Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1127921 original size:11 final size:10
Alignment explanation
Indices: 1127894--1127931 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1127884 TTATTCTAAA
1127894 AAAATATT-T
1 AAAATATTAT
*
1127903 ATAATATTAT
1 AAAATATTAT
1127913 AAAAATATTAT
1 -AAAATATTAT
1127924 AAAATATT
1 AAAATATT
1127932 TATTTAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.28
10 9 0.36
11 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAATATTAT
Found at i:1129856 original size:24 final size:22
Alignment explanation
Indices: 1129822--1129867 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1129812 GATATTTTAT
**
1129822 TATATAAAAATATTCAAGATTA
1 TATATAAAAATATAAAAGATTA
1129844 TATATAGATAAATATAAAAGATTA
1 TATATA-A-AAATATAAAAGATTA
1129868 CATTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
TATATAAAAATATAAAAGATTA
Found at i:1130195 original size:29 final size:28
Alignment explanation
Indices: 1130159--1130220 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
1130149 TAAATATTTG
* *
1130159 TATTTATATTTAGGACTCTTAATTTTTAT
1 TATTTATAATTAGGACAC-TAATTTTTAT
*
1130188 TATTTATAATTAGGTCACTAATTTTTAT
1 TATTTATAATTAGGACACTAATTTTTAT
*
1130216 AATTT
1 TATTT
1130221 CTTAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (28 bp):
TATTTATAATTAGGACACTAATTTTTAT
Found at i:1130220 original size:28 final size:29
Alignment explanation
Indices: 1130160--1130220 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1130150 AAATATTTGT
* * *
1130160 ATTTATATTTAGGACTCTTAATTTTTATT
1 ATTTATAATTAGGACACTTAATTTTTATA
*
1130189 ATTTATAATTAGGTCAC-TAATTTTTATA
1 ATTTATAATTAGGACACTTAATTTTTATA
1130217 ATTT
1 ATTT
1130221 CTTAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (29 bp):
ATTTATAATTAGGACACTTAATTTTTATA
Found at i:1132490 original size:28 final size:28
Alignment explanation
Indices: 1132455--1132509 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1132445 ATCAGAACGA
* *
1132455 GGAACATAGTCCCATGTAGAATCAGAAT
1 GGAACATAGTCCCAAGCAGAATCAGAAT
*
1132483 GGAACATAGTGCCAAGCAGAATCAGAA
1 GGAACATAGTCCCAAGCAGAATCAGAA
1132510 AGAAATCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (28 bp):
GGAACATAGTCCCAAGCAGAATCAGAAT
Found at i:1136640 original size:20 final size:18
Alignment explanation
Indices: 1136598--1136639 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1136588 TATATATACG
1136598 TTATTATATATAATAATA
1 TTATTATATATAATAATA
1136616 TTATTATAT-T-ATAAATA
1 TTATTATATATAAT-AATA
1136633 TTATTAT
1 TTATTAT
1136640 TTGTAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTATATATAATAATA
Found at i:1136697 original size:21 final size:21
Alignment explanation
Indices: 1136671--1136751 Score: 144
Period size: 21 Copynumber: 3.9 Consensus size: 21
1136661 TTACAAAGTG
1136671 AGGCATACAGGCCCGATTACA
1 AGGCATACAGGCCCGATTACA
*
1136692 AGGCATACATGCCCGATTACA
1 AGGCATACAGGCCCGATTACA
1136713 AGGCATACAGGCCCGATTACA
1 AGGCATACAGGCCCGATTACA
*
1136734 AGGCACACAGGCCCGATT
1 AGGCATACAGGCCCGATT
1136752 CAGATGCAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (21 bp):
AGGCATACAGGCCCGATTACA
Found at i:1137005 original size:42 final size:42
Alignment explanation
Indices: 1136951--1137043 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
1136941 CCGGCCACCG
*
1136951 TCTCCATAAGCTCCAACCGAAGGTTGCCACGCCATTACCGCC
1 TCTCCACAAGCTCCAACCGAAGGTTGCCACGCCATTACCGCC
* *
1136993 TCTCTACAAGCTCCAACCGAAGGTTGCCACGCCATTTCCGCC
1 TCTCCACAAGCTCCAACCGAAGGTTGCCACGCCATTACCGCC
1137035 TCTCCACAA
1 TCTCCACAA
1137044 TCCATTAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (42 bp):
TCTCCACAAGCTCCAACCGAAGGTTGCCACGCCATTACCGCC
Found at i:1137817 original size:13 final size:13
Alignment explanation
Indices: 1137799--1137823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1137789 AGGTTTATTC
1137799 GTATTTTAATTTG
1 GTATTTTAATTTG
1137812 GTATTTTAATTT
1 GTATTTTAATTT
1137824 TATTTATTTA
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
GTATTTTAATTTG
Found at i:1142162 original size:43 final size:43
Alignment explanation
Indices: 1142093--1142380 Score: 328
Period size: 43 Copynumber: 6.7 Consensus size: 43
1142083 ATAGCAGGCT
* *
1142093 CCTTTGCTGTGTGTAATGGTAAGCCTTACAGTTTCCCTAGGTC
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTC
*
1142136 CCTTTGCTGTGTGCAAGGGTAGGCCTTACAGTTTCCCTAGGTTC
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGG-TC
* * * *
1142180 CTTTTGCTTTGTTCAAGAGTAAGCCTTACAGTTTCCCTAGGTC
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTC
* * * *
1142223 CCTTTTGCTGTGTGTAAGGGTAAGCATTACAGTTTCCCCAGGTT
1 CC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTC
* * * *
1142267 CCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCAC-AAGTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTC
* * * *
1142309 CCTTTGTTGTGTTCAAGGGTAAACCTTACAGTTTCCCCAGG-C
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTC
* * *
1142351 TCTTTTGCTATGTGCAAGGATAAGACCTTA
1 -CCTTTGCTGTGTGCAAGGGTAAG-CCTTA
1142381 TCGTTTTTGC
Statistics
Matches: 206, Mismatches: 34, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
42 36 0.17
43 91 0.44
44 79 0.38
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (43 bp):
CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTAGGTC
Found at i:1142206 original size:87 final size:87
Alignment explanation
Indices: 1142111--1142368 Score: 360
Period size: 87 Copynumber: 3.0 Consensus size: 87
1142101 GTGTGTAATG
* *
1142111 GTAAGCCTTACAGTTTCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAGGCCTTACAGTTTCCCTAG
1 GTAAGCCTTACAGTTTCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
* *
1142176 GTTCCTTTTGCTTTGTTCAAGA
66 GTTCCTTTTGCTATGTGCAAGA
* *
1142198 GTAAGCCTTACAGTTTCCCTAGGTCCCTTTTGCTGTGTGTAAGGGTAAGCATTACAGTTTCCCCA
1 GTAAGCCTTACAGTTTCCCTAGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
*
1142263 GGTTCC-TTTGCTATGTGCAAGG
65 GGTTCCTTTTGCTATGTGCAAGA
* * * * * *
1142285 GTAAGCCTTACAGTTTCAC-AAGTTCCTTTGTTGTGTTCAAGGGTAAACCTTACAGTTTCCCCAG
1 GTAAGCCTTACAGTTTCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
*
1142349 GCT-CTTTTGCTATGTGCAAG
66 GTTCCTTTTGCTATGTGCAAG
1142369 GATAAGACCT
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
84 1 0.01
85 50 0.33
86 5 0.03
87 58 0.38
88 39 0.25
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (87 bp):
GTAAGCCTTACAGTTTCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAG
GTTCCTTTTGCTATGTGCAAGA
Found at i:1148267 original size:22 final size:22
Alignment explanation
Indices: 1148242--1148289 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1148232 TACATTTTGT
*
1148242 AAAGATGATAGACTCTCTTTTC
1 AAAGATGATAGACTCTCTTTTA
*
1148264 AAAGATGATAGATTCTCTTTTA
1 AAAGATGATAGACTCTCTTTTA
1148286 AAAG
1 AAAG
1148290 GCAAGAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAGATGATAGACTCTCTTTTA
Found at i:1149187 original size:90 final size:89
Alignment explanation
Indices: 1149043--1149215 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
1149033 AAACTCCACG
* *
1149043 GAATAGTAGTGGAACAAATTTTTTAGCAAAGTATCAAAATCCATGGAAGAGTAGTGGAAGCAAAT
1 GAATAGTAGTGGAACAAATTTTTTAACAAAGTATCAAAATCCACGGAAGAGTAGTGGAAGCAAAT
1149108 TCAATCATAAATATGGACTCCATA
66 TCAATCATAAATATGGACTCCATA
* *
1149132 GAATAGTAGTGGAACATATTTTTTTAACAAAGTATCAAACTCCACGGAAGAGTAGTGGAAGCAAA
1 GAATAGTAGTGGAACA-AATTTTTTAACAAAGTATCAAAATCCACGGAAGAGTAGTGGAAGCAAA
*
1149197 TTCAATCATAAATCTGGAC
65 TTCAATCATAAATATGGAC
1149216 AAATTTTTCA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 16 0.21
90 62 0.79
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (89 bp):
GAATAGTAGTGGAACAAATTTTTTAACAAAGTATCAAAATCCACGGAAGAGTAGTGGAAGCAAAT
TCAATCATAAATATGGACTCCATA
Found at i:1149917 original size:90 final size:89
Alignment explanation
Indices: 1149762--1150088 Score: 465
Period size: 89 Copynumber: 3.7 Consensus size: 89
1149752 AAACTCCACG
* *
1149762 GAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATCAAACTCCATGGAAGAGTAGTGGAAGAAAAT
1 GAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAGTGGAAGCAAAT
*
1149827 TCAATCATAAATCTGGACTCTATA
66 TCAATCATAAATCTGGACTCCATA
* * *
1149851 GAAGAGTAGTGGAACAGATTTTTTTAACAAAGTATCAAACTCCACGGAAGAGTAGTGGAAGCAAA
1 GAAGAGTAGTGGAAC-GAATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAGTGGAAGCAAA
1149916 TTCAATCATAAATCTGGACTCCATA
65 TTCAATCATAAATCTGGACTCCATA
* * * *
1149941 GAAGAGTAGTGGAACAAAATTTTCAGCAAAGAAACAAACTCCACGGAAGAGTAGTGGAAGCAAAT
1 GAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAGTGGAAGCAAAT
* * * *
1150006 TCAATCATAATTATGAACTCCACA
66 TCAATCATAAATCTGGACTCCATA
* * * * *
1150030 AAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATGAGAACTTCACGAAAGCGTAGTGGA
1 GAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATCA-AACTCCACGGAAGAGTAGTGGA
1150089 GTAATCCAAG
Statistics
Matches: 210, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
89 108 0.51
90 102 0.49
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (89 bp):
GAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATCAAACTCCACGGAAGAGTAGTGGAAGCAAAT
TCAATCATAAATCTGGACTCCATA
Found at i:1149948 original size:44 final size:44
Alignment explanation
Indices: 1149798--1150043 Score: 176
Period size: 44 Copynumber: 5.5 Consensus size: 44
1149788 CAAAGTATCA
** *
1149798 AACTCCATGGAAGAGTAGTGGAAGAAAATTCAATCATAAATCTG
1 AACTCCACAGAAGAGTAGTGGAAGCAAATTCAATCATAAATCTG
* * * * *** * * * *
1149842 GACTCTATAGAAGAGTAGTGGAA-CAGATTTTTTTAACAAAGTATCA
1 AACTCCACAGAAGAGTAGTGGAAGCA-AATTCAATCATAAA-TCT-G
*
1149888 AACTCCACGGAAGAGTAGTGGAAGCAAATTCAATCATAAATCTG
1 AACTCCACAGAAGAGTAGTGGAAGCAAATTCAATCATAAATCTG
* * * * * *
1149932 GACTCCATAGAAGAGTAGTGGAA-CAAAATTTTC-AGCAAAGAAAC-A
1 AACTCCACAGAAGAGTAGTGGAAGC-AAA--TTCAATCATA-AATCTG
* * *
1149977 AACTCCACGGAAGAGTAGTGGAAGCAAATTCAATCATAATTATG
1 AACTCCACAGAAGAGTAGTGGAAGCAAATTCAATCATAAATCTG
*
1150021 AACTCCACAAAAGAGTAGTGGAA
1 AACTCCACAGAAGAGTAGTGGAA
1150044 CGAATTTTTC
Statistics
Matches: 149, Mismatches: 42, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
43 6 0.04
44 76 0.51
45 31 0.21
46 34 0.23
47 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (44 bp):
AACTCCACAGAAGAGTAGTGGAAGCAAATTCAATCATAAATCTG
Found at i:1150087 original size:179 final size:179
Alignment explanation
Indices: 1149762--1150088 Score: 467
Period size: 179 Copynumber: 1.8 Consensus size: 179
1149752 AAACTCCACG
* * * * *
1149762 GAAGAGTAGTGGAACGAATTTTTCAGCAAAGTATCAAACTCCATGGAAGAGTAGTGGAAGAAAAT
1 GAAGAGTAGTGGAACAAAATTTTCAGCAAAGAAACAAACTCCACGGAAGAGTAGTGGAAGAAAAT
* * * * * * *
1149827 TCAATCATAAATCTGGACTCTATAGAAGAGTAGTGGAACAGATTTTTTTAACAAAGTATCAAACT
66 TCAATCATAAATATGAACTCCACAAAAGAGTAGTGGAACAGAATTTTTCAACAAAGTATCAAACT
*
1149892 CCACGGAAGAGTAGTGGAAGCAAATTCAATCATAAATCTGGACTCCATA
131 CCACGAAAGAGTAGTGGAAGCAAATTCAATCATAAATCTGGACTCCATA
*
1149941 GAAGAGTAGTGGAACAAAATTTTCAGCAAAGAAACAAACTCCACGGAAGAGTAGTGGAAGCAAAT
1 GAAGAGTAGTGGAACAAAATTTTCAGCAAAGAAACAAACTCCACGGAAGAGTAGTGGAAGAAAAT
* * *
1150006 TCAATCATAATTATGAACTCCACAAAAGAGTAGTGGAAC-GAATTTTTCAGCAAAGTATGAGAAC
66 TCAATCATAAATATGAACTCCACAAAAGAGTAGTGGAACAGAATTTTTCAACAAAGTATCA-AAC
* *
1150070 TTCACGAAAGCGTAGTGGA
130 TCCACGAAAGAGTAGTGGA
1150089 GTAATCCAAG
Statistics
Matches: 128, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
178 17 0.13
179 111 0.87
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (179 bp):
GAAGAGTAGTGGAACAAAATTTTCAGCAAAGAAACAAACTCCACGGAAGAGTAGTGGAAGAAAAT
TCAATCATAAATATGAACTCCACAAAAGAGTAGTGGAACAGAATTTTTCAACAAAGTATCAAACT
CCACGAAAGAGTAGTGGAAGCAAATTCAATCATAAATCTGGACTCCATA
Found at i:1150621 original size:21 final size:21
Alignment explanation
Indices: 1150514--1150619 Score: 131
Period size: 21 Copynumber: 5.0 Consensus size: 21
1150504 AAAGTGAGGT
*
1150514 ATACAGGTCCGATTACAAGGC
1 ATACAGGCCCGATTACAAGGC
* *
1150535 ATACAGACCTGATTACAAGGC
1 ATACAGGCCCGATTACAAGGC
**
1150556 ATACATTCCCGATTACAAGGC
1 ATACAGGCCCGATTACAAGGC
** *
1150577 ATACATTCCCGATTAAAAGGC
1 ATACAGGCCCGATTACAAGGC
*
1150598 ACACAGGCCCGATTACAAGGC
1 ATACAGGCCCGATTACAAGGC
1150619 A
1 A
1150620 CATGGCCAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATACAGGCCCGATTACAAGGC
Found at i:1154104 original size:29 final size:30
Alignment explanation
Indices: 1154060--1154131 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
1154050 AACTTTTTCA
*
1154060 ATCAAAGTCAAAGGTCAAC-GGTCAGAC-CG
1 ATCAAAGTCAACGGTCAACAGGT-AGACTCG
*
1154089 ATCAAAGTCAACGGTCAACAGGTTGACTCG
1 ATCAAAGTCAACGGTCAACAGGTAGACTCG
*
1154119 GTCAAAGTCAACG
1 ATCAAAGTCAACG
1154132 AGTTAACCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (30 bp):
ATCAAAGTCAACGGTCAACAGGTAGACTCG
Found at i:1154192 original size:14 final size:14
Alignment explanation
Indices: 1154170--1154212 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1154160 TGGACTGAAC
*
1154170 CAGGTGGGTCGAGT
1 CAGGAGGGTCGAGT
*
1154184 CAGGAGGGTC-AGG
1 CAGGAGGGTCGAGT
*
1154197 CAGGAGGGTAGAGT
1 CAGGAGGGTCGAGT
1154211 CA
1 CA
1154213 ACCCGGTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.23, C:0.14, G:0.49, T:0.14
Consensus pattern (14 bp):
CAGGAGGGTCGAGT
Found at i:1156146 original size:10 final size:10
Alignment explanation
Indices: 1156131--1156155 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1156121 ATTATTTTAA
1156131 TTATTATGTT
1 TTATTATGTT
1156141 TTATTATGTT
1 TTATTATGTT
1156151 TTATT
1 TTATT
1156156 TTTAATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
TTATTATGTT
Found at i:1160946 original size:7 final size:7
Alignment explanation
Indices: 1160934--1160958 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1160924 CGATAGAAGA
1160934 GGAAAAG
1 GGAAAAG
1160941 GGAAAAG
1 GGAAAAG
1160948 GGAAAAG
1 GGAAAAG
1160955 GGAA
1 GGAA
1160959 GAGATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GGAAAAG
Found at i:1173657 original size:18 final size:18
Alignment explanation
Indices: 1173634--1173678 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1173624 TAAATGAAAT
1173634 GGCATGCAAGCTGTCACC
1 GGCATGCAAGCTGTCACC
1173652 GGCATGCAAGCTGTCACC
1 GGCATGCAAGCTGTCACC
1173670 GGCATGCAA
1 GGCATGCAA
1173679 AAGGAATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (18 bp):
GGCATGCAAGCTGTCACC
Found at i:1187625 original size:72 final size:69
Alignment explanation
Indices: 1187519--1187665 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 69
1187509 TGAAAGTATT
1187519 AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
1 AAAATGGTTTTCAAGTTTGGTAATCAACTTTG-AAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
1187583 CTTTA
65 CTTGA
*** *
1187588 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGT
1 AAAATGGTTTTC-AAGTTTGGT-AAT-CAACTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGT
*
1187653 TTGTTGA
63 TTCTTGA
1187660 AAAATG
1 AAAATG
1187666 ATAATGGGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 12 0.18
70 9 0.13
71 11 0.16
72 36 0.53
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTTC
TTGA
Found at i:1187645 original size:37 final size:36
Alignment explanation
Indices: 1187546--1187664 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
1187536 TGGTAATCAA
1187546 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
1187583 CTTT-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
1187618 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
1187655 -GTTGAAAAAT
1 CTTTGAAAAAT
1187665 GATAATGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 16 0.21
37 26 0.34
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1192153 original size:21 final size:21
Alignment explanation
Indices: 1192129--1192189 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1192119 AACTTTGAAA
1192129 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1192150 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1192164 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1192185 AAATG
1 AAATG
1192190 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1192220 original size:37 final size:37
Alignment explanation
Indices: 1192121--1192239 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1192111 TGGTAACCAA
1192121 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1192158 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1192193 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1192230 -GTTGAAAAAT
1 CTTTGAAAAAT
1192240 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1203387 original size:20 final size:20
Alignment explanation
Indices: 1203336--1203390 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1203326 TTCATATTTT
* *
1203336 CATCTTTACAGTTGCGTTCG
1 CATCTTTACATTTGCGTTCA
*
1203356 CATCTTTACATTTACGTTCA
1 CATCTTTACATTTGCGTTCA
*
1203376 CATCTTTGCATTTGC
1 CATCTTTACATTTGC
1203391 ACTCTCATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.44
Consensus pattern (20 bp):
CATCTTTACATTTGCGTTCA
Found at i:1203996 original size:22 final size:23
Alignment explanation
Indices: 1203948--1203996 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1203938 GACCCGAAAT
* * *
1203948 AATAAAAATAATTATTTTTATTC
1 AATAAAAACAATGATTTTAATTC
*
1203971 AATAAAAACAATGA-TTTAATTG
1 AATAAAAACAATGATTTTAATTC
1203993 AATA
1 AATA
1203997 TATATATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
AATAAAAACAATGATTTTAATTC
Found at i:1204427 original size:32 final size:32
Alignment explanation
Indices: 1204386--1204447 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1204376 AACAGGGTTG
*
1204386 GTCGCCATCCCTTCCATGCGATACCAAAGGAA
1 GTCGCCATCCCTTCCATGCGACACCAAAGGAA
*
1204418 GTCGCCATCCTTTCCATGCGACACCAAAGG
1 GTCGCCATCCCTTCCATGCGACACCAAAGG
1204448 GTATTTCTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (32 bp):
GTCGCCATCCCTTCCATGCGACACCAAAGGAA
Found at i:1211033 original size:13 final size:13
Alignment explanation
Indices: 1211017--1211042 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1211007 AAAAATTTAT
1211017 TTAAAAATTAAAA
1 TTAAAAATTAAAA
1211030 TTAAAAATTAAAA
1 TTAAAAATTAAAA
1211043 AAACATAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAAATTAAAA
Found at i:1214554 original size:13 final size:13
Alignment explanation
Indices: 1214529--1214562 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
1214519 CTAAATTGAA
1214529 CAAATATAAAATTT
1 CAAATA-AAAATTT
1214543 CAAATAAAAATTT
1 CAAATAAAAATTT
1214556 -AAATAAA
1 CAAATAAA
1214563 TTAAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 7 0.35
14 6 0.30
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (13 bp):
CAAATAAAAATTT
Found at i:1214777 original size:20 final size:19
Alignment explanation
Indices: 1214739--1214786 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1214729 TATATATATG
*
1214739 AACTATATATATATGTATA
1 AACTATATATACATGTATA
*
1214758 AACTATATATACCGTGTATA
1 AACTATATATA-CATGTATA
1214778 AACTATATA
1 AACTATATA
1214787 GTTTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (19 bp):
AACTATATATACATGTATA
Found at i:1214786 original size:2 final size:2
Alignment explanation
Indices: 1214678--1214768 Score: 71
Period size: 2 Copynumber: 44.5 Consensus size: 2
1214668 ACTATAATTA
*
1214678 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * * *
1214721 TT AT -T TT AT AT AT AT AT GA- ACT AT AT AT AT AT GT AT AA ACT
1 AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT A-T
1214762 AT AT AT A
1 AT AT AT A
1214769 CCGTGTATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
1 3 0.04
2 64 0.89
3 5 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1214857 original size:11 final size:11
Alignment explanation
Indices: 1214841--1214878 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1214831 AATATAAATC
*
1214841 ATATAGTTTAT
1 ATATAGATTAT
1214852 ATATAGATTAT
1 ATATAGATTAT
1214863 ATAT-GAATTAT
1 ATATAG-ATTAT
1214874 ATATA
1 ATATA
1214879 ACTATACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (11 bp):
ATATAGATTAT
Found at i:1215084 original size:2 final size:2
Alignment explanation
Indices: 1215077--1215281 Score: 137
Period size: 2 Copynumber: 98.5 Consensus size: 2
1215067 TATTTAAACA
* * * * *
1215077 AT AT AT AT AT AT AT AT AT AT AA AT -T AG GT AGT TT AT AG AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T
* * * *
1215120 AGT AT AT AA ACT AT AT AT AA AC A- AT AT AT ACT AT AT AT AT AA
1 A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * * * *
1215162 ACT AT GT AGT TT AT ACT ACT AT CT AT AA AC A- AT AT AGT TT AT AT
1 A-T AT AT A-T AT AT A-T A-T AT AT AT AT AT AT AT AT A-T AT AT AT
* *
1215206 AC AT AGT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1215249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1215282 CTATCTATAA
Statistics
Matches: 161, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
1 3 0.02
2 140 0.87
3 18 0.11
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1215108 original size:66 final size:67
Alignment explanation
Indices: 1215024--1215160 Score: 240
Period size: 66 Copynumber: 2.1 Consensus size: 67
1215014 TTTATGGAAT
* *
1215024 TATATATAAACTATGTAGTTTATAGATAGTAGTATATAAACTATATTTAAACAATATATA-TATA
1 TATATATAAACTAGGTAGTTTATAGATAGTAGTATATAAACTATATATAAACAATATATACTATA
1215088 TA
66 TA
*
1215090 TATATATAAATTAGGTAGTTTATAGATAGTAGTATATAAACTATATATAAACAATATATACTATA
1 TATATATAAACTAGGTAGTTTATAGATAGTAGTATATAAACTATATATAAACAATATATACTATA
1215155 TA
66 TA
1215157 TATA
1 TATA
1215161 AACTATGTAG
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 57 0.85
67 10 0.15
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.40
Consensus pattern (67 bp):
TATATATAAACTAGGTAGTTTATAGATAGTAGTATATAAACTATATATAAACAATATATACTATA
TA
Found at i:1215136 original size:11 final size:11
Alignment explanation
Indices: 1215122--1215166 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1215112 TAGATAGTAG
1215122 TATATAAACTA
1 TATATAAACTA
*
1215133 TATATAAACAA
1 TATATAAACTA
*
1215144 TATATACTA-TA
1 TATATA-AACTA
1215155 TATATAAACTA
1 TATATAAACTA
1215166 T
1 T
1215167 GTAGTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 1 0.04
11 26 0.93
12 1 0.04
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (11 bp):
TATATAAACTA
Found at i:1215294 original size:10 final size:11
Alignment explanation
Indices: 1215216--1215295 Score: 57
Period size: 10 Copynumber: 7.9 Consensus size: 11
1215206 ACATAGTTTA
*
1215216 TATATA-TATA
1 TATATACTATC
*
1215226 TATATA-TATA
1 TATATACTATC
*
1215236 TATATA-TATA
1 TATATACTATC
*
1215246 TATATA-TATA
1 TATATACTATC
*
1215256 TATATA-TATA
1 TATATACTATC
*
1215266 TATATA-TATA
1 TATATACTATC
1215276 TATATACTATC
1 TATATACTATC
1215287 TATA-ACTAT
1 TATATACTAT
1215296 GGTTTAGGGT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
10 61 0.90
11 7 0.10
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATACTATC
Found at i:1217465 original size:31 final size:31
Alignment explanation
Indices: 1217427--1217508 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
1217417 GAACCTCGAC
*
1217427 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1217458 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* *
1217489 AACTGTCCATATGTCTCGAA
1 AACTGTCCATAGGTCCCGAA
1217509 AGACAAAGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:1217519 original size:31 final size:31
Alignment explanation
Indices: 1217427--1217522 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
1217417 GAACCTCGAC
* **
1217427 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACAAAGGTA
**
1217458 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACAAAGGTA
* *
1217489 AACTGTCCATATGTCTCGAA-AGACAAAGGTA
1 AACTGTCCATAGGTCCCGAAGA-ACAAAGGTA
1217520 AAC
1 AAC
1217523 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.02
31 58 0.98
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACAAAGGTA
Found at i:1218434 original size:20 final size:22
Alignment explanation
Indices: 1218409--1218466 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1218399 TTCCCCTTGA
1218409 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
1218429 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
1218452 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1218467 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:1221570 original size:30 final size:30
Alignment explanation
Indices: 1221502--1221612 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 30
1221492 GAAGGACCTA
* * *
1221502 TCCAGAGGTCACAAAG-ACCCCGATAACTA
1 TCCAGAGGTCACAAAGAACCTCGAAAACTG
*
1221531 TCCAGAGGTCATAAAGAACCTCGAAAACTG
1 TCCAGAGGTCACAAAGAACCTCGAAAACTG
* * * * * *
1221561 TCCATAGGTCCCGACGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGAACCT-CGAAAACTG
* *
1221592 TCCATAGGTCCCAAAGAACCT
1 TCCAGAGGTCACAAAGAACCT
1221613 AGGTAAACTA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 15 0.22
30 26 0.39
31 26 0.39
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGAAAACTG
Found at i:1221593 original size:31 final size:31
Alignment explanation
Indices: 1221555--1221651 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 31
1221545 AGAACCTCGA
* *
1221555 AAACTGTCCATAGGTCCCGACGAACCTAGGT
1 AAACTGTCCATAGGTCCCAAAGAACCTAGGT
1221586 AAACTGTCCATAGGTCCCAAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCAAAGAACCTAGGT
* * * *
1221617 AAACTATCCATATGTCTCGAAAG-ACATAGGT
1 AAACTGTCCATAGGTC-CCAAAGAACCTAGGT
1221648 AAAC
1 AAAC
1221652 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 54 0.92
32 5 0.08
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (31 bp):
AAACTGTCCATAGGTCCCAAAGAACCTAGGT
Found at i:1222627 original size:20 final size:22
Alignment explanation
Indices: 1222602--1222659 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1222592 TTCCCCTTGA
1222602 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
1222622 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
1222645 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1222660 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:1222725 original size:64 final size:63
Alignment explanation
Indices: 1222647--1222787 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
1222637 TCTTTAACAT
* *
1222647 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * * *
1222710 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTACAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
1222774 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1222788 ATTGAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 21 0.32
64 45 0.68
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:1224886 original size:22 final size:22
Alignment explanation
Indices: 1224861--1224926 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
1224851 GCATGTGAAC
*
1224861 TATGTCTCGAATGACCTATGTA
1 TATGTCTCGAAGGACCTATGTA
1224883 TATGTCTCGAAGGACCTATGTA
1 TATGTCTCGAAGGACCTATGTA
1224905 TATGTCTCGAAGGACCTATGTA
1 TATGTCTCGAAGGACCTATGTA
1224927 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (22 bp):
TATGTCTCGAAGGACCTATGTA
Found at i:1231982 original size:14 final size:14
Alignment explanation
Indices: 1231963--1232012 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
1231953 CGGTAATATA
1231963 TTCATTTATGTTCG
1 TTCATTTATGTTCG
1231977 TTCATTTA---TC-
1 TTCATTTATGTTCG
*
1231987 TTCGTTTATGTTCG
1 TTCATTTATGTTCG
*
1232001 TTCGTTTATGTT
1 TTCATTTATGTT
1232013 TGTTTATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
13 2 0.06
14 20 0.65
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (14 bp):
TTCATTTATGTTCG
Found at i:1232034 original size:24 final size:24
Alignment explanation
Indices: 1231967--1232037 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
1231957 AATATATTCA
* *
1231967 TTTATGTTCGTTCATTTATCTTCG
1 TTTATGTTCGTTCATTTATGTTTG
*
1231991 TTTATGTTCGTTCGTTTATGTTTG
1 TTTATGTTCGTTCATTTATGTTTG
* *
1232015 TTTATGTGCATTCATTTATGTTT
1 TTTATGTTCGTTCATTTATGTTT
1232038 AGCTCAATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.61
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTATGTTTG
Found at i:1232354 original size:60 final size:60
Alignment explanation
Indices: 1232289--1232489 Score: 237
Period size: 60 Copynumber: 3.3 Consensus size: 60
1232279 ACCCAGTTTC
* * * *
1232289 CAAATTCGCAACACGAATTTGTAAATGGCAACCCATAATTCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACACAAAAGT
* * *
1232349 CAAATTCGCAACGCG-A-TAGTCAAATTCGCAACAC-TGAAGTCAAATTCGCAACACAAAAAT
1 CAAATTCGCAACACGAATTTGT-AAA-TCGCAACACAT-AAGTCAAATTCGCAACACAAAAGT
* * * *
1232409 CAAATTTGCAACGCGAATCTGTAAATCGCAACACATAAGTCAAATTAGCAACACAAAAGT
1 CAAATTCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACACAAAAGT
*
1232469 CAAATTTGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
1232490 CAAATTCGCA
Statistics
Matches: 120, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
58 3 0.03
59 5 0.04
60 100 0.83
61 10 0.08
62 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (60 bp):
CAAATTCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACACAAAAGT
Found at i:1232553 original size:20 final size:19
Alignment explanation
Indices: 1232481--1232578 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
1232471 AATTTGCAAC
1232481 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
1232500 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
1232519 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
* *
1232538 ACTCGATTTTCGAATTCGCA
1 ACT-GAATTTCAAATTCGCA
* *
1232558 ACACGAATTT-AATTTCGCA
1 AC-TGAATTTCAAATTCGCA
1232577 AC
1 AC
1232579 ACAAATGTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 50 0.70
20 21 0.30
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (19 bp):
ACTGAATTTCAAATTCGCA
Found at i:1232575 original size:39 final size:39
Alignment explanation
Indices: 1232468--1232578 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 39
1232458 AACACAAAAG
*
1232468 TCAAATTTGCAACACTGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACTGAATT
* *
1232508 TCAAATTCGCAAC-TGAATTTCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACT-GAATT
* *
1232547 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAACACGAATTTCAAATTCGCAAC
1232579 ACAAATGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 19 0.30
39 26 0.41
40 18 0.29
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (39 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACTGAATT
Found at i:1232579 original size:19 final size:20
Alignment explanation
Indices: 1232249--1232580 Score: 202
Period size: 20 Copynumber: 16.7 Consensus size: 20
1232239 AAATGACCAA
* * *
1232249 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* * *
1232269 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACACGAATTT
1232288 CCAAATTCGCAACACGAATTT
1 -CAAATTCGCAACACGAATTT
* * * *
1232309 GTAAA-TGGCAAC-CCATAATT
1 -CAAATTCGCAACACGA-ATTT
*
1232329 CAAATTCGCAACACAGAA-GT
1 CAAATTCGCAACAC-GAATTT
* *
1232349 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACACGAAT-TT
*
1232369 CAAATTCGCAACACTGAA-GT
1 CAAATTCGCAACAC-GAATTT
* **
1232389 CAAATTCGCAACACAAAAAT
1 CAAATTCGCAACACGAATTT
* *
1232409 CAAATTTGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
**
1232431 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACACGA-ATTT
* * **
1232449 CAAATTAGCAACACAAAAGT
1 CAAATTCGCAACACGAATTT
*
1232469 CAAATTTGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
1232490 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
1232509 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
1232528 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
1232548 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
1232568 -AATTTCGCAACAC
1 CAAATTCGCAACAC
1232581 AAATGTTTTG
Statistics
Matches: 249, Mismatches: 44, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
18 2 0.01
19 63 0.25
20 152 0.61
21 29 0.12
22 3 0.01
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:1232752 original size:16 final size:15
Alignment explanation
Indices: 1232717--1232755 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1232707 TCTCCATCTC
*
1232717 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1232732 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1232748 TAATTTTT
1 TAATTTTT
1232756 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1233371 original size:12 final size:12
Alignment explanation
Indices: 1233350--1233383 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1233340 ACCACATTTC
*
1233350 CAATACCAAACA
1 CAATATCAAACA
1233362 CAATATCAAACA
1 CAATATCAAACA
*
1233374 CAATCTCAAA
1 CAATATCAAA
1233384 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1233536 original size:24 final size:24
Alignment explanation
Indices: 1233509--1233562 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1233499 GTATTCAAAA
1233509 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
1233533 TTTGATCTTGGTGAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1233557 TTTGAT
1 TTTGAT
1233563 GATGTTTCAG
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:0.17, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1236409 original size:37 final size:37
Alignment explanation
Indices: 1236363--1236448 Score: 172
Period size: 37 Copynumber: 2.3 Consensus size: 37
1236353 CTTTTACAAG
1236363 TCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCA
1 TCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCA
1236400 TCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCA
1 TCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCA
1236437 TCAATTAAACAA
1 TCAATTAAACAA
1236449 ATCAACTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (37 bp):
TCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCA
Found at i:1237857 original size:21 final size:21
Alignment explanation
Indices: 1237818--1237892 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
1237808 GTGAATCGGG
* **
1237818 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGACAGGGAC
*
1237839 C-CATTGAACGATGACAGGGGC
1 CTC-TTGAACGATGACAGGGAC
*
1237860 CTCTTGAACGATGAGA-GGAGC
1 CTCTTGAACGATGACAGGGA-C
1237881 CTCTTGAACGAT
1 CTCTTGAACGAT
1237893 AGGAGGCGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.07
21 41 0.91
22 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGAC
Found at i:1237898 original size:21 final size:21
Alignment explanation
Indices: 1237842--1237915 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1237832 GAGGGACCCA
* *
1237842 TTGAACGATGACAGGGGCCTC
1 TTGAACGATGAGAGGAGCCTC
1237863 TTGAACGATGAGAGGAGCCTC
1 TTGAACGATGAGAGGAGCCTC
*
1237884 TTGAACGAT-AGGAGGCGCCTC
1 TTGAACGATGA-GAGGAGCCTC
*
1237905 TTGAATGATGA
1 TTGAACGATGA
1237916 AAGGTGAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (21 bp):
TTGAACGATGAGAGGAGCCTC
Found at i:1238217 original size:21 final size:21
Alignment explanation
Indices: 1238193--1238242 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1238183 TGAAACAATC
* *
1238193 TCACGTAGAGCGGCTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
1238214 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
1238235 TCACGTAG
1 TCACGTAG
1238243 CACACCATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:1240057 original size:14 final size:14
Alignment explanation
Indices: 1240038--1240069 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1240028 ACGTGAAAAT
1240038 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
1240052 GAAAATCGCAACGC
1 GAAAATCGCAACGA
1240066 GAAA
1 GAAA
1240070 CTAAAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1240483 original size:20 final size:21
Alignment explanation
Indices: 1240458--1240515 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
1240448 TTTGAGAGAT
1240458 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
1240478 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* *
1240500 GAAGATGGGGACGGAT
1 GGAGAT-GAGACGGAT
1240516 GTCGTCGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
22 27 0.82
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:1240520 original size:22 final size:22
Alignment explanation
Indices: 1240465--1240522 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1240455 GATGGAGATA
* *
1240465 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGAAGATGGG
1240487 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGTCGAAGATGGG
*
1240509 GACGGATGTCGTCG
1 GACGGATTTCGTCG
1240523 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.43, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGAAGATGGG
Found at i:1240918 original size:20 final size:21
Alignment explanation
Indices: 1240893--1240985 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1240883 TTTTCCCAAT
*
1240893 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1240913 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1240934 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1240954 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1240975 TCGCAATGCGA
1 TCGCAATGCGA
1240986 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1240938 original size:41 final size:41
Alignment explanation
Indices: 1240893--1240985 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1240883 TTTTCCCAAT
1240893 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1240934 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1240975 TCGCAATGCGA
1 TCGCAATGCGA
1240986 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1240998 original size:41 final size:41
Alignment explanation
Indices: 1240912--1241046 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
1240902 GAATAAGTAA
* *
1240912 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1240953 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * *
1240994 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1241035 TTCGCAACGCGA
1 ATCGCAACGCGA
1241047 TTCTGACTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1240999 original size:20 final size:20
Alignment explanation
Indices: 1240974--1241067 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1240964 AATTGGGAAA
*
1240974 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1240994 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1241015 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1241035 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1241055 TTTGCAACGCGAT
1 ATCGCAACGCGAT
1241068 TTACATAGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.72
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1241618 original size:19 final size:19
Alignment explanation
Indices: 1241558--1241638 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1241548 TTCGAGAATG
1241558 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1241578 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
1241594 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1241611 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1241630 AAAATCGCA
1 AAAATCGCA
1241639 TTGCGATTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1241669 original size:19 final size:19
Alignment explanation
Indices: 1241634--1241817 Score: 156
Period size: 20 Copynumber: 10.1 Consensus size: 19
1241624 GAAACCAAAA
*
1241634 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
1241652 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1241671 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1241690 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1241710 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1241726 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1241743 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1241757 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1241776 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1241796 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1241816 TC
1 TC
1241818 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 17, Indels: 27
0.75 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 11 0.08
19 48 0.36
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1241691 original size:24 final size:20
Alignment explanation
Indices: 1241644--1241721 Score: 117
Period size: 19 Copynumber: 4.0 Consensus size: 20
1241634 TCGCATTGCG
1241644 ATTTCATTTCGCGTTGCGAT
1 ATTTCATTTCGCGTTGCGAT
1241664 -TTTCATTTCGCGTTGCGAT
1 ATTTCATTTCGCGTTGCGAT
*
1241683 -TTTTATTTCGCGGTTGCGAT
1 ATTTCATTTCGC-GTTGCGAT
1241703 -TTTCATTTCGCGTTGCGAT
1 ATTTCATTTCGCGTTGCGAT
1241722 TGTCTGGTCG
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
19 37 0.67
20 18 0.33
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (20 bp):
ATTTCATTTCGCGTTGCGAT
Found at i:1241703 original size:39 final size:38
Alignment explanation
Indices: 1241634--1241817 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
1241624 GAAACCAAAA
*
1241634 TCGCATTGCGA-TTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1241671 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1241710 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
1241743 TCGCGTTGTGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1241776 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1241816 TC
1 TC
1241818 AACCAAAAGA
Statistics
Matches: 121, Mismatches: 15, Indels: 20
0.78 0.10 0.13
Matches are distributed among these distances:
31 3 0.02
33 37 0.31
34 9 0.07
35 1 0.01
36 3 0.02
37 10 0.08
38 10 0.08
39 30 0.25
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1243879 original size:42 final size:42
Alignment explanation
Indices: 1243819--1243911 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1243809 GCCCGACTCG
* * *
1243819 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1243861 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
1243903 ACTGTCATC
1 CCTATCATC
1243912 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1245318 original size:14 final size:14
Alignment explanation
Indices: 1245298--1245334 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1245288 GATTGTTTAA
1245298 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
1245311 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
1245326 TTGATTTGT
1 TTGATTTGT
1245335 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1245535 original size:19 final size:19
Alignment explanation
Indices: 1245513--1245663 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1245503 CGAAATTAAA
1245513 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1245532 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1245547 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1245565 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1245579 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1245598 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1245613 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1245631 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1245650 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1245664 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1245559 original size:33 final size:32
Alignment explanation
Indices: 1245517--1245643 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1245507 ATTAAATTCG
1245517 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1245550 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1245583 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1245616 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1245644 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1245606 original size:66 final size:66
Alignment explanation
Indices: 1245510--1245642 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1245500 ACGCGAAATT
*
1245510 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1245575 G
66 G
*
1245576 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1245641 G
66 G
1245642 A
1 A
1245643 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1247947 original size:12 final size:12
Alignment explanation
Indices: 1247930--1247954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1247920 TCTTCGGGGA
1247930 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1247942 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1247954 C
1 C
1247955 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1249264 original size:20 final size:20
Alignment explanation
Indices: 1249239--1249296 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1249229 ATTCATTTGA
1249239 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1249259 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1249279 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1249297 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1249339 original size:14 final size:16
Alignment explanation
Indices: 1249319--1249392 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1249309 TGAAAATCGC
1249319 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1249334 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1249351 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1249370 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1249386 -TTGCGAT
1 ATTGCGAT
1249393 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1249356 original size:19 final size:19
Alignment explanation
Indices: 1249315--1249382 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1249305 GAAATGAAAA
1249315 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1249331 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1249348 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1249367 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1249383 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1251427 original size:20 final size:19
Alignment explanation
Indices: 1251392--1251447 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
1251382 CGAAACTTAA
1251392 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1251411 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
1251431 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
1251448 AAATCGTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1251453 original size:19 final size:19
Alignment explanation
Indices: 1251390--1251490 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1251380 CACGAAACTT
1251390 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
** *
1251409 CTATCGCAACGCGGAAATGG
1 AAATCGCAACGC-GAAATGA
** *
1251429 CTATCGCAATGCGAAATGA
1 AAATCGCAACGCGAAATGA
* *
1251448 AAATCGTAA--CG--A-CA
1 AAATCGCAACGCGAAATGA
1251462 AAATCGCAACGCGAAATG-
1 AAATCGCAACGCGAAATGA
1251480 AAATCGCAACG
1 AAATCGCAACG
1251491 ACAAAATCGC
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 12 0.18
19 22 0.34
20 17 0.26
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.14
Consensus pattern (19 bp):
AAATCGCAACGCGAAATGA
Found at i:1251466 original size:14 final size:14
Alignment explanation
Indices: 1251447--1251504 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1251437 ATGCGAAATG
*
1251447 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
1251461 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1251477 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1251493 AAAATCGCAACG
1 AAAATCGCAACG
1251505 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1251491 original size:32 final size:33
Alignment explanation
Indices: 1251431--1251509 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1251421 GGAAATGGCT
* *
1251431 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1251464 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1251496 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1251510 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1251557 original size:14 final size:14
Alignment explanation
Indices: 1251538--1251595 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1251528 TTTCATTTCG
1251538 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
1251552 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
*
1251568 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
1251584 CGTTGCGATTTT
1 CGTTGCGATTTT
1251596 CATTTTGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1251606 original size:33 final size:33
Alignment explanation
Indices: 1251521--1251611 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
1251511 ACAAATCGCA
* *
1251521 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1251554 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1251586 TTGCGATTTTCATTTTGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1251612 AGCCATTTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1251630 original size:20 final size:19
Alignment explanation
Indices: 1251596--1251640 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1251586 TTGCGATTTT
1251596 CATTTTGCATTGCGATAGC
1 CATTTTGCATTGCGATAGC
* *
1251615 CATTTCTGCGTTGCGATAGT
1 CATTT-TGCATTGCGATAGC
1251635 CATTTT
1 CATTTT
1251641 CGTTTTGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (19 bp):
CATTTTGCATTGCGATAGC
Found at i:1252154 original size:18 final size:18
Alignment explanation
Indices: 1252128--1252172 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1252118 GTCGATCAGA
*
1252128 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1252146 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1252164 TGATGGCTC
1 TGATGGCTC
1252173 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1253801 original size:22 final size:22
Alignment explanation
Indices: 1253776--1253819 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1253766 GATTTAGATA
1253776 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1253798 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1253820 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1254109 original size:20 final size:20
Alignment explanation
Indices: 1254007--1254117 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
1253997 GATTATGTAT
*
1254007 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1254027 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1254047 TATCGCGTTGCGA-AGTAAG
1 TATCGCGTTGCGATAGTCAG
* ***
1254066 TATC-CGTTGCGAT-TTTTT
1 TATCGCGTTGCGATAGTCAG
*
1254084 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1254104 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1254118 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
18 13 0.17
19 17 0.22
20 48 0.62
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1254135 original size:21 final size:21
Alignment explanation
Indices: 1254106--1254198 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
1254096 ATAGTCAGTA
1254106 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1254127 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1254147 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
1254168 TAGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1254188 TCGCATTGCGA
1 TCGCATTGCGA
1254199 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1254151 original size:41 final size:41
Alignment explanation
Indices: 1254106--1254198 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1254096 ATAGTCAGTA
*
1254106 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTAGCGTTGCGATTTACTTAT
1254147 TCGCATTGCGATTTTCCCAATTAGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTAGCGTTGCGATTTACTTAT
1254188 TCGCATTGCGA
1 TCGCATTGCGA
1254199 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTAGCGTTGCGATTTACTTAT
Found at i:1254465 original size:41 final size:40
Alignment explanation
Indices: 1254408--1254719 Score: 161
Period size: 40 Copynumber: 7.8 Consensus size: 40
1254398 TTATTTTCTC
1254408 TTGCGAATTTGACTATCGCGTTGCGAATTTGAAATTCA-GTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTG-AATT-ATGTG
*
1254449 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGAATTATGTG
** * * *
1254489 TTGCGAATTTGACT-TCTGTATTGCG-ATTTACAAATT-CGCG
1 TTGCGAATTTGACTATC-GCGTTGCGAATTT--GAATTATGTG
* * ** *
1254529 TTGCG-ATTT-ACAGATTCGCGTTGTGAATTTGGCTTTTGCT-
1 TTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGAATTATG-TG
** * *
1254569 TTGCGAATTTGACT-TCAGTATTGCGAATTTG-ACTATCGCG
1 TTGCGAATTTGACTATC-GCGTTGCGAATTTGAATTAT-GTG
**
1254609 TTGCGAATTTGACT-TCTTTGTTGCGAATTT-AACTTATGTG
1 TTGCGAATTTGACTATC-GCGTTGCGAATTTGAA-TTATGTG
* * *
1254649 TTGCG-ATTT-ACAAATTCTCGTTGCGAATTTCGAA--ACTGGG
1 TTGCGAATTTGAC-TA-TCGCGTTGCGAATTT-GAATTA-TGTG
* *
1254689 TTGCGAAATTGGAGT-TCGCGTTGCGAATTTG
1 TTGCG-AATTTGACTATCGCGTTGCGAATTTG
1254720 TTGGTCATTT
Statistics
Matches: 209, Mismatches: 36, Indels: 54
0.70 0.12 0.18
Matches are distributed among these distances:
38 4 0.02
39 23 0.11
40 125 0.60
41 49 0.23
42 7 0.03
43 1 0.00
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGAATTATGTG
Found at i:1254593 original size:60 final size:60
Alignment explanation
Indices: 1254529--1254678 Score: 157
Period size: 60 Copynumber: 2.5 Consensus size: 60
1254519 CAAATTCGCG
* * * *
1254529 TTGCGATTTACAGATTCGCGTTGTGAATTTGGC-T-TTTGCTTTGCGAATTTGACTTCA-GTA
1 TTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCTTTG--TTGCGAATTTAACTT-ATGTA
* *
1254589 TTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTTCTTTGTTGCGAATTTAACTTATGTG
1 TTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGACTTCTTTGTTGCGAATTTAACTTATGTA
*
1254649 TTGCGATTTACAAATTCTCGTTGCGAATTT
1 TTGCGATTTACAAATTCGCGTTGCGAATTT
1254679 CGAAACTGGG
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
58 2 0.03
59 6 0.08
60 56 0.74
61 6 0.08
62 6 0.08
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.43
Consensus pattern (60 bp):
TTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCTTTGTTGCGAATTTAACTTATGTA
Found at i:1254608 original size:80 final size:80
Alignment explanation
Indices: 1254464--1254654 Score: 214
Period size: 80 Copynumber: 2.4 Consensus size: 80
1254454 AATTTGACTA
*
1254464 TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACTTCTGTATTGCGATTTACAAATTCGCG
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACTTCAGTATTGCGATTTACAAATTCGCG
1254529 TTGCGATTTACAGAT
66 TTGCGATTTACAGAT
* * * *
1254544 TCGCGTTGTGAATTTGGCTTTTGCT-TTGCGAATTTGACTTCAGTATTGCGAATTTGAC-TA-TC
1 TCGCGTTGCGAATTTGACTTATG-TGTTGCGAATTTGACTTCAGTATTGCG-ATTT-ACAAATTC
1254606 GCGTTGCGAATTT---GACT
63 GCGTTGCG-ATTTACAGA-T
** *
1254623 TCTTTGTTGCGAATTTAACTTATGTGTTGCGA
1 TC-GCGTTGCGAATTTGACTTATGTGTTGCGA
1254655 TTTACAAATT
Statistics
Matches: 93, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
78 2 0.02
79 4 0.04
80 75 0.81
81 10 0.11
82 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (80 bp):
TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACTTCAGTATTGCGATTTACAAATTCGCG
TTGCGATTTACAGAT
Found at i:1254631 original size:20 final size:20
Alignment explanation
Indices: 1254408--1254654 Score: 172
Period size: 20 Copynumber: 12.3 Consensus size: 20
1254398 TTATTTTCTC
*
1254408 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGTG
* *
1254428 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTG-ACTTCTGTG
*
1254449 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGTG
*
1254469 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGTG
*
1254489 TTGCGAATTTGACTTCTGTA
1 TTGCGAATTTGACTTCTGTG
*
1254509 TTGCG-ATTT-ACAAATTC-GCG
1 TTGCGAATTTGAC---TTCTGTG
*
1254529 TTGCG-ATTT-ACAGATTC-GCG
1 TTGCGAATTTGAC---TTCTGTG
* * *
1254549 TTGTGAATTTGGCTTTTGCT-
1 TTGCGAATTTGACTTCTG-TG
* *
1254569 TTGCGAATTTGACTTCAGTA
1 TTGCGAATTTGACTTCTGTG
*
1254589 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGTG
*
1254609 TTGCGAATTTGACTTCTTTG
1 TTGCGAATTTGACTTCTGTG
* *
1254629 TTGCGAATTTAACTTATGTG
1 TTGCGAATTTGACTTCTGTG
1254649 TTGCGA
1 TTGCGA
1254655 TTTACAAATT
Statistics
Matches: 187, Mismatches: 26, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
18 2 0.01
19 10 0.05
20 148 0.79
21 26 0.14
22 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:1254919 original size:10 final size:10
Alignment explanation
Indices: 1254904--1254933 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1254894 ACTCATCTGT
1254904 GTTCGTTTAC
1 GTTCGTTTAC
*
1254914 GTTCGTTTAT
1 GTTCGTTTAC
1254924 GTTCGTTTAC
1 GTTCGTTTAC
1254934 ATCTGTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (10 bp):
GTTCGTTTAC
Found at i:1254946 original size:24 final size:21
Alignment explanation
Indices: 1254914--1254968 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 21
1254904 GTTCGTTTAC
*
1254914 GTTCGTTTATGTTCGTTTACATCT
1 GTTCGTTTATATTCG-TTA-AT-T
1254938 GTTCGTTTATATTCGTTAATT
1 GTTCGTTTATATTCGTTAATT
1254959 GTTCGTTTAT
1 GTTCGTTTAT
1254969 CATTTAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.37
22 2 0.07
23 3 0.10
24 14 0.47
ACGTcount: A:0.15, C:0.13, G:0.16, T:0.56
Consensus pattern (21 bp):
GTTCGTTTATATTCGTTAATT
Found at i:1257425 original size:3 final size:3
Alignment explanation
Indices: 1257417--1257471 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1257407 ATTCAACTGA
1257417 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1257465 -TT ATT AT
1 ATT ATT AT
1257472 AACAATAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1263088 original size:13 final size:13
Alignment explanation
Indices: 1263072--1263101 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1263062 ATAGTATATG
1263072 TATATATGTAAAC
1 TATATATGTAAAC
*
1263085 TATATATGTAACC
1 TATATATGTAAAC
1263098 TATA
1 TATA
1263102 GTATATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (13 bp):
TATATATGTAAAC
Found at i:1263182 original size:14 final size:15
Alignment explanation
Indices: 1263158--1263186 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1263148 CTATATATGT
1263158 AACATATAGTTTATA
1 AACATATAGTTTATA
1263173 AACA-ATAGTTTATA
1 AACATATAGTTTATA
1263187 TTAGTGTACT
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:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AACATATAGTTTATA
Found at i:1263222 original size:21 final size:21
Alignment explanation
Indices: 1263196--1263243 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1263186 ATTAGTGTAC
* *
1263196 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
1263217 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
1263238 TTTATA
1 TATATA
1263244 TTAATGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:1263316 original size:146 final size:153
Alignment explanation
Indices: 1263161--1263562 Score: 371
Period size: 157 Copynumber: 2.6 Consensus size: 153
1263151 TATATGTAAC
* * * * *
1263161 ATATAGTTTATAAACAATAGTTTATATTAGTGTACTATATAGTTTATAACCTATAG-TATA-TAA
1 ATATAGTTTATAAACAATAATTTATATTAATGTACTAGATAGTTTATAAACTATAGTTACATTAA
* *
1263224 T-TT-ATA-AACTATAGTTTATATTAATGTA-T-TAT-ATACTTAATATTAATGTTAATTATTTT
66 TATTAATATAACTATAGTTTATATTAATATAGTATATAATA-TTAATATTAATATTAATTATTTT
1263283 AACTATAATTTATATTAATATATT
130 AACTATAATTTATATTAATATATT
* * *
1263307 ATATAGTTTATAAACTATAATTTGTATTAATGTAGTAGATAGTTTATAAACTATAGTTTACATTA
1 ATATAGTTTATAAACAATAATTTATATTAATGTACTAGATAGTTTATAAACTATAG-TTACATTA
1263372 ATATTAACATATTAACTATAGTTTATATTAATATAGTATATAATATTAATATTAATATTAATTAT
65 ATATT-A-ATA-TAACTATAGTTTATATTAATATAGTATATAATATTAATATTAATATTAATTAT
** * * *
1263437 AGT--CTATAAATCATA-TACTATATT
127 TTTAACTATAATTTATATTAATATATT
* * * * * * * *
1263461 AATATTAATTATATTAACTATAGTTTATA--AACTGTACTATATAATTTATAAAATATAGTTTAT
1 -ATA-TAGTT-TATAAACAATAATTTATATTAA-TGTACTAGATAGTTTATAAACTATAG-TTAC
*
1263524 ATTAATATTAATTTTATAAACTATATTTTATATTAATAT
61 ATTAATATTAA---TAT-AACTATAGTTTATATTAATAT
1263563 TAATTACAAA
Statistics
Matches: 211, Mismatches: 25, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
146 49 0.23
148 3 0.01
149 4 0.02
150 2 0.01
153 3 0.01
154 9 0.04
155 37 0.18
156 41 0.19
157 60 0.28
158 3 0.01
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (153 bp):
ATATAGTTTATAAACAATAATTTATATTAATGTACTAGATAGTTTATAAACTATAGTTACATTAA
TATTAATATAACTATAGTTTATATTAATATAGTATATAATATTAATATTAATATTAATTATTTTA
ACTATAATTTATATTAATATATT
Found at i:1263325 original size:36 final size:36
Alignment explanation
Indices: 1263283--1263375 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
1263273 TAATTATTTT
* *
1263283 AACTATAATTTATATTAATATATTATATAGTTTATA
1 AACTATAATTTATATTAATATAGTAGATAGTTTATA
* *
1263319 AACTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATATAGTAGATAGTTTATA
* *
1263355 AACTATAGTTTACATTAATAT
1 AACTATAATTTATATTAATAT
1263376 TAACATATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGTAGATAGTTTATA
Found at i:1263416 original size:42 final size:44
Alignment explanation
Indices: 1263368--1263490 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 44
1263358 TATAGTTTAC
* * *
1263368 ATTAATATTAA-CATATTAACTATAGTTTATATTAATATAGTAT
1 ATTAATATTAATAATATTAACTATAGTTTATAATAATATACTAT
* * *
1263411 A-TAATATTAATATTAATATTAATTATAGTCTATAAATCATATACTAT
1 ATTAATATT-A-A-TAATATTAACTATAGTTTAT-AATAATATACTAT
*
1263458 ATTAATATTAATTATATTAACTATAGTTTATAA
1 ATTAATATTAATAATATTAACTATAGTTTATAA
1263491 ACTGTACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
42 7 0.11
43 2 0.03
44 3 0.05
45 17 0.26
46 17 0.26
47 12 0.18
48 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (44 bp):
ATTAATATTAATAATATTAACTATAGTTTATAATAATATACTAT
Found at i:1263419 original size:18 final size:15
Alignment explanation
Indices: 1263380--1263562 Score: 74
Period size: 15 Copynumber: 11.7 Consensus size: 15
1263370 TAATATTAAC
1263380 ATATTAACTATAGTTT
1 ATATTAA-TATAGTTT
*
1263396 ATATTAATATAGTAT
1 ATATTAATATAGTTT
* * *
1263411 ATAATATTAATA-TTA
1 ATATTAAT-ATAGTTT
*
1263426 ATATTAATTATAGTCT
1 ATATTAA-TATAGTTT
*
1263442 ATA--AATCATA-TACT
1 ATATTAAT-ATAGT-TT
*
1263456 ATATTAATATTA-ATT
1 ATATTAATA-TAGTTT
1263471 ATATTAACTATAGTTT
1 ATATTAA-TATAGTTT
*
1263487 ATAAACTGTACTATATAATTT
1 AT--A-T-TA--ATATAGTTT
*
1263508 ATA-AAATATAGTTT
1 ATATTAATATAGTTT
*
1263522 ATATTAATATTAATTT
1 ATATTAATA-TAGTTT
* *
1263538 -TATAAACTATATTTT
1 ATATTAA-TATAGTTT
1263553 ATATTAATAT
1 ATATTAATAT
1263563 TAATTACAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 41
0.68 0.11 0.22
Matches are distributed among these distances:
13 2 0.02
14 21 0.17
15 50 0.39
16 39 0.31
18 1 0.01
19 2 0.02
20 2 0.02
21 9 0.07
22 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATTAATATAGTTT
Found at i:1263421 original size:6 final size:6
Alignment explanation
Indices: 1263396--1263433 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1263386 ACTATAGTTT
*
1263396 ATATTA ATA-TA GTATATA ATATTA ATATTA ATATTA AT
1 ATATTA ATATTA ATAT-TA ATATTA ATATTA ATATTA AT
1263434 TATAGTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 19 0.68
7 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:1263437 original size:24 final size:24
Alignment explanation
Indices: 1263368--1263437 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
1263358 TATAGTTTAC
* *
1263368 ATTAATATTAACATATTAACTATAGT
1 ATTAATATT-A-ATATTAATTATAAT
*
1263394 -TT-ATATTAATA-TAGTATATAAT
1 ATTAATATTAATATTAAT-TATAAT
1263416 ATTAATATTAATATTAATTATA
1 ATTAATATTAATATTAATTATA
1263438 GTCTATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 2 0.06
22 8 0.22
23 3 0.08
24 18 0.50
25 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
ATTAATATTAATATTAATTATAAT
Found at i:1263516 original size:14 final size:14
Alignment explanation
Indices: 1263499--1263555 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1263489 AAACTGTACT
1263499 ATATAATTTATAAA
1 ATATAATTTATAAA
* *
1263513 ATATAGTTTATATTA
1 ATATAATTTATA-AA
1263528 ATATTAATTTTATAAA
1 ATA-TAA-TTTATAAA
* *
1263544 CTATATTTTATA
1 ATATAATTTATA
1263556 TTAATATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 17 0.50
15 6 0.18
16 5 0.15
17 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATAATTTATAAA
Found at i:1263533 original size:6 final size:6
Alignment explanation
Indices: 1263522--1263644 Score: 50
Period size: 6 Copynumber: 21.2 Consensus size: 6
1263512 AATATAGTTT
* * * *
1263522 ATATTA ATATTA ATTTTA TAAACT- ATATTTT ATATTA ATATT- A-ATTA
1 ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA ATATTA
* * *
1263569 CAAATTA CAAATT- ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATTA
1 -ATATTA -ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
1263615 AT-TATA ATCTATA AT-TT- ATATTA ATATTA A
1 ATAT-TA ATAT-TA ATATTA ATATTA ATATTA A
1263645 GTATAAGTGA
Statistics
Matches: 94, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
4 5 0.05
5 22 0.23
6 46 0.49
7 21 0.22
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:1263543 original size:31 final size:31
Alignment explanation
Indices: 1263455--1263567 Score: 129
Period size: 31 Copynumber: 3.5 Consensus size: 31
1263445 AATCATATAC
* *
1263455 TATATTAATATTAATTATATTAACTATAGTT
1 TATATTAATATTAATTTTATAAACTATAGTT
* *
1263486 TATAAACTGTACTATATAA-TTTATAAAATATAGTT
1 TAT--A-T-TAATAT-TAATTTTATAAACTATAGTT
*
1263521 TATATTAATATTAATTTTATAAACTATATTT
1 TATATTAATATTAATTTTATAAACTATAGTT
1263552 TATATTAATATTAATT
1 TATATTAATATTAATT
1263568 ACAAATTACA
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
30 3 0.04
31 38 0.55
32 1 0.01
33 2 0.03
34 1 0.01
35 21 0.30
36 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (31 bp):
TATATTAATATTAATTTTATAAACTATAGTT
Found at i:1263611 original size:50 final size:52
Alignment explanation
Indices: 1263553--1263652 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 52
1263543 ACTATATTTT
1263553 ATATTAATATTAATTACAAAT-TACAAATTATATT-ATATTAA-TATAAGTTA
1 ATATTAATATTAATTA-AAATCTACAAATTATATTAATATTAAGTATAAGTTA
* * *
1263603 ATATTAATATTAATTATAATCTATAATTTATATTAATATTAAGTATAAGT
1 ATATTAATATTAATTAAAATCTACAAATTATATTAATATTAAGTATAAGT
1263653 GATAATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 3 0.07
50 27 0.61
51 7 0.16
52 7 0.16
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (52 bp):
ATATTAATATTAATTAAAATCTACAAATTATATTAATATTAAGTATAAGTTA
Found at i:1263635 original size:23 final size:23
Alignment explanation
Indices: 1263585--1263639 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1263575 ACAAATTATA
1263585 TTATATTAA-TATAAGTTAATAT
1 TTATATTAATTATAAGTTAATAT
*
1263607 TAATATTAATTATAA-TCT-ATAAT
1 TTATATTAATTATAAGT-TAAT-AT
1263630 TTATATTAAT
1 TTATATTAAT
1263640 ATTAAGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATATTAATTATAAGTTAATAT
Found at i:1263637 original size:29 final size:29
Alignment explanation
Indices: 1263594--1263667 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
1263584 ATTATATTAA
* *
1263594 TATAAGTTAATATTAATATTAATTATAA-T
1 TATAA-TTTATATTAATATTAAGTATAAGT
1263623 CTATAATTTATATTAATATTAAGTATAAGT
1 -TATAATTTATATTAATATTAAGTATAAGT
*
1263653 GATAATTTATATTAA
1 TATAATTTATATTAA
1263668 CACTATTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 34 0.85
30 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (29 bp):
TATAATTTATATTAATATTAAGTATAAGT
Found at i:1263663 original size:79 final size:79
Alignment explanation
Indices: 1263512--1263666 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 79
1263502 TAATTTATAA
* * * *
1263512 AATATAGTTTATATTAATATTAATTTTATAAACTATATTTTATATTAATATTAATTACAAATTAC
1 AATATAGTTAATATTAATATTAA-TTTATAAACTATAATTTATATTAATATTAAGTACAAATGAC
1263577 AAATTATATTATATT
65 AAATTATATTATATT
* * * *
1263592 AATATAAGTTAATATTAATATTAA-TTATAATCTATAATTTATATTAATATTAAGTATAAGTGAT
1 AATAT-AGTTAATATTAATATTAATTTATAAACTATAATTTATATTAATATTAAGTACAAATGAC
*
1263656 AATTTATATTA
65 AAATTATATTA
1263667 ACACTATTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
79 43 0.66
80 5 0.08
81 17 0.26
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (79 bp):
AATATAGTTAATATTAATATTAATTTATAAACTATAATTTATATTAATATTAAGTACAAATGACA
AATTATATTATATT
Found at i:1264389 original size:6 final size:6
Alignment explanation
Indices: 1264372--1264454 Score: 69
Period size: 6 Copynumber: 14.0 Consensus size: 6
1264362 TTCTGTAACT
* * * ** *
1264372 CAAACC CGAACC CAAACC CGAACC CAAATC TGAACC CAAATC CAAA-C
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC
* * * *
1264419 CAAACC CATACC CAAACC AAAATC CAAACC CGAACC
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAAACC
1264455 TAAAAAACCT
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
5 5 0.09
6 53 0.91
ACGTcount: A:0.46, C:0.43, G:0.05, T:0.06
Consensus pattern (6 bp):
CAAACC
Found at i:1264389 original size:12 final size:12
Alignment explanation
Indices: 1264372--1264454 Score: 80
Period size: 12 Copynumber: 7.0 Consensus size: 12
1264362 TTCTGTAACT
1264372 CAAACCCGAACC
1 CAAACCCGAACC
1264384 CAAACCCGAACC
1 CAAACCCGAACC
* *
1264396 CAAATCTGAACC
1 CAAACCCGAACC
* *
1264408 CAAATCC-AAAC
1 CAAACCCGAACC
1264419 CAAACCC-ATACC
1 CAAACCCGA-ACC
** *
1264431 CAAACCAAAATC
1 CAAACCCGAACC
1264443 CAAACCCGAACC
1 CAAACCCGAACC
1264455 TAAAAAACCT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
11 10 0.17
12 47 0.81
13 1 0.02
ACGTcount: A:0.46, C:0.43, G:0.05, T:0.06
Consensus pattern (12 bp):
CAAACCCGAACC
Found at i:1264795 original size:19 final size:21
Alignment explanation
Indices: 1264771--1264815 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1264761 GTTCATTCAT
*
1264771 TTTGTTTATTTTAA-T-ATTG
1 TTTGTTTATTATAATTCATTG
*
1264790 TTTGTTTGTTATAATTCATTG
1 TTTGTTTATTATAATTCATTG
1264811 TTTGT
1 TTTGT
1264816 ATAACTGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 1 0.05
21 9 0.41
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (21 bp):
TTTGTTTATTATAATTCATTG
Found at i:1265133 original size:36 final size:36
Alignment explanation
Indices: 1265093--1265482 Score: 254
Period size: 38 Copynumber: 10.6 Consensus size: 36
1265083 ACGGTTTTCT
* * * *
1265093 AAAATATGTATACTATATAGTTTCGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
* *
1265129 AAAATATATATATTATATAGTTTT-AAAAAATTTTG
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
* * *
1265164 AAAACATATATAATGTATAATTTTTGAAAATGC-TTTTG
1 AAAATATATATAATATAT-AGTTTTGAAAA--CATTTTG
*
1265202 AAAATATATATAATATATAGTTTTGAAATCATTTTG
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
*
1265238 AATATATATATATATATATATATATATAGTTTTTAAAACATTTTTTG
1 -----A-A-A-ATATATATA-ATATATAGTTTTGAAAACA--TTTTG
*
1265285 AAAACT-TATATAATATATAGTTTTTAAAACATTTTTG
1 AAAA-TATATATAATATATAGTTTTGAAAACA-TTTTG
*
1265322 AAAA-ATTATATAATATATAGTTTTAAAAACATATTTTG
1 AAAATA-TATATAATATATAGTTTTGAAAAC--ATTTTG
1265360 AAAACT-TATAT-A-ATAT--TTTT-AAATTA-ATTTTG
1 AAAA-TATATATAATATATAGTTTTGAAA--ACATTTTG
* *** *
1265392 AAAA-CTATATAATATATAGTTTTG-AATTTTTTTT
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
* * *
1265426 AAAA-AAATATAATATATAG-TTTAAAAATATTTTTG
1 AAAATATATATAATATATAGTTTTGAAAACA-TTTTG
* *
1265461 -AAATATATATATTACATAGTTT
1 AAAATATATATAATATATAGTTT
1265483 ATATTATATT
Statistics
Matches: 289, Mismatches: 29, Indels: 72
0.74 0.07 0.18
Matches are distributed among these distances:
31 5 0.02
32 11 0.04
33 10 0.03
34 31 0.11
35 48 0.17
36 37 0.13
37 47 0.16
38 54 0.19
39 8 0.03
40 2 0.01
41 2 0.01
42 2 0.01
43 1 0.00
44 9 0.03
45 17 0.06
47 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTGAAAACATTTTG
Found at i:1265246 original size:2 final size:2
Alignment explanation
Indices: 1265239--1265265 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1265229 ATCATTTTGA
1265239 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 A
1265266 GTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1265320 original size:37 final size:36
Alignment explanation
Indices: 1265252--1265482 Score: 217
Period size: 37 Copynumber: 6.5 Consensus size: 36
1265242 TATATATATA
1265252 TATATATATATATAGTTTTTAAAACATTTTTTGAAAAC
1 TATATA-ATATATAGTTTTTAAAACA-TTTTTGAAAAC
*
1265290 TTATATAATATATAGTTTTTAAAACATTTTTGAAAAAT
1 -TATATAATATATAGTTTTTAAAACATTTTTG-AAAAC
*
1265328 TATATAATATATAGTTTTAAAAACATATTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACAT-TTTTGAAAAC
** *
1265365 T-TAT-ATA-ATA-TTTTTAAATTAATTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
* ** * *
1265397 TATATAATATATAG-TTTT-GAATTTTTTTTAAAAA
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
* * *
1265431 AATATAATATATAG-TTTAAAAATATTTTTGAAATA-
1 TATATAATATATAGTTTTTAAAACATTTTTGAAA-AC
* *
1265466 TATATATTACATAGTTT
1 TATATAATATATAGTTT
1265483 ATATTATATT
Statistics
Matches: 162, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
32 11 0.07
33 11 0.07
34 32 0.20
35 32 0.20
36 6 0.04
37 36 0.22
38 28 0.17
39 6 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
Done.