i:1330884 original size:174 final size:174
Alignment explanation
Indices: 1330594--1330942 Score: 698
Period size: 174 Copynumber: 2.0 Consensus size: 174
1330584 AAGAGAGAGC
1330594 ATGGATTGAAGCTCGTGATGCAGCTTTAATAAAAGCTTTACAAAACCTGACAGGAAAAAAATTTA
1 ATGGATTGAAGCTCGTGATGCAGCTTTAATAAAAGCTTTACAAAACCTGACAGGAAAAAAATTTA
1330659 AGGGCGACGATCTGATAGCAACTGAATCTGTTAAGGAAGATGGCTGGCAAGAATCTGAGGTTTCA
66 AGGGCGACGATCTGATAGCAACTGAATCTGTTAAGGAAGATGGCTGGCAAGAATCTGAGGTTTCA
1330724 TGGCTTATACAGCTGAGAACCTGCATGGAATCAAGGTTCGAAGA
131 TGGCTTATACAGCTGAGAACCTGCATGGAATCAAGGTTCGAAGA
1330768 ATGGATTGAAGCTCGTGATGCAGCTTTAATAAAAGCTTTACAAAACCTGACAGGAAAAAAATTTA
1 ATGGATTGAAGCTCGTGATGCAGCTTTAATAAAAGCTTTACAAAACCTGACAGGAAAAAAATTTA
1330833 AGGGCGACGATCTGATAGCAACTGAATCTGTTAAGGAAGATGGCTGGCAAGAATCTGAGGTTTCA
66 AGGGCGACGATCTGATAGCAACTGAATCTGTTAAGGAAGATGGCTGGCAAGAATCTGAGGTTTCA
1330898 TGGCTTATACAGCTGAGAACCTGCATGGAATCAAGGTTCGAAGA
131 TGGCTTATACAGCTGAGAACCTGCATGGAATCAAGGTTCGAAGA
1330942 A
1 A
1330943 GAAGAAGGGT
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 175 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (174 bp):
ATGGATTGAAGCTCGTGATGCAGCTTTAATAAAAGCTTTACAAAACCTGACAGGAAAAAAATTTA
AGGGCGACGATCTGATAGCAACTGAATCTGTTAAGGAAGATGGCTGGCAAGAATCTGAGGTTTCA
TGGCTTATACAGCTGAGAACCTGCATGGAATCAAGGTTCGAAGA
Found at i:1333735 original size:36 final size:34
Alignment explanation
Indices: 1333653--1333766 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 34
1333643 AAAACAATTC
*
1333653 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
1333688 TCAATTTCATTCTAAACCCTAAATTCCAAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCC-AAAATAAT
* * *
1333724 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
1333759 TCAATTTC
1 TCAATTTC
1333767 TGTCTTTTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 1 0.01
35 39 0.55
36 25 0.35
37 6 0.08
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.33
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1334845 original size:33 final size:33
Alignment explanation
Indices: 1334779--1334865 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
1334769 TTTCTCCTTA
* * * *
1334779 AATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
1 AATTGAATTACTTTGGAA-TTAGAGTTTAGAATG
1334813 TAATTGAATTA-TTTGGAATTAGAGTTTAGAATG
1 -AATTGAATTACTTTGGAATTAGAGTTTAGAATG
* *
1334846 AAATGAATTACTTTGAAATT
1 AATTGAATTACTTTGGAATT
1334866 TGGGATTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 9 0.20
33 22 0.48
34 6 0.13
35 9 0.20
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (33 bp):
AATTGAATTACTTTGGAATTAGAGTTTAGAATG
Found at i:1336940 original size:27 final size:27
Alignment explanation
Indices: 1336910--1336981 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
1336900 TTTAAAGTTT
1336910 TCGAGTTCGAGTCGAGCTCAGCAATAC
1 TCGAGTTCGAGTCGAGCTCAGCAATAC
1336937 TCGAGTTCGAGTCGAGCTCAGCAATAC
1 TCGAGTTCGAGTCGAGCTCAGCAATAC
*
1336964 TCGAGTTCGACTCG-GCTC
1 TCGAGTTCGAGTCGAGCTC
1336982 GTTTAACAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 4 0.09
27 40 0.91
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (27 bp):
TCGAGTTCGAGTCGAGCTCAGCAATAC
Found at i:1337106 original size:30 final size:30
Alignment explanation
Indices: 1337044--1337106 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1337034 GAACCGGCGG
* * * *
1337044 TTCACAGCGGTTTTGTCGGTTTTCAGCCGA
1 TTCACACCGGTTTTATCGGTTCTAAGCCGA
*
1337074 TTCACACCGGTTTTATCGGTTCTAAGCTGA
1 TTCACACCGGTTTTATCGGTTCTAAGCCGA
1337104 TTC
1 TTC
1337107 TACCAGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (30 bp):
TTCACACCGGTTTTATCGGTTCTAAGCCGA
Found at i:1339688 original size:28 final size:28
Alignment explanation
Indices: 1339649--1339712 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
1339639 AAAAAATTAT
1339649 TTTAG-GTAGGGATGTACCGATACACTC
1 TTTAGTGTAGGGATGTACCGATACACTC
1339676 TTTAGTGTAGGGATGTACCGATACACTC
1 TTTAGTGTAGGGATGTACCGATACACTC
1339704 TTTAGTGTA
1 TTTAGTGTA
1339713 TCGATGCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.14
28 31 0.86
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (28 bp):
TTTAGTGTAGGGATGTACCGATACACTC
Found at i:1341439 original size:20 final size:20
Alignment explanation
Indices: 1341412--1341458 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1341402 AAGAAAATTC
1341412 AAAA-GAAATGAAGGCTTCA
1 AAAATGAAATGAAGGCTTCA
1341431 AAAATGAAATGAAGGCTTCA
1 AAAATGAAATGAAGGCTTCA
1341451 AAAATGAA
1 AAAATGAA
1341459 CCAAAGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATGAAATGAAGGCTTCA
Found at i:1341465 original size:20 final size:20
Alignment explanation
Indices: 1341422--1341465 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1341412 AAAAGAAATG
**
1341422 AAGGCTTCAAAAATGAAATG
1 AAGGCTTCAAAAATGAAACA
*
1341442 AAGGCTTCAAAAATGAACCA
1 AAGGCTTCAAAAATGAAACA
1341462 AAGG
1 AAGG
1341466 AGAAGAACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.16
Consensus pattern (20 bp):
AAGGCTTCAAAAATGAAACA
Found at i:1345671 original size:44 final size:44
Alignment explanation
Indices: 1345608--1345708 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
1345598 TGCAAAGTGT
*
1345608 ATCGATACACTATCAAAGTGTACCAATGCATTCCTTGAATGTGC
1 ATCGATACACTATCAAAGTGCACCAATGCATTCCTTGAATGTGC
** * * *
1345652 ATCGATACACTATGTAAGTGCATCGATGCATTCCTTGAATGTGT
1 ATCGATACACTATCAAAGTGCACCAATGCATTCCTTGAATGTGC
1345696 ATCGATACACTAT
1 ATCGATACACTAT
1345709 ACAATATACT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
ATCGATACACTATCAAAGTGCACCAATGCATTCCTTGAATGTGC
Found at i:1347630 original size:16 final size:16
Alignment explanation
Indices: 1347609--1347641 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1347599 AGGGGATGAG
1347609 TAATTTTCAAAATTGA
1 TAATTTTCAAAATTGA
1347625 TAATTTTCAAAATTGA
1 TAATTTTCAAAATTGA
1347641 T
1 T
1347642 TTTGATTTCA
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:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATTTTCAAAATTGA
Found at i:1347652 original size:18 final size:18
Alignment explanation
Indices: 1347629--1347664 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1347619 AATTGATAAT
* *
1347629 TTTCAAAATTGATTTTGA
1 TTTCAAAAATAATTTTGA
1347647 TTTCAAAAATAATTTTGA
1 TTTCAAAAATAATTTTGA
1347665 AAGAAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATAATTTTGA
Found at i:1349536 original size:28 final size:28
Alignment explanation
Indices: 1349496--1349549 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1349486 ATTTTAAAGA
* **
1349496 ACAGAGGTGCCAGATTTTAGATTGAAGC
1 ACAGAGGTACCAGATCCTAGATTGAAGC
1349524 ACAGAGGTACCAGATCCTAGATTGAA
1 ACAGAGGTACCAGATCCTAGATTGAA
1349550 ATATAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (28 bp):
ACAGAGGTACCAGATCCTAGATTGAAGC
Found at i:1349761 original size:82 final size:80
Alignment explanation
Indices: 1349602--1349761 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 80
1349592 TTCTAGACTG
*
1349602 AAGCACAGAGGTGATAAGTCATTTTTAACTACACAGGTGTCAGTTTGTCGATTGAAGAACAAAGG
1 AAGCACAGAGGTGATAAGTCATTTTTAACTACACAGGTGTCAGTTTGTCGAGTGAAGAACAAAGG
**
1349667 TGTTTAATCATTACA
66 TACTTAATCATTACA
* * * * * * * **
1349682 AAGCACAGAGGTGCTCAGTCATTTTTATCTGCACAGAGGTGTCAGTTTGTTGAGTGAAGCATATT
1 AAGCACAGAGGTGATAAGTCATTTTTAACT--ACACAGGTGTCAGTTTGTCGAGTGAAGAACAAA
1349747 GGTACTTAATCATTA
64 GGTACTTAATCATTA
1349762 ATTCAAGCAC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 27 0.41
82 39 0.59
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (80 bp):
AAGCACAGAGGTGATAAGTCATTTTTAACTACACAGGTGTCAGTTTGTCGAGTGAAGAACAAAGG
TACTTAATCATTACA
Found at i:1353662 original size:13 final size:14
Alignment explanation
Indices: 1353646--1353683 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
1353636 AACAAAAAAC
1353646 AAAAAAAAAGGCAA
1 AAAAAAAAAGGCAA
1353660 AAAAAAAAAGGCAA
1 AAAAAAAAAGGCAA
1353674 AAAAACAAAA
1 AAAAA-AAAA
1353684 AAAGAGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGGCAA
Found at i:1353675 original size:33 final size:32
Alignment explanation
Indices: 1353631--1353696 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
1353621 TTTTTTTTTC
*
1353631 AAAAAAAC-AAAAAACAAAAAAAAAGGCAAAA
1 AAAAAAACAAAAAAACAAAAAAAAAGCCAAAA
*
1353662 AAAAAAAGGCAAAAAAACAAAAAAAGAGCCAAAA
1 AAAAAAA--CAAAAAAACAAAAAAAAAGCCAAAA
1353696 A
1 A
1353697 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 7 0.23
33 1 0.03
34 22 0.73
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAAAAACAAAAAAAAAGCCAAAA
Found at i:1358246 original size:20 final size:22
Alignment explanation
Indices: 1358203--1358247 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1358193 AAGGTATCGG
*
1358203 TACCATAGTATAGGAGTATCGA
1 TACCATAGTATAGGAGTATAGA
*
1358225 TACCATGGTA-AGG-GTATAGA
1 TACCATAGTATAGGAGTATAGA
1358245 TAC
1 TAC
1358248 TATTGAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 9 0.43
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (22 bp):
TACCATAGTATAGGAGTATAGA
Found at i:1358654 original size:54 final size:54
Alignment explanation
Indices: 1358568--1359173 Score: 694
Period size: 54 Copynumber: 11.3 Consensus size: 54
1358558 TTACCAAATA
* * **
1358568 GGCACTAAGTGTGCAAC-C-CATGAAATTTATCATATGTTTATGAACAACTATTTC
1 GGCACTAAGTGTGCAACTCACA-G-AATTCATCATATGTTGATGAACAACCGTTTC
*
1358622 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTT
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
1358676 GGCACTAAGTGTGCAACTCACGGAATTCATCATATGTTGATGCACAACTGTGTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
1358730 GGCACTATGTGTGTAACTCACAGAATTCATCATATGTTGATGAACAACTC-TGTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAAC-CGTTTC
* * * * *
1358784 GGTACTATGTGTGCAACTCACAAAATTCACCATATATTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
*
1358838 GGCACT-AGTGTGCAACTCAC-GAAATTCATCATATGTTGATGAACAACCATTTC
1 GGCACTAAGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
1358891 GACACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACTGTTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
1358945 AGCACTAAGTGTGCAACTCACGGAATTAATCATATGTTGATGAATAACCGTTTT
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
1358999 GGCACTAAGTGTGCAAC-C-CATGAACTTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAACTCACA-GAA-TTCATCATATGTTGATGAACAACCGTTTC
** * * * *
1359053 AACACT--GTCTGTAACTCACGGAATTCATCATATGTTGATGAACAACCG-TAC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * * * *
1359104 AAGCACTATA-TGTGCAACTCATAGAATTCATCATGTATTGATGAACGACCGTATA
1 -GGCACTA-AGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
1359159 GGCACTAAGTGTGCA
1 GGCACTAAGTGTGCA
1359174 TCTTAATAAA
Statistics
Matches: 472, Mismatches: 63, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
51 2 0.00
52 38 0.08
53 56 0.12
54 371 0.79
55 3 0.01
56 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:1359499 original size:46 final size:46
Alignment explanation
Indices: 1359447--1359609 Score: 222
Period size: 46 Copynumber: 3.6 Consensus size: 46
1359437 ATTTGACATA
1359447 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATT
1 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATT
* * **
1359493 AAAGGCATGAAGGGATGCCATAAATAAAAATGCATAACAGTGCATT
1 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATT
* * *
1359539 AAATGCATGAAATGG-TGCCATAAATG-AAATGCATAATGGTTCATA
1 AAAGGCATGAAA-GGATGCCATAAATGAAAATGCATAATGGTGCATT
* *
1359584 AAAGGCATGAAAGGGTTCCATAAATG
1 AAAGGCATGAAAGGATGCCATAAATG
1359610 TGAAATTGAT
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
44 2 0.02
45 36 0.35
46 62 0.61
47 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (46 bp):
AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATT
Found at i:1360600 original size:14 final size:15
Alignment explanation
Indices: 1360581--1360609 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1360571 TTGTTAATTG
1360581 GAGTAAGAGG-AAAT
1 GAGTAAGAGGTAAAT
1360595 GAGTAAGAGGTAAAT
1 GAGTAAGAGGTAAAT
1360610 ACATTGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (15 bp):
GAGTAAGAGGTAAAT
Found at i:1361293 original size:2 final size:2
Alignment explanation
Indices: 1361286--1361358 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1361276 GATGTCAGAA
1361286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1361328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1361359 GTTTTTCTGC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1364765 original size:54 final size:54
Alignment explanation
Indices: 1364700--1365230 Score: 681
Period size: 54 Copynumber: 9.8 Consensus size: 54
1364690 TTACCAAATA
* ***
1364700 GGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAGTTATTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* * *
1364754 GGCACTAAGTGTGTAACTCACGGAATTCATCATATGTTGATGAACAATCATTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* ** *
1364808 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGCTGATGAACAACTGTTTT
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* * ** * *
1364862 GGCAGTATGTGTGCAACTCATGGAATTTATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* * * *
1364916 GACACTAAGTGTGTAACTCACGGAATTCATCATACGTTGATGAACAACCATTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* * * * *
1364970 GGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGTTGAACAACCGTTTT
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* ***
1365024 GGTACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAATTGTTTC
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
* *
1365078 GGCACTAAGTGTGCAACCCAC-GAAATTCATCATATATTGATGAACAACCATTTC
1 GGCACTAAGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCATTTC
* *
1365132 GGCACTATGTGTGCAACTCAC-GAAATTCATCATATGTTGATGAACAACCA-TAC
1 GGCACTAAGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCATTTC
* * *
1365185 ATGCACTATGTGTGCAACTCACAGAATTCATCATGTGTTGATGAAC
1 -GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAAC
1365231 GACCGTATAG
Statistics
Matches: 418, Mismatches: 56, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
53 3 0.01
54 414 0.99
55 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (54 bp):
GGCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTC
Found at i:1364975 original size:162 final size:162
Alignment explanation
Indices: 1364700--1365251 Score: 766
Period size: 162 Copynumber: 3.4 Consensus size: 162
1364690 TTACCAAATA
* * ****
1364700 GGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAGTTATTTCGGCACTAAGTG
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
* *
1364765 TGTAACTCACGGAATTCATCATATGTTGATGAACAATCATTTCGGCACTAAGTGTGCAACTCACA
66 TGTAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACA
* *
1364830 GAATTCATCATATGCTGATGAACAACTGTTTT
131 GAATTCATCATATGTTGATGAACAACCGTTTT
* ** * *
1364862 GGCAGTATGTGTGCAACTCATGGAATTTATCATATGTTGATGAACAACCGTTTCGACACTAAGTG
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
* *
1364927 TGTAACTCACGGAATTCATCATACGTTGATGAACAACCATTTCGGCACTATGTGTGCAACCCACA
66 TGTAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACA
*
1364992 GAATTCATCATATGTTGTTGAACAACCGTTTT
131 GAATTCATCATATGTTGATGAACAACCGTTTT
* * **
1365024 GGTACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAATTGTTTCGGCACTAAGTG
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
* * * *
1365089 TGCAACCCACGAAATTCATCATATATTGATGAACAACCATTTCGGCACTATGTGTGCAACTCAC-
66 TGTAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACA
* **
1365153 GAAATTCATCATATGTTGATGAACAACCATACAT
131 G-AATTCATCATATGTTGATGAACAACCGT-TTT
* * * * *
1365187 -GCACTATGTGTGCAACTCACAGAATTCATCATGTGTTGATGAACGACCGTATAGGCACTACGTG
1 GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
1365251 T
66 T
1365252 ATATCTTAAT
Statistics
Matches: 342, Mismatches: 46, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
161 1 0.00
162 340 0.99
163 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (162 bp):
GGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
TGTAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACA
GAATTCATCATATGTTGATGAACAACCGTTTT
Found at i:1365586 original size:46 final size:46
Alignment explanation
Indices: 1365534--1365651 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 46
1365524 ATTTGTCATA
* *
1365534 AAAGGCATGAAAGGATGCCATAAATGAACATGCATAATGGTGCATT
1 AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
1365580 AAAGGCAT-AAAGGGATGCCATAAATGAAAATGCATAACGGTGCATT
1 AAAGGCATGAAA-GGATGCCATAAATGAAAATGCATAACGGTGCATT
*
1365626 AAAGGCATGAAAGGGTGCCATAAATG
1 AAAGGCATGAAAGGATGCCATAAATG
1365652 TGAAATTGAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
45 3 0.04
46 61 0.91
47 3 0.04
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.19
Consensus pattern (46 bp):
AAAGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
Found at i:1371398 original size:6 final size:6
Alignment explanation
Indices: 1371387--1371414 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1371377 ATAAAACATA
1371387 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
1371415 GGAGTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:1373556 original size:20 final size:21
Alignment explanation
Indices: 1373533--1373575 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1373523 AATTAAAGTT
1373533 TTTA-ATTTTAATTTTTT-TAA
1 TTTACATTTT-ATTTTTTATAA
*
1373553 TTTACCTTTTATTTTTTATAA
1 TTTACATTTTATTTTTTATAA
1373574 TT
1 TT
1373576 AGTTATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTACATTTTATTTTTTATAA
Found at i:1374174 original size:21 final size:21
Alignment explanation
Indices: 1374150--1374194 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1374140 ATTGTCCAAT
1374150 AAACATGAAATCCATAACAAC
1 AAACATGAAATCCATAACAAC
* *
1374171 AAACTTGAAATCCATAATAAC
1 AAACATGAAATCCATAACAAC
1374192 AAA
1 AAA
1374195 TCAAAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.20, G:0.04, T:0.18
Consensus pattern (21 bp):
AAACATGAAATCCATAACAAC
Found at i:1377514 original size:19 final size:19
Alignment explanation
Indices: 1377490--1377564 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
1377480 TATGCATGTA
*
1377490 AGCTGAGTAAGCAACAGTC
1 AGCTGAGTAAGCAGCAGTC
*
1377509 AGCTGAGTAAGCAGCAATC
1 AGCTGAGTAAGCAGCAGTC
1377528 AGCTGAGTAAGCAGCAGTC
1 AGCTGAGTAAGCAGCAGTC
*
1377547 AGCTGAGTCAGCAGCAGT
1 AGCTGAGTAAGCAGCAGT
1377565 TGGAAGTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.16
Consensus pattern (19 bp):
AGCTGAGTAAGCAGCAGTC
Found at i:1382912 original size:40 final size:42
Alignment explanation
Indices: 1382845--1382936 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 42
1382835 GTTTTCAAAC
* *
1382845 AAAACGCCACTAATGTTTCAACATATTGC-G-ATGTT-TTTAA
1 AAAACGCCACAAATGTTCCAACATATTGCGGAAT-TTGTTTAA
*
1382885 AAAACGCCACAAATGTTCCGAA-TTATTGCGGAATTTGTTTAA
1 AAAACGCCACAAATGTTCC-AACATATTGCGGAATTTGTTTAA
*
1382927 AAAACACCAC
1 AAAACGCCAC
1382937 TAAAGAACGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
40 23 0.52
41 5 0.11
42 16 0.36
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (42 bp):
AAAACGCCACAAATGTTCCAACATATTGCGGAATTTGTTTAA
Found at i:1383103 original size:40 final size:41
Alignment explanation
Indices: 1383031--1383113 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
1383021 TATATGTACC
*
1383031 CTATTACGGCATTTGTTTAAAAATGCTACTAAAGAACGATT
1 CTATTACGGCATTTGTTTAAAAATGCCACTAAAGAACGATT
* * * * *
1383072 CTATTATGGCGTTTG-TTAGAAATGCCACTAAAGTAGGATT
1 CTATTACGGCATTTGTTTAAAAATGCCACTAAAGAACGATT
1383112 CT
1 CT
1383114 GTGCCAGTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 23 0.64
41 13 0.36
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (41 bp):
CTATTACGGCATTTGTTTAAAAATGCCACTAAAGAACGATT
Found at i:1383978 original size:22 final size:22
Alignment explanation
Indices: 1383906--1383983 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
1383896 TACCACGAAA
1383906 TAAACGAACATGTT-CGTGGACAT
1 TAAACGAACATGTTAC--GGACAT
* * * **
1383929 TAAAGGAATATGTTCACGAACGC
1 TAAACGAACATGTT-ACGGACAT
1383952 TAAACGAACATGTTACGGACAT
1 TAAACGAACATGTTACGGACAT
1383974 TAAACGAACA
1 TAAACGAACA
1383984 CATTCACGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 15 0.35
23 27 0.63
25 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (22 bp):
TAAACGAACATGTTACGGACAT
Found at i:1383990 original size:45 final size:45
Alignment explanation
Indices: 1383906--1383994 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
1383896 TACCACGAAA
* * **
1383906 TAAACGAACATGTTCGTGGACATTAAAGGAATATGTTCACGAACGC
1 TAAACGAACATGTTCG-GGACATTAAACGAACACATTCACGAACGC
1383952 TAAACGAACATGTTAC-GGACATTAAACGAACACATTCACGAAC
1 TAAACGAACATGTT-CGGGACATTAAACGAACACATTCACGAAC
1383995 ATTAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 23 0.61
46 14 0.37
47 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (45 bp):
TAAACGAACATGTTCGGGACATTAAACGAACACATTCACGAACGC
Found at i:1384798 original size:42 final size:42
Alignment explanation
Indices: 1384724--1384834 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
1384714 TATTATTTAT
** *
1384724 ATTTGTGACGA-AAACA-TTTTGTCACTAGTCTTAG-TTGATG
1 ATTTGTGACGATAATTATTTTTGTCACTAATCTTAGTTTG-TG
* * *
1384764 ATTTGTGACGGTAATTATTTTTGTTACTAATCTTAGTTTGTT
1 ATTTGTGACGATAATTATTTTTGTCACTAATCTTAGTTTGTG
1384806 ATTTGTGACGATAATTATTTTTGTCACTA
1 ATTTGTGACGATAATTATTTTTGTCACTA
1384835 TTGAAATGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 10 0.17
41 3 0.05
42 44 0.73
43 3 0.05
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (42 bp):
ATTTGTGACGATAATTATTTTTGTCACTAATCTTAGTTTGTG
Found at i:1386065 original size:24 final size:24
Alignment explanation
Indices: 1386031--1386077 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1386021 CAACAATAGT
*
1386031 TTAACATAAATA-TTGTTTTTTTG
1 TTAACATAAATATTTCTTTTTTTG
1386054 TTAACAATAAATATTTCTTTTTTT
1 TTAAC-ATAAATATTTCTTTTTTT
1386078 TAGCATAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 7 0.33
25 9 0.43
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAACATAAATATTTCTTTTTTTG
Found at i:1386074 original size:23 final size:23
Alignment explanation
Indices: 1386031--1386085 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1386021 CAACAATAGT
*
1386031 TTAACATAAATATTGTTTTTTTG
1 TTAACATAAATATTGTCTTTTTG
*
1386054 TTAACAATAAATATT-TCTTTTTT
1 TTAAC-ATAAATATTGTCTTTTTG
*
1386077 TTAGCATAA
1 TTAACATAA
1386086 GGGTTAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 15 0.54
24 9 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (23 bp):
TTAACATAAATATTGTCTTTTTG
Found at i:1386695 original size:34 final size:34
Alignment explanation
Indices: 1386644--1386731 Score: 140
Period size: 34 Copynumber: 2.5 Consensus size: 34
1386634 ATCGAACAAT
1386644 TGGTCACTAAAAAAATACTTAGTGTGACAACACAGG
1 TGGT-ACT-AAAAAATACTTAGTGTGACAACACAGG
*
1386680 TGGTATTAAAAAATACTTAGTGTGACAACACAGG
1 TGGTACTAAAAAATACTTAGTGTGACAACACAGG
*
1386714 TGGTACTAAAATATACTT
1 TGGTACTAAAAAATACTT
1386732 TTAGCGTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
34 43 0.88
35 2 0.04
36 4 0.08
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (34 bp):
TGGTACTAAAAAATACTTAGTGTGACAACACAGG
Found at i:1388095 original size:43 final size:43
Alignment explanation
Indices: 1388025--1388138 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
1388015 CGTTTGGTAA
* *** *
1388025 CAAAAAACGCCACAATAGGTAACGAGATATAGCA-GCGTTTGTC
1 CAAAAAACGCCGCAATAGGTGTTGAGATATAG-AGGCATTTGTC
* *
1388068 CAAAAAACGTCGCAATAGGTGTTGAGATTTAGAGGCATTTGTC
1 CAAAAAACGCCGCAATAGGTGTTGAGATATAGAGGCATTTGTC
* *
1388111 CCACAAACGCCGCAATAGGTGTTGAGAT
1 CAAAAAACGCCGCAATAGGTGTTGAGAT
1388139 TTAGGGGCGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 59 0.98
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (43 bp):
CAAAAAACGCCGCAATAGGTGTTGAGATATAGAGGCATTTGTC
Found at i:1388177 original size:44 final size:43
Alignment explanation
Indices: 1388072--1388205 Score: 171
Period size: 43 Copynumber: 3.1 Consensus size: 43
1388062 TTTGTCCAAA
* * *
1388072 AAACGTCGCAATAGGTGTTGAGATTTAGAGGCATTTGTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGAGGCGTTTTTCCCAC
* *
1388115 AAACGCCGCAATAGGTGTTGAGATTTAGGGGCGTTTTTTCTCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGAGGCG-TTTTTCCCAC
* * *
1388159 AAATGCCGCAATCA-GTGTTGAGATTTAGTGACGTTTTTCCCAC
1 AAACGCCGCAAT-AGGTGTTGAGATTTAGAGGCGTTTTTCCCAC
1388202 AAAC
1 AAAC
1388206 ATCGTAAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
43 42 0.53
44 36 0.46
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGAGGCGTTTTTCCCAC
Found at i:1388387 original size:42 final size:42
Alignment explanation
Indices: 1388230--1388386 Score: 197
Period size: 42 Copynumber: 3.7 Consensus size: 42
1388220 ATGTATATAA
* * * *
1388230 AAACGCCGCAAAAGATCTGGTATATAGCAACATTTTTTGGATAC
1 AAACGCCGCAAAAGGTCTGGTATATAGCGACA-TTTTT-CATAT
* *
1388274 AAACGCCGCTAAAGGTCTGGTATATAGCGACGTTTTTCATAT
1 AAACGCCGCAAAAGGTCTGGTATATAGCGACATTTTTCATAT
* * *
1388316 AAACGTCGCAAAAGGTTTGGTATATAGCGGCATTTTTCATAT
1 AAACGCCGCAAAAGGTCTGGTATATAGCGACATTTTTCATAT
* *
1388358 AAACACCGCAAAAGGTTTGGTATATAGCG
1 AAACGCCGCAAAAGGTCTGGTATATAGCG
1388387 GTGTTTTTAG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 67 0.67
43 5 0.05
44 28 0.28
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCTGGTATATAGCGACATTTTTCATAT
Found at i:1388394 original size:42 final size:42
Alignment explanation
Indices: 1388230--1388415 Score: 192
Period size: 42 Copynumber: 4.3 Consensus size: 42
1388220 ATGTATATAA
* * ** * * *
1388230 AAACGCCGCAAAAGATCTGGTATATAGCAACATTTTTTGGATAC
1 AAACGCCGCAAAAGGTTTGGTATATAGCGGC-GTTTTT-CATAT
* * *
1388274 AAACGCCGCTAAAGGTCTGGTATATAGCGACGTTTTTCATAT
1 AAACGCCGCAAAAGGTTTGGTATATAGCGGCGTTTTTCATAT
* *
1388316 AAACGTCGCAAAAGGTTTGGTATATAGCGGCATTTTTCATAT
1 AAACGCCGCAAAAGGTTTGGTATATAGCGGCGTTTTTCATAT
* * *
1388358 AAACACCGCAAAAGGTTTGGTATATAGCGGTGTTTTTAGGATAT
1 AAACGCCGCAAAAGGTTTGGTATATAGCGGCGTTTTT--CATAT
*
1388402 AAACGCCGCTAAAG
1 AAACGCCGCAAAAG
1388416 AACACAGAAT
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 73 0.60
43 5 0.04
44 44 0.36
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTTTGGTATATAGCGGCGTTTTTCATAT
Found at i:1388402 original size:86 final size:86
Alignment explanation
Indices: 1388230--1388416 Score: 216
Period size: 86 Copynumber: 2.2 Consensus size: 86
1388220 ATGTATATAA
* * *
1388230 AAACGCCGCAAAAGATCTGGTATATAGCAACATTTTTTGGATACAAACGCCGCTAAAGGTCTGGT
1 AAACGCCGCAAAAGATCTGGTATATAGCAACATTTTTTGCATACAAACACCGCAAAAGGTCTGGT
1388295 ATATAGCGACGTTTTTCATAT
66 ATATAGCGACGTTTTTCATAT
* * * ** * *
1388316 AAACGTCGCAAAAGGTTTGGTATATAGCGGCA-TTTTT-CATATAAACACCGCAAAAGGTTTGGT
1 AAACGCCGCAAAAGATCTGGTATATAGCAACATTTTTTGCATACAAACACCGCAAAAGGTCTGGT
** *
1388379 ATATAGCGGTGTTTTTAGGATAT
66 ATATAGCGACGTTTTT--CATAT
*
1388402 AAACGCCGCTAAAGA
1 AAACGCCGCAAAAGA
1388417 ACACAGAATT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
84 35 0.42
85 5 0.06
86 43 0.52
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (86 bp):
AAACGCCGCAAAAGATCTGGTATATAGCAACATTTTTTGCATACAAACACCGCAAAAGGTCTGGT
ATATAGCGACGTTTTTCATAT
Found at i:1388779 original size:21 final size:21
Alignment explanation
Indices: 1388735--1388803 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1388725 ACTGATATGT
*
1388735 TGCTTCTCTCTGTGCTGCCAC
1 TGCTTCTCTCTGTGCTTCCAC
* *
1388756 TGCTTCTCTCTGTGCTTTCGC
1 TGCTTCTCTCTGTGCTTCCAC
* *
1388777 TGCTGCTCTCTCTGCTTCC-C
1 TGCTTCTCTCTGTGCTTCCAC
1388797 TTGCTTC
1 -TGCTTC
1388804 ATTTTCGGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.01, C:0.38, G:0.17, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTTCCAC
Found at i:1391348 original size:122 final size:122
Alignment explanation
Indices: 1391217--1391481 Score: 273
Period size: 122 Copynumber: 2.2 Consensus size: 122
1391207 ACTATTGATT
* ** *
1391217 AACCCTATTATGGCATTTGTCT-CAAAATGCCATTAAAAACAACCCTATTAAGGCATTTTTCCTA
1 AACCCTATTATGGCATTTGT-TGCAAAATACCACGAAAAACAACCCTATTAAGGCATTTATCCTA
* * * *
1391281 AAAACATCTCTAAATTATAACTCTATTACGACATTTATTGGAAAACA-CCACTATAAAC
65 AAAACACCACTAAATTACAACTCTATTACAACATTTATTGGAAAA-AGCCACTATAAAC
*** * * * * ** * *
1391339 AACCCTATTACATCGTTTATTGGAAAATACCACGATAAACAACCCTATTTTGGCATTTATGCTAT
1 AACCCTATTATGGCATTTGTTGCAAAATACCACGAAAAACAACCCTATTAAGGCATTTATCCTAA
* * *
1391404 AAACACCACTAAATTACCACTCTATTACAACATTTGTTTGAAAAATGCCACTATAAAC
66 AAACACCACTAAATTACAACTCTATTACAACATTTATTGGAAAAA-GCCACTATAAAC
* *
1391462 AACCATATTCTGGCATTTGT
1 AACCCTATTATGGCATTTGT
1391482 GCTATAAACG
Statistics
Matches: 111, Mismatches: 29, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
121 2 0.02
122 85 0.77
123 24 0.22
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (122 bp):
AACCCTATTATGGCATTTGTTGCAAAATACCACGAAAAACAACCCTATTAAGGCATTTATCCTAA
AAACACCACTAAATTACAACTCTATTACAACATTTATTGGAAAAAGCCACTATAAAC
Found at i:1391398 original size:40 final size:40
Alignment explanation
Indices: 1391303--1391387 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
1391293 AATTATAACT
*
1391303 CTATTAC-GACATTTATTGGAAAACACCACTATAAACAACC
1 CTATTACAG-CATTTATTGGAAAACACCACGATAAACAACC
* * *
1391343 CTATTACATCGTTTATTGGAAAATACCACGATAAACAACC
1 CTATTACAGCATTTATTGGAAAACACCACGATAAACAACC
1391383 CTATT
1 CTATT
1391388 TTGGCATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (40 bp):
CTATTACAGCATTTATTGGAAAACACCACGATAAACAACC
Found at i:1391523 original size:83 final size:83
Alignment explanation
Indices: 1391343--1391531 Score: 236
Period size: 83 Copynumber: 2.3 Consensus size: 83
1391333 ATAAACAACC
* * * * *
1391343 CTATTACATCGTTTATTGG-AAAATACCACGATAAACAACCCTATTTTGGCATTTATGCTATAAA
1 CTATTACAACATTTGTTGGAAAAATACCACGATAAACAACCATATTCTGGCATTTATGCTATAAA
1391407 CACCACTAAATTACCACT
66 CACCACTAAATTACCACT
* * * *
1391425 CTATTACAACATTTGTTTGAAAAATGCCACTATAAACAACCATATTCTGGCATTTGTGCTATAAA
1 CTATTACAACATTTGTTGGAAAAATACCACGATAAACAACCATATTCTGGCATTTATGCTATAAA
* * *
1391490 CGCCGCTAAATTACTACT
66 CACCACTAAATTACCACT
** *
1391508 CTATTACGGCGTTTGTTGGAAAAA
1 CTATTACAACATTTGTTGGAAAAA
1391532 CGCCGCTAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 15 0.17
83 75 0.83
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (83 bp):
CTATTACAACATTTGTTGGAAAAATACCACGATAAACAACCATATTCTGGCATTTATGCTATAAA
CACCACTAAATTACCACT
Found at i:1395984 original size:32 final size:33
Alignment explanation
Indices: 1395942--1396004 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
1395932 CAAATTTTGC
1395942 ATTGTTTAAAAGTATGA-TTGGGATT-AATTAT
1 ATTGTTTAAAAGTATGATTTGGGATTGAATTAT
*
1395973 ATTGTTTTAAAAGTGTGATTTGGGATTGAATT
1 ATTG-TTTAAAAGTATGATTTGGGATTGAATT
1396005 TTATGTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 12 0.43
33 8 0.29
34 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (33 bp):
ATTGTTTAAAAGTATGATTTGGGATTGAATTAT
Found at i:1399961 original size:17 final size:17
Alignment explanation
Indices: 1399924--1399957 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1399914 TGAGGTTACT
*
1399924 ATTTCTATGAATAGTGA
1 ATTTCTATGAATAGTAA
1399941 ATTTC-ATGAATAGTAA
1 ATTTCTATGAATAGTAA
1399957 A
1 A
1399958 ATTTAATCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
ATTTCTATGAATAGTAA
Found at i:1400118 original size:19 final size:19
Alignment explanation
Indices: 1400094--1400136 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1400084 TGAGCTCAAG
1400094 AGGGAGCTGCTCATATGCA
1 AGGGAGCTGCTCATATGCA
1400113 AGGGAGCTGCTCATATGCA
1 AGGGAGCTGCTCATATGCA
1400132 AGGGA
1 AGGGA
1400137 ACAATGAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.19, G:0.35, T:0.19
Consensus pattern (19 bp):
AGGGAGCTGCTCATATGCA
Found at i:1404766 original size:23 final size:23
Alignment explanation
Indices: 1404740--1404814 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
1404730 AGAATAGAGG
* *
1404740 ATTCTACGCGGTCCTTCGGGATA
1 ATTCTACGTGGTCCTTCGGGACA
*
1404763 ATTCTACGTGGTCCTTCAGGACA
1 ATTCTACGTGGTCCTTCGGGACA
* * *
1404786 ATACTATGTGGTCTTTCGGGACA
1 ATTCTACGTGGTCCTTCGGGACA
*
1404809 TTTCTA
1 ATTCTA
1404815 TGTGTCACTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTCTACGTGGTCCTTCGGGACA
Found at i:1404848 original size:24 final size:24
Alignment explanation
Indices: 1404808--1404859 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1404798 CTTTCGGGAC
* * *
1404808 ATTTCTATGTGTCACTTTGGTGTA
1 ATTTCTATGGGTCACTTTAGTGCA
1404832 ATTTCTATGCGGT-ACTTTAGTGCA
1 ATTTCTATG-GGTCACTTTAGTGCA
1404856 ATTT
1 ATTT
1404860 ATACAAGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (24 bp):
ATTTCTATGGGTCACTTTAGTGCA
Found at i:1405001 original size:3 final size:3
Alignment explanation
Indices: 1404969--1405012 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1404959 TGAACAGTGA
* * * *
1404969 ATG ATA ATG ATA ATG ATA ATG ATA ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1405013 ATATATGCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1405012 original size:6 final size:6
Alignment explanation
Indices: 1404968--1405009 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1404958 ATGAACAGTG
* *
1404968 AATGAT AATGAT AATGAT AATGAT AATGAT GATGAT GATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
1405010 GATATATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (6 bp):
AATGAT
Found at i:1408164 original size:18 final size:19
Alignment explanation
Indices: 1408130--1408165 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1408120 TGGTTATTTC
*
1408130 TTGAATTTTTGGGTTGGTT
1 TTGAATCTTTGGGTTGGTT
1408149 TTGAATCTTT-GGTTGGT
1 TTGAATCTTTGGGTTGGT
1408166 GTAAAAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.11, C:0.03, G:0.31, T:0.56
Consensus pattern (19 bp):
TTGAATCTTTGGGTTGGTT
Found at i:1408691 original size:20 final size:20
Alignment explanation
Indices: 1408666--1408716 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1408656 GATTGAAGTA
*
1408666 GTATCGATACTGATGTG-GAG
1 GTATCGATACTCATG-GCGAG
1408686 GTATCGATAC-CATGGCTGAG
1 GTATCGATACTCATGGC-GAG
1408706 GTATCGATACT
1 GTATCGATACT
1408717 ATAATTGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 23 0.85
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCATGGCGAG
Found at i:1409418 original size:24 final size:24
Alignment explanation
Indices: 1409353--1409423 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
1409343 TCGAGGGTTC
* *
1409353 TACGCGGTCCTTCGGGACAAATTTC
1 TACGTGGTCCTTCGGGACAAA-TTA
* * * *
1409378 TACATAGTCCTTTGGGATAAATTA
1 TACGTGGTCCTTCGGGACAAATTA
1409402 TACGTGGTCCTTCGGGACAAAT
1 TACGTGGTCCTTCGGGACAAAT
1409424 CTATGTGGAA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (24 bp):
TACGTGGTCCTTCGGGACAAATTA
Found at i:1409480 original size:24 final size:24
Alignment explanation
Indices: 1409411--1409481 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1409401 ATACGTGGTC
*
1409411 CTTCGG-GACAAA-TCTATGTGGAA
1 CTTCGGTG-CAAATTCTATGTGGCA
* * *
1409434 CTTCTGTGCATATTCTACGTGGCA
1 CTTCGGTGCAAATTCTATGTGGCA
1409458 CTTCGGTGCAAATTCTATGTGGCA
1 CTTCGGTGCAAATTCTATGTGGCA
1409482 ATGGTGACTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 8 0.21
24 31 0.79
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTATGTGGCA
Found at i:1415668 original size:20 final size:20
Alignment explanation
Indices: 1415623--1415672 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
1415613 GGATGAACAA
1415623 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
*
1415644 TATCGATACTGATGTGGAG-G
1 TATCGATACTGAT-TGAAGAG
1415664 TATCGATAC
1 TATCGATAC
1415673 CAAGGTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:1416395 original size:24 final size:25
Alignment explanation
Indices: 1416322--1416395 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
1416312 GAGTCGAGGG
1416322 TTCTACGCGGTCCTTCGGGAAAAAT
1 TTCTACGCGGTCCTTCGGGAAAAAT
** * *
1416347 TTCTACGTTGTCATTCGGGACAAAT
1 TTCTACGCGGTCCTTCGGGAAAAAT
* *
1416372 TT-TACGCGGTCCTTCAGGATAAAT
1 TTCTACGCGGTCCTTCGGGAAAAAT
1416396 CTTTGTGGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 17 0.43
25 23 0.57
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (25 bp):
TTCTACGCGGTCCTTCGGGAAAAAT
Found at i:1416436 original size:24 final size:24
Alignment explanation
Indices: 1416400--1416453 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1416390 ATAAATCTTT
*
1416400 GTGGCACTACGGTGCATATTCTAC
1 GTGGCACTACGGTGCAAATTCTAC
* *
1416424 GTGGCACTTCGGTGCAAATTCTAT
1 GTGGCACTACGGTGCAAATTCTAC
1416448 GTGGCA
1 GTGGCA
1416454 GTGGTGACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (24 bp):
GTGGCACTACGGTGCAAATTCTAC
Found at i:1417481 original size:66 final size:62
Alignment explanation
Indices: 1417348--1417500 Score: 180
Period size: 66 Copynumber: 2.4 Consensus size: 62
1417338 AGGGATAATG
* * *
1417348 GTTTCAAGAGAAATCGACTCAAAGATGATGCTTCAAGAGAAGCTGTCTCAAGAGACAAAATTC
1 GTTTCAAGAGAAA-CGACTCAAAGATGATGCTTCAAAAGAAACTGTCTAAAGAGACAAAATTC
* * *
1417411 GTTTCAAGGGAAACGATCTCAAAGATAGGTGTTTCAAAAGAAACTGTCTAAAGGGAGACAAAATT
1 GTTTCAAGAGAAACGA-CTCAAAGAT-GATGCTTCAAAAGAAACTGTCTAAA--GAGACAAAATT
*
1417476 T
62 C
*
1417477 GTTTCAAGAGAAACAGACTAAAAG
1 GTTTCAAGAGAAAC-GACTCAAAG
1417501 TTTTTTTCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
62 3 0.04
63 21 0.28
64 20 0.26
66 30 0.39
67 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (62 bp):
GTTTCAAGAGAAACGACTCAAAGATGATGCTTCAAAAGAAACTGTCTAAAGAGACAAAATTC
Found at i:1424614 original size:23 final size:23
Alignment explanation
Indices: 1424571--1424614 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1424561 ACCCCCATAA
*
1424571 GGGAACCGATTCCCACTTTGAAT
1 GGGAACCGATTCCCACCTTGAAT
* *
1424594 GGGAACTGATTCCCTCCTTGA
1 GGGAACCGATTCCCACCTTGA
1424615 GGGAATCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
GGGAACCGATTCCCACCTTGAAT
Found at i:1428160 original size:2 final size:2
Alignment explanation
Indices: 1428148--1428197 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1428138 AGTTTTATTG
*
1428148 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1428190 T- TA TA TA T
1 TA TA TA TA T
1428198 TCTATAGGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1432282 original size:15 final size:15
Alignment explanation
Indices: 1432262--1432291 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1432252 GTAAAATAAA
1432262 AATGAATTAACAATT
1 AATGAATTAACAATT
1432277 AATGAATTAACAATT
1 AATGAATTAACAATT
1432292 GATATTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
AATGAATTAACAATT
Found at i:1432667 original size:30 final size:28
Alignment explanation
Indices: 1432612--1432767 Score: 80
Period size: 30 Copynumber: 5.3 Consensus size: 28
1432602 TCAAAGGATT
*
1432612 AAAATAGAAAATTAAAGGGAAAATAGCA
1 AAAATAGAAAATTAAAGGGAAAATAGAA
* * *
1432640 ATAATAGAAAGTTAAAGTGCTAAAATAGAA
1 AAAATAGAAAATTAAAG-G-GAAAATAGAA
* * ** *
1432670 AAAATAGACATTTAAAAGACTAAAATAGTA
1 AAAATAGAAAATT-AAAG-GGAAAATAGAA
* * *
1432700 AAAATATAAACTT-AAGAGACTAAATAGAA
1 AAAATAGAAAATTAAAGGGA--AAATAGAA
* * * * *
1432729 AATACAGACATTTAAAGGACTAAAATAGAA
1 AAAATAGAAAATTAAAGG--GAAAATAGAA
1432759 AAAATAGAA
1 AAAATAGAA
1432768 GCTTAAGGAC
Statistics
Matches: 94, Mismatches: 26, Indels: 14
0.70 0.19 0.10
Matches are distributed among these distances:
27 1 0.01
28 18 0.19
29 16 0.17
30 54 0.57
31 4 0.04
32 1 0.01
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.20
Consensus pattern (28 bp):
AAAATAGAAAATTAAAGGGAAAATAGAA
Found at i:1432725 original size:29 final size:30
Alignment explanation
Indices: 1432631--1432783 Score: 134
Period size: 30 Copynumber: 5.2 Consensus size: 30
1432621 AATTAAAGGG
* * * *
1432631 AAAATAGCAATAATAGAAAGTTAA-AGTGCT
1 AAAATAGAAAAAATAGAAACTTAAGAG-ACT
* * *
1432661 AAAATAGAAAAAATAGACATTTAAAAGACT
1 AAAATAGAAAAAATAGAAACTTAAGAGACT
* *
1432691 AAAATAGTAAAAATATAAACTTAAGAGACT
1 AAAATAGAAAAAATAGAAACTTAAGAGACT
* * * *
1432721 -AAATAGAAAATACAGACATTTAA-AGGACT
1 AAAATAGAAAAAATAGAAACTTAAGA-GACT
*
1432750 AAAATAGAAAAAATAGAAGCTTAAG-GACT
1 AAAATAGAAAAAATAGAAACTTAAGAGACT
1432779 AAAAT
1 AAAAT
1432784 GGTATTAACA
Statistics
Matches: 98, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
28 1 0.01
29 30 0.31
30 65 0.66
31 2 0.02
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (30 bp):
AAAATAGAAAAAATAGAAACTTAAGAGACT
Done.