Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008796.1 Hibiscus syriacus cultivar Beakdansim tig00111941_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: 1607457
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 7
Found at i:963132 original size:2 final size:2
Alignment explanation
Indices: 963125--963156 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
963115 CAAACTATCC
963125 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
963157 TCTTTCAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:964228 original size:74 final size:76
Alignment explanation
Indices: 964058--964262 Score: 290
Period size: 75 Copynumber: 2.7 Consensus size: 76
964048 CCGTTGTACA
* * * * *
964058 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCAGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAG
* *
964122 CAAAACTATTT
66 CAAAACCATTC
*
964133 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAG
*
964197 CCAAACCATTC
66 CAAAACCATTC
* *
964208 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
964263 TTTTTGGCTT
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
74 21 0.18
75 95 0.81
76 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAG
CAAAACCATTC
Found at i:964876 original size:17 final size:17
Alignment explanation
Indices: 964854--964897 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
964844 TTCATAAATC
964854 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
964871 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
964888 -AAATATCCAA
1 CAAA-ATCCAA
964898 AAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:964889 original size:9 final size:8
Alignment explanation
Indices: 964849--964900 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
964839 CACTATTCAT
964849 AAATCC-A
1 AAATCCAA
964856 AAATCCAA
1 AAATCCAA
*
964864 CAATCCACA
1 AAATCCA-A
964873 AAAT-CAA
1 AAATCCAA
964880 ACAATCCAA
1 A-AATCCAA
964889 AATATCCAA
1 AA-ATCCAA
964898 AAA
1 AAA
964901 GTTGAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 8 0.21
8 14 0.37
9 16 0.42
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATCCAA
Found at i:966895 original size:21 final size:23
Alignment explanation
Indices: 966823--966895 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
966813 CAGAACCCCA
* *
966823 GGGGGGTATCGATTCCCCTGT--G
1 GGGGGGAATCGGTTCCCCT-TCAG
*
966845 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAG
*
966868 AGGGGGAATCGGTT-CCC-TCAG
1 GGGGGGAATCGGTTCCCCTTCAG
966889 GGGGGGA
1 GGGGGGA
966896 TCAATTCCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.23
22 20 0.47
23 13 0.30
ACGTcount: A:0.15, C:0.22, G:0.42, T:0.21
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAG
Found at i:972840 original size:75 final size:76
Alignment explanation
Indices: 972677--972880 Score: 263
Period size: 74 Copynumber: 2.7 Consensus size: 76
972667 GTTGTACAAT
* * * *
972677 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACT-GAAATTCTCGGAGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATTCTCGGAGC
** *
972740 AAAACTGTTTA
66 AAAACCATTCA
*
972751 GGGGGAATCGGTTCCTCCTAT-GGGGGAATTGGTTCCCTCCGAGCATTCTGGAAA-TCTCGGAGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATTCTCGGAGC
*
972814 CAAACCATTCA
66 AAAACCATTCA
* *
972825 GGGGGGAATCGGTTCCTCCTATGAGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 -GGGGGAATCGGTTCCTCCTATG-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
972881 TTTTTGGCTT
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
74 58 0.51
75 26 0.23
77 29 0.26
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATTCTCGGAGC
AAAACCATTCA
Found at i:975251 original size:31 final size:31
Alignment explanation
Indices: 975200--975355 Score: 231
Period size: 31 Copynumber: 5.0 Consensus size: 31
975190 CCCGAAGGAC
* * * *
975200 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
* *
975231 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
*
975262 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
975293 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
* *
975324 CAGTCCATATATCCCGAAGAAAATAGATAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
975355 C
1 C
975356 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATATATCCCGAAGAACATAGGTAAA
Found at i:978766 original size:3 final size:3
Alignment explanation
Indices: 978758--978806 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
978748 GTAAAATGTA
* *
978758 AAT AAT AAT AAT AAT AAT AAC AAT AA- AAT -TT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
978804 AAT
1 AAT
978807 TAAAATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 3 0.08
3 37 0.93
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:978793 original size:19 final size:20
Alignment explanation
Indices: 978758--978807 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
978748 GTAAAATGTA
*
978758 AATAATAATAATAATAATAAC
1 AATAATAAT-TTAATAATAAC
*
978779 AATAA-AATTTAATAATAAT
1 AATAATAATTTAATAATAAC
978798 AATAATAATT
1 AATAATAATT
978808 AAAATATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 14 0.54
20 7 0.27
21 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAATAATTTAATAATAAC
Found at i:978813 original size:9 final size:10
Alignment explanation
Indices: 978760--978813 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 10
978750 AAAATGTAAA
978760 TAATAATAA-
1 TAATAATAAT
978769 TAATAATAA-
1 TAATAATAAT
*
978778 CAATAA-AATT
1 TAATAATAA-T
978788 TAATAATAA-
1 TAATAATAAT
978797 TAATAATAAT
1 TAATAATAAT
978807 TAA-AATA
1 TAATAATA
978814 TAACAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 2 0.05
9 27 0.69
10 8 0.21
11 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
TAATAATAAT
Found at i:979277 original size:134 final size:135
Alignment explanation
Indices: 979031--979328 Score: 402
Period size: 134 Copynumber: 2.2 Consensus size: 135
979021 GTTCTTACAT
* * * * * *
979031 GATGAGGAAATTTGGTCGTGGGATG-CTACTGCTCATACGTGATGAAGATTTCTTGGCCATCTTT
1 GATGAGGAGATCTGGTCGGGGGATGAC-ACGGCTCATACGTGATGAAGAGTTCTTAGCCATCTTT
* * * *
979095 AGGAAGGGTGACAACTCAGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTT
65 AGGAAGGGTAACAACACAGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTGACACGGCTC
979160 CTACGC
130 CTACGC
979166 GATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTC-TAGCCATCTTTA
1 GATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTA
* * * * * *
979230 GGTAGGGTAATAACACGGTTCCTACGCGATGAGGACGGCTGATTATCTATGGTTGACGCGGCTCC
66 GGAAGGGTAACAACACAGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTGACACGGCTCC
979295 TACGC
131 TACGC
* * *
979300 GATGAGGAGGTCTGGTCAGGGTATGACAC
1 GATGAGGAGATCTGGTCGGGGGATGACAC
979329 AGTTCCTATG
Statistics
Matches: 143, Mismatches: 19, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
134 97 0.68
135 45 0.31
136 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.26
Consensus pattern (135 bp):
GATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTA
GGAAGGGTAACAACACAGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTGACACGGCTCC
TACGC
Found at i:979360 original size:134 final size:134
Alignment explanation
Indices: 979031--979365 Score: 361
Period size: 134 Copynumber: 2.5 Consensus size: 134
979021 GTTCTTACAT
* * * * * * *
979031 GATGAGGAAATTTGGTC-GTGGGATG-CTACTGCTCATACGTGATGAAGATTTCTTGGCCATCTT
1 GATGAGGAGATCTGGTCAG-GGGATGAC-ACAGCTCATACGTGATGAAGAGTAC-TAGACATCTT
* * *
979094 TAGGAAGGGTGACAACTCAGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGGCT
63 TAGGAAGGGTAACAACACAGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTGACACGGCT
*
979159 TCTACGC
128 CCTACGC
* * * *
979166 GATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTAGCCATCTTTAG
1 GATGAGGAGATCTGGTCAGGGGATGACACAGCTCATACGTGATGAAGAGTACTAGACATCTTTAG
* * * * * *
979231 GTAGGGTAATAACACGGTTCCTACGCGATGAGGACGGCTGATTATCTATGGTTGACGCGGCTCCT
66 GAAGGGTAACAACACAGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTGACACGGCTCCT
979296 ACGC
131 ACGC
* * * * * * *
979300 GATGAGGAGGTCTGGTCAGGGTATGACACAGTTCCTATGTGATGAGGA-TAACTTGACATCTTTA
1 GATGAGGAGATCTGGTCAGGGGATGACACAGCTCATACGTGATGAAGAGT-ACTAGACATCTTTA
979364 GG
65 GG
979366 GATTTTGGTT
Statistics
Matches: 171, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
133 1 0.01
134 124 0.73
135 44 0.26
136 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (134 bp):
GATGAGGAGATCTGGTCAGGGGATGACACAGCTCATACGTGATGAAGAGTACTAGACATCTTTAG
GAAGGGTAACAACACAGTTCCTACGCGATGAGGACGGCTGATTATCTAGGGGTGACACGGCTCCT
ACGC
Found at i:979413 original size:28 final size:28
Alignment explanation
Indices: 979373--979435 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
979363 AGGGATTTTG
* * *
979373 GTTTCAAGGAAAACCAACTCAACGATTT
1 GTTTCAAGAAAAACAAACTCAAAGATTT
*
979401 GTTTCAATAAAAACAAACTCAAAGATTT
1 GTTTCAAGAAAAACAAACTCAAAGATTT
979429 GTTTCAA
1 GTTTCAA
979436 AAGCAACGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (28 bp):
GTTTCAAGAAAAACAAACTCAAAGATTT
Found at i:979628 original size:66 final size:63
Alignment explanation
Indices: 979444--979628 Score: 153
Period size: 66 Copynumber: 2.8 Consensus size: 63
979434 AAAAGCAACG
* *
979444 GTCTCCAAAGAGACGAAATTTGTTTCAAGGGAAATGA-CTC-ATAGATGATT-TTTAAAGGAAGT
1 GTCT-CAAAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAT-GATG-TTGTTTAAAGGAAGT
979506 T
63 T
* * * * * * * **
979507 GTCTCAAGCGAGATAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGTTCGGTGTTTCATGGGAAA
1 GTCTCAA-AGAGACAAAATTTG-TTTCAAGGGAAACGATCTCAATGAT-GTTGTTT-AAAGG-AA
979572 G-T
61 GTT
979574 GTCTCAAATGAGACAAAATTTGTTTCAAGGGAAACGATCTCAATGATGTTTGTTT
1 GTCTCAAA-GAGACAAAATTTGTTTCAAGGGAAACGATCTCAATGATG-TTGTTT
979629 TATTTCAAGG
Statistics
Matches: 94, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
62 3 0.03
63 15 0.16
64 12 0.13
65 7 0.07
66 31 0.33
67 23 0.24
68 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (63 bp):
GTCTCAAAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAATGATGTTGTTTAAAGGAAGTT
Found at i:980046 original size:31 final size:31
Alignment explanation
Indices: 979963--980038 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
979953 GATAAAATTA
* * *
979963 ATTTCAAGGGAAAC-GATTCAAAGATGGTTTT
1 ATTTCAAGAGAAACAAACTCAAAGAT-GTTTT
979994 ATTTCAAGAGAAACAAACTCAAAGAT-TTTGT
1 ATTTCAAGAGAAACAAACTCAAAGATGTTT-T
*
980025 ATTTCTAGAGAAAC
1 ATTTCAAGAGAAAC
980039 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 27 0.69
32 9 0.23
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (31 bp):
ATTTCAAGAGAAACAAACTCAAAGATGTTTT
Found at i:980154 original size:29 final size:29
Alignment explanation
Indices: 980122--980372 Score: 136
Period size: 29 Copynumber: 8.4 Consensus size: 29
980112 AAGATAGGTA
*
980122 TTTCAAAAGAAATGACTCAAAGATTTTTG
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
**
980151 TTTCAAAAGAAACGACTTGAA-ATTTTT-
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
* ** * *
980178 TTACAAAA-AATTGTCTCAAGCAAGACAAAATTTTG
1 TTTCAAAAGAAACGACTC-A--AAG----ATTTTTG
* * *
980213 TTTCAAAATAGACAGACTCAAA-A-TTGT-
1 TTTCAAAAGAAAC-GACTCAAAGATTTTTG
* *
980240 TTTCAAAAGAAACAACTCAAAGATTTTTA
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
* * *
980269 TTTCAAAAGAAACAACTCACAGACTTTTG
1 TTTCAAAAGAAACGACTCAAAGATTTTTG
*
980298 TTTCAAGAGAAACAGACTCAAAGATAGGTTTTG
1 TTTCAAAAGAAAC-GACTCAAAGAT---TTTTG
** * *
980331 TTTCAAGGGAAACAATCTCAAAGATGTTTG
1 TTTCAAAAGAAACGA-CTCAAAGATTTTTG
* *
980361 TTTTAAGAGAAA
1 TTTCAAAAGAAA
980373 TTGTCTCAAA
Statistics
Matches: 171, Mismatches: 32, Indels: 37
0.71 0.13 0.15
Matches are distributed among these distances:
26 12 0.07
27 19 0.11
28 12 0.07
29 59 0.35
30 22 0.13
32 1 0.01
33 26 0.15
34 7 0.04
35 7 0.04
36 2 0.01
37 4 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TTTCAAAAGAAACGACTCAAAGATTTTTG
Found at i:980330 original size:33 final size:30
Alignment explanation
Indices: 980240--980372 Score: 146
Period size: 29 Copynumber: 4.4 Consensus size: 30
980230 TCAAAATTGT
* *
980240 TTTCAAAAGAAACAACTCAAAGAT-TTTTA
1 TTTCAAGAGAAACAACTCAAAGATGTTTTG
* * *
980269 TTTCAAAAGAAACAACTCACAGA-CTTTTG
1 TTTCAAGAGAAACAACTCAAAGATGTTTTG
980298 TTTCAAGAGAAACAGACTCAAAGATAGGTTTTG
1 TTTCAAGAGAAACA-ACTCAAAGAT--GTTTTG
*
980331 TTTCAAGGGAAACAATCTCAAAGATG-TTTG
1 TTTCAAGAGAAACAA-CTCAAAGATGTTTTG
*
980361 TTTTAAGAGAAA
1 TTTCAAGAGAAA
980373 TTGTCTCAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
29 39 0.43
30 22 0.24
31 1 0.01
32 1 0.01
33 27 0.30
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTG
Found at i:980372 original size:63 final size:58
Alignment explanation
Indices: 980236--980372 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 58
980226 AGACTCAAAA
* *
980236 TTGTTTTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCACAGACTT
1 TTGTTTT-AAGAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCAAAGACTT
* * **
980295 TTGTTTCAAGAGAAACAGACTCAAAGATAGGTTTTGTTTCAAGGGAAACAATCTCAAAGA-TGT
1 TTGTTTTAAGAGAAACA-ACTCAAAGAT---TTTTATTTCAAAAGAAACAA-CTCAAAGACT-T
980358 TTGTTTTAAGAGAAA
1 TTGTTTTAAGAGAAA
980373 TTGTCTCAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 9 0.14
59 16 0.25
62 18 0.28
63 22 0.34
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (58 bp):
TTGTTTTAAGAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCAAAGACTT
Found at i:980480 original size:66 final size:62
Alignment explanation
Indices: 980326--980555 Score: 234
Period size: 66 Copynumber: 3.6 Consensus size: 62
980316 CAAAGATAGG
* * *
980326 TTTTGTTTCAAGGGAAACA-ATCTCAAAGATGTTTGTTTTAAGAGAAATTGTCTCAAAATAGACA
1 TTTTGTTTCAA-AGAAACATA-CTCAAAGA--TTT-TTTTAAAAGAAACTGTCTCAAAA-AGACA
980390 AAA
60 AAA
* *
980393 CTTTGTTTTCATAA-AAACATACTCAAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGACAA
1 TTTTG-TTTCA-AAGAAACATACTCAAAGATTTTT-TT-AAAAGAAACTGTCTCAAAA-AGACAA
980457 AA
61 AA
* * * *
980459 TTTTATTTCCAAAGAAGCATACTCAAAGATTCTTTTAAAAGAAACTTTCTCAAAAAGAC--AA
1 TTTTGTTT-CAAAGAAACATACTCAAAGATTTTTTTAAAAGAAACTGTCTCAAAAAGACAAAA
980520 TTTTGTTATCAAAGAAACATACTCAAAGATTTTTTT
1 TTTTGTT-TCAAAGAAACATACTCAAAGATTTTTTT
980556 TTGTGTTTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 22
0.79 0.08 0.12
Matches are distributed among these distances:
61 33 0.24
62 1 0.01
63 4 0.03
64 19 0.14
65 12 0.09
66 47 0.34
67 17 0.12
68 6 0.04
69 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (62 bp):
TTTTGTTTCAAAGAAACATACTCAAAGATTTTTTTAAAAGAAACTGTCTCAAAAAGACAAAA
Found at i:980769 original size:36 final size:35
Alignment explanation
Indices: 980716--980853 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 35
980706 ATAATTTGGA
980716 AAATTGTCTCAAGTGAGACAATATTTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGACAA-ATTTGTTTTTAGAG
* * *
980752 AAATTGTTTCAAATGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGAC-AAATTTGTTTTTAGAG
980788 AAATTGTCTCAAGTGAGACAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGTGAGACAAA-TTTGTTTTTAGAG
** *
980823 AAAACGATCTCAAGTGAGATCAACTTTGTTT
1 AAATTG-TCTCAAGTGAGA-CAAATTTGTTT
980854 AATGTGAAAC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
35 10 0.11
36 74 0.83
37 5 0.06
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (35 bp):
AAATTGTCTCAAGTGAGACAAATTTGTTTTTAGAG
Found at i:980973 original size:106 final size:105
Alignment explanation
Indices: 980820--981032 Score: 286
Period size: 106 Copynumber: 2.0 Consensus size: 105
980810 GTTTGTTTTT
* * *
980820 GAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTTGAAATTTGTATTCTC
1 GAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA-TATC
*
980885 AAAGG-AAAATGTCTCAAACGATACGAAATTTGTTTTGAAA
65 AAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
* * * * *
980925 GAGATAACAATCTCATGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATAT
1 GAGAAAACAATCTCAAGTGAGATCAA-CTTTGTTT-AATGTGAAACAAATTCGAAATTTGTATAT
**
980989 CAAAGGAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAA
64 CAAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
981031 GA
1 GA
981033 AAATGTCTCA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
105 30 0.32
106 62 0.66
107 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (105 bp):
GAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATATCA
AAGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
Found at i:981041 original size:36 final size:36
Alignment explanation
Indices: 980996--981134 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
980986 TATCAAAGGA
* *
980996 AAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAAG
1 AAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAG
*
981032 AAAATGTCTCAAGTGAGACAAAATTTGTTTT--AAG
1 AAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAG
*
981066 AAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGAG
1 AAAA-TGTCTCAAGCGAGACAAAATTTGTTTTGAAAG
*
981103 AAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 AAAATGTCTCAAGCGAGAC-AAAATTTGTTTT
981135 AAAATTCTCA
Statistics
Matches: 95, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
34 7 0.07
35 26 0.27
36 45 0.47
37 17 0.18
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (36 bp):
AAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAG
Found at i:981075 original size:71 final size:72
Alignment explanation
Indices: 980994--981136 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 72
980984 TATATCAAAG
* * *
980994 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAAGAAAATGTCTCAAGTGAGAC-AAAATTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAAATGTCTCAAGCGAGACAAAAATTT
981058 GTTTTAA
66 GTTTTAA
* * *
981065 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAAATTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAAATGTCTCAAGCGAGACAAAAATTT
981130 GTTTTAA
66 GTTTTAA
981137 AATTCTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 51 0.78
72 14 0.22
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (72 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAAATGTCTCAAGCGAGACAAAAATTT
GTTTTAA
Found at i:981667 original size:14 final size:15
Alignment explanation
Indices: 981637--981671 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
981627 ATTTGTTTTC
981637 TTTGCCCCATCAAAAT
1 TTTGCCCCA-CAAAAT
981653 TTTGCCCCA-AAAAT
1 TTTGCCCCACAAAAT
981667 TTTGC
1 TTTGC
981672 TTATCTTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
16 9 0.47
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (15 bp):
TTTGCCCCACAAAAT
Found at i:988134 original size:3 final size:3
Alignment explanation
Indices: 988126--988174 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
988116 ATAAAATGTA
* * *
988126 AAT AAT AAT AAT AAT AAC AAC AA- AAT -TT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
988172 AAT
1 AAT
988175 TAAATATAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:988183 original size:22 final size:22
Alignment explanation
Indices: 988132--988180 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
988122 TGTAAATAAT
*
988132 AATAATAATAACAACAAAATTT
1 AATAATAATAACAACAAAATTA
* *
988154 AATAATAATAATAATAATAATTA
1 AATAATAATAACAACAA-AATTA
988177 AATA
1 AATA
988181 TAACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAATAACAACAAAATTA
Found at i:996846 original size:28 final size:28
Alignment explanation
Indices: 996814--996868 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
996804 CTCCGCTTAT
* *
996814 ATTATGTCGTCGAGTAAGTGCTTGAAAC
1 ATTATGCCGTCAAGTAAGTGCTTGAAAC
* *
996842 ATTATGCCGTTAAGTTAGTGCTTGAAA
1 ATTATGCCGTCAAGTAAGTGCTTGAAA
996869 GCAACGATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (28 bp):
ATTATGCCGTCAAGTAAGTGCTTGAAAC
Found at i:1007450 original size:14 final size:14
Alignment explanation
Indices: 1007431--1007459 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1007421 AGTCTCTCTA
1007431 TAGACAATTACATG
1 TAGACAATTACATG
1007445 TAGACAATTACATG
1 TAGACAATTACATG
1007459 T
1 T
1007460 GTTTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (14 bp):
TAGACAATTACATG
Found at i:1007899 original size:232 final size:229
Alignment explanation
Indices: 1007484--1008368 Score: 905
Period size: 240 Copynumber: 3.8 Consensus size: 229
1007474 CGTCTATTAG
* * * *
1007484 TTTTCATTTGAAATTTAAGCAAAATCAGCAGTGAATTGTTGATTTATAAGAATATGTCTATATGT
1 TTTTCATTTGAAATTTAAACAAATTCAGCAGTGAATTGTTGATTTATAAGAATCTGTCTATCTGT
* * * * ** * *
1007549 ACAGAGATTTGTTTGTTTGTGAGAATCTGTTAGTCTATTAACATTTTTCTCGTGATTTAGGTGAA
66 AAAGTGATGTATCAGTTTGTGAGAATCTGTCAGTCTATTAACATTTTTCTCGTGATTTAGGTAAA
** * ** *
1007614 TACATTAAACGTTTT-TTATAGAAAGTTAGTTTCATATATTTTTAGTTTTTTTATGAATAAGCCT
131 TACATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTTTTAG-ATTTTTATGAATAAGCCT
*
1007678 CTCTATAGATAATTACACGTGTTTTTGT-ATTTAA
195 CTCTATAGACAATTACACGTGTTTTTGTAATTTAA
*
1007712 TTTTCATTTGAAATTTAAACAAATGCTA-CAGTGAATTGTTGATTTATAAGAATCTGTCTGTCTA
1 TTTTCATTTGAAATTTAAACAAATTC-AGCAGTGAATTGTTGATTTATAAGAA----TCTGTCTA
* * * **
1007776 TCTGTAAAGTGATTTATCAGTTTGTGAAAATATGTTTGTCTATTAA-ATTTTTTCTCGTGATTTA
61 TCTGTAAAGTGATGTATCAGTTTGTGAGAATCTGTCAGTCTATTAACA-TTTTTCTCGTGATTTA
* * *
1007840 GGTAAATATATTAAACGTTTTCAAATATAAAATTAGTTTCATACCTTTTAAGATTTTTATGAATA
125 GGTAAATACATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTTTTAGATTTTTATGAAT-
* * * *
1007905 AATCTCGCTATATAGACAATTGCACGTGTTTTTGTATTTGACGTTTATTA
189 AAGC-CTCTCTATAGACAATTACACGTGTTTTTGTA----A--TTTA--A
* * * * ** * *
1007955 GTTTTCTTTTGAAATTTAAACTAATTCATCAGTGAATTGTTGGTTTATATTAATTTGTCTATCTA
1 -TTTTCATTTGAAATTTAAACAAATTCAGCAGTGAATTGTTGATTTATAAGAATCTGTCTATCTG
* * * *
1008020 TACAGTGGTGTATAAGTTTATGAGAATCTGTCAGTCTATTAACATTTTTCTCGTGATTTAGGTAA
65 TAAAGTGATGTATCAGTTTGTGAGAATCTGTCAGTCTATTAACATTTTTCTCGTGATTTAGGTAA
* * * * *
1008085 ATGCATTAAACGTTTTCAAATAGAAAATTAGCTTCATGCCTTTTTAGATTTTTACGAATAAGTCT
130 ATACATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTTTTAGATTTTTATGAATAAGCCT
* * * *
1008150 CTCTATAAACAATTACACATTTTTTTTATATTTAACATCTATCAA
195 CTCTATAGACAATTACAC---GTGTTT-T-TGT-A-AT-T-T-AA
* *
1008195 TTTTCATTTGAAATTTAAACAAATTCAGCAGTGAATTGTTGGTTTATAAGAATCTATCTATCTGT
1 TTTTCATTTGAAATTTAAACAAATTCAGCAGTGAATTGTTGATTTATAAGAATCTGTCTATCTGT
* * * * *
1008260 AAAAACTGATGTATCAGTTTGTGAGAATCTATCAGTTTATTAACATGTTTCTCGTAATTTAGGTA
66 --AAAGTGATGTATCAGTTTGTGAGAATCTGTCAGTCTATTAACATTTTTCTCGTGATTTAGGTA
** *
1008325 AATGTATTAAATGTTTTCAAATAGAAAATTAGTTTCATACCTTT
129 AATACATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTT
1008369 CTCCCAACAA
Statistics
Matches: 542, Mismatches: 83, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
228 47 0.09
229 1 0.00
231 1 0.00
232 90 0.17
233 26 0.05
234 26 0.05
238 16 0.03
239 61 0.11
240 118 0.22
241 105 0.19
242 2 0.00
243 4 0.01
244 45 0.08
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (229 bp):
TTTTCATTTGAAATTTAAACAAATTCAGCAGTGAATTGTTGATTTATAAGAATCTGTCTATCTGT
AAAGTGATGTATCAGTTTGTGAGAATCTGTCAGTCTATTAACATTTTTCTCGTGATTTAGGTAAA
TACATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTTTTAGATTTTTATGAATAAGCCTC
TCTATAGACAATTACACGTGTTTTTGTAATTTAA
Found at i:1008074 original size:240 final size:240
Alignment explanation
Indices: 1006956--1008368 Score: 1322
Period size: 258 Copynumber: 5.8 Consensus size: 240
1006946 TATAGATATC
* * * *** *
1006956 TACACGTGTTTTTGTATTTAACGTTTATTCA-TTTTTA-TTGAAATTTTAAATAAATTCAATGGC
1 TACACGTGTTTTTGTATTTAACGTCTATT-AGTTTTCATTTGAAA-TTTAAACAAATTCAGCAGT
* * * * * *
1007019 GAATTGTTGATTTTTGAGAATATGTCTATCTGTAAAGTTGATTTATCAATTTGTGAGAATCTGTC
64 GAATTGTTGATTTATAAGAATTTGTCTATCTATAAAG-TGATGTATCAGTTTGTGAGAATCTGTC
** * * * * * *
1007084 AGTCTGCTAACATGTTTCTCGTGATTTACGTAAATGCATTAAACGTTTTCGAATGGAAAGTTAGT
128 AGTCTATTAACATTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAAATTAGT
* * **
1007149 TTCATATCTTTTTAGATTTTTATGAATAAGTCTCTC--TATAGGTAAT
193 TTCATACCTTTTTAGATTTTTATGAATAAATCTCTCTATATAGACAAT
* * * * * *
1007195 TACACGTGTTTTTGTATTTAACATTTATTAATTTTCATTTGAAATTTAAACAAATTCAACAATAA
1 TACACGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAACAAATTCAGCAGTGA
* * * * * * * * *
1007260 ACTGTCGATTTATAAGAATCTATCTATATGTAAAGTGATTTATCAATTTGTGAGAATTTGTCAGT
66 ATTGTTGATTTATAAGAATTTGTCTATCTATAAAGTGATGTATCAGTTTGTGAGAATCTGTCAGT
* * * *
1007325 -TAACTAACATGTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCGAATAGAAAGTCAGTTT
131 CT-ATTAACATTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAA---A--TT
* * * *
1007389 CAGTTTCTTACTTTTTTAGCTTTTTATGAATAAGTCTCTCTATAGACAATTACATGTAGACAAT
190 -AGTTTCATACCTTTTTAGATTTTTATGAATAAATCTCTC--T-----A-T--A--TAGACAAT
* * *
1007453 TACATGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAGCAAAATCAGCAGTGA
1 TACACGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAACAAATTCAGCAGTGA
* * * * * * * ** *
1007518 ATTGTTGATTTATAAGAATATGTCTATATGTACAGAGATTTGTTTGTTTGTGAGAATCTGTTAGT
66 ATTGTTGATTTATAAGAATTTGTCTATCTATAAAGTGATGTATCAGTTTGTGAGAATCTGTCAGT
* ** *
1007583 CTATTAACATTTTTCTCGTGATTTAGGTGAATACATTAAACGTTTT-TTATAGAAAGTTAGTTTC
131 CTATTAACATTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAAATTAGTTTC
** * * * *
1007647 ATATATTTTTAGTTTTTTTATGAAT-AAGC-CTCTCTATAGATAAT
196 ATACCTTTTTAG-ATTTTTATGAATAAATCTCTCTATATAGACAAT
*
1007691 TACACGTGTTTTTGTA--T----T-TA--A-TTTTCATTTGAAATTTAAACAAATGCTA-CAGTG
1 TACACGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAACAAATTC-AGCAGTG
* * * *
1007745 AATTGTTGATTTATAAGAATCTGTCTGTCTATCTGTAAAGTGATTTATCAGTTTGTGAAAATATG
65 AATTGTTGATTTATAAGAA--T-T-TGTCTATCTATAAAGTGATGTATCAGTTTGTGAGAATCTG
** * *
1007810 TTTGTCTATTAA-ATTTTTTCTCGTGATTTAGGTAAATATATTAAACGTTTTCAAATATAAAATT
126 TCAGTCTATTAACA-TTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAAATT
* *
1007874 AGTTTCATACCTTTTAAGATTTTTATGAATAAATCTCGCTATATAGACAAT
190 AGTTTCATACCTTTTTAGATTTTTATGAATAAATCTCTCTATATAGACAAT
* * * * * *
1007925 TGCACGTGTTTTTGTATTTGACGTTTATTAGTTTTCTTTTGAAATTTAAACTAATTCATCAGTGA
1 TACACGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAACAAATTCAGCAGTGA
* ** * * * *
1007990 ATTGTTGGTTTATATTAATTTGTCTATCTATACAGTGGTGTATAAGTTTATGAGAATCTGTCAGT
66 ATTGTTGATTTATAAGAATTTGTCTATCTATAAAGTGATGTATCAGTTTGTGAGAATCTGTCAGT
* *
1008055 CTATTAACATTTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCAAATAGAAAATTAGCTTC
131 CTATTAACATTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAAATTAGTTTC
* * *
1008120 ATGCCTTTTTAGATTTTTACGAATAAGTCTCTCTATA-A-ACAAT
196 ATACCTTTTTAGATTTTTATGAATAAATCTCTCTATATAGACAAT
* * * * * *
1008163 TACACATTTTTTTTATATTTAACATCTATCAATTTTCATTTGAAATTTAAACAAATTCAGCAGTG
1 TACAC-GTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAACAAATTCAGCAGTG
* * * * * *
1008228 AATTGTTGGTTTATAAGAATCTATCTATCTGTAAAAACTGATGTATCAGTTTGTGAGAATCTATC
65 AATTGTTGATTTATAAGAATTTGTCTATC--TATAAAGTGATGTATCAGTTTGTGAGAATCTGTC
* * * ** *
1008293 AGTTTATTAACATGTTTCTCGTAATTTAGGTAAATGTATTAAATGTTTTCAAATAGAAAATTAGT
128 AGTCTATTAACATTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAAATTAGT
1008358 TTCATACCTTT
193 TTCATACCTTT
1008369 CTCCCAACAA
Statistics
Matches: 979, Mismatches: 146, Indels: 96
0.80 0.12 0.08
Matches are distributed among these distances:
228 47 0.05
229 2 0.00
230 1 0.00
231 3 0.00
232 90 0.09
233 26 0.03
234 27 0.03
236 2 0.00
237 1 0.00
238 112 0.11
239 150 0.15
240 134 0.14
241 100 0.10
242 2 0.00
243 4 0.00
244 79 0.08
248 1 0.00
250 3 0.00
251 17 0.02
252 13 0.01
254 1 0.00
256 1 0.00
257 7 0.01
258 155 0.16
259 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (240 bp):
TACACGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAACAAATTCAGCAGTGA
ATTGTTGATTTATAAGAATTTGTCTATCTATAAAGTGATGTATCAGTTTGTGAGAATCTGTCAGT
CTATTAACATTTTTCTCGTGATTTAGGTAAATACATTAAACGTTTTCAAATAGAAAATTAGTTTC
ATACCTTTTTAGATTTTTATGAATAAATCTCTCTATATAGACAAT
Found at i:1008146 original size:472 final size:472
Alignment explanation
Indices: 1006956--1008368 Score: 1506
Period size: 472 Copynumber: 2.9 Consensus size: 472
1006946 TATAGATATC
* *
1006956 TACACGTGTTTTTGTATTTAACGTTTATTCA-TTTT-TATTGAAATTTTAAA-TAAATTCAAT-G
1 TACACGTGTTTTTGTATTTAACGTTTATT-AGTTTTCTTTTGAAA-TTTAAACT-AATTC-ATCA
* * *
1007017 GCGAATTGTTGATTTTTGAGAATATGTCTATCTGTAAAGTTGATTTATCAA-TTTGTGAGAATCT
62 GTGAATTGTTGATTTAT-AGAATATGTCTATCTGTACAG-TGATTTAT-AAGTTTGTGAGAATCT
** * * * *
1007081 GTCAGTCTGCTAACATGTTTCTCGTGATTTACGTAAATGCATTAAACGTTTTCGAATGGAAAGTT
124 GTCAGTCTATTAACATTTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCAAATAGAAAGTT
*
1007146 AGTTTCATATCTTTTTAGATTTTTATGAATAAGTCTCTCTATAGGTAATTACACGTGTTTTTGTA
189 AGTTTCATATCTTTTTAGATTTTTATGAATAAGTCTCTCTATAGATAATTACACGTGTTTTTG--
* * * *
1007211 TTTAACATTTATTAATTTTCATTTGAAATTTAAACAAATTCAACAATAAACTGTCGATTTATAAG
252 --T-A-A--TATTAATTTTCATTTGAAATTTAAACAAATTC-ACAGTGAATTGTTGATTTATAAG
* * * *
1007276 AATCTATCTATATGTAAAGTGATTTATCAATTTGTGAGAATTTGTCAGTTAACTAACATGTTTCT
310 AATCTATCTATCTGTAAAGTGATTTATCAGTTTGTGAGAATATGTCAGTT-ATTAACATGTTTCT
* * * * *
1007341 CGTGATTTAGGTAAATGCATTAAACGTTTTCGAATAGAAAGTCAGTTTCAGTTTCTTACTTTTTT
374 CGTGATTTAGGTAAATGTATTAAACGTTTTCAAATAGAAA---A--TT-AGTTTCATACCTTTTA
* * *
1007406 AGCTTTTTATGAATAAGTCTCTCTATAGACAATTACATGTAGACAAT
433 AGATTTTTATGAATAAG-ATCTC---AGAC-A-TA-ATATAGACAAT
* * * * * * *
1007453 TACATGTGTTTTTGTATTTAACGTCTATTAGTTTTCATTTGAAATTTAAGCAAAATCAGCAGTGA
1 TACACGTGTTTTTGTATTTAACGTTTATTAGTTTTCTTTTGAAATTTAAACTAATTCATCAGTGA
* * * ** *
1007518 ATTGTTGATTTATAAGAATATGTCTATATGTACAGAGATTTGTTTGTTTGTGAGAATCTGTTAGT
66 ATTGTTGATTTAT-AGAATATGTCTATCTGTACAGTGATTTATAAGTTTGTGAGAATCTGTCAGT
* * **
1007583 CTATTAACATTTTTCTCGTGATTTAGGTGAATACATTAAACGTTTT-TTATAGAAAGTTAGTTTC
130 CTATTAACATTTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCAAATAGAAAGTTAGTTTC
* * *
1007647 ATATATTTTTAGTTTTTTTATGAATAAGCCTCTCTATAGATAATTACACGTGTTTTTGT-AT-TT
195 ATATCTTTTTAG-ATTTTTATGAATAAGTCTCTCTATAGATAATTACACGTGTTTTTGTAATATT
* *
1007710 AATTTTCATTTGAAATTTAAACAAATGCTACAGTGAATTGTTGATTTATAAGAATCTGTCTGTCT
259 AATTTTCATTTGAAATTTAAACAAATTC-ACAGTGAATTGTTGATTTATAAGAA----TCTATCT
* ** *
1007775 ATCTGTAAAGTGATTTATCAGTTTGTGAAAATATGTTTGTCTATTAA-ATTTTTTCTCGTGATTT
319 ATCTGTAAAGTGATTTATCAGTTTGTGAGAATATGTCAGT-TATTAACA-TGTTTCTCGTGATTT
* *
1007839 AGGTAAATATATTAAACGTTTTCAAATATAAAATTAGTTTCATACCTTTTAAGATTTTTATGAAT
382 AGGTAAATGTATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTTTAAGATTTTTATGAAT
1007904 AA-ATCTC-G-C-T-ATATAGACAAT
447 AAGATCTCAGACATAATATAGACAAT
* *
1007925 TGCACGTGTTTTTGTATTTGACGTTTATTAGTTTTCTTTTGAAATTTAAACTAATTCATCAGTGA
1 TACACGTGTTTTTGTATTTAACGTTTATTAGTTTTCTTTTGAAATTTAAACTAATTCATCAGTGA
* * * * * * *
1007990 ATTGTTGGTTTATATTAATTTGTCTATCTATACAGTGGTGTATAAGTTTATGAGAATCTGTCAGT
66 ATTGTTGATTTATA-GAATATGTCTATCTGTACAGTGATTTATAAGTTTGTGAGAATCTGTCAGT
* *
1008055 CTATTAACATTTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCAAATAGAAAATTAGCTTC
130 CTATTAACATTTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCAAATAGAAAGTTAGTTTC
** * * * * *
1008120 ATGCCTTTTTAGATTTTTACGAATAAGTCTCTCTATAAACAATTACACAT-TTTTTTTATATTTA
195 ATATCTTTTTAGATTTTTATGAATAAGTCTCTCTATAGATAATTACACGTGTTTTTGTA-A--T-
*
1008184 ACATCTATCAATTTTCATTTGAAATTTAAACAAATTCAGCAGTGAATTGTTGGTTTATAAGAATC
256 --A--T-T-AATTTTCATTTGAAATTTAAACAAATTCA-CAGTGAATTGTTGATTTATAAGAATC
* * * *
1008249 TATCTATCTGTAAAAACTGATGTATCAGTTTGTGAGAATCTATCAGTTTATTAACATGTTTCTCG
314 TATCTATCTGT--AAAGTGATTTATCAGTTTGTGAGAATATGTCAG-TTATTAACATGTTTCTCG
* *
1008314 TAATTTAGGTAAATGTATTAAATGTTTTCAAATAGAAAATTAGTTTCATACCTTT
376 TGATTTAGGTAAATGTATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTT
1008369 CTCCCAACAA
Statistics
Matches: 775, Mismatches: 110, Indels: 78
0.80 0.11 0.08
Matches are distributed among these distances:
471 7 0.01
472 192 0.25
473 24 0.03
474 1 0.00
475 1 0.00
477 1 0.00
478 1 0.00
479 12 0.02
481 92 0.12
482 8 0.01
483 50 0.06
484 28 0.04
485 2 0.00
486 50 0.06
487 2 0.00
489 2 0.00
490 86 0.11
491 1 0.00
492 1 0.00
495 26 0.03
496 108 0.14
497 74 0.10
498 6 0.01
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (472 bp):
TACACGTGTTTTTGTATTTAACGTTTATTAGTTTTCTTTTGAAATTTAAACTAATTCATCAGTGA
ATTGTTGATTTATAGAATATGTCTATCTGTACAGTGATTTATAAGTTTGTGAGAATCTGTCAGTC
TATTAACATTTTTCTCGTGATTTAGGTAAATGCATTAAACGTTTTCAAATAGAAAGTTAGTTTCA
TATCTTTTTAGATTTTTATGAATAAGTCTCTCTATAGATAATTACACGTGTTTTTGTAATATTAA
TTTTCATTTGAAATTTAAACAAATTCACAGTGAATTGTTGATTTATAAGAATCTATCTATCTGTA
AAGTGATTTATCAGTTTGTGAGAATATGTCAGTTATTAACATGTTTCTCGTGATTTAGGTAAATG
TATTAAACGTTTTCAAATAGAAAATTAGTTTCATACCTTTTAAGATTTTTATGAATAAGATCTCA
GACATAATATAGACAAT
Found at i:1008898 original size:29 final size:30
Alignment explanation
Indices: 1008861--1008922 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
1008851 GTATGTTTTT
*
1008861 GTTCCAGTTTAGTGCCTAACGTTT-ATTTC
1 GTTCCAGTTTAGTGCCTAACGTTTCATTCC
* *
1008890 GTTCTAGTTTGGTGCCTAACGTTTCATTCC
1 GTTCCAGTTTAGTGCCTAACGTTTCATTCC
1008920 GTT
1 GTT
1008923 AATAAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (30 bp):
GTTCCAGTTTAGTGCCTAACGTTTCATTCC
Found at i:1009988 original size:13 final size:13
Alignment explanation
Indices: 1009972--1009997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1009962 TAATTATGAA
1009972 AAATAAAATAAGT
1 AAATAAAATAAGT
1009985 AAATAAAATAAGT
1 AAATAAAATAAGT
1009998 GGCAGAGCCA
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:0.08, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAGT
Found at i:1012672 original size:14 final size:14
Alignment explanation
Indices: 1012630--1012687 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
1012620 TTGAATATCT
1012630 AACATATATTATAAA
1 AACATATATTA-AAA
* * **
1012645 AAAATTTACCAAAA
1 AACATATATTAAAA
1012659 AACATATATTAAAA
1 AACATATATTAAAA
*
1012673 AACATACATTAAAA
1 AACATATATTAAAA
1012687 A
1 A
1012688 TACTAAAAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
14 27 0.79
15 7 0.21
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATATTAAAA
Found at i:1016972 original size:19 final size:19
Alignment explanation
Indices: 1016948--1016984 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1016938 AAATAATATG
*
1016948 CTTCATAATCTCGTGGACA
1 CTTCATAATCTCGGGGACA
*
1016967 CTTCATATTCTCGGGGAC
1 CTTCATAATCTCGGGGAC
1016985 CTCACGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (19 bp):
CTTCATAATCTCGGGGACA
Found at i:1019214 original size:26 final size:26
Alignment explanation
Indices: 1019154--1019214 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
1019144 ATATCAGATC
*
1019154 GGGTTGGGCTTATAATTTAAAATTTT
1 GGGTTGGGTTTATAATTTAAAATTTT
*
1019180 GGGTTGGGTTTATACTTTAAAATTTT
1 GGGTTGGGTTTATAATTTAAAATTTT
*
1019206 GGGTCGGGT
1 GGGTTGGGT
1019215 GGATGATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (26 bp):
GGGTTGGGTTTATAATTTAAAATTTT
Found at i:1020236 original size:23 final size:22
Alignment explanation
Indices: 1020192--1020261 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
1020182 GTCATTTTGG
*
1020192 CACGTCTTAACTTTGTTTTTATGA
1 CACGT-TTTACTTTG-TTTTATGA
*
1020216 CACGTTTTACTTAGTTCTTATGA
1 CACGTTTTACTTTGTT-TTATGA
*
1020239 CA--TTTTTCTTTGTTTTATGA
1 CACGTTTTACTTTGTTTTATGA
1020259 CAC
1 CAC
1020262 ATTGTTTGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 8 0.20
21 10 0.25
22 2 0.05
23 15 0.38
24 5 0.12
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.51
Consensus pattern (22 bp):
CACGTTTTACTTTGTTTTATGA
Found at i:1020693 original size:40 final size:40
Alignment explanation
Indices: 1020649--1020748 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
1020639 CGTGTGTATG
1020649 GTGCGGGGCAGAGGCCGCGCCTTACGCCACGTAAGATATA
1 GTGCGGGGCAGAGGCCGCGCCTTACGCCACGTAAGATATA
* *
1020689 GTGCGGGGCAGGGGTCGCGCCTTACGCCACGTAAGATATA
1 GTGCGGGGCAGAGGCCGCGCCTTACGCCACGTAAGATATA
* *
1020729 GCGCAGGGCA-AGGGCCGCGC
1 GTGCGGGGCAGA-GGCCGCGC
1020749 TATTCAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.20, C:0.28, G:0.39, T:0.13
Consensus pattern (40 bp):
GTGCGGGGCAGAGGCCGCGCCTTACGCCACGTAAGATATA
Found at i:1025257 original size:111 final size:111
Alignment explanation
Indices: 1025120--1025341 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
1025110 ATTACAAAAA
* * * *
1025120 TTAATTCTTAATTTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
1025185 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
1025231 TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1025296 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
1025342 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:1025679 original size:48 final size:49
Alignment explanation
Indices: 1025627--1025733 Score: 135
Period size: 50 Copynumber: 2.2 Consensus size: 49
1025617 AGATATCCAG
* *
1025627 GTATAGCGCGGATCAGGGGG-CGCTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGGAGCAGGGGGACGCTATACCCACGTGGCGCCAAATCACC
* * * *
1025675 GTATATCGCGGGGCAGGGGGCACGCTATACTCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGAGCAGGGGG-ACGCTATACCCACGTGGCGCCAAATCACC
*
1025725 ATATAGCGC
1 GTATAGCGC
1025734 AATGCAGGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 17 0.35
50 32 0.65
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (49 bp):
GTATAGCGCGGAGCAGGGGGACGCTATACCCACGTGGCGCCAAATCACC
Found at i:1025741 original size:50 final size:48
Alignment explanation
Indices: 1025640--1025747 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 48
1025630 TAGCGCGGAT
* * * **
1025640 CAGGGGGCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGG
1 CAGGGGGCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCAAGG
* * *
1025688 CAGGGGGCACGCTATACTCACGTGGCGCCAAATCAGCATATAGCGCAATG
1 CAGGGGG--CGCTATACCCACGTGGCGCCAAATCACCATATAGCGCAAGG
*
1025738 CAGGGCGCGC
1 CAGGGGGCGC
1025748 GCTTTTCTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
48 10 0.20
50 39 0.80
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.14
Consensus pattern (48 bp):
CAGGGGGCGCTATACCCACGTGGCGCCAAATCACCATATAGCGCAAGG
Found at i:1027537 original size:15 final size:15
Alignment explanation
Indices: 1027517--1027547 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1027507 AACTCATAAT
1027517 CTACTCTATAAATGG
1 CTACTCTATAAATGG
1027532 CTACTCTATAAATGG
1 CTACTCTATAAATGG
1027547 C
1 C
1027548 GTGTAGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (15 bp):
CTACTCTATAAATGG
Found at i:1031690 original size:19 final size:19
Alignment explanation
Indices: 1031666--1031741 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
1031656 GCTCAAAAAG
*
1031666 ATATTATTTTATTCA-TTTA
1 ATATTATTTTAAT-ATTTTA
*
1031685 ATATTAATTTAATATTTTA
1 ATATTATTTTAATATTTTA
*
1031704 ATATTATTTTGATAAAATATTTA
1 ATATTA-TTT--TAATAT-TTTA
*
1031727 ATATTATTATAATAT
1 ATATTATTTTAATAT
1031742 AACTTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 1 0.02
19 21 0.46
20 7 0.15
22 7 0.15
23 10 0.22
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
ATATTATTTTAATATTTTA
Found at i:1032550 original size:14 final size:15
Alignment explanation
Indices: 1032524--1032553 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1032514 ATTTCAATTT
1032524 AATTTATAATATTAA
1 AATTTATAATATTAA
1032539 AATTTA-AATATTAA
1 AATTTATAATATTAA
1032553 A
1 A
1032554 CGTTATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTATAATATTAA
Found at i:1033511 original size:22 final size:22
Alignment explanation
Indices: 1033485--1033529 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1033475 TAATAAATTA
*
1033485 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATAT
1033507 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1033529 T
1 T
1033530 AATAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1033536 original size:22 final size:22
Alignment explanation
Indices: 1033483--1033535 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1033473 AATAATAAAT
*
1033483 TATT-TAAAATAAATCAATCTA
1 TATTATAAAATAAATCAATCCA
*
1033504 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
1033526 TATTAATAAA
1 TATT-ATAAA
1033536 TTATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:1033538 original size:54 final size:54
Alignment explanation
Indices: 1033475--1033737 Score: 317
Period size: 54 Copynumber: 5.0 Consensus size: 54
1033465 ACAACTACAA
*
1033475 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAT
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* **
1033529 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* **
1033583 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* *** * * *
1033637 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCTATA-TTTTAAAATAAATCAATCCATAC
*
1033690 T-AT--A-T-TTTAAAATAAATCAAT-TCATATTTTAAAATAAATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATCT-ATATTTTAAAATAAATCAATCCATA
1033738 TTTTAAAATA
Statistics
Matches: 186, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
47 5 0.03
48 27 0.15
49 1 0.01
50 1 0.01
52 2 0.01
53 2 0.01
54 143 0.77
55 5 0.03
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
Found at i:1033573 original size:18 final size:18
Alignment explanation
Indices: 1033547--1033632 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
1033537 TATTTAAAAT
* *
1033547 AAATCAATCCATATTTTA
1 AAATAAATCAATATTTTA
*
1033565 AAATAAATCAATA-TATA
1 AAATAAATCAATATTTTA
*
1033582 CTAATAAAT---TA-TTTA
1 -AAATAAATCAATATTTTA
1033597 AAATAAATCAATCCATATTTTA
1 AAATAAATC-A---ATATTTTA
1033619 AAATAAATCAATAT
1 AAATAAATCAATAT
1033633 ATACTAATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
14 7 0.13
15 5 0.09
17 3 0.06
18 22 0.42
21 3 0.06
22 13 0.25
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAAATCAATATTTTA
Found at i:1033641 original size:18 final size:18
Alignment explanation
Indices: 1033566--1033644 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
1033556 CATATTTTAA
1033566 AATAAATCAATATATACT
1 AATAAATCAATATATACT
* *
1033584 AATAAAT---TATTTA-A
1 AATAAATCAATATATACT
**
1033598 AATAAATCAATCCATATTTT
1 AATAAATCAAT--ATATACT
1033618 AAAATAAATCAATATATACT
1 --AATAAATCAATATATACT
1033638 AATAAAT
1 AATAAAT
1033645 TATTTAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
14 7 0.15
15 5 0.11
17 1 0.02
18 14 0.30
19 3 0.07
20 5 0.11
22 11 0.24
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAATCAATATATACT
Found at i:1033768 original size:22 final size:22
Alignment explanation
Indices: 1033678--1033817 Score: 145
Period size: 22 Copynumber: 6.2 Consensus size: 22
1033668 CAACTACAAT
*
1033678 AATAAATCAATCTATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
1033700 AATAAATCAATTCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
1033722 AATAAATCAATTCATATTTTAA
1 AATAAATCAATCCATATTTTAA
**
1033744 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
1033767 ATTATTTAAAATAAATTATTTTAA
1 AATAAAT-CAATCCA-TATTTTAA
*
1033791 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
1033813 AATAA
1 AATAA
1033818 TTTATTTTAA
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
22 69 0.73
23 12 0.13
24 12 0.13
25 2 0.02
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:1033791 original size:15 final size:15
Alignment explanation
Indices: 1033762--1033946 Score: 192
Period size: 15 Copynumber: 11.5 Consensus size: 15
1033752 AATCCATACT
1033762 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1033776 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1033791 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1033813 AATAATTTATTTTAA
1 AATAAATTATTTTAA
1033828 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1033843 AATAAACCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1033865 AATAATTTATTTTAA
1 AATAAATTATTTTAA
1033880 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1033895 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1033910 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1033925 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1033940 AATAAAT
1 AATAAAT
1033947 AACCTTATTA
Statistics
Matches: 146, Mismatches: 10, Indels: 29
0.79 0.05 0.16
Matches are distributed among these distances:
14 9 0.06
15 103 0.71
17 2 0.01
18 4 0.03
19 6 0.04
20 2 0.01
22 20 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1033854 original size:52 final size:52
Alignment explanation
Indices: 1033736--1033946 Score: 284
Period size: 52 Copynumber: 4.3 Consensus size: 52
1033726 AATCAATTCA
*
1033736 TATTTTAAAATAAATCAATCCATA----CTAATAAATTA-TTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
*
1033783 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
* *
1033835 TATTTTAAAATAAACCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
* *
1033887 TATTTTAAAAT--A--AAT---TATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
1033932 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1033947 AACCTTATTA
Statistics
Matches: 150, Mismatches: 6, Indels: 15
0.88 0.04 0.09
Matches are distributed among these distances:
45 38 0.25
47 25 0.17
48 3 0.02
50 1 0.01
51 9 0.06
52 74 0.49
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (52 bp):
TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAAT
Found at i:1035483 original size:32 final size:32
Alignment explanation
Indices: 1035445--1035606 Score: 175
Period size: 32 Copynumber: 5.7 Consensus size: 32
1035435 CAAACTATAT
1035445 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1035477 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1035499 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1035531 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1035553 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1035585 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
1035607 AACTACAATA
Statistics
Matches: 109, Mismatches: 1, Indels: 40
0.73 0.01 0.27
Matches are distributed among these distances:
22 32 0.29
23 3 0.03
24 2 0.02
25 1 0.01
26 6 0.06
28 6 0.06
29 1 0.01
30 2 0.02
31 2 0.02
32 54 0.50
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1035557 original size:22 final size:22
Alignment explanation
Indices: 1035531--1035573 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1035521 TAATAAATTA
1035531 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1035553 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1035574 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1035582 original size:22 final size:22
Alignment explanation
Indices: 1035533--1035581 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1035523 ATAAATTATT
**
1035533 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1035555 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1035578 TAAA
1 TAAA
1035582 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1035600 original size:54 final size:54
Alignment explanation
Indices: 1035413--1035698 Score: 397
Period size: 54 Copynumber: 5.4 Consensus size: 54
1035403 ACAACTACAA
* *
1035413 TAATAAATTATTTAAAATAAATCAAACTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1035467 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1035521 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
1035575 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* * *
1035628 -CAT--A-T-TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1035677 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
1035699 TATTTTAAAA
Statistics
Matches: 202, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
47 5 0.02
48 28 0.14
49 2 0.01
50 3 0.01
52 3 0.01
53 2 0.01
54 154 0.76
55 5 0.02
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1035641 original size:22 final size:22
Alignment explanation
Indices: 1035616--1035675 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
1035606 CAACTACAAT
*
1035616 AATAAATCAATCCATATTTTAA
1 AATAAATCAATACATATTTTAA
*
1035638 AATAAATCAATTCATATTTTAA
1 AATAAATCAATACATATTTTAA
1035660 AATAAATCAATACATA
1 AATAAATCAATACATA
1035676 CTAATAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATCAATACATATTTTAA
Found at i:1035684 original size:22 final size:21
Alignment explanation
Indices: 1035590--1035684 Score: 57
Period size: 22 Copynumber: 4.3 Consensus size: 21
1035580 AATTATTTAA
* * *
1035590 AATAAATCAATCCATACAACTAC
1 AATAAATAAATCAATAC-A-TAT
*
1035613 AAT-AATAAATCAATCCATAT
1 AATAAATAAATCAATACATAT
** *
1035633 TTTAAAATAAATCAATTCATAT
1 AAT-AAATAAATCAATACATAT
**
1035655 TTTAAAATAAATCAATACATACT
1 AAT-AAATAAATCAATACATA-T
1035678 AATAAAT
1 AATAAAT
1035685 TATTTAAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.05
21 1 0.02
22 50 0.85
23 5 0.08
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (21 bp):
AATAAATAAATCAATACATAT
Found at i:1035707 original size:15 final size:15
Alignment explanation
Indices: 1035678--1035743 Score: 107
Period size: 15 Copynumber: 4.5 Consensus size: 15
1035668 AATACATACT
1035678 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1035692 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1035707 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1035722 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1035737 AATAAAT
1 AATAAAT
1035744 AACCTTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
14 9 0.19
15 39 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1035816 original size:10 final size:10
Alignment explanation
Indices: 1035810--1035840 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1035800 CTTGAAGATG
1035810 TTTGAAGACA
1 TTTGAAGACA
1035820 TTTGAAGACA
1 TTTGAAGACA
1035830 TTTGAAGACA
1 TTTGAAGACA
1035840 T
1 T
1035841 AAAATCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (10 bp):
TTTGAAGACA
Found at i:1040094 original size:268 final size:269
Alignment explanation
Indices: 1039611--1040101 Score: 939
Period size: 268 Copynumber: 1.8 Consensus size: 269
1039601 CATATTTGTG
*
1039611 TTCATAATTGTCAGGTTTAACACGAGTTTCTAACAGACAGAGAACATCTACTTTGAAAAGATTAG
1 TTCAGAATTGTCAGGTTTAACACGAGTTTCTAACAGACAGAGAACATCTACTTTGAAAAGATTAG
1039676 CTCTATTCATAACTTTTTTCCTGTTTGTGAGGATTGTTGAATCCTCTAATATTCCAAAAACAAAT
66 CTCTATTCATAACTTTTTTCCTGTTTGTGAGGATTGTTGAATCCTCTAATATTCCAAAAACAAAT
*
1039741 TAACATTCAATTTGTGTTCATATTCTTTATATTTGATTTGAGGTAATGTTTCGGTATGTGTCTGT
131 TAACATTCAATTTGTGTTCAGATTCTTTATATTTGATTTGAGGTAATGTTTCGGTATGTGTCTGT
1039806 TTATTCATTCATATTATTTTCCAAGTCAATTCCTTTGATCAGTTGAGTGACAGAGGGAAAGGTCA
196 TTATTCATTCATATTATTTTCCAAGTCAATTCCTTTGATCAGTTGAGTGACAGAGGGAAAGGTCA
1039871 ATTCCTTTT
261 ATTCCTTTT
1039880 TTCAGAATTGTCAGGTTTAACACGAGTTTCTAACAGACAGAGAACATCTACTTTGAAAAGATTAG
1 TTCAGAATTGTCAGGTTTAACACGAGTTTCTAACAGACAGAGAACATCTACTTTGAAAAGATTAG
*
1039945 CTTTATTCATAACTTTTTT-CTGTTTGTGAGGATTGTTGAATCCTCTAATATTCCAAAAACAAAT
66 CTCTATTCATAACTTTTTTCCTGTTTGTGAGGATTGTTGAATCCTCTAATATTCCAAAAACAAAT
1040009 TAACATTCAATTTGTGTTCAGATTCTTTATATTTGATTTGAGGTAATGTTTCGGTATGTGTCTGT
131 TAACATTCAATTTGTGTTCAGATTCTTTATATTTGATTTGAGGTAATGTTTCGGTATGTGTCTGT
*
1040074 TTATTCATTCATATTATTTTCCAGGTCA
196 TTATTCATTCATATTATTTTCCAAGTCA
1040102 TCTTGAAGCA
Statistics
Matches: 218, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
268 136 0.62
269 82 0.38
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (269 bp):
TTCAGAATTGTCAGGTTTAACACGAGTTTCTAACAGACAGAGAACATCTACTTTGAAAAGATTAG
CTCTATTCATAACTTTTTTCCTGTTTGTGAGGATTGTTGAATCCTCTAATATTCCAAAAACAAAT
TAACATTCAATTTGTGTTCAGATTCTTTATATTTGATTTGAGGTAATGTTTCGGTATGTGTCTGT
TTATTCATTCATATTATTTTCCAAGTCAATTCCTTTGATCAGTTGAGTGACAGAGGGAAAGGTCA
ATTCCTTTT
Found at i:1040819 original size:23 final size:23
Alignment explanation
Indices: 1040801--1040861 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1040791 CTCATATAAA
*
1040801 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1040824 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1040847 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1040862 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1040995 original size:18 final size:18
Alignment explanation
Indices: 1040972--1041008 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1040962 GAATACATAT
1040972 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
*
1040990 ATGTCCTGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1041008 A
1 A
1041009 ATCATTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.22, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:1041082 original size:121 final size:121
Alignment explanation
Indices: 1040868--1041231 Score: 640
Period size: 121 Copynumber: 3.0 Consensus size: 121
1040858 GCCATATAAT
* * *
1040868 AATGTCCAT-AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATG
1 AATGTCC-TGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATG
*
1040932 CGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
65 TGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
1040989 AATGTCCTGAAGGACCACAAATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1041054 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* *
1041110 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTTTGT
1 AATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
*
1041175 GTCTCACCAGACTTCACACATGTTCCGAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
1041231 A
1 A
1041232 TAGACCCTCA
Statistics
Matches: 233, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 1 0.00
121 232 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (121 bp):
AATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:1041116 original size:18 final size:18
Alignment explanation
Indices: 1041093--1041128 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1041083 GAATACATAT
1041093 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1041111 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1041129 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:1041164 original size:59 final size:59
Alignment explanation
Indices: 1040980--1041164 Score: 150
Period size: 59 Copynumber: 3.1 Consensus size: 59
1040970 ATATGTCCCG
*
1040980 AAGGACCACAATGTCCTGAAGGACCACAAATCATTCCTTAAGAATCATATACATATGCC
1 AAGGACCACAATGTCCCGAAGGACCACAAATCATTCCTTAAGAATCATATACATATGCC
* * * * * *
1041039 AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTTCC-AAAGAATACATAT--ATGT
1 AAGGACCACA--A--TGTC-C-CGAAGGAC--CACAAATCATTCCTTAAGAAT-CATATACATAT
*
1041097 CCC
57 GCC
*
1041100 GAAGGACCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCC
1 -AAGGACCACAATGTCCCGAAGGACCACAAATCATTCCTTAAGAATCATATACATATGCC
1041160 AAGGA
1 AAGGA
1041165 TCAAGTTTGT
Statistics
Matches: 94, Mismatches: 15, Indels: 34
0.66 0.10 0.24
Matches are distributed among these distances:
57 7 0.07
58 12 0.13
59 25 0.27
60 6 0.06
61 6 0.06
62 20 0.21
63 12 0.13
64 6 0.06
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (59 bp):
AAGGACCACAATGTCCCGAAGGACCACAAATCATTCCTTAAGAATCATATACATATGCC
Found at i:1041226 original size:62 final size:62
Alignment explanation
Indices: 1040920--1041226 Score: 202
Period size: 62 Copynumber: 5.0 Consensus size: 62
1040910 CATATACTAG
*
1040920 GGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
1 GGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
* * * * * * * *
1040982 GGACCACA--ATGT-CCTGA--AGGAC--CACAAATCATTCCTTAAGAAT-CATATACATATGCC
1 GGATCA-AGTATGTGTCTCACCA-GACTTCACACAT-GTTCC-AAAGAATACATAT--ATGTCCC
1041039 -AA
60 GAA
1041041 GGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
1 GGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
* * * * * * *
1041103 GGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATTCCTTAAGAAT-CATATACATATGC
1 GGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTTCC-AAAGAATACATAT--ATGTCC
1041159 C-AA
59 CGAA
* *
1041162 GGATCAAGTTTGTGTCTCACCAGACTTCACACATGTTCCGAAGAATACATATATGTCCCGAA
1 GGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
1041224 GGA
1 GGA
1041227 CCACATAGAC
Statistics
Matches: 181, Mismatches: 32, Indels: 64
0.65 0.12 0.23
Matches are distributed among these distances:
57 13 0.07
58 23 0.13
59 36 0.20
60 17 0.09
61 17 0.09
62 39 0.22
63 23 0.13
64 13 0.07
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (62 bp):
GGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
Found at i:1042535 original size:21 final size:21
Alignment explanation
Indices: 1042509--1042552 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1042499 ATTTTATTCG
*
1042509 CTTGAA-GGGTTATCGGTTCCC
1 CTTGAATGGG-TATCGATTCCC
1042530 CTTGAATGGGTATCGATTCCC
1 CTTGAATGGGTATCGATTCCC
1042551 CT
1 CT
1042553 ATCCCAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (21 bp):
CTTGAATGGGTATCGATTCCC
Found at i:1046320 original size:23 final size:23
Alignment explanation
Indices: 1046294--1046354 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1046284 CTCATATAAA
*
1046294 TGCACTGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* * *
1046317 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
1046340 TGCACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
1046355 TATAATAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:1046488 original size:18 final size:18
Alignment explanation
Indices: 1046465--1046500 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1046455 GAATACATAT
1046465 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1046483 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1046501 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:1046536 original size:59 final size:58
Alignment explanation
Indices: 1046473--1046657 Score: 157
Period size: 59 Copynumber: 3.1 Consensus size: 58
1046463 ATATGTCCCG
1046473 AAGGACCACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCC
1 AAGGACCACAATGTCCCGAAGGACCACATAT-ATTCCTTAAGAATCATATACATATGCC
* * * * * * *
1046532 AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACATGTTCC-AAAGAATACATAT--ATGTC
1 AAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATATTCCTTAAGAAT-CATATACATATG
1046591 CC
57 CC
1046593 GAAGGACCACAATGTCCCGAAGGACCACATATAATTCCTTAAGAATCATATACATATGCC
1 -AAGGACCACAATGTCCCGAAGGACCACATAT-ATTCCTTAAGAATCATATACATATGCC
1046653 AAGGA
1 AAGGA
1046658 TCAAGTTTGT
Statistics
Matches: 95, Mismatches: 14, Indels: 34
0.66 0.10 0.24
Matches are distributed among these distances:
57 7 0.07
58 12 0.13
59 25 0.26
60 6 0.06
61 6 0.06
62 20 0.21
63 12 0.13
64 7 0.07
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (58 bp):
AAGGACCACAATGTCCCGAAGGACCACATATATTCCTTAAGAATCATATACATATGCC
Found at i:1046575 original size:121 final size:121
Alignment explanation
Indices: 1046374--1046724 Score: 630
Period size: 121 Copynumber: 2.9 Consensus size: 121
1046364 GTCCATAAGA
* * * *
1046374 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1046439 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGAAGG
1046495 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1046560 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGAAGG
* * *
1046616 ACCACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTTTGTGTCTTACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
*
1046681 TCACACATGTTCCAAAGAATACATATATATCCCGAAGGACCACA
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
1046725 TAGATCCTCG
Statistics
Matches: 222, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 222 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (121 bp):
ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGAAGG
Found at i:1046578 original size:62 final size:63
Alignment explanation
Indices: 1046391--1046719 Score: 186
Period size: 62 Copynumber: 5.4 Consensus size: 63
1046381 ATCATTCCTT
* * * *
1046391 AAGAAT-CATATACATATACTAGGGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * *
1046453 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATATCCC-AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
1046508 CCTT
61 CC-A
*
1046512 AAGAAT-CATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * *
1046574 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATAATT
1 AAGAATACATATACATATCCC-AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
1046629 CCTT
61 CC-A
* * *
1046633 AAGAAT-CATATACATATGCCAAGGATCAAGTTTGTGTCTTACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1046695 AAGAATACATAT--ATATCCCGAAGGA
1 AAGAATACATATACATATCCC-AAGGA
1046720 CCACATAGAT
Statistics
Matches: 197, Mismatches: 34, Indels: 72
0.65 0.11 0.24
Matches are distributed among these distances:
57 14 0.07
58 24 0.12
59 39 0.20
60 11 0.06
61 17 0.09
62 50 0.25
63 28 0.14
64 14 0.07
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (63 bp):
AAGAATACATATACATATCCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
Found at i:1046609 original size:18 final size:18
Alignment explanation
Indices: 1046586--1046621 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1046576 GAATACATAT
1046586 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1046604 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1046622 TATAATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:1066954 original size:20 final size:20
Alignment explanation
Indices: 1066926--1067032 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
1066916 ACTATCGCGT
*
1066926 TGCGAATACGTAAATTGCAA
1 TGCGAATACGTAAATCGCAA
*
1066946 TGTGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
1066966 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
1066986 TGCGAATACGTAAATCACAA
1 TGCGAATACGTAAATCGCAA
*
1067006 TGCGAATATGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
1067026 CGCGAAT
1 TGCGAAT
1067033 CTGACTATCG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (20 bp):
TGCGAATACGTAAATCGCAA
Found at i:1067043 original size:60 final size:60
Alignment explanation
Indices: 1066900--1067050 Score: 189
Period size: 60 Copynumber: 2.5 Consensus size: 60
1066890 GTTTCCAAAT
* ** ** *
1066900 TCGCAACGCGATTCTGACTATCGCGTTGCGAATACGTAAATTGCAATGTGAATACGTAAA
1 TCGCAACGCGAATCTGACTATCGCAATGCGAATACGTAAATCACAATGCGAATACGTAAA
* * *
1066960 TCGCAATGCGAATAC-GTA-AATCGCAATGCGAATACGTAAATCACAATGCGAATATGTAAA
1 TCGCAACGCGAAT-CTG-ACTATCGCAATGCGAATACGTAAATCACAATGCGAATACGTAAA
1067020 TCGCAACGCGAATCTGACTATCGCAATGCGA
1 TCGCAACGCGAATCTGACTATCGCAATGCGA
1067051 TTTACATAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.03
60 72 0.95
61 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (60 bp):
TCGCAACGCGAATCTGACTATCGCAATGCGAATACGTAAATCACAATGCGAATACGTAAA
Found at i:1067244 original size:22 final size:22
Alignment explanation
Indices: 1067230--1067294 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
1067220 ACGACATCCA
*
1067230 TCCCCATCTCTGACGAAATCAG
1 TCCCCATCTCCGACGAAATCAG
*
1067252 TCCCCATCTCCGACGATATCAG
1 TCCCCATCTCCGACGAAATCAG
* *
1067274 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
1067295 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAG
Found at i:1067658 original size:33 final size:34
Alignment explanation
Indices: 1067610--1067682 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
1067600 ACTATCGCAA
** *
1067610 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
1067643 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
1067677 TGCGAT
1 TGCGAT
1067683 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:1067678 original size:20 final size:20
Alignment explanation
Indices: 1067653--1067702 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1067643 TGCGATTCTT
1067653 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
1067673 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
1067693 GTGTTGCGAT
1 GCGTTGCGAT
1067703 TTAAAGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1069562 original size:20 final size:20
Alignment explanation
Indices: 1069537--1069673 Score: 104
Period size: 20 Copynumber: 7.5 Consensus size: 20
1069527 AGAATAGTTT
1069537 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1069557 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1069573 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
1069590 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
1069606 A--ATTGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1069624 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1069644 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1069664 ACTATCGCAA
1 ACTATCGCAA
1069674 CGAAAGAATC
Statistics
Matches: 96, Mismatches: 7, Indels: 28
0.73 0.05 0.21
Matches are distributed among these distances:
14 13 0.14
16 10 0.10
17 8 0.08
18 5 0.05
19 7 0.07
20 53 0.55
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1069583 original size:34 final size:34
Alignment explanation
Indices: 1069540--1069694 Score: 152
Period size: 34 Copynumber: 4.4 Consensus size: 34
1069530 ATAGTTTACT
*
1069540 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
** *
1069574 ATCGCAATGCG-AAATGAAAATCGCAAC-AACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AGA
* *
1069607 ATTGCAACGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
1069645 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
*
1069681 ATCACAATGCGAAA
1 ATCGCAATGCGAAA
1069695 TGAAAATCAC
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
32 1 0.01
33 25 0.26
34 36 0.37
36 3 0.03
37 4 0.04
38 5 0.05
40 23 0.24
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:1069745 original size:20 final size:20
Alignment explanation
Indices: 1069718--1069786 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1069708 GTGATTCTCT
**
1069718 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1069738 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1069758 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1069778 CGTTGCGAT
1 CGTTGCGAT
1069787 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1069796 original size:20 final size:20
Alignment explanation
Indices: 1069718--1069796 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
1069708 GTGATTCTCT
*
1069718 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* * *
1069738 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
1069758 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
1069778 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
1069797 AGATTCTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:1070098 original size:14 final size:14
Alignment explanation
Indices: 1070079--1070132 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1070069 CATTTTAGCA
1070079 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1070093 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1070110 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1070126 TTGCGAT
1 TTGCGAT
1070133 AGTCATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1070118 original size:33 final size:33
Alignment explanation
Indices: 1070057--1070152 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1070047 TATTTATATG
*
1070057 CGTTGCGATTTTCATTTTAGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1070091 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
1070124 CGTTGCGATAGTCATTTCTGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
1070153 AGTCAATTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 34 0.60
34 23 0.40
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1070149 original size:20 final size:19
Alignment explanation
Indices: 1070124--1070212 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 19
1070114 GCGATTCTCT
1070124 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
*
1070144 CGTTGCGATAGTCAATTACG
1 CGTTGCGATAGTC-ATTTCG
1070164 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1070184 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
1070204 CGTTGCGAT
1 CGTTGCGAT
1070213 TTCCGCGTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.05
20 53 0.85
21 6 0.10
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1070179 original size:40 final size:40
Alignment explanation
Indices: 1070124--1070212 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
1070114 GCGATTCTCT
*
1070124 CGTTGCGATAGTCATTTCTGCGTTGCGATAGTCA-ATTACG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-CG
*
1070164 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
1070204 CGTTGCGAT
1 CGTTGCGAT
1070213 TTCCGCGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:1073787 original size:17 final size:17
Alignment explanation
Indices: 1073765--1073798 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1073755 CGTTGAACAG
1073765 GGGGGAATCGGTACCCT
1 GGGGGAATCGGTACCCT
*
1073782 GGGGGAATCGGTTCCCT
1 GGGGGAATCGGTACCCT
1073799 CCGAGCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.21
Consensus pattern (17 bp):
GGGGGAATCGGTACCCT
Found at i:1076470 original size:21 final size:21
Alignment explanation
Indices: 1076444--1076524 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
1076434 CAGAACCTCA
*
1076444 GGGGGGTATCGATTCCCCTAT
1 GGGGGGAATCGATTCCCCTAT
* *
1076465 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-T-AT
* * *
1076488 AGGGGGAATTGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCT-AT
1076509 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
1076525 TCTGCACTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 5 0.10
21 26 0.54
22 4 0.08
23 13 0.27
ACGTcount: A:0.16, C:0.23, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTAT
Found at i:1083025 original size:20 final size:20
Alignment explanation
Indices: 1083000--1083046 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1082990 AAATTCAGTA
*
1083000 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1083020 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1083040 TTGCGAT
1 TTGCGAT
1083047 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1083056 original size:20 final size:20
Alignment explanation
Indices: 1083033--1083185 Score: 261
Period size: 20 Copynumber: 7.7 Consensus size: 20
1083023 CGATAGTCAG
*
1083033 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
**
1083053 ATTCATATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1083073 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1083093 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1083113 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1083133 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1083153 ATTCTCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1083173 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1083186 ATTTGGAAAA
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 124 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1086317 original size:30 final size:30
Alignment explanation
Indices: 1086283--1086343 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1086273 GTTACTAAAG
1086283 GCCCAAAATTTTCAATATTTATTATCAGGA
1 GCCCAAAATTTTCAATATTTATTATCAGGA
** * *
1086313 GCCCAATTTTTTCAATATTTGTTATTAGGA
1 GCCCAAAATTTTCAATATTTATTATCAGGA
1086343 G
1 G
1086344 AGTAGCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (30 bp):
GCCCAAAATTTTCAATATTTATTATCAGGA
Found at i:1090387 original size:2 final size:2
Alignment explanation
Indices: 1090380--1090407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1090370 TATGTAAGAA
1090380 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
1090408 TAAGAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1091484 original size:15 final size:16
Alignment explanation
Indices: 1091464--1091494 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1091454 CATCCACATC
1091464 CTTTTC-TTTTCTTTT
1 CTTTTCTTTTTCTTTT
1091479 CTTTTCTTTTTCTTTT
1 CTTTTCTTTTTCTTTT
1091495 GGATTTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTCTTTTTCTTTT
Found at i:1091491 original size:6 final size:5
Alignment explanation
Indices: 1091464--1091494 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1091454 CATCCACATC
1091464 CTTTT CTTTT CTTTT CTTTT CTTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT C-TTTT CTTTT
1091495 GGATTTCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
CTTTT
Found at i:1095430 original size:83 final size:83
Alignment explanation
Indices: 1095269--1095434 Score: 251
Period size: 83 Copynumber: 2.0 Consensus size: 83
1095259 TGAGAGACTC
* *
1095269 ATCAAAACAACGTGTTATAGTCAGAGGAATATTTTGTAACTTTTAATAGTCGATGGACTCAACAA
1 ATCAAAACAACGTGTTATAGTCAGAGGAATATTTTGTAACTTTCAATAATCGATGGACTCAACAA
* *
1095334 AGCAGTGTCCTATAGTTG
66 AACAATGTCCTATAGTTG
* * *
1095352 ATCAAAGCAATGTGTTATAGTCAGAGGAGTATTTTGTAACTTTCAATAATCGATGGACTCAACAA
1 ATCAAAACAACGTGTTATAGTCAGAGGAATATTTTGTAACTTTCAATAATCGATGGACTCAACAA
* *
1095417 AATAATGTTCTATAGTTG
66 AACAATGTCCTATAGTTG
1095435 GGGTTCATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (83 bp):
ATCAAAACAACGTGTTATAGTCAGAGGAATATTTTGTAACTTTCAATAATCGATGGACTCAACAA
AACAATGTCCTATAGTTG
Found at i:1104643 original size:19 final size:19
Alignment explanation
Indices: 1104593--1104643 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1104583 TATGTTTTTC
* *
1104593 TTTTTAAAAATAGATAATT
1 TTTTTAAAATTATATAATT
**
1104612 TTTTTAATTTTATATAATT
1 TTTTTAAAATTATATAATT
1104631 TTTTTAAAATTAT
1 TTTTTAAAATTAT
1104644 CATATTGTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTTAAAATTATATAATT
Found at i:1125999 original size:20 final size:20
Alignment explanation
Indices: 1125961--1126000 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1125951 AGATATTATA
*
1125961 CTATATTGTTCATTGCATTG
1 CTATATTGATCATTGCATTG
1125981 CTATATTGATC-TTGCCATTG
1 CTATATTGATCATTG-CATTG
1126001 TTGTGGTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (20 bp):
CTATATTGATCATTGCATTG
Found at i:1129399 original size:2 final size:2
Alignment explanation
Indices: 1129392--1129418 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1129382 AACACGTTTG
1129392 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1129419 GCCTTTGCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1135354 original size:6 final size:6
Alignment explanation
Indices: 1135343--1135373 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1135333 TTTCACCCTA
1135343 AACCCG AACCCG -ACCCG AACCCG AACCCG AA
1 AACCCG AACCCG AACCCG AACCCG AACCCG AA
1135374 TTTTTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:1135360 original size:11 final size:12
Alignment explanation
Indices: 1135343--1135373 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1135333 TTTCACCCTA
1135343 AACCCGAACCCG
1 AACCCGAACCCG
1135355 -ACCCGAACCCG
1 AACCCGAACCCG
1135366 AACCCGAA
1 AACCCGAA
1135374 TTTTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (12 bp):
AACCCGAACCCG
Found at i:1135582 original size:20 final size:20
Alignment explanation
Indices: 1135557--1135596 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1135547 GTTTGGCAAT
*
1135557 GAACCGGTTGAAAACCGATA
1 GAACCGGCTGAAAACCGATA
*
1135577 GAACCGGCTGAAAATCGATA
1 GAACCGGCTGAAAACCGATA
1135597 AAACTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (20 bp):
GAACCGGCTGAAAACCGATA
Found at i:1139270 original size:14 final size:14
Alignment explanation
Indices: 1139251--1139320 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
1139241 TGATTGTATC
1139251 ATCTTAAACCCTAA
1 ATCTTAAACCCTAA
*
1139265 ATCTTAAACTCTAA
1 ATCTTAAACCCTAA
*
1139279 A--TTAAGACCCTAT
1 ATCTTAA-ACCCTAA
* * * **
1139292 ACCCTAAGCTATAA
1 ATCTTAAACCCTAA
1139306 ATCTTAAACCCTAA
1 ATCTTAAACCCTAA
1139320 A
1 A
1139321 ATCATAAATA
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
14 27 0.68
15 3 0.08
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (14 bp):
ATCTTAAACCCTAA
Found at i:1141593 original size:19 final size:19
Alignment explanation
Indices: 1141542--1141593 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1141532 AGGAGCACAC
*
1141542 GACGACCTATGGAATACTT
1 GACGACCTATGGAGTACTT
*
1141561 GGCGACCTATGGAGTACTT
1 GACGACCTATGGAGTACTT
1141580 GACGACCTATGGAG
1 GACGACCTATGGAG
1141594 CTGCAATAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (19 bp):
GACGACCTATGGAGTACTT
Found at i:1141675 original size:19 final size:19
Alignment explanation
Indices: 1141651--1141687 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1141641 TTGTCGCAAG
*
1141651 GAGCACTTGGCGACCTATT
1 GAGCACTTGACGACCTATT
1141670 GAGCACTTGACGACCTAT
1 GAGCACTTGACGACCTAT
1141688 GGAGTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (19 bp):
GAGCACTTGACGACCTATT
Found at i:1155163 original size:21 final size:21
Alignment explanation
Indices: 1155128--1155187 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
1155118 TTTTAATCTC
*
1155128 AAATATTAAACCCTAAATCCTA
1 AAATCTTAAA-CCTAAATCCTA
* *
1155150 AAATCTTAAACCTAAA-CTTT
1 AAATCTTAAACCTAAATCCTA
*
1155170 AAATCTTAGACCTTAAAT
1 AAATCTTAAACC-TAAAT
1155188 TTTAAACCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.41
21 10 0.31
22 9 0.28
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATCTTAAACCTAAATCCTA
Found at i:1155175 original size:20 final size:21
Alignment explanation
Indices: 1155150--1155193 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1155140 CTAAATCCTA
1155150 AAATCTTAAACC-TAAACTTT
1 AAATCTTAAACCTTAAACTTT
* *
1155170 AAATCTTAGACCTTAAATTTT
1 AAATCTTAAACCTTAAACTTT
1155191 AAA
1 AAA
1155194 CCCTAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATCTTAAACCTTAAACTTT
Found at i:1155338 original size:2 final size:2
Alignment explanation
Indices: 1155331--1155398 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1155321 GATCATAACC
1155331 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
1155373 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
1155399 TTTTATTATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155475 original size:2 final size:2
Alignment explanation
Indices: 1155468--1155506 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1155458 TGTGTATTTC
1155468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1155507 AAGGTTAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1156427 original size:21 final size:23
Alignment explanation
Indices: 1156386--1156428 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1156376 AAGAGTGCCG
1156386 GCGTGGAGGGAGTTATGGTGGAC
1 GCGTGGAGGGAGTTATGGTGGAC
*
1156409 GCGTGGTGGG-GTT-TGGTGGA
1 GCGTGGAGGGAGTTATGGTGGA
1156429 GAAAGATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.12, C:0.07, G:0.56, T:0.26
Consensus pattern (23 bp):
GCGTGGAGGGAGTTATGGTGGAC
Found at i:1160820 original size:22 final size:21
Alignment explanation
Indices: 1160777--1160832 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
1160767 ATGTAGAAAT
*
1160777 TAAATGAATATAATAAATATAA
1 TAAAT-AATATAAAAAATATAA
*
1160799 TAAATAATTTAAAAAATAATAA
1 TAAATAATATAAAAAAT-ATAA
*
1160821 TATATAAATATA
1 TAAAT-AATATA
1160833 GTAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.36
22 13 0.46
23 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATAATATAAAAAATATAA
Found at i:1160843 original size:14 final size:14
Alignment explanation
Indices: 1160783--1160844 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
1160773 AAATTAAATG
* *
1160783 AATATAATAAATAT
1 AATATAATAATTAA
1160797 AATA-AATAATTTAA
1 AATATAATAA-TTAA
*
1160811 AAAATAATAATATATA
1 AATATAATAAT-TA-A
*
1160827 AATATAGTAATTAA
1 AATATAATAATTAA
1160841 AATA
1 AATA
1160845 GATATTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.13
14 15 0.38
15 9 0.23
16 10 0.26
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:1162811 original size:2 final size:2
Alignment explanation
Indices: 1162804--1162839 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1162794 ACATGCTATT
1162804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1162840 TAATGTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1162894 original size:25 final size:26
Alignment explanation
Indices: 1162864--1162920 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
1162854 TTAACTTAAG
1162864 TTAACTTTAAAAAATATATTTTAT-A
1 TTAACTTTAAAAAATATATTTTATGA
**
1162889 TTAAC-TTATTAAATATATTTTATGA
1 TTAACTTTAAAAAATATATTTTATGA
*
1162914 TGAACTT
1 TTAACTT
1162921 AATTTACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 16 0.59
25 10 0.37
26 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAACTTTAAAAAATATATTTTATGA
Found at i:1162907 original size:24 final size:25
Alignment explanation
Indices: 1162875--1162921 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1162865 TAACTTTAAA
*
1162875 AAATATATTTTAT-ATTAACTTATT
1 AAATATATTTTATGATGAACTTATT
1162899 AAATATATTTTATGATGAACTTA
1 AAATATATTTTATGATGAACTTA
1162922 ATTTACTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
AAATATATTTTATGATGAACTTATT
Found at i:1165608 original size:12 final size:12
Alignment explanation
Indices: 1165591--1165639 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1165581 CATTATATTG
1165591 TATTATTTTTAT
1 TATTATTTTTAT
1165603 TATTATTTTTAT
1 TATTATTTTTAT
*
1165615 TAATTTATATATTAT
1 T-A-TTAT-TTTTAT
*
1165630 AATTATTTTT
1 TATTATTTTT
1165640 TTGCCGGCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 16 0.52
13 5 0.16
14 5 0.16
15 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATTTTTAT
Found at i:1165635 original size:21 final size:20
Alignment explanation
Indices: 1165598--1165636 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1165588 TTGTATTATT
**
1165598 TTTATTATTATTTTTATTAA
1 TTTATTATTATAATTATTAA
1165618 TTTATATATTATAATTATT
1 TTTAT-TATTATAATTATT
1165637 TTTTTGCCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTATTATAATTATTAA
Found at i:1165942 original size:17 final size:17
Alignment explanation
Indices: 1165917--1165950 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1165907 CCGGTTTCGA
1165917 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
1165934 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
1165951 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1166715 original size:33 final size:33
Alignment explanation
Indices: 1166670--1166768 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1166660 AACTCAACAT
* * *
1166670 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1166703 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1166736 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1166768 A
1 A
1166769 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1166787 original size:21 final size:21
Alignment explanation
Indices: 1166763--1166804 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166753 ACTTCAAGTT
1166763 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1166784 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1166805 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Done.