Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2856328 original size:21 final size:21
Alignment explanation
Indices: 2856306--2856381 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
2856296 TACCTCATAT
* *
2856306 CTCAAACCCTAAATCTTAAAT
1 CTCAAACCCTAAATCATAAAC
* * * *
2856327 CTTAAATCCTCAATCCTAAAC
1 CTCAAACCCTAAATCATAAAC
2856348 CTCAAACCCT-AATCATAAAC
1 CTCAAACCCTAAATCATAAAC
*
2856368 CT-AAACCTTAAATC
1 CTCAAACCCTAAATC
2856382 CTAACCCTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 6 0.13
20 15 0.33
21 24 0.53
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (21 bp):
CTCAAACCCTAAATCATAAAC
Found at i:2856358 original size:14 final size:14
Alignment explanation
Indices: 2856306--2856385 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
2856296 TACCTCATAT
* *
2856306 CTCAAACCCTAAAT
1 CTCAAATCCTAAAC
* *
2856320 CTTAAATCTTAAATC
1 CTCAAATCCTAAA-C
2856335 CTC-AATCCTAAAC
1 CTCAAATCCTAAAC
* *
2856348 CTCAAACCCTAATC
1 CTCAAATCCTAAAC
*
2856362 AT-AAA-CCTAAAC
1 CTCAAATCCTAAAC
*
2856374 CTTAAATCCTAA
1 CTCAAATCCTAA
2856386 CCCTAACAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
12 7 0.14
13 10 0.20
14 32 0.63
15 2 0.04
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.26
Consensus pattern (14 bp):
CTCAAATCCTAAAC
Found at i:2856381 original size:20 final size:19
Alignment explanation
Indices: 2856309--2856391 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 19
2856299 CTCATATCTC
* *
2856309 AAACCCTAAATCTTAAATCTT
1 AAACCCT-AATCCTAAA-CCT
*
2856330 AAATCCTCAATCCTAAACCT
1 AAACCCT-AATCCTAAACCT
*
2856350 CAAACCCTAATCATAAACCT
1 -AAACCCTAATCCTAAACCT
* *
2856370 AAACCTTAAATCCTAACCCT
1 AAACCCT-AATCCTAAACCT
2856390 AA
1 AA
2856392 CAAGAAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.12
20 25 0.49
21 20 0.39
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.25
Consensus pattern (19 bp):
AAACCCTAATCCTAAACCT
Found at i:2856926 original size:13 final size:13
Alignment explanation
Indices: 2856886--2856931 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
2856876 AATAAATTCA
2856886 ATTATAAATAAAT
1 ATTATAAATAAAT
*
2856899 AATT-TAAATTGAAT
1 -ATTATAAA-TAAAT
2856913 ATTATAAATAAAT
1 ATTATAAATAAAT
2856926 ATTATA
1 ATTATA
2856932 TACATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
ATTATAAATAAAT
Found at i:2857072 original size:2 final size:2
Alignment explanation
Indices: 2857065--2857114 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2857055 TATCCCATGT
2857065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2857107 -A TA TA TA T
1 TA TA TA TA T
2857115 TTAATTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2858626 original size:20 final size:21
Alignment explanation
Indices: 2858588--2858627 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2858578 CCGTTAAACA
2858588 GGGGGGAATCGGTACTCCCTTG
1 GGGGGGAATCGGTA-TCCCTTG
2858610 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
2858628 CCGAGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTATCCCTTG
Found at i:2859732 original size:18 final size:19
Alignment explanation
Indices: 2859688--2859737 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
2859678 CCTATGGTTG
*
2859688 TGCTTGTTCCTC-TGCTAT
1 TGCTGGTTCCTCGTGCTAT
* *
2859706 TGCTTGTTCCTCGTGCTGT
1 TGCTGGTTCCTCGTGCTAT
*
2859725 T-CTGGTTCATCGT
1 TGCTGGTTCCTCGT
2859738 TGGAGTCGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.04, C:0.26, G:0.22, T:0.48
Consensus pattern (19 bp):
TGCTGGTTCCTCGTGCTAT
Found at i:2861309 original size:21 final size:21
Alignment explanation
Indices: 2861283--2861364 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
2861273 AGAACCCCAG
2861283 GGGGGTATCGATTCCCCTACA
1 GGGGGTATCGATTCCCCTACA
* * *
2861304 GGGGGTATTGGTTCCCCTTCAAA
1 GGGGGTATCGATTCCCC-T-ACA
* * *
2861327 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTAC-A
2861349 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
2861365 TCTGCACTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 15 0.31
22 17 0.35
23 17 0.35
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.26
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTACA
Found at i:2861365 original size:21 final size:22
Alignment explanation
Indices: 2861283--2861364 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
2861273 AGAACCCCAG
*
2861283 GGGGGTATCGATTCCCCTAC-A
1 GGGGGTATCGATTCCCCTTCAA
* *
2861304 GGGGGTATTGGTTCCCCTTCAAA
1 GGGGGTATCGATTCCCCTTC-AA
* *
2861327 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTTCAA
2861349 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
2861365 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.33
22 16 0.31
23 19 0.37
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTCAA
Found at i:2867871 original size:25 final size:23
Alignment explanation
Indices: 2867824--2867898 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 23
2867814 AAGAAAGGGT
*
2867824 AATAAAAAATAAGGAAAATAAATA
1 AATAAAAAAAAAGGAAAA-AAATA
2867848 AATAAAATAAAAAGGAAGAAAAATA
1 AATAAAA-AAAAAGGAA-AAAAATA
* * *
2867873 AATACAAGAAAAACGAAATAAATA
1 AATA-AAAAAAAAGGAAAAAAATA
2867897 AA
1 AA
2867899 CAAAGTATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
24 15 0.34
25 25 0.57
26 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (23 bp):
AATAAAAAAAAAGGAAAAAAATA
Found at i:2868150 original size:24 final size:24
Alignment explanation
Indices: 2868123--2868178 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
2868113 AAGAAAGGAA
2868123 TAAAAAATAAAAATATATATATA-
1 TAAAAAATAAAAATATATATATAG
* *
2868146 TTAAAAA-AAAAATGTATATATAG
1 TAAAAAATAAAAATATATATATAG
*
2868169 TAAAATATAA
1 TAAAAAATAA
2868179 TATAAAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 14 0.52
23 11 0.41
24 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
TAAAAAATAAAAATATATATATAG
Found at i:2868151 original size:22 final size:22
Alignment explanation
Indices: 2868126--2868175 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2868116 AAAGGAATAA
*
2868126 AAAATAAAAATATATATATATT
1 AAAATAAAAATATATATATAGT
* *
2868148 AAAAAAAAAATGTATATATAGT
1 AAAATAAAAATATATATATAGT
2868170 AAAATA
1 AAAATA
2868176 TAATATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATAAAAATATATATATAGT
Found at i:2870238 original size:43 final size:43
Alignment explanation
Indices: 2870184--2870310 Score: 146
Period size: 43 Copynumber: 3.0 Consensus size: 43
2870174 CTTGTGTAGA
* * * *
2870184 TGGGCATGATATCCTTCATTGTGAAGTTGAAATTGTGGATTTG
1 TGGGCACGATATCCTTCATTGTGGAGTTGAAATCGTGGATGTG
* * * *
2870227 TGGGCACGATATCCTCCATCGTGGAGTTGAAATCATAGATGTG
1 TGGGCACGATATCCTTCATTGTGGAGTTGAAATCGTGGATGTG
* * * *
2870270 TGGGTACGATATCCTTCGTTATGGAGTTAAAATCGTGGATG
1 TGGGCACGATATCCTTCATTGTGGAGTTGAAATCGTGGATG
2870311 GCCCATTCGT
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.34
Consensus pattern (43 bp):
TGGGCACGATATCCTTCATTGTGGAGTTGAAATCGTGGATGTG
Found at i:2871256 original size:6 final size:6
Alignment explanation
Indices: 2871245--2871287 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
2871235 ACCCACCTTA
2871245 TTTTTC TTTTTC -TTTTC TCTTTTC TTTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC -TTTTTC TTTTTC TTTTTC
2871288 AATTTAGGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 18 0.53
7 10 0.29
8 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:2880221 original size:26 final size:25
Alignment explanation
Indices: 2880170--2880240 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 25
2880160 AATAAAAAAT
* * *
2880170 AAGGAAAATAAATAAATAAAATAAA
1 AAGGAAAAAAAATAAAGAAAAGAAA
*
2880195 AAGGAAGAAAAAATAAAGACAAGAAA
1 AAGGAA-AAAAAATAAAGAAAAGAAA
* * *
2880221 AA-CAAAATAAATAAACAAAA
1 AAGGAAAAAAAATAAAGAAAA
2880241 TATAGGTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
24 12 0.32
25 8 0.22
26 17 0.46
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (25 bp):
AAGGAAAAAAAATAAAGAAAAGAAA
Found at i:2880467 original size:12 final size:12
Alignment explanation
Indices: 2880441--2880472 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
2880431 AATAATAAAT
2880441 AAATAAAAGGAA
1 AAATAAAAGGAA
2880453 AAATAGAAAGGAA
1 AAATA-AAAGGAA
2880466 AAATAAA
1 AAATAAA
2880473 TAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAATAAAAGGAA
Found at i:2880494 original size:25 final size:25
Alignment explanation
Indices: 2880466--2880514 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2880456 TAGAAAGGAA
*
2880466 AAATAAATAAATATATATATTAAAT
1 AAATAAATAAATATATATAGTAAAT
**
2880491 AAATAAATATGTATATATAGTAAA
1 AAATAAATAAATATATATAGTAAA
2880515 ATATAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
AAATAAATAAATATATATAGTAAAT
Found at i:2880514 original size:21 final size:21
Alignment explanation
Indices: 2880466--2880506 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2880456 TAGAAAGGAA
2880466 AAATAAATAAATATATATATT
1 AAATAAATAAATATATATATT
*
2880487 AAATAAATAAATATGTATAT
1 AAATAAATAAATATATATAT
2880507 ATAGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATAAATAAATATATATATT
Found at i:2884922 original size:2 final size:2
Alignment explanation
Indices: 2884915--2884939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2884905 CATTTTTCAA
2884915 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 A
2884940 CTTCTTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2886930 original size:180 final size:182
Alignment explanation
Indices: 2886561--2887270 Score: 646
Period size: 179 Copynumber: 3.9 Consensus size: 182
2886551 TAGGTTGTGT
* * * * *
2886561 CTAAAATGTTACTAGAGTTTAAGCTAATGGGGCCTTAGACATTCCTACGATAAAAAATAATTTAA
1 CTAAAATGTTACCAGAGTTTAAGCTAATGAGG-CTTAGACATTCCCACGATAACAAATAAGTTAA
* * **
2886626 AAG-TTGAAATGTTATGAATA--TATAAGAAATGTGGTTGCGCCCAAAGAATGTCATGGTTCACT
65 AAGCTTAAAATGTTATGAATATCTATAATAAATACGGTTGCGCCCAAAGAATGTCATGGTTCACT
* * * * * * *
2886688 GAGAAA-TAGGTTGCGATATGTAATGTTAATATATTTATTAGT-AAATAGATTGCG
130 AAGAAAGTAGGTTGC--TATGAAATATTAATATTTTTATTA-TAAAATGGGTTGCC
* * * * * *
2886742 CT-AAATGTTACCAGAGTTTAAGTTGATGAGGCTTAGACAATCCCATGATAAGAAATAAGTTAAT
1 CTAAAATGTTACCAGAGTTTAAGCTAATGAGGCTTAGACATTCCCACGATAACAAATAAGTTAAA
* * * *
2886806 AG-TTAAAACTGATATGTATATCTATAATAAATACGGTTGCG-CC-AAGAATATCATGATTCACT
66 AGCTTAAAA-TGTTATGAATATCTATAATAAATACGGTTGCGCCCAAAGAATGTCATGGTTCACT
* **
2886868 AAGAAAGTAGGTTGCTATGGAATACGAATATTTTTATTATAAAATGGGTT-CAC
130 AAGAAAGTAGGTTGCTATGAAATATTAATATTTTTATTATAAAATGGGTTGC-C
* * * * * *
2886921 CTAAAATGTTACTAGAGTCTAAGCTAATAAGACTTA-A-ATTTTCC-CGATAACAAAAAAGTTAA
1 CTAAAATGTTACCAGAGTTTAAGCTAATGAGGCTTAGACA-TTCCCACGATAACAAATAAGTTAA
* * * * *
2886983 AAGCTGAAAATGTTATGAATATCTATAATAAATACGGTTGCG-TCTAATAATGTCATGG-TAACT
65 AAGCTTAAAATGTTATGAATATCTATAATAAATACGGTTGCGCCCAAAGAATGTCATGGTTCACT
* * * *
2887046 AAGAATGTA-GTTACGATATGAAATATTAATATTTTTATTGATAAAATGAGTTGTGC
130 AAGAAAGTAGGTT--GCTATGAAATATTAATATTTTTATT-ATAAAATGGGTTG-CC
* * * * * **
2887102 CTAAACTGTTACCATAATTTAAGCTGATGGAGCCTTAGATTTTCCCACGATAACAAATAAGTTAA
1 CTAAAATGTTACCAGAGTTTAAGCTAAT-GAGGCTTAGACATTCCCACGATAACAAATAAGTTAA
* * * *
2887167 AAGCTTAAAATGTTATGAATATCTACAATAAATACGATTG-G-CCTAAGATTGTCATGGTTCACT
65 AAGCTTAAAATGTTATGAATATCTATAATAAATACGGTTGCGCCCAAAGAATGTCATGGTTCACT
* * *
2887230 AAGAAAGTAGGTTACGAATTGAAACATTAATATTTTTATTA
130 AAGAAAGTAGGTTGC-TA-TGAAATATTAATATTTTTATTA
2887271 ATATATTGTG
Statistics
Matches: 429, Mismatches: 77, Indels: 43
0.78 0.14 0.08
Matches are distributed among these distances:
177 3 0.01
178 63 0.15
179 102 0.24
180 94 0.22
181 35 0.08
182 22 0.05
183 19 0.04
184 68 0.16
185 23 0.05
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (182 bp):
CTAAAATGTTACCAGAGTTTAAGCTAATGAGGCTTAGACATTCCCACGATAACAAATAAGTTAAA
AGCTTAAAATGTTATGAATATCTATAATAAATACGGTTGCGCCCAAAGAATGTCATGGTTCACTA
AGAAAGTAGGTTGCTATGAAATATTAATATTTTTATTATAAAATGGGTTGCC
Found at i:2887230 original size:362 final size:359
Alignment explanation
Indices: 2886561--2887242 Score: 808
Period size: 362 Copynumber: 1.9 Consensus size: 359
2886551 TAGGTTGTGT
* ** * * *
2886561 CTAAAATGTTACTAGAGTTTAAGCTAATGGGGCCTTAGACATTCCTACGATAAAAAATAATTTAA
1 CTAAAATGTTACTAGAGTCTAAGCTAATGAAGACTTAAACATTCC-ACGATAAAAAATAAGTTAA
* ** * *
2886626 AAGTTGAAATGTTATGAATATATAAGAAATGTGGTTGCGCCCAAAGAATGTCATGGTTCACTGAG
65 AAGCTGAAATGTTATGAATATATAAGAAATACGGTTGCGCCCAAAGAATGTCATGGTTAACTAAG
* * *
2886691 AAATAGGTTGCGATATGTAATGTTAATATATTTATTAGTAAATAGATTGCGCTAAATGTTACCAG
130 AAATAGGTTACGATATGAAATATTAATATATTTATTAGTAAATAGATTGCGCTAAATGTTACCAG
* * * * * *
2886756 AGTTTAAGTTGATGAGGCTTAGACAATCCCATGATAAGAAATAAGTTAATAGTTAAAACTGATAT
195 AATTTAAGCTGATGAGCCTTAGACAATCCCACGATAACAAATAAGTTAAAAGTTAAAACTGATAT
* * *
2886821 GTATATCTATAATAAATACGGTTGCGCCAAGAATATCATGATTCACTAAGAAAGTAGGTTGCTAT
260 GAATATCTACAATAAATACGATTGCGCCAAGAATATCATGATTCACTAAGAAAGTAGGTTGCTAT
2886886 GGAATACGAATATTTTTATTATAAAATGGGTTCAC
325 GGAATACGAATATTTTTATTATAAAATGGGTTCAC
**
2886921 CTAAAATGTTACTAGAGTCTAAGCTAAT-AAGACTTAAATTTTCC-CGATAACAAAA-AAGTTAA
1 CTAAAATGTTACTAGAGTCTAAGCTAATGAAGACTTAAACATTCCACGATAA-AAAATAAGTTAA
* * * *
2886983 AAGCTGAAAATGTTATGAATATCTATAATAAATACGGTTGCG-TCTAATAATGTCATGG-TAACT
65 AAGCTG-AAATGTTATGAATA--TATAAGAAATACGGTTGCGCCCAAAGAATGTCATGGTTAACT
* * *
2887046 AAGAATGTA-GTTACGATATGAAATATTAATATTTTTATT-GATAAA-ATGAGTTGTGCCTAAAC
127 AAGAA-ATAGGTTACGATATGAAATATTAATATATTTATTAG-TAAATA-GA-TTGCG-CTAAA-
* ***
2887108 TGTTACCATAATTTAAGCTGATGGAGCCTTAGATTTTCCCACGATAACAAATAAGTTAAAAGCTT
186 TGTTACCAGAATTTAAGCTGAT-GAGCCTTAGACAATCCCACGATAACAAATAAGTTAAAAG-TT
* * * *
2887173 AAAA-TGTTATGAATATCTACAATAAATACGATTG-GCCTAAGATTGTCATGGTTCACTAAGAAA
249 AAAACTGATATGAATATCTACAATAAATACGATTGCGCC-AAGAATATCATGATTCACTAAGAAA
2887236 GTAGGTT
313 GTAGGTT
2887243 ACGAATTGAA
Statistics
Matches: 269, Mismatches: 40, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
357 19 0.07
358 58 0.22
359 29 0.11
360 48 0.18
361 22 0.08
362 87 0.32
363 6 0.02
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (359 bp):
CTAAAATGTTACTAGAGTCTAAGCTAATGAAGACTTAAACATTCCACGATAAAAAATAAGTTAAA
AGCTGAAATGTTATGAATATATAAGAAATACGGTTGCGCCCAAAGAATGTCATGGTTAACTAAGA
AATAGGTTACGATATGAAATATTAATATATTTATTAGTAAATAGATTGCGCTAAATGTTACCAGA
ATTTAAGCTGATGAGCCTTAGACAATCCCACGATAACAAATAAGTTAAAAGTTAAAACTGATATG
AATATCTACAATAAATACGATTGCGCCAAGAATATCATGATTCACTAAGAAAGTAGGTTGCTATG
GAATACGAATATTTTTATTATAAAATGGGTTCAC
Found at i:2887621 original size:72 final size:72
Alignment explanation
Indices: 2887497--2887631 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 72
2887487 TTATGTGGTA
* *
2887497 ATGATCGATACTTTTAAATATTGAAAAAAATTGATAAAAATATCAAATTTAAAA-ATTGATACTT
1 ATGATCGATACTTTTAAATATTG-AAAAAATTGATAAAAATATCAAAGTTAAAATATCGATACTT
2887561 ATGCAATG
65 ATGCAATG
* * *
2887569 ATGATCGATACTTTTATATATTG-AAAAATTGATGAAGAAGAT-TGATAGTTAAAATATCGATAC
1 ATGATCGATACTTTTAAATATTGAAAAAATTGAT-AA-AA-ATATCAAAGTTAAAATATCGATAC
2887632 ATATTATGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
70 10 0.19
71 2 0.04
72 33 0.61
73 9 0.17
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (72 bp):
ATGATCGATACTTTTAAATATTGAAAAAATTGATAAAAATATCAAAGTTAAAATATCGATACTTA
TGCAATG
Found at i:2889531 original size:267 final size:267
Alignment explanation
Indices: 2889029--2889556 Score: 992
Period size: 267 Copynumber: 2.0 Consensus size: 267
2889019 CCTCCAAACT
2889029 GCTATGATTGGAATGAGCTTGCATCTGCCAAAAATTATCTTTTGATAAAACGTAAGCATGAATCC
1 GCTATGATTGGAATGAGCTTGCATCTGCCAAAAATTATCTTTTGATAAAACGTAAGCATGAATCC
2889094 AAACAACCCAAATAGGCCCCCTGTAAGATAGCCTAATAAGTAAACTAGGGCAACATTATTTCAAG
66 AAACAACCCAAATAGGCCCCCTGTAAGATAGCCTAATAAGTAAACTAGGGCAACATTATTTCAAG
2889159 TTTCATATCCTTGAGCCCTAACCCCCTTCAAGATTTAGGGCAACAAATAATTCTACAACTAACTC
131 TTTCATATCCTTGAGCCCTAACCCCCTTCAAGATTTAGGGCAACAAATAATTCTACAACTAACTC
2889224 GAGCCCTTCTCGCTGTAATATCACAATTCTTCTAAAAAAAACTGGAACAAATATGCTTAATTATA
196 GAGCCCTTCTCGCTGTAATATCACAATTCTTCTAAAAAAAACTGGAACAAATATGCTTAATTATA
2889289 AAACATG
261 AAACATG
2889296 GCTATGATTGGAATGAGCTTGCATCTGCCAAAAATTATCTTTTGATAAAACGTAAGCATGAATCC
1 GCTATGATTGGAATGAGCTTGCATCTGCCAAAAATTATCTTTTGATAAAACGTAAGCATGAATCC
2889361 AAACAACCCAAATAGG-CCCCTGTAAGATAGCCTTAATAAGTAAAACTA-GGCAAACATTATTTC
66 AAACAACCCAAATAGGCCCCCTGTAAGATAGCC-TAATAAGT-AAACTAGGGC-AACATTATTTC
2889424 AAGTTTTCATATCCTTGAGCCCTAACCCCCTTC-AGATTTAGGGCAACAAATAATTCTACAACTA
128 AAG-TTTCATATCCTTGAGCCCTAACCCCCTTCAAGATTTAGGGCAACAAATAATTCTACAACTA
2889488 ACTCGAGCCCTTCTCGCTGTAATATCACAATTCTTCT-AAAAAAACTGGAACAAATATGCTTAAT
192 ACTCGAGCCCTTCTCGCTGTAATATCACAATTCTTCTAAAAAAAACTGGAACAAATATGCTTAAT
2889552 TATAA
257 TATAA
2889557 GAAGAACAAT
Statistics
Matches: 257, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
266 16 0.06
267 124 0.48
268 88 0.34
269 29 0.11
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (267 bp):
GCTATGATTGGAATGAGCTTGCATCTGCCAAAAATTATCTTTTGATAAAACGTAAGCATGAATCC
AAACAACCCAAATAGGCCCCCTGTAAGATAGCCTAATAAGTAAACTAGGGCAACATTATTTCAAG
TTTCATATCCTTGAGCCCTAACCCCCTTCAAGATTTAGGGCAACAAATAATTCTACAACTAACTC
GAGCCCTTCTCGCTGTAATATCACAATTCTTCTAAAAAAAACTGGAACAAATATGCTTAATTATA
AAACATG
Found at i:2893734 original size:21 final size:21
Alignment explanation
Indices: 2893708--2893792 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
2893698 ATCGAGGGTT
2893708 ATATGTGGTCATTCGGGACAA
1 ATATGTGGTCATTCGGGACAA
*
2893729 ATATGTGGTCTTTCGGGACAA
1 ATATGTGGTCATTCGGGACAA
* *
2893750 ATATGTGGTCCTCCGGGACAA
1 ATATGTGGTCATTCGGGACAA
* **
2893771 ATAT-AGGTCATTCAAGACAA
1 ATATGTGGTCATTCGGGACAA
2893791 AT
1 AT
2893793 TCTATGTGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 13 0.23
21 43 0.77
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (21 bp):
ATATGTGGTCATTCGGGACAA
Found at i:2898725 original size:42 final size:42
Alignment explanation
Indices: 2898665--2898745 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
2898655 GGGTTCTATG
* * * *
2898665 TGGTCCTTCTGGACAAATATGTAGTCATTTGGGATAAATATA
1 TGGTCCTCCAGGACAAATATATAGTCATTTGGGACAAATATA
* * *
2898707 TGGTCCTCCAGGATAAATATATGGTCTTTTGGGACAAAT
1 TGGTCCTCCAGGACAAATATATAGTCATTTGGGACAAAT
2898746 TCTATGTACC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
TGGTCCTCCAGGACAAATATATAGTCATTTGGGACAAATATA
Found at i:2898745 original size:21 final size:21
Alignment explanation
Indices: 2898675--2898745 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2898665 TGGTCCTTCT
* *
2898675 GGACAAATATGTAGTCATTTG
1 GGACAAATATATGGTCATTTG
* * ***
2898696 GGATAAATATATGGTCCTCCA
1 GGACAAATATATGGTCATTTG
* *
2898717 GGATAAATATATGGTCTTTTG
1 GGACAAATATATGGTCATTTG
2898738 GGACAAAT
1 GGACAAAT
2898746 TCTATGTACC
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (21 bp):
GGACAAATATATGGTCATTTG
Found at i:2899516 original size:16 final size:17
Alignment explanation
Indices: 2899487--2899522 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2899477 AAATTTTAAT
2899487 TGTTTTGTAAAAGTAAA
1 TGTTTTGTAAAAGTAAA
*
2899504 TGTTTTG-AAAAGTCAA
1 TGTTTTGTAAAAGTAAA
2899520 TGT
1 TGT
2899523 GACACATCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (17 bp):
TGTTTTGTAAAAGTAAA
Found at i:2904605 original size:218 final size:218
Alignment explanation
Indices: 2904207--2904639 Score: 793
Period size: 219 Copynumber: 2.0 Consensus size: 218
2904197 TAGAGAATTG
2904207 TTATATTAAATGATGTGTTTTTAAGATAAATCTATTACAAATTTCTTTATTTGAGCATAATTATT
1 TTATATTAAATGATGTGTTTTTAAGATAAATCTATTACAAATTTCTTTATTTGAGCATAATTATT
2904272 ATTGACAAGGATATATTTGATACACTTAAAACGAGATTCTTCTGAAAGATAAATCTTGACGGTGG
66 ATTGACAAGGATATATTTGATACACTTAAAACGAGATTCTTCTGAAAGATAAATCTTGACGGTGG
2904337 AAAACCATGTCTAGCAAATAATCTTGTTGGAAAAAAAGTAATTTTTCCTTGT-AAATTTACTTAT
131 AAAACCATGTCTAGCAAATAATCTTGTTGGAAAAAAAGTAATTTTTCCTTGTAAAATTTACTTAT
2904401 CGGATA-AGAGAAATTTATAATGTT
196 CGGA-AGA-AGAAATTTATAATGTT
2904425 TTATATTAAATGATGTGTTTTTAAGATAAATCTATTACAAATTTTCTTTATTTGAGCATAATTAT
1 TTATATTAAATGATGTGTTTTTAAGATAAATCTATTACAAA-TTTCTTTATTTGAGCATAATTAT
2904490 TATTTGACAAGGATATATTTGATACACTT-AAACGAGATTCTTCTGAAAGATAAATCTTGACGGT
65 TA-TTGACAAGGATATATTTGATACACTTAAAACGAGATTCTTCTGAAAGATAAATCTTGACGGT
2904554 GGAAAACCATGTCTAGCAAATAATCTTGTTGG-AAAAAAGTAATTTTTCCTTGTAAAATTTACTT
129 GGAAAACCATGTCTAGCAAATAATCTTGTTGGAAAAAAAGTAATTTTTCCTTGTAAAATTTACTT
2904618 ATCGGAAGTAAGAAATTTATAA
194 ATCGGAAG-AAGAAATTTATAA
2904640 AAAGATTCTT
Statistics
Matches: 210, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
218 63 0.30
219 120 0.57
220 27 0.13
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (218 bp):
TTATATTAAATGATGTGTTTTTAAGATAAATCTATTACAAATTTCTTTATTTGAGCATAATTATT
ATTGACAAGGATATATTTGATACACTTAAAACGAGATTCTTCTGAAAGATAAATCTTGACGGTGG
AAAACCATGTCTAGCAAATAATCTTGTTGGAAAAAAAGTAATTTTTCCTTGTAAAATTTACTTAT
CGGAAGAAGAAATTTATAATGTT
Found at i:2908351 original size:20 final size:20
Alignment explanation
Indices: 2908303--2908354 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2908293 TGAATTGGTA
*
2908303 GTATCGATACAAAGAGTATG
1 GTATCGATACCAAGAGTATG
*
2908323 GTACCGATACCAAGAGTATG
1 GTATCGATACCAAGAGTATG
*
2908343 GTATAGATACCA
1 GTATCGATACCA
2908355 TTTCCATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (20 bp):
GTATCGATACCAAGAGTATG
Found at i:2923243 original size:30 final size:30
Alignment explanation
Indices: 2923209--2923378 Score: 259
Period size: 30 Copynumber: 5.7 Consensus size: 30
2923199 GTAAATAATA
* *
2923209 TTATCGTTTGTTACAAAATGGTCATTAACG
1 TTATCGTTTGTTACAAAATGGCCACTAACG
* *
2923239 TTATCGTTTGTTACAAAATGGTCATTAACG
1 TTATCGTTTGTTACAAAATGGCCACTAACG
*
2923269 TTATCGTTTGTTACAAAATGGCCACTAAAG
1 TTATCGTTTGTTACAAAATGGCCACTAACG
* * *
2923299 TTATTGTTTGTTATAAAATGACCACTAACG
1 TTATCGTTTGTTACAAAATGGCCACTAACG
*
2923329 TTATCGTTTGTTACAAAATGGCCACTAAAG
1 TTATCGTTTGTTACAAAATGGCCACTAACG
2923359 TTATCGTTTGTTACAAAATG
1 TTATCGTTTGTTACAAAATG
2923379 ATCAATCGAC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 129 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (30 bp):
TTATCGTTTGTTACAAAATGGCCACTAACG
Found at i:2926301 original size:23 final size:24
Alignment explanation
Indices: 2926259--2926308 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
2926249 ATATGTACAT
* *
2926259 GAACATATAAACGAACATGTTCGC
1 GAACATATAAACCAAAATGTTCGC
2926283 GAACAT-TAAACCAAAATGTTCGC
1 GAACATATAAACCAAAATGTTCGC
2926306 GAA
1 GAA
2926309 TAAACGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (24 bp):
GAACATATAAACCAAAATGTTCGC
Found at i:2927220 original size:25 final size:25
Alignment explanation
Indices: 2927192--2927267 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
2927182 TTCATCGACT
2927192 ATTAAAAATATGAAATTATCTATTG
1 ATTAAAAATATGAAATTATCTATTG
* * *
2927217 ATTATAAGATAT-TAATTCGT-TGATT-
1 ATTA-AAAATATGAAATT-ATCT-ATTG
2927242 ATTAAAAATTATGAAATTATCTATTG
1 ATTAAAAA-TATGAAATTATCTATTG
2927268 TTTATAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 13
0.67 0.11 0.23
Matches are distributed among these distances:
24 3 0.08
25 20 0.53
26 15 0.39
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTAAAAATATGAAATTATCTATTG
Found at i:2927265 original size:51 final size:50
Alignment explanation
Indices: 2927188--2927300 Score: 181
Period size: 51 Copynumber: 2.2 Consensus size: 50
2927178 TGAATTCATC
2927188 GACTATTAAAAATATGAAATTATCTATTGATTATAAGATATTAATTCGTT
1 GACTATTAAAAATATGAAATTATCTATTGATTATAAGATATTAATTCGTT
* * * *
2927238 GATTATTAAAAATTATGAAATTATCTATTGTTTATAAGGTATTAATTTGTT
1 GACTATTAAAAA-TATGAAATTATCTATTGATTATAAGATATTAATTCGTT
2927289 GACTATTAAAAA
1 GACTATTAAAAA
2927301 CTAGATTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 11 0.19
51 46 0.81
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (50 bp):
GACTATTAAAAATATGAAATTATCTATTGATTATAAGATATTAATTCGTT
Found at i:2932406 original size:41 final size:42
Alignment explanation
Indices: 2932328--2932412 Score: 163
Period size: 41 Copynumber: 2.0 Consensus size: 42
2932318 AGAAGCAAGC
2932328 TTCGTATAGTTCACTTCAATGGAGGCTTCCAATGGCGCTTCG
1 TTCGTATAGTTCACTTCAATGGAGGCTTCCAATGGCGCTTCG
2932370 TTCGTATAGTTCACTTCAAT-GAGGCTTCCAATGGCGCTTCG
1 TTCGTATAGTTCACTTCAATGGAGGCTTCCAATGGCGCTTCG
2932411 TT
1 TT
2932413 GAGGAAGGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (42 bp):
TTCGTATAGTTCACTTCAATGGAGGCTTCCAATGGCGCTTCG
Found at i:2932698 original size:15 final size:16
Alignment explanation
Indices: 2932679--2932720 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2932669 GCATTTAAAC
2932679 ATATTTGCATTT-TTT
1 ATATTTGCATTTCTTT
* *
2932694 TTATTTTCATTTCTTT
1 ATATTTGCATTTCTTT
*
2932710 ATATTCGCATT
1 ATATTTGCATT
2932721 AGCTAACAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
ATATTTGCATTTCTTT
Found at i:2933638 original size:100 final size:100
Alignment explanation
Indices: 2933450--2933709 Score: 307
Period size: 100 Copynumber: 2.6 Consensus size: 100
2933440 TAAATTTATA
* * *
2933450 TATAC-ATAAAGCTTTAGTTATCCCTCTAAAGCAATTGGTTAAATGCTCCAGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGTTATCCCTCTAAAGAAATTGGTTAAATGCCCCAGCTTTATGGATAAG
*
2933514 ATTCAGCTAAGCCTGATAAAGGTGATTATAATATC
66 ATTCAGCTAAGCCTAATAAAGGTGATTATAATATC
* *
2933549 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAAATTGGTTAAACT-CCCC-GACTTTATGGAT
1 TATACAATAAAGCTTGAGTTATCCCTCTAAAG-AAATTGGTTAAA-TGCCCCAG-CTTTATGGAT
* *
2933612 AATATTCAGCT-AGCCTAATAAAGGTGATTATAATATT
63 AAGATTCAGCTAAGCCTAATAAAGGTGATTATAATATC
* * * * * * *
2933649 TATACAATGATA--TTAAGCTATCCCTCTAGAGCAATTGGTTAAACGCCTCAGCTTTATGGAT
1 TATACAAT-AAAGCTTGAGTTATCCCTCTAAAGAAATTGGTTAAATGCCCCAGCTTTATGGAT
2933710 TCAGCTAGCC
Statistics
Matches: 139, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
98 24 0.17
99 22 0.16
100 56 0.40
101 36 0.26
102 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (100 bp):
TATACAATAAAGCTTGAGTTATCCCTCTAAAGAAATTGGTTAAATGCCCCAGCTTTATGGATAAG
ATTCAGCTAAGCCTAATAAAGGTGATTATAATATC
Found at i:2935539 original size:124 final size:123
Alignment explanation
Indices: 2935129--2935541 Score: 517
Period size: 124 Copynumber: 3.3 Consensus size: 123
2935119 TAAGAGCCAA
*
2935129 TTTTAACTTCACGACGAATGATATTG-GACTCGA--AGCAACATTCATCTTTAGATTGGATTTCA
1 TTTTAACTTCACGACGAAGGA-ATTGTG-CTC-ACTAGCAACATTCATCTTTAGATTGGATTTCA
* * * *
2935191 ACTTCATTACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGG
63 ACTTCATGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGG
* * *
2935252 TTTTAACTTCACGACGAAGGGAATCGTGCTCACTAGTATCATTCATCTTTAGATTGGATTTCAAC
1 TTTTAACTTCACGACGAA-GGAATTGTGCTCACTAGCAACATTCATCTTTAGATTGGATTTCAAC
* * * *
2935317 TTCATGATGAAGAATATTCAATTCAGGGCTCAACTTCACAACGAAAGGGCCATCCACGG
65 TTCATGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGG
* * * * * *
2935376 TTTTAGCTTCACGATGAGAGGAATTGTGCCCACCAGCAACATTCATCTTCAGATTAGATTTCAAC
1 TTTTAACTTCACGACGA-AGGAATTGTGCTCACTAGCAACATTCATCTTTAGATTGGATTTCAAC
* * * *
2935441 TTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCCTCCACGA
65 TTCATGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGG
* * * *
2935500 TTTCAACTTCACGACGAAGGATATTGTGTTCATTTGCAACAT
1 TTTTAACTTCACGACGAAGGA-ATTGTGCTCACTAGCAACAT
2935542 AGCTCAAGGC
Statistics
Matches: 247, Mismatches: 37, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
122 1 0.00
123 28 0.11
124 217 0.88
125 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (123 bp):
TTTTAACTTCACGACGAAGGAATTGTGCTCACTAGCAACATTCATCTTTAGATTGGATTTCAACT
TCATGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGG
Found at i:2935725 original size:84 final size:84
Alignment explanation
Indices: 2935529--2935962 Score: 497
Period size: 84 Copynumber: 5.2 Consensus size: 84
2935519 GATATTGTGT
* * * * *
2935529 TCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
2935594 CGCTCAGCTCTAAGG-AAA
66 CGCTCAGCTCCAAGGCACA
* * * *
2935612 TCATTTGCAGCATAACTCAAGGCTAGAAGGATTATCTGCCAACCAAAGGCCTTCTAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
2935677 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
*
2935696 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAAGACCTTCGAGTTCAACT
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACT
* *
2935760 ATGCTCAGCTCCAAGGCATA
65 ACGCTCAGCTCCAAGGCACA
* * * *
2935780 TCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * *
2935841 CACTCAGCTTCGAGGGCACA
66 CGCTCAGC-TCCAAGGCACA
* * * * * *
2935861 TCATTTACAACATAACTCAAGGCTAGAAGGGTTTATCTGTCAA-CAAAGACCTTTGAGTTCGATT
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGG-TTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
2935925 ACACTCAGCT-CAGCGGCACA
65 ACGCTCAGCTCCA-AGGCACA
* *
2935945 TCATTTGTAGTATAGCTC
1 TCATTTGCAGCATAGCTC
2935963 GATCACACTA
Statistics
Matches: 300, Mismatches: 42, Indels: 17
0.84 0.12 0.05
Matches are distributed among these distances:
80 24 0.08
81 37 0.12
82 6 0.02
83 74 0.25
84 131 0.44
85 28 0.09
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:2935911 original size:165 final size:165
Alignment explanation
Indices: 2935529--2935962 Score: 518
Period size: 165 Copynumber: 2.6 Consensus size: 165
2935519 GATATTGTGT
* *
2935529 TCATTTGCAACATAGCTCAAGGCAAGAAGGGTTAT-TTTCCAACAAAAGACCTTCGAGTTCGACT
1 TCATTTGCAACATAGCTCAAGGCTAGAAGGGTTATCTGT-CAACAAAAGACCTTCGAGTTCGACT
* * * *
2935593 ACGCTCAGCTCTAAGG-AAATCATTTGCAGCATAACTCAAGGCTAGAAGGATTATCTGCCAACCA
65 ACGCTCAGCTCCAAGGCAAATCATTTGCAGTATAGCTCAAGGCTAGAAGGACTATCTG---ACCA
* * * *
2935657 AAGGCCTTCTAGTTCGACTACGCTCAGCTCCAAGGCACA
127 AAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACA
* * * *
2935696 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCAACTA
1 TCATTTGCAACATAGCTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTA
* * *
2935761 TGCTCAGCTCCAAGGCATATCATTTGCAGTATAGCTCAAGGCTAGAAGGGCTATCTG-CCAAAGA
66 CGCTCAGCTCCAAGGCAAATCATTTGCAGTATAGCTCAAGGCTAGAAGGACTATCTGACCAAAGA
* * *
2935825 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
131 CCCTCGAGTTCGACTACACTCAGC-TCCAAGGCACA
* * * *
2935861 TCATTTACAACATAACTCAAGGCTAGAAGGGTTTATCTGTCAAC-AAAGACCTTTGAGTTCGATT
1 TCATTTGCAACATAGCTCAAGGCTAGAAGGG-TTATCTGTCAACAAAAGACCTTCGAGTTCGACT
* * * *
2935925 ACACTCAGCT-CAGCGGCACATCATTTGTAGTATAGCTC
65 ACGCTCAGCTCCA-AGGCAAATCATTTGCAGTATAGCTC
2935963 GATCACACTA
Statistics
Matches: 229, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
164 28 0.12
165 84 0.37
166 10 0.04
167 70 0.31
168 37 0.16
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
TCATTTGCAACATAGCTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCAAATCATTTGCAGTATAGCTCAAGGCTAGAAGGACTATCTGACCAAAGA
CCCTCGAGTTCGACTACACTCAGCTCCAAGGCACA
Found at i:2936355 original size:36 final size:35
Alignment explanation
Indices: 2936310--2936555 Score: 152
Period size: 36 Copynumber: 7.0 Consensus size: 35
2936300 TTAAAACGGT
* * *
2936310 TTTCTAAAATATGTATAATATATAGTTTCGAAAAC
1 TTTCGAAAATATATATAATATATAGTTTTGAAAAC
* * **
2936345 ATTTCGAAAATTTATATATTATATAGTTTTGAAATTT
1 -TTTCGAAAATATATATAATATATAGTTTTGAAA-AC
* * * *
2936382 TTTTGGAAATATTTATAATGTATAGTTTTTGAAAATTC
1 TTTCGAAAATATATATAATATATAG-TTTTGAAAA--C
*
2936420 TTTTGAAAATATATATAATATATAGTTTTG-AAA-
1 TTTCGAAAATATATATAATATATAGTTTTGAAAAC
*
2936453 -TT-----ATATATATAATATATAGTTTTTAAAAC
1 TTTCGAAAATATATATAATATATAGTTTTGAAAAC
* * *
2936482 ATTTTTTGAAAACT-TATATAGTATATAGTTTTAAAAAC
1 ---TTTCGAAAA-TATATATAATATATAGTTTTGAAAAC
* *
2936520 ATTTTTGAAAA-ATTATATAATATATAGTTTTAAAAA
1 --TTTCGAAAATA-TATATAATATATAGTTTTGAAAA
2936556 TATTTTTTGA
Statistics
Matches: 169, Mismatches: 23, Indels: 35
0.74 0.10 0.15
Matches are distributed among these distances:
27 21 0.12
28 3 0.02
32 2 0.01
33 2 0.01
36 50 0.30
37 45 0.27
38 45 0.27
39 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (35 bp):
TTTCGAAAATATATATAATATATAGTTTTGAAAAC
Found at i:2936446 original size:74 final size:72
Alignment explanation
Indices: 2936316--2936454 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 72
2936306 CGGTTTTCTA
* *
2936316 AAATATGTATAATATATAGTTTCGAAAACATTTCGAAAATTTATATATTATATAGTTTTGAAATT
1 AAATATGTATAATATATAGTTTCGAAAACATTTCGAAAATATATATAATATATAGTTTTGAAATT
2936381 TTTTTGG
66 TTTTTGG
* * * *
2936388 AAATATTTATAATGTATAGTTTTTGAAAATTC-TTTTGAAAATATATATAATATATAGTTTTGAA
1 AAATATGTATAATATATAG-TTTCGAAAA--CATTTCGAAAATATATATAATATATAGTTTTGAA
2936452 ATT
63 ATT
2936455 ATATATATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 17 0.29
73 8 0.14
74 32 0.55
75 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (72 bp):
AAATATGTATAATATATAGTTTCGAAAACATTTCGAAAATATATATAATATATAGTTTTGAAATT
TTTTTGG
Found at i:2936458 original size:27 final size:25
Alignment explanation
Indices: 2936420--2936480 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 25
2936410 TTGAAAATTC
2936420 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAATATATATAATATATAG
2936445 TTTTGAAATTATATATATAATATATAG
1 TTTTGAAA--ATATATATAATATATAG
*
2936472 TTTTTAAAA
1 TTTTGAAAA
2936481 CATTTTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
27 24 0.73
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (25 bp):
TTTTGAAAATATATATAATATATAG
Found at i:2936465 original size:65 final size:65
Alignment explanation
Indices: 2936390--2936578 Score: 184
Period size: 65 Copynumber: 2.8 Consensus size: 65
2936380 TTTTTTGGAA
* * *
2936390 ATATTTATAATGTATAGTTTTTGAAA-ATTCTTTTGAAAA-TATATATAATATATAGTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATT-TTTTGAAAACT-TATATAATATATAGTTTTGAAA
2936453 TT
64 TT
* *
2936455 ATATATATAATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAGTATATAGTTTTAAAAAC
1 ATATATATAATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAATATATAGTTTT--GAA-
2936520 ATTTTT
63 A---TT
* * *
2936526 GAAAAATTATATAATATATAGTTTTAAAAATATTTTTTGAAAACTTATATAAT
1 ---ATA-TATATAATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAAT
2936579 GTTTTTAAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
65 49 0.48
66 4 0.04
67 2 0.02
68 1 0.01
71 2 0.02
74 2 0.02
75 43 0.42
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (65 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAATATATAGTTTTGAAATT
Found at i:2936563 original size:38 final size:36
Alignment explanation
Indices: 2936457--2936686 Score: 233
Period size: 37 Copynumber: 6.5 Consensus size: 36
2936447 TTGAAATTAT
*
2936457 ATATATAATATATAGTTTTTAAAACATTTTTTGAAAA
1 ATATATAATATATAGTTTTAAAAACA-TTTTTGAAAA
* *
2936494 CTTATATAGTATATAGTTTTAAAAACATTTTTGAAAA
1 -ATATATAATATATAGTTTTAAAAACATTTTTGAAAA
*
2936531 ATTATATAATATATAGTTTTAAAAATATTTTTTGAAAA
1 A-TATATAATATATAGTTTTAAAAACA-TTTTTGAAAA
* * ** *
2936569 CT-TAT-ATA-AT-GTTTTTAAATTAATTTTGAAAA
1 ATATATAATATATAGTTTTAAAAACATTTTTGAAAA
* **
2936601 ATATATAATATATAGTTTTGAAAACATTTTT--TTA
1 ATATATAATATATAGTTTTAAAAACATTTTTGAAAA
* *
2936635 A-ATATAATATATAG-TTTAAAAATATTTTTGAAAT
1 ATATATAATATATAGTTTTAAAAACATTTTTGAAAA
*
2936669 ATATATATTATATAGTTT
1 ATATATAATATATAGTTT
2936687 ATATTATATT
Statistics
Matches: 159, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
32 23 0.14
33 26 0.16
34 8 0.05
35 17 0.11
36 18 0.11
37 34 0.21
38 33 0.21
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATATAATATATAGTTTTAAAAACATTTTTGAAAA
Found at i:2936575 original size:68 final size:68
Alignment explanation
Indices: 2936457--2936686 Score: 250
Period size: 68 Copynumber: 3.3 Consensus size: 68
2936447 TTGAAATTAT
* *
2936457 ATATATAATATATAGTTTTTAAAACATTTTTTGAAAACTTATATAGTATATAGTTTTAAAAACAT
1 ATATATAATATATAGTTTTAAAAACATTTTTTG--AA---ATATA-TATATAGTTTTAAAAATAT
2936522 TTTTGAAAA
60 TTTTGAAAA
* * * *
2936531 ATTATATAATATATAGTTTTAAAAATATTTTTTGAAA-ACT-TATATAATGTTTTTAAATTAATT
1 A-TATATAATATATAGTTTTAAAAACATTTTTTGAAATA-TATATAT-A-GTTTTAAAAATATTT
2936594 TTGAAAA
62 TTGAAAA
* *
2936601 ATATATAATATATAGTTTTGAAAACATTTTTTTAAATATAATATATAG-TTTAAAAATATTTTTG
1 ATATATAATATATAGTTTTAAAAACATTTTTTGAAATAT-ATATATAGTTTTAAAAATATTTTTG
*
2936665 AAAT
65 AAAA
*
2936669 ATATATATTATATAGTTT
1 ATATATAATATATAGTTT
2936687 ATATTATATT
Statistics
Matches: 135, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
68 38 0.28
69 36 0.27
70 23 0.17
71 5 0.04
73 2 0.01
74 1 0.01
75 30 0.22
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (68 bp):
ATATATAATATATAGTTTTAAAAACATTTTTTGAAATATATATATAGTTTTAAAAATATTTTTGA
AAA
Found at i:2936663 original size:31 final size:33
Alignment explanation
Indices: 2936459--2936676 Score: 137
Period size: 33 Copynumber: 6.3 Consensus size: 33
2936449 GAAATTATAT
*
2936459 ATATAATATATAGTTTTTAAAACATTTTTTGAAA
1 ATATAATATATAGTTTTGAAAACATTTTTTG-AA
*
2936493 ACTTATATAGTATATAGTTTTAAAAACA-TTTTTGAAAAA
1 A--TATA-A-TATATAGTTTTGAAAACATTTTTTG---AA
* *
2936532 TTATATAATATATAGTTTTAAAAATATTTTTTGAA
1 --ATATAATATATAGTTTTGAAAACATTTTTTGAA
* * ***
2936567 A-ACTTATATA-ATGTTTTTAAATTA-ATTTTGAAAAA
1 ATA-TAATATATA-GTTTTGAAA--ACATTTT-TTGAA
*
2936602 TATATAATATATAGTTTTGAAAACATTTTTTTAA
1 -ATATAATATATAGTTTTGAAAACATTTTTTGAA
2936636 ATATAATATATAG-TTT-AAAA-ATATTTTTGAA
1 ATATAATATATAGTTTTGAAAACAT-TTTTTGAA
2936667 ATAT-ATATAT
1 ATATAATATAT
2936677 TATATAGTTT
Statistics
Matches: 152, Mismatches: 13, Indels: 42
0.73 0.06 0.20
Matches are distributed among these distances:
30 8 0.05
31 15 0.10
32 5 0.03
33 28 0.18
34 9 0.06
35 10 0.07
36 19 0.12
37 26 0.17
38 24 0.16
39 7 0.05
41 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (33 bp):
ATATAATATATAGTTTTGAAAACATTTTTTGAA
Found at i:2936708 original size:21 final size:24
Alignment explanation
Indices: 2936668--2936718 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
2936658 ATTTTTGAAA
*
2936668 TATATATATTATATAGTTTAT-AT
1 TATATTTATTATATAGTTTATGAT
2936691 TATATTTATTAT-TA-TTTATGAT
1 TATATTTATTATATAGTTTATGAT
2936713 T-TATTT
1 TATATTT
2936719 TATTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.38
22 5 0.19
23 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TATATTTATTATATAGTTTATGAT
Found at i:2936714 original size:17 final size:15
Alignment explanation
Indices: 2936684--2936723 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2936674 TATTATATAG
2936684 TTTATATTATATTTAT
1 TTTAT-TTATATTTAT
2936700 TATTATTTATGATTTAT
1 T-TTATTTAT-ATTTAT
2936717 TTTATTT
1 TTTATTT
2936724 TTCTTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATATTTAT
Found at i:2936730 original size:22 final size:22
Alignment explanation
Indices: 2936690--2936739 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
2936680 ATAGTTTATA
2936690 TTATATTTATTATTATTTA-TGAT
1 TTAT-TTTATTATTATTTATTG-T
* *
2936713 TTATTTTATTTTTCTTTATTGT
1 TTATTTTATTATTATTTATTGT
2936735 TTATT
1 TTATT
2936740 AATTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (22 bp):
TTATTTTATTATTATTTATTGT
Found at i:2937857 original size:10 final size:10
Alignment explanation
Indices: 2937842--2937871 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2937832 AATCCATTAA
2937842 TTTCAATTTG
1 TTTCAATTTG
2937852 TTTCAATTTG
1 TTTCAATTTG
2937862 TTTCAATTTG
1 TTTCAATTTG
2937872 ATCCTCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (10 bp):
TTTCAATTTG
Found at i:2938024 original size:21 final size:20
Alignment explanation
Indices: 2938009--2938164 Score: 67
Period size: 21 Copynumber: 7.8 Consensus size: 20
2937999 TTTTTCGTTT
2938009 TTCTTTGTTTTATTTTATTTA
1 TTCTTT-TTTTATTTTATTTA
2938030 TTCTTTTTTTA-TTTA-TT-
1 TTCTTTTTTTATTTTATTTA
* * * * *
2938047 TTATTATTTTCTTTGATTTT
1 TTCTTTTTTTATTTTATTTA
* *
2938067 TTCTTACTTTGATTTT-TCTTA
1 TTCTT-TTTTTATTTTAT-TTA
* *
2938088 TT-TTTCAATTTATTTAATTT-
1 TTCTTT--TTTTATTTTATTTA
2938108 TTACTTTTATTTA-TTTATTTA
1 TT-CTTTT-TTTATTTTATTTA
* *
2938129 AT-TTTATTTATTTTACTTTA
1 TTCTTTTTTTATTTTA-TTTA
*
2938149 TTTTATTTTTTATTTT
1 TTCT-TTTTTTATTTT
2938165 TTTCATAACT
Statistics
Matches: 99, Mismatches: 20, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
17 8 0.08
18 9 0.09
19 13 0.13
20 25 0.25
21 30 0.30
22 14 0.14
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTTTTTATTTTATTTA
Found at i:2938029 original size:9 final size:9
Alignment explanation
Indices: 2938017--2938167 Score: 88
Period size: 8 Copynumber: 16.9 Consensus size: 9
2938007 TTTTCTTTGT
2938017 TTTATTTTA
1 TTTATTTTA
*
2938026 TTTA--TTC
1 TTTATTTTA
2938033 TTT-TTTTA
1 TTTATTTTA
2938041 TTTATTTTA
1 TTTATTTTA
*
2938050 -TTATTTTC
1 TTTATTTTA
*
2938058 TTTGATTTTT
1 TTT-ATTTTA
*
2938068 TCTTACTTTGA
1 T-TTA-TTTTA
2938079 TTT-TTCTTA
1 TTTATT-TTA
**
2938088 TTT-TTCAA
1 TTTATTTTA
*
2938096 TTTATTTAATT
1 TTTATTT--TA
2938107 TTTACTTTTA
1 TTTA-TTTTA
2938117 TTTA-TTTA
1 TTTATTTTA
2938125 TTTAATTTTA
1 TTT-ATTTTA
2938135 TTTATTTTA
1 TTTATTTTA
2938144 CTTTATTTTA
1 -TTTATTTTA
2938154 -TT-TTTTA
1 TTTATTTTA
2938161 TTT-TTTT
1 TTTATTTT
2938168 CATAACTTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
7 10 0.09
8 33 0.29
9 27 0.24
10 30 0.27
11 10 0.09
12 3 0.03
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2938120 original size:4 final size:4
Alignment explanation
Indices: 2938095--2938163 Score: 52
Period size: 4 Copynumber: 16.0 Consensus size: 4
2938085 TTATTTTTCA
*
2938095 ATTT ATTT AATT -TTT ACTTTT ATTT ATTT ATTT AATTTT ATTT ATTTT
1 ATTT ATTT ATTT ATTT A--TTT ATTT ATTT ATTT -A-TTT ATTT A-TTT
2938143 ACTTT ATTTT ATTT -TTT ATTT
1 A-TTT A-TTT ATTT ATTT ATTT
2938164 TTTTCATAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
3 5 0.09
4 28 0.52
5 14 0.26
6 7 0.13
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:2938134 original size:14 final size:14
Alignment explanation
Indices: 2938117--2938156 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2938107 TTTACTTTTA
*
2938117 TTTATTTATTTAAT
1 TTTATTTATTTAAC
*
2938131 TTTATTTATTTTAC
1 TTTATTTATTTAAC
2938145 TTTATTTTATTT
1 TTTA-TTTATTT
2938157 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTATTTAAC
Found at i:2938164 original size:5 final size:5
Alignment explanation
Indices: 2938016--2938157 Score: 77
Period size: 5 Copynumber: 28.8 Consensus size: 5
2938006 TTTTTCTTTG
* * *
2938016 TTTTA TTTTA -TTTA TTCTTT TTTTA -TTTA TTTTA --TTA TTTTC TTTGA
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * *
2938063 TTTT- TTCTTA CTTTGA TTTT- TCTTA TTTTTCA ATTTA TTTAA TTTTTA
1 TTTTA TT-TTA -TTTTA TTTTA TTTTA -TTTT-A TTTTA TTTTA -TTTTA
* *
2938111 CTTTTA -TTTA -TTTA TTTAA TTTTA -TTTA TTTTA CTTTA TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
2938158 TTATTTTTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 28
0.69 0.13 0.19
Matches are distributed among these distances:
3 3 0.03
4 25 0.24
5 52 0.50
6 21 0.20
7 3 0.03
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:2938779 original size:19 final size:17
Alignment explanation
Indices: 2938755--2938801 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
2938745 ACCTAATTTT
2938755 GGTATCGATACCATAAAGG
1 GGTATCGATACCAT--AGG
*
2938774 GGTATC-AGTACCATAGT
1 GGTATCGA-TACCATAGG
2938791 GGTATCGATAC
1 GGTATCGATAC
2938802 TGGGATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.44
18 2 0.08
19 12 0.48
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (17 bp):
GGTATCGATACCATAGG
Found at i:2938873 original size:22 final size:22
Alignment explanation
Indices: 2938845--2938918 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
2938835 CTAGAAGAGG
2938845 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
2938867 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
* *
2938889 GTATTGATACCATGGT-GGG-A
1 GTATCGATACCATAGTAGGGTA
*
2938909 GTATCAATAC
1 GTATCGATAC
2938919 TGACAAACCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.19
21 3 0.06
22 36 0.75
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:2939314 original size:59 final size:59
Alignment explanation
Indices: 2939251--2939647 Score: 606
Period size: 59 Copynumber: 6.8 Consensus size: 59
2939241 CACTAAGTGA
*
2939251 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGAGCA-CTTCGTGT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTT-GTGT
*
2939310 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGT
* *
2939369 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG-AGCTTATTGT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTT-GTGT
* *
2939428 GCTAAAATGATAAGAAATTCATACTAA--GTATGAATTTCCGTATAGGG-AGCTTATTGT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTT-GTGT
* ** * *
2939485 GCTAAAATGATAAGAAATTCATACTAAGTGTTTGAATTTCTATATTGGGCACCTTGTTT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGT
* *
2939544 GCTAAAATGATAAGAAATTCATACTAAGTGTATGGATTTCCGTATTGGGCACCTTGTGT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGT
*
2939603 GCTAAAATGATAAGAAATTAATACTAAGTGTATGAATTTCCGTAT
1 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
2939648 GAGAAATAAT
Statistics
Matches: 314, Mismatches: 19, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
57 57 0.18
58 3 0.01
59 248 0.79
60 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (59 bp):
GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGT
Found at i:2939549 original size:175 final size:176
Alignment explanation
Indices: 2939251--2939647 Score: 611
Period size: 175 Copynumber: 2.2 Consensus size: 176
2939241 CACTAAGTGA
*
2939251 GCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGAGCACTTCGTGTGCTAAA
1 GCTAAAATGATAAGAAATTCATACTAAG-GTATGAATTTCCGTATAGAGCACTTAGTGTGCTAAA
* *
2939316 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTTGTGTGCTAAAATGATA
65 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACCTTGTGTGCTAAAATGATA
* *
2939381 AGAAATTCATACTAAGTGTATGAATTTCCGTATAGGG-AGCTTATTGT
130 AGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTT-GTGT
* *
2939428 GCTAAAATGATAAGAAATTCATACTAA-GTATGAATTTCCGTATAG-GGAGCTTATTGTGCTAAA
1 GCTAAAATGATAAGAAATTCATACTAAGGTATGAATTTCCGTATAGAGCA-CTTAGTGTGCTAAA
* * * *
2939491 ATGATAAGAAATTCATACTAAGTGTTTGAATTTCTATATTGGGCACCTTGTTTGCTAAAATGATA
65 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACCTTGTGTGCTAAAATGATA
* *
2939556 AGAAATTCATACTAAGTGTATGGATTTCCGTATTGGGCACCTTGTGT
130 AGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGT
*
2939603 GCTAAAATGATAAGAAATTAATACTAAGTGTATGAATTTCCGTAT
1 GCTAAAATGATAAGAAATTCATACTAAG-GTATGAATTTCCGTAT
2939648 GAGAAATAAT
Statistics
Matches: 202, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
174 2 0.01
175 153 0.76
176 4 0.02
177 43 0.21
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (176 bp):
GCTAAAATGATAAGAAATTCATACTAAGGTATGAATTTCCGTATAGAGCACTTAGTGTGCTAAAA
TGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACCTTGTGTGCTAAAATGATAA
GAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGT
Found at i:2945023 original size:20 final size:21
Alignment explanation
Indices: 2944974--2945027 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2944964 TACCATAAAG
*
2944974 GGGTATCGGTACCATAGTATA
1 GGGTATCGATACCATAGTATA
* *
2944995 GTAGTATCGATACCATGGTA-A
1 G-GGTATCGATACCATAGTATA
2945016 GGGTATCGATAC
1 GGGTATCGATAC
2945028 TGGGCCACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 15 0.54
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCATAGTATA
Found at i:2945117 original size:20 final size:22
Alignment explanation
Indices: 2945071--2945122 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2945061 CCGGAAGGGG
2945071 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
2945093 GTATCGATACCATGGT-GGG-A
1 GTATCGATACCATAGTAGGGTA
2945113 GTATCGATAC
1 GTATCGATAC
2945123 TGAGGAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 15 0.52
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:2945124 original size:95 final size:95
Alignment explanation
Indices: 2944898--2945124 Score: 296
Period size: 95 Copynumber: 2.4 Consensus size: 95
2944888 GGTACCAATG
* * *
2944898 GGGTAGTATCGATACCATAGTAAGGGTATCGATACTAGATAACATCGAACTTAATTTTGGTATCA
1 GGGTAGTATCGATACCATGGTAAGGGTATCGATACTGGACAACATCGAACTTAATTTTGGTATCA
* *
2944963 ATACCATAAAGGGGTATCGGTACCATAGTA
66 ATACCAGAAAGGGGTATCGATACCATAGTA
** * * *
2944993 TAGTAGTATCGATACCATGGTAAGGGTATCGATACTGGGCCACATTGAA-TCTAATTTTGGTATC
1 GGGTAGTATCGATACCATGGTAAGGGTATCGATACTGGACAACATCGAACT-TAATTTTGGTATC
* * *
2945057 TATACCGGAAGGGGGTATCGATACCATAGTA
65 AATACCAGAAAGGGGTATCGATACCATAGTA
*
2945088 GGGTAGTATCGATACCATGGT-GGGAGTATCGATACTG
1 GGGTAGTATCGATACCATGGTAAGG-GTATCGATACTG
2945125 AGGAACCATA
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
94 3 0.03
95 111 0.97
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (95 bp):
GGGTAGTATCGATACCATGGTAAGGGTATCGATACTGGACAACATCGAACTTAATTTTGGTATCA
ATACCAGAAAGGGGTATCGATACCATAGTA
Found at i:2945528 original size:59 final size:59
Alignment explanation
Indices: 2945456--2945965 Score: 715
Period size: 59 Copynumber: 8.8 Consensus size: 59
2945446 ATGGTAGTAA
2945456 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2945515 TTGTGCTAAAATGATAA-AACTTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2945573 GTGTGCTAAATTGATAAGAAATTCATACTAAGTGTATGAATCTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2945632 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCGCTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
2945691 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCGCTTA
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
2945750 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATAAATTTTCGTATAGGGCGCTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* **
2945809 GTGTGCTAAAATGATAAG------A-A-T-A--GTATGAATTTCTGTATTTGGCACCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-CTTC
* * * *
2945857 GTGTGTTAAAATGATAAAAAAATTCATACTAAGTGTATGAATTTCCTTATTGGGCACCTT-
1 GTGTGCTAAAATGAT-AAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-CTTC
* *
2945917 GTGTGCTAAAATGATAAGAAATTCATACTAAATGTATGAATTTTCGTAT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
2945966 GGGAAATAAT
Statistics
Matches: 406, Mismatches: 31, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
48 30 0.07
49 5 0.01
50 1 0.00
51 1 0.00
52 1 0.00
53 1 0.00
55 1 0.00
56 1 0.00
57 1 0.00
58 56 0.14
59 271 0.67
60 37 0.09
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:2945895 original size:60 final size:59
Alignment explanation
Indices: 2945831--2945959 Score: 197
Period size: 60 Copynumber: 2.2 Consensus size: 59
2945821 GATAAGAATA
* * *
2945831 GTATGAATTT-CTGTATTTGGCACCTTGTGTGTTAAAATGATAAAAAAATTCATACTAAGT
1 GTATGAATTTCCT-TATTGGGCACCTTGTGTGCTAAAATGAT-AAAAAATTCATACTAAAT
*
2945891 GTATGAATTTCCTTATTGGGCACCTTGTGTGCTAAAATGATAAGAAATTCATACTAAAT
1 GTATGAATTTCCTTATTGGGCACCTTGTGTGCTAAAATGATAAAAAATTCATACTAAAT
2945950 GTATGAATTT
1 GTATGAATTT
2945960 TCGTATGGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 26 0.41
60 36 0.56
61 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (59 bp):
GTATGAATTTCCTTATTGGGCACCTTGTGTGCTAAAATGATAAAAAATTCATACTAAAT
Found at i:2945921 original size:108 final size:107
Alignment explanation
Indices: 2945724--2945936 Score: 286
Period size: 108 Copynumber: 2.0 Consensus size: 107
2945714 CATACTAAGT
* *
2945724 GTATGAATTTCCGTATAGGGCGCTTAGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATAA
1 GTATGAATTTCCGTATAGGGCCCTTAGTGTGCTAAAATGATAAAAAATTCATACTAAGTGTATAA
* *
2945789 ATTTTCGTATAGGGCGCTTCGTGTGCTAAAATGATAAGAATA
66 ATTTCCGTATAGGGCCCTTCGTGTGCTAAAATGATAAGAATA
* ** *
2945831 GTATGAATTTCTGTATTTGGCACCTT-GTGTGTTAAAATGATAAAAAAATTCATACTAAGTGTAT
1 GTATGAATTTCCGTATAGGGC-CCTTAGTGTGCTAAAATGAT-AAAAAATTCATACTAAGTGTAT
* * *
2945895 GAATTTCCTTATTGGGCACCTT-GTGTGCTAAAATGATAAGAA
64 AAATTTCCGTATAGGGC-CCTTCGTGTGCTAAAATGATAAGAA
2945937 ATTCATACTA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
107 32 0.35
108 57 0.62
109 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (107 bp):
GTATGAATTTCCGTATAGGGCCCTTAGTGTGCTAAAATGATAAAAAATTCATACTAAGTGTATAA
ATTTCCGTATAGGGCCCTTCGTGTGCTAAAATGATAAGAATA
Found at i:2959796 original size:60 final size:60
Alignment explanation
Indices: 2959703--2959823 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
2959693 ATAAAAGAAA
* * * *
2959703 CCTTAAAGAATCCTAATTGTTGTCTTTGCCGTCATCTTCCCCTATTCATTTCCCTTTGTT
1 CCTTAAAGAATCCTAATTGTTGCCGTTACCGTCATCTTCCCCTATTCATTCCCCTTTGTT
* *
2959763 CCTTAAAGAATCCTAGTTGTTGCCGTTATCGTCATCTTCCCCTATTCATTCCCCTTTGTT
1 CCTTAAAGAATCCTAATTGTTGCCGTTACCGTCATCTTCCCCTATTCATTCCCCTTTGTT
2959823 C
1 C
2959824 TTCATCGAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.43
Consensus pattern (60 bp):
CCTTAAAGAATCCTAATTGTTGCCGTTACCGTCATCTTCCCCTATTCATTCCCCTTTGTT
Found at i:2963017 original size:15 final size:15
Alignment explanation
Indices: 2962997--2963075 Score: 77
Period size: 15 Copynumber: 5.1 Consensus size: 15
2962987 CTCCTCGTAA
2962997 CTATGGTGGTGGCGG
1 CTATGGTGGTGGCGG
*
2963012 CTATGGTGGTGGTGG
1 CTATGGTGGTGGCGG
*** *
2963027 CGGCGGCTATGGTGGTGG
1 CTATGG---TGGTGGCGG
*
2963045 CTATGGAGGTGGCGG
1 CTATGGTGGTGGCGG
2963060 CTATGGTGGTGGCGG
1 CTATGGTGGTGGCGG
2963075 C
1 C
2963076 GGCGGCTATG
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
15 39 0.76
18 12 0.24
ACGTcount: A:0.08, C:0.14, G:0.53, T:0.25
Consensus pattern (15 bp):
CTATGGTGGTGGCGG
Found at i:2963026 original size:21 final size:21
Alignment explanation
Indices: 2963000--2963093 Score: 107
Period size: 21 Copynumber: 4.2 Consensus size: 21
2962990 CTCGTAACTA
*
2963000 TGGTGGTGGCGGCTATGGTGG
1 TGGTGGCGGCGGCTATGGTGG
2963021 TGGTGGCGGCGGCTATGGTGG
1 TGGTGGCGGCGGCTATGGTGG
*
2963042 TGGCTATGGAGGTGGCGGCTATGGTGG
1 TGG---T---GGCGGCGGCTATGGTGG
*
2963069 TGGCGGCGGCGGCTATGGTGG
1 TGGTGGCGGCGGCTATGGTGG
2963090 TGGT
1 TGGT
2963094 AATTATGGCG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
21 42 0.68
24 1 0.02
27 19 0.31
ACGTcount: A:0.06, C:0.13, G:0.55, T:0.26
Consensus pattern (21 bp):
TGGTGGCGGCGGCTATGGTGG
Found at i:2963068 original size:48 final size:48
Alignment explanation
Indices: 2962997--2963092 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
2962987 CTCCTCGTAA
* *
2962997 CTATGGTGGTGGCGGCTATGGTGGTGGTGGCGGCGGCTATGGTGGTGG
1 CTATGGAGGTGGCGGCTATGGTGGTGGCGGCGGCGGCTATGGTGGTGG
2963045 CTATGGAGGTGGCGGCTATGGTGGTGGCGGCGGCGGCTATGGTGGTGG
1 CTATGGAGGTGGCGGCTATGGTGGTGGCGGCGGCGGCTATGGTGGTGG
2963093 TAATTATGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.07, C:0.14, G:0.54, T:0.25
Consensus pattern (48 bp):
CTATGGAGGTGGCGGCTATGGTGGTGGCGGCGGCGGCTATGGTGGTGG
Found at i:2968735 original size:9 final size:9
Alignment explanation
Indices: 2968709--2968750 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
2968699 AAAGGAATAA
2968709 ATGATAAT-
1 ATGATAATG
2968717 ATTGATAATG
1 A-TGATAATG
2968727 ATG-TGAATG
1 ATGAT-AATG
2968736 ATGATAATG
1 ATGATAATG
2968745 ATGATA
1 ATGATA
2968751 TACATATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.07
9 26 0.87
10 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (9 bp):
ATGATAATG
Found at i:2975237 original size:19 final size:19
Alignment explanation
Indices: 2975213--2975275 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
2975203 GATATCAGAA
**
2975213 ATCAGAAAAGAGGTCAAAG
1 ATCAGAAAAGAAATCAAAG
*
2975232 ATCAGAACAA-AAATCAGAG
1 ATCAGAA-AAGAAATCAAAG
*
2975251 ATCAGAAAAGATATCAAAG
1 ATCAGAAAAGAAATCAAAG
*
2975270 TTCAGA
1 ATCAGA
2975276 GCATAAATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 2 0.06
19 32 0.89
20 2 0.06
ACGTcount: A:0.54, C:0.13, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCAGAAAAGAAATCAAAG
Found at i:2975257 original size:38 final size:38
Alignment explanation
Indices: 2975206--2975293 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
2975196 AAATAGAGAT
* *
2975206 ATCAGAAATCAGAAAAGAGGTCAAAGATCAGAACAAAA
1 ATCAGAGATCAGAAAAGAGATCAAAGATCAGAACAAAA
* * * *
2975244 ATCAGAGATCAGAAAAGATATCAAAGTTCAGAGCATAA
1 ATCAGAGATCAGAAAAGAGATCAAAGATCAGAACAAAA
*
2975282 ATCAGAGCTCAG
1 ATCAGAGATCAG
2975294 GCTATATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15
Consensus pattern (38 bp):
ATCAGAGATCAGAAAAGAGATCAAAGATCAGAACAAAA
Found at i:2979860 original size:185 final size:186
Alignment explanation
Indices: 2979510--2979877 Score: 641
Period size: 185 Copynumber: 2.0 Consensus size: 186
2979500 GTATGATCAG
*
2979510 GGAACACACTAGAGGTTCCAGATATTATTCGGAGGCGATTGGTATTTATCATATAGGAAGTCATG
1 GGAACACACTAGAGGTTCCAGATATTATTCAGAGGCGATTGGTATTTATCATATAGGAAGTCATG
*
2979575 AAACTTCTATAAACTGATTAAACTCAGAGATGAGATCCCCATAAAAAAGGTTTGATAGCTTACAG
66 AAACTTCTATAAACTGATTAAACTCAGAGATGAGATCCCCATAAAAAAGGTTTGATAGCTGACAG
* * *
2979640 ATTCATCAGTTATTCAGAACGTGATTTATCAGGATCATATAGTATTCAGTTATTCTT
131 ATTCATCAATTATTCAGAACATGATTTATCAGGATCATATA-TATTCAGATATTCTT
2979697 GGAACACACTAGAGGTTCCAGATATTATTCAGAGGCGATTGGTATTTATCATATA-GAAGTCATG
1 GGAACACACTAGAGGTTCCAGATATTATTCAGAGGCGATTGGTATTTATCATATAGGAAGTCATG
* * *
2979761 AAACTTTTGTAAACTGGTTAAACTCAGAGATGAGATCCCCAT-AAAAAGGTTTGATAGCTGACAG
66 AAACTTCTATAAACTGATTAAACTCAGAGATGAGATCCCCATAAAAAAGGTTTGATAGCTGACAG
2979825 ATTCATCAATTATTCAGAACATGATTTATCAGGATCATATATATTCAGATATT
131 ATTCATCAATTATTCAGAACATGATTTATCAGGATCATATATATTCAGATATT
2979878 TTTCGAAGGC
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
184 11 0.06
185 60 0.35
186 48 0.28
187 54 0.31
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (186 bp):
GGAACACACTAGAGGTTCCAGATATTATTCAGAGGCGATTGGTATTTATCATATAGGAAGTCATG
AAACTTCTATAAACTGATTAAACTCAGAGATGAGATCCCCATAAAAAAGGTTTGATAGCTGACAG
ATTCATCAATTATTCAGAACATGATTTATCAGGATCATATATATTCAGATATTCTT
Found at i:2983717 original size:19 final size:20
Alignment explanation
Indices: 2983693--2983743 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2983683 TATATGTTTT
*
2983693 TATGAACAGTAA-AATATGG
1 TATGAACAGTAACAATATCG
*
2983712 TATGAATAGTGAACAATATCG
1 TATGAACAGT-AACAATATCG
*
2983733 TGTGAACAGTA
1 TATGAACAGTA
2983744 CCGTGAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.35
20 3 0.12
21 14 0.54
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (20 bp):
TATGAACAGTAACAATATCG
Found at i:2987591 original size:19 final size:20
Alignment explanation
Indices: 2987567--2987615 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
2987557 AATATATTTT
2987567 TATGAACAGTAA-AATACAG
1 TATGAACAGTAACAATACAG
*
2987586 TATGAACAG-AACAATACCG
1 TATGAACAGTAACAATACAG
2987605 TATGAACAGTA
1 TATGAACAGTA
2987616 GCGTGAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.07
19 24 0.89
20 1 0.04
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.20
Consensus pattern (20 bp):
TATGAACAGTAACAATACAG
Found at i:2987702 original size:21 final size:21
Alignment explanation
Indices: 2987663--2987702 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2987653 TCAATTGTGT
* *
2987663 ATCGATGCAATGTTGCAGTGC
1 ATCGATGCAATGCTACAGTGC
*
2987684 ATCGATGCACTGCTACAGT
1 ATCGATGCAATGCTACAGT
2987703 AACTTCAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
ATCGATGCAATGCTACAGTGC
Found at i:2988410 original size:31 final size:31
Alignment explanation
Indices: 2988375--2988512 Score: 109
Period size: 31 Copynumber: 4.4 Consensus size: 31
2988365 TAGATTCCGA
* * *
2988375 AGAACCTAGGTAAATTGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCCT
* * *
2988406 AGAACATAGTTATACTGTCCATATG-TCCCG
1 AGAACATAGGTAAACTGTCCATATGTTCCCT
* ** * *
2988436 AAAGACATAGGTAATTTTGTCTATATGTTCCGT
1 AGA-ACATAGGTAA-ACTGTCCATATGTTCCCT
* *
2988469 AGAACATAGGTATACTGTCCATATG-TCCCG
1 AGAACATAGGTAAACTGTCCATATGTTCCCT
*
2988499 AAAGACATAGGTAA
1 AGA-ACATAGGTAA
2988513 TTCTTCGACT
Statistics
Matches: 80, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
30 10 0.12
31 47 0.59
32 18 0.22
33 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCCT
Found at i:2988463 original size:32 final size:32
Alignment explanation
Indices: 2988420--2988516 Score: 126
Period size: 32 Copynumber: 3.1 Consensus size: 32
2988410 CATAGTTATA
2988420 CTGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAAAGACATAGGTAATT
* * * * *
2988452 TTGTCTATATGTTCCG-TAGAACATAGGT-ATA
1 CTGTCCATATGTCCCGAAAG-ACATAGGTAATT
2988483 CTGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAAAGACATAGGTAATT
2988515 CT
1 CT
2988517 TCGACTCTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
31 25 0.48
32 27 0.52
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (32 bp):
CTGTCCATATGTCCCGAAAGACATAGGTAATT
Found at i:2988472 original size:63 final size:63
Alignment explanation
Indices: 2988381--2988514 Score: 225
Period size: 63 Copynumber: 2.1 Consensus size: 63
2988371 CCGAAGAACC
* * *
2988381 TAGGTAA-ATTGTCCATATGTTCCTTAGAACATAGTTATACTGTCCATATGTCCCGAAAGACA
1 TAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
*
2988443 TAGGTAATTTTGTCTATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
1 TAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
2988506 TAGGTAATT
1 TAGGTAATT
2988515 CTTCGACTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 7 0.10
63 60 0.90
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (63 bp):
TAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACA
Found at i:3006943 original size:5 final size:5
Alignment explanation
Indices: 3006933--3007042 Score: 68
Period size: 5 Copynumber: 22.4 Consensus size: 5
3006923 AATTTTCAAA
* *
3006933 AAAAT AAAAT -AAAT AAACT AAAAT AAAGT AAAAT AAAAAT AAAAAT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT
* * * * ** * *
3006983 AACA- CAAAT AAAAT -AAAC AAAAT -ACAT AAACG AACAT AAAAT AAAACA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
3007031 AAAAT AAAAT AA
1 AAAAT AAAAT AA
3007043 TGGGATCAAA
Statistics
Matches: 79, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
4 15 0.19
5 49 0.62
6 15 0.19
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:3006957 original size:19 final size:17
Alignment explanation
Indices: 3006933--3006999 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 17
3006923 AATTTTCAAA
3006933 AAAATAAAATAAATAAAC
1 AAAATAAAATAAA-AAAC
* *
3006951 TAAAATAAAGTAAAATA-
1 -AAAATAAAATAAAAAAC
3006968 AAAATAAAAATAAAAAAC
1 AAAAT-AAAATAAAAAAC
3006986 ACAAATAAAATAAA
1 A-AAATAAAATAAA
3007000 CAAAATACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.12
17 9 0.22
18 11 0.27
19 16 0.39
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAAAAAAC
Found at i:3006971 original size:35 final size:35
Alignment explanation
Indices: 3006932--3006999 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
3006922 CAATTTTCAA
*
3006932 AAAAAT-AAAATAAATAAACTA-AAATAAAGTAAAAT
1 AAAAATAAAAATAAA-AAAC-ACAAATAAAATAAAAT
3006967 AAAAATAAAAATAAAAAACACAAATAAAATAAA
1 AAAAATAAAAATAAAAAACACAAATAAAATAAA
3007000 CAAAATACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 1 0.03
35 21 0.70
36 8 0.27
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.16
Consensus pattern (35 bp):
AAAAATAAAAATAAAAAACACAAATAAAATAAAAT
Found at i:3007288 original size:19 final size:19
Alignment explanation
Indices: 3007264--3007302 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3007254 GTAACAGAAA
*
3007264 AAAATAATAATAAATAAAT
1 AAAATAAAAATAAATAAAT
3007283 AAAATAAAAATAAATAAAT
1 AAAATAAAAATAAATAAAT
3007302 A
1 A
3007303 TATGCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATAAAAATAAATAAAT
Found at i:3007295 original size:15 final size:16
Alignment explanation
Indices: 3007269--3007323 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
3007259 AGAAAAAAAT
3007269 AATAATAAATAAATAA
1 AATAATAAATAAATAA
3007285 AATAA-AAATAAAT-A
1 AATAATAAATAAATAA
**
3007299 AATATATGCATATAATAA
1 AATA-ATAAATA-AATAA
3007317 AATAATA
1 AATAATA
3007324 TTAGATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 8 0.25
17 5 0.16
18 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
AATAATAAATAAATAA
Found at i:3009344 original size:85 final size:85
Alignment explanation
Indices: 3009220--3010374 Score: 1465
Period size: 85 Copynumber: 13.7 Consensus size: 85
3009210 AGATGAATAG
* * * ** *
3009220 AATCGAACTCGACA-GTTTTTGTTGATAGATAGCCTTTCTCAACTTAAGCTATGCTGTAAATTTG
1 AATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
* *
3009284 ATATGCCCTTGAGATGAATGG
65 ATATGCCCTTGAGCTGAATGT
* * * * * * *
3009305 AATCGATCTCGGAGGTATTTGTTGACGGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
3009370 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * * * *
3009390 AATTGAACTCGAAGGTCTTTGTTGATAGATACCCCTTCTCACCTTGAGATATGTTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
*
3009455 TATACCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * *
3009475 AATCGAACTTGAGGGTCTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGCTGTAAATTTCA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
*
3009540 TAT-CCCTTTGAGCTGAATAT
66 TATGCCC-TTGAGCTGAATGT
* * * * * * *
3009560 AATCGAACTTGAAGGTTTTTGTTGACAGATGGTCCTTCTCACCTTGAGCTATGTTGTATATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
3009625 TATGCCTTTGAGCTGAATAT
66 TATGCCCTTGAGCTGAATGT
* * *
3009645 AATCGAACTCAAAGGTCTTTTTTGACATATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
3009710 TATACCCTTGAACTGAATGT
66 TATGCCCTTGAGCTGAATGT
* ** * *
3009730 AATCGAACTCGAA--TGTTTGTTGGTAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAA-TAGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
3009792 TATGCCCTTGAGTTAAATGT
66 TATGCCCTTGAGCTGAATGT
* *
3009812 AATCGAACTCGAAGATCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
3009877 TGTGCCTTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
3009897 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
3009962 TATGCCTTTGAGCTGAATAT
66 TATGCCCTTGAGCTGAATGT
* *
3009982 AATTGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAG-TAATACTGTAAATTTG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCT-ATGCTGTAAATTTG
3010046 ATATGCCCTTGAGCTGAATGT
65 ATATGCCCTTGAGCTGAATGT
* * * * * * * *
3010067 AATTGAAATCGAAGG--TTTGTTGGCAGATAGCCCTTCTCGCCTTGAGTTATACTGCATA-TAGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
3010129 TATGCCTTTGAGTTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * *
3010149 AATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
3010214 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
** * * * *
3010234 AATCGAACTCGAAGG--TTTGTTGGTAGATAGCCCTTCTCGCCATGAGCTATACTGCAAA-TAGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
3010296 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * *
3010316 AATCGAACTTGAAGG--TTTGTTGGCAGATAGCCCTTCTCACCTTGAGCTATGCTGCAAAT
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAAT
3010375 AGTTCCTTTA
Statistics
Matches: 933, Mismatches: 125, Indels: 26
0.86 0.12 0.02
Matches are distributed among these distances:
82 141 0.15
83 112 0.12
84 83 0.09
85 595 0.64
86 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
TATGCCCTTGAGCTGAATGT
Found at i:3009920 original size:337 final size:337
Alignment explanation
Indices: 3009220--3010374 Score: 1541
Period size: 337 Copynumber: 3.4 Consensus size: 337
3009210 AGATGAATAG
* * * *
3009220 AATCGAACTCGACA-GTTTTTGTTGATAGATAGCCTTTCTCAACTTAAGCTATGCTGTAAATTTG
1 AATCGAACTCGA-AGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTG
* ** * * * * *
3009284 ATATGCCCTTGAGATGAATGGAATCGATCTCGGAGGTATTTGTTGACGGATAACCCTTCTCGCCT
65 ATATGCCCTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCT
* * *
3009349 TGAGTTATGCTATAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTCTTTGTTG
130 TGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAA--TGTTTGTTG
* * * * * * * *
3009414 ATAGATACCCCTTCTCACCTTGAGATATGTTGTAAATTTGATATACCCTTGAGCTGAATGTAATC
193 GTAGATAGCCCTTCTCGCCTTGAGATATGCTGCAAA-TAGATATGCCCTTGAGTTGAATGTAATC
* * * * *
3009479 GAACTTGAGGGTCTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGCTGTAAATTTCATATC
257 GAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
*
3009544 CCTTTGAGCTGAATAT
322 CCTTTGAGCTGAATGT
* * * * *
3009560 AATCGAACTTGAAGGTTTTTGTTGACAGATGGTCCTTCTCACCTTGAGCTATGTTGTATATTTGA
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
* * * *
3009625 TATGCCTTTGAGCTGAATATAATCGAACTCAAAGGTCTTTTTTGACATATAGCCCTTCTCGCCTT
66 TATGCCCTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
* * *
3009690 GAGCTATGCTGTAAATTTGATATACCCTTGAACTGAATGTAATCGAACTCGAATGTTTGTTGGTA
131 GAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAATGTTTGTTGGTA
* *
3009755 GATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATAGATATGCCCTTGAGTTAAATGTAATCGAAC
196 GATAGCCCTTCTCGCCTTGAGATATGCTGCAAATAGATATGCCCTTGAGTTGAATGTAATCGAAC
* * *
3009820 TCGAAGATCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATGTGCCTT
261 TCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTT
3009885 TGAGCTGAATGT
326 TGAGCTGAATGT
* *
3009897 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
* *
3009962 TATGCCTTTGAGCTGAATATAATTGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
66 TATGCCCTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
* * * *
3010027 GAG-TAATACTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAAATCGAAGGTTTGTTGGC
131 GAGCT-ATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAATGTTTGTTGGT
* * * * *
3010091 AGATAGCCCTTCTCGCCTTGAGTTATACTGCATATAGATATGCCTTTGAGTTGAATGTAATCAAA
195 AGATAGCCCTTCTCGCCTTGAGATATGCTGCAAATAGATATGCCCTTGAGTTGAATGTAATCGAA
* * * *
3010156 CTCGAAGGTCTTTGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCTGTAAATTTGATATGCCC
260 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
3010221 TTGAGCTGAATGT
325 TTGAGCTGAATGT
** * * * * *
3010234 AATCGAACTCGAAGG--TTTGTTGGTAGATAGCCCTTCTCGCCATGAGCTATACTGCAAA-TAGA
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
* * * *
3010296 TATGCCCTTGAGCTGAATGTAATCGAACTTGAAGG--TTTGTTGGCAGATAGCCCTTCTCACCTT
66 TATGCCCTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
*
3010359 GAGCTATGCTGCAAAT
131 GAGCTATGCTGTAAAT
3010375 AGTTCCTTTA
Statistics
Matches: 721, Mismatches: 91, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
332 38 0.05
333 1 0.00
334 34 0.05
335 38 0.05
336 1 0.00
337 415 0.58
338 38 0.05
339 1 0.00
340 155 0.21
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (337 bp):
AATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
TATGCCCTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
GAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAATGTTTGTTGGTA
GATAGCCCTTCTCGCCTTGAGATATGCTGCAAATAGATATGCCCTTGAGTTGAATGTAATCGAAC
TCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTT
TGAGCTGAATGT
Found at i:3011845 original size:95 final size:95
Alignment explanation
Indices: 3011676--3011862 Score: 302
Period size: 95 Copynumber: 2.0 Consensus size: 95
3011666 GACAACTCAG
* * * * *
3011676 TATTATAATCACCTTTATCAGGCTAGTTGAATCTTATCCATATAGTCGGGGCGTTTAACTAATTG
1 TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
3011741 CTCTAGAGGGACAACTCAAGCTTTATTGTA
66 CTCTAGAGGGACAACTCAAGCTTTATTGTA
*
3011771 TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGTGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
* *
3011836 CTTTGGAGGGACAACTCAAGCTTTATT
66 CTCTAGAGGGACAACTCAAGCTTTATT
3011863 ATAATCTGGG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (95 bp):
TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTGTA
Found at i:3016293 original size:4 final size:4
Alignment explanation
Indices: 3016284--3016310 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3016274 CAGTTCATAT
3016284 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
3016311 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:3017117 original size:39 final size:38
Alignment explanation
Indices: 3017060--3017192 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 38
3017050 TAAAATAAAC
* *
3017060 AAAATAAATAAATGAAAATAAAAGAAAAATAAGGAAAAGA
1 AAAAGAAAAAAAT-AAAAT-AAAGAAAAATAAGGAAAAGA
3017100 AAAAGAAAAAAATAAAATAATAGAATTAAATAA--AAAAGA
1 AAAAGAAAAAAATAAAATAA-AGAA--AAATAAGGAAAAGA
3017139 AAAA-AAACAAAATAAAAT--AGAAAACA-AAGAGAAAAGA
1 AAAAGAAA-AAAATAAAATAAAGAAAA-ATAAG-GAAAAGA
* *
3017176 ATAGGAAAAAAATAAAA
1 AAAAGAAAAAAATAAAA
3017193 ATAGAATATA
Statistics
Matches: 80, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
34 4 0.05
35 1 0.01
36 4 0.05
37 17 0.21
38 8 0.10
39 29 0.36
40 11 0.14
41 6 0.08
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (38 bp):
AAAAGAAAAAAATAAAATAAAGAAAAATAAGGAAAAGA
Found at i:3017418 original size:6 final size:6
Alignment explanation
Indices: 3017409--3017479 Score: 142
Period size: 6 Copynumber: 11.8 Consensus size: 6
3017399 TACATATATA
3017409 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
3017457 CATACG CATACG CATACG CATAC
1 CATACG CATACG CATACG CATAC
3017480 ATACATACAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (6 bp):
CATACG
Found at i:3017484 original size:4 final size:4
Alignment explanation
Indices: 3017475--3017530 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
3017465 TACGCATACG
3017475 CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3017520 -ATA CATA CATA
1 CATA CATA CATA
3017531 TACATATACA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
4 44 0.92
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:3017498 original size:26 final size:26
Alignment explanation
Indices: 3017469--3017701 Score: 115
Period size: 24 Copynumber: 9.6 Consensus size: 26
3017459 TACGCATACG
*
3017469 CATACGCATACATACATACATACATA
1 CATACACATACATACATACATACATA
*
3017495 CATACATATACATACATACATACATATA
1 CATACACATACATACATACATAC--ATA
*
3017523 CATACATATACAT--ATACAT--ATA
1 CATACACATACATACATACATACATA
*
3017545 CATATACAT--ATACAT--ATACAT-
1 CATACACATACATACATACATACATA
* * * *
3017566 -ATACATATACATATACATATACATA
1 CATACACATACATACATACATACATA
*
3017591 CATATACAT--ATACAT--ATACATA
1 CATACACATACATACATACATACATA
* * * *
3017613 TATACATATACAT--ATACATATACA
1 CATACACATACATACATACATACATA
* * * * *
3017637 TATACATATACATACATATACATATA
1 CATACACATACATACATACATACATA
* * * *
3017663 CATATACAT--ATACATATACATATA
1 CATACACATACATACATACATACATA
*
3017687 CATATACATACATAC
1 CATACACATACATAC
3017702 GCATACGCAT
Statistics
Matches: 164, Mismatches: 23, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
20 10 0.06
22 33 0.20
24 54 0.33
26 51 0.31
28 16 0.10
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.31
Consensus pattern (26 bp):
CATACACATACATACATACATACATA
Found at i:3017507 original size:6 final size:6
Alignment explanation
Indices: 3017496--3018501 Score: 1198
Period size: 6 Copynumber: 167.5 Consensus size: 6
3017486 ACATACATAC
* * *
3017496 ATACAT ATACAT ACATAC ATACAT ATAC-- ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3017542 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3017588 ATACAT ATACAT ATACAT ATACATAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATAC--AT ATACAT ATACAT ATACAT ATACAT
3017638 ATACAT ATAC-- ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
** ** ** ** **
3017684 ATACAT ATAC-- ATACAT ACGCAT ACGCAT ACGCAT AGCATACGC ATACGC
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ---ATACAT ATACAT
** ** * * * *
3017733 ATACGC ATACGC ATACAC ATACGT ATACAC ATACGCAT ATACAT ATACAC
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATA--CAT ATACAT ATACAT
* ** ** ** * **
3017783 ATACGCAT ATACAT ATACAC ATACGC ATACGC ATACGC ATACGT ATACGC
1 ATA--CAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
** * * * * * *
3017833 ATACGC ATACAC ATACGTAT ACACAT ATGCAT ATGCAT ATCCAT ATGCAT
1 ATACAT ATACAT ATAC--AT ATACAT ATACAT ATACAT ATACAT ATACAT
* * ** * *
3017883 ATGCAT ATCCAT ATACAT ATACAT ATACAT ATGTAT ATGCAT ATGCAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* ** * * ** * * **
3017931 ATGCAT ATGTAT ATGCAT ATGCAT ATGGAT ATGCAT ATGCAT ATGGAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
3017979 ATGCAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018027 ATACAT ATACAT ATACAT A-ACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018074 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018122 AT-CAT ATACAT ATACAT ATACAT ATAC-- ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018167 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018215 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018261 ATACAT ATACAT ATACATAT ATACAT ATAC-- ATACAT ATACATAT ATACAT
1 ATACAT ATACAT ATAC--AT ATACAT ATACAT ATACAT ATAC--AT ATACAT
3018311 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018359 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
3018407 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * * *
3018455 ATGCAT ATACGCAT ATGCAT ATGCAT ATGCAT ATACAT ATACAT ATA
1 ATACAT ATA--CAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
3018502 ATAAAAAATA
Statistics
Matches: 920, Mismatches: 47, Indels: 66
0.89 0.05 0.06
Matches are distributed among these distances:
4 28 0.03
5 10 0.01
6 843 0.92
8 37 0.04
9 2 0.00
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:3020567 original size:28 final size:30
Alignment explanation
Indices: 3020495--3020573 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 30
3020485 ATATTTTAAA
* * *
3020495 TATTAAAATATCTTTTGTTTTTGTTTTAACT
1 TATT-AAATATATTTTGATTTTGGTTTAACT
3020526 TATTAAAT-TATTTT-ATTTTGGTTTAACT
1 TATTAAATATATTTTGATTTTGGTTTAACT
* *
3020554 TATTAAATATTTTTTTATTT
1 TATTAAATATATTTTGATTT
3020574 AATGTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 20 0.48
29 10 0.24
30 8 0.19
31 4 0.10
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (30 bp):
TATTAAATATATTTTGATTTTGGTTTAACT
Found at i:3020668 original size:15 final size:15
Alignment explanation
Indices: 3020638--3020692 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3020628 TCTTATTTTC
*
3020638 TAAAATATATT--TT
1 TAAAATATATTAAAT
*
3020651 TAAAATATCTTAAAT
1 TAAAATATATTAAAT
*
3020666 TAAAATATATTTAAT
1 TAAAATATATTAAAT
3020681 TATAAATTATAT
1 TA-AAA-TATAT
3020693 ATTTATTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 10 0.29
15 16 0.47
16 3 0.09
17 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATATATTAAAT
Found at i:3020740 original size:28 final size:28
Alignment explanation
Indices: 3020695--3020780 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
3020685 AATTATATAT
*
3020695 TTATTGATCTTCATTTAAAATATATTTTA
1 TTATT-ATCTTCAATTAAAATATATTTTA
*
3020724 TTATTATTTTCAATTAAAGA-ATATATTT-
1 TTATTATCTTCAATTAAA-ATATAT-TTTA
3020752 TTATTATCTT-AACTTCAAAATATATTTTA
1 TTATTATCTTCAA-TT-AAAATATATTTTA
3020781 ACTAATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
27 2 0.04
28 30 0.62
29 16 0.33
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (28 bp):
TTATTATCTTCAATTAAAATATATTTTA
Found at i:3020789 original size:14 final size:15
Alignment explanation
Indices: 3020770--3020810 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3020760 TTAACTTCAA
3020770 AATATATTTTAA-CT
1 AATATATTTTAAGCT
*
3020784 AATATATTTTAAGTT
1 AATATATTTTAAGCT
*
3020799 AAAATATTTTAA
1 AATATATTTTAA
3020811 AAACATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATATTTTAAGCT
Done.