Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008056.1 Hibiscus syriacus cultivar Beakdansim tig00110551_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: 2370532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:976173 original size:26 final size:27
Alignment explanation
Indices: 976133--976190 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
976123 CTTTAATTAC
**
976133 CCCTAACTTGCTTAAACC-TTTATGTA
1 CCCTAACTTAATTAAACCTTTTATGTA
976159 CCCTAACTTAATTAAACCTTTTATGTA
1 CCCTAACTTAATTAAACCTTTTATGTA
976186 CCCTA
1 CCCTA
976191 GGTTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.29, C:0.28, G:0.05, T:0.38
Consensus pattern (27 bp):
CCCTAACTTAATTAAACCTTTTATGTA
Found at i:982733 original size:16 final size:17
Alignment explanation
Indices: 982697--982734 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
982687 TACTTTATTA
*
982697 CTTTTATTATTTAATCG
1 CTTTTATTATTTAATAG
*
982714 CTTTTATT-TTTAATAT
1 CTTTTATTATTTAATAG
982730 CTTTT
1 CTTTT
982735 TACCAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
CTTTTATTATTTAATAG
Found at i:987028 original size:23 final size:25
Alignment explanation
Indices: 986993--987047 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
986983 TTGAATGAAA
986993 GAAAGAAG-AAAAAAATAGC-AGTTC
1 GAAAGAAGAAAAAAAATAGCTA-TTC
987017 GAAA-AAGAAAAAAAATAGCTATTC
1 GAAAGAAGAAAAAAAATAGCTATTC
987041 GAAAGAA
1 GAAAGAA
987048 AAATAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.11
24 22 0.79
25 3 0.11
ACGTcount: A:0.62, C:0.07, G:0.18, T:0.13
Consensus pattern (25 bp):
GAAAGAAGAAAAAAAATAGCTATTC
Found at i:991250 original size:30 final size:29
Alignment explanation
Indices: 991214--991280 Score: 116
Period size: 30 Copynumber: 2.3 Consensus size: 29
991204 ACCCTTTTAT
991214 TTTAAGACTATTGAAAGCGACCTCTTAGGC
1 TTTAAGACTATTGAAAGCGACCTCTTA-GC
*
991244 TTTAAGACTATTGAAAGCGACCTCTTATC
1 TTTAAGACTATTGAAAGCGACCTCTTAGC
991273 TTTAAGAC
1 TTTAAGAC
991281 AATCACTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 9 0.25
30 27 0.75
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (29 bp):
TTTAAGACTATTGAAAGCGACCTCTTAGC
Found at i:992741 original size:3 final size:3
Alignment explanation
Indices: 992735--992777 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
992725 GATGATGATG
992735 ATA ATA ATA ATA A-A TATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
992778 CGGTCTCCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:995049 original size:5 final size:5
Alignment explanation
Indices: 995029--995068 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
995019 AATATAATAA
995029 GAAAT G-AAT G-AAT GAAAT GAAAT GAAAAT GAAAT GAAAT G
1 GAAAT GAAAT GAAAT GAAAT GAAAT G-AAAT GAAAT GAAAT G
995069 TTAGAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:995059 original size:11 final size:11
Alignment explanation
Indices: 995035--995066 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
995025 ATAAGAAATG
995035 AATG-AATG-A
1 AATGAAATGAA
995044 AATGAAATGAA
1 AATGAAATGAA
995055 AATGAAATGAA
1 AATGAAATGAA
995066 A
1 A
995067 TGTTAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 4 0.19
10 4 0.19
11 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (11 bp):
AATGAAATGAA
Found at i:995060 original size:16 final size:17
Alignment explanation
Indices: 995029--995068 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
995019 AATATAATAA
995029 GAAATGAATGAATGAAAT
1 GAAATGAA-GAATGAAAT
995047 GAAATGAA-AATGAAAT
1 GAAATGAAGAATGAAAT
995063 GAAATG
1 GAAATG
995069 TTAGAGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (17 bp):
GAAATGAAGAATGAAAT
Found at i:1000067 original size:24 final size:24
Alignment explanation
Indices: 1000035--1000098 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1000025 TCATTAACGC
*
1000035 TAAACAAACACGTTCATAAACATA
1 TAAACAAACACGTTCACAAACATA
* *
1000059 TAAATAAACACGTTCGCAAACATA
1 TAAACAAACACGTTCACAAACATA
* *
1000083 -AAACGAACATGTTCAC
1 TAAACAAACACGTTCAC
1000099 GACGTCCACA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 12 0.36
24 21 0.64
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.20
Consensus pattern (24 bp):
TAAACAAACACGTTCACAAACATA
Found at i:1011416 original size:133 final size:134
Alignment explanation
Indices: 1010609--1012442 Score: 1429
Period size: 134 Copynumber: 13.6 Consensus size: 134
1010599 GCGAATCGAA
* * ** * ** * *
1010609 CTCGATTCAATTTTCCCTGAAGAGTAGTGGAATAAATCAACATTTTTAGATATGACTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * * *
1010674 AAAAGCAGTGAAATAGATCCCTCTTTTTTCCAG-TTTGATCTTCCCTGAGTAATAGTGGAACAAG
66 AGAAGAAGTGGAACAGATCCCTC-TTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAG
1010738 T-TTGC
130 TCTT-C
* * * ** * * *
1010743 CTCGATTCAATCTTCCTTAAAGAAAAGTGGAATGAATCAATATCCCCATAGCTGATTTTACCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * * * * * *
1010808 AGAAGAAGTGTAAAATATCCCTCTCTTTCAAGATTTAATCTTCCCTAAGTAACAGTGGAACAAGG
66 AGAAGAAGTGGAACAGATCCCTCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGT
1010873 CTGT-
131 CT-TC
* * * *
1010877 CTCGATTCAATCTTCCCTAAAGAACAATGAAATGAATCAACATTTCCAGATCTAATTTT-CCTTA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* ** * * * *
1010941 AGAA-CAGCAGAACATATCCCT-TTTTTCAAGAATTGATCTTCCCTGAGGAATAGTGGAACAAGT
66 AGAAGAAGTGGAACAGATCCCTCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGT
*
1011004 TTTC
131 CTTC
* * * * * *
1011008 CTCGGTTCAATCTTCCCTGAAA-AATAGTGGAATGAATCAACATTTCTAGAACTGATCTTCCCCC
1 CTCGATTCAATCTTCCCT-AAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTC
* * * * * * * *
1011072 AATAAAAAGTGGAATAGATCCCTCTTTTCCCATATTTGATCTTCCTTAAGGAACAGTGTAACAAG
65 AAGAAGAAGTGGAACAGATCCCTCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAG
*
1011137 TCTGC
130 TCTTC
* * * * * * * * * *
1011142 CTCTATTCAATATTTCCTGAAGAACAATGGAATGGATCAACATTTTCATATCTAATTTTTCCCTT
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGA-TTTTCCCTC
* * * * * * *
1011207 AAGAA-ACAATGAAACATATTCCTCTTTTTTCCAGATTTGATTTTTCCT-ATGGAACAGTGAAAC
65 AAGAAGA-AGTGGAACAGATCCCTC-TTTTTCCAGATTTGATCTTCCCTGA-GGAACAGTGGAAC
*
1011270 AAGTCTGC
127 AAGTCTTC
* * * * * * * *
1011278 CTCGATTTAAGCATCCCTAAAGAACAGTGGAATGATTCAACGTCTCCAGATCTTATTTTACCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * *
1011343 AGAA-AAGTGGAATAGCTCCCTCTCTTTT-AAGATTTGATCTTCCATGAGTAACAGTGGAACAAG
66 AGAAGAAGTGGAACAGATCCCTCT-TTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAG
1011406 TCTTC
130 TCTTC
* * * * * * *
1011411 CTCGATTCAATCTTCCCAAAAGAACAATAGAACGAATCAAGATTTTCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* ** * * * * * *
1011476 AGAAGCAGCAGAACATATCCCT-TTTTTCAAGATTTGATATTCCATAAGGAACAGTGGAAAAAGT
66 AGAAGAAGTGGAACAGATCCCTCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGT
1011540 CTTC
131 CTTC
* * * *
1011544 CTCGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAACATTTCCAGATCTGGTTTTCTCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * ** * * * *
1011609 ATAAGCAGCAGAACAAATCCATCCTTTTTTCCAGATTTGATATTCCCTGAGGAACAGTGAAACAA
66 AGAAGAAGTGGAACAGATCCCT-C-TTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAA
*
1011674 GTCTGC
129 GTCTTC
* * * * * * *
1011680 CTCGATTCAATCTTCCTTGAAGAACACTGAAATGAATCAATATTTCTAGATCTGATTTT-CCTAA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * *** * * * * *
1011744 AAAAGTAGCAAAACAAATCCATCTTTTCTCCAGATTTGATCTTCTAC-GAGGAATAATGGAACAA
66 AGAAGAAGTGGAACAGATCCCTCTTTT-TCCAGATTTGATCTTC-CCTGAGGAACAGTGGAACAA
*
1011808 GTGTTC
129 GTCTTC
* * * ** ** * *
1011814 CTTGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATGTCCCCAGATCTGAATTTACCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * ** * * * * * *
1011879 ATAAGAAGCGGAACAAATCCCTATCATTCAATATTTAATATTCCCTGAGTAATA-TGGAACAAGT
66 AGAAGAAGTGGAACAGATCCCTCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGT
* *
1011943 ATGC
131 CTTC
* * ** * * *
1011947 CTCGATTCAATCTTCTCTATAGAATTGTGGAATGAATCAACATTTCTATATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
** * ** *
1012012 AGAATTAGCGGAACAGATCTAT-TTTCTTCCAGATTTGATCTTCCTTGAGGAACAGTGGAACAAG
66 AGAAGAAGTGGAACAGATCCCTCTTT-TTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAG
*
1012076 TCTAC
130 TCTTC
*
1012081 CTCGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * *
1012146 AGAAGCAGCGGAACATG-TCCTTCTTTTCTATTTTCCAGATTTGATCTTCCCCGAGGAACATTGA
66 AGAAGAAGTGGAACA-GATCC--C---TCT-TTTTCCAGATTTGATCTTCCCTGAGGAACAGTGG
*
1012210 AACAAGTCTAC
124 AACAAGTCTTC
** * * * * * * *
1012221 CTTAATTCAATCTTCCCTGAAGAATAGTGCAATGAATCAACATTCCCATATATGATTTTCCCTTA
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * * * * * **
1012286 AGAAGAAATAGAGCATATCCATCTTCTTTCGAGATTTGATATTCCCTGAGTAGTAGTGGAACAAG
66 AGAAGAAGTGGAACAGATCCCTCTT-TTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAG
*
1012351 TCTAC
130 TCTTC
* * * * * * * *
1012356 CTCTATTCAATCCTCCCTGAAGAAAAGTGGAATGAATCAACATTTCTC-GATATGATCTACCCTT
1 CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTC-CAGATCTGATTTTCCCTC
*
1012420 AAGAA-ACAGTGGAACAAATCCCT
65 AAGAAGA-AGTGGAACAGATCCCT
1012443 TATCAGATTT
Statistics
Matches: 1354, Mismatches: 308, Indels: 75
0.78 0.18 0.04
Matches are distributed among these distances:
130 1 0.00
131 83 0.06
132 26 0.02
133 330 0.24
134 437 0.32
135 192 0.14
136 172 0.13
139 1 0.00
140 110 0.08
141 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
AGAAGAAGTGGAACAGATCCCTCTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGT
CTTC
Found at i:1011778 original size:536 final size:536
Alignment explanation
Indices: 1010693--1012395 Score: 1733
Period size: 536 Copynumber: 3.2 Consensus size: 536
1010683 GAAATAGATC
* * * * *
1010693 CCTCTTTTTTCCAG-TTTGATCTTC-CCTGAGTAATAGTGGAACAAGTTTGCCTCGATTCAATCT
1 CCTCTTTTCTCCAGATTTGATCTTCTAC-GAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCT
* * * * *
1010756 TCCTTAAAGAAAAGTGGAATGAATCAATATCCCCATAGCTGATTTTACCTCAAGAAGAAGTGTAA
65 TCCCTAAAGAAAAGTGGAATGAATCAATGTCCCCAGATCTGATTTTACCTCAAGAAGAAGTGGAA
* * *
1010821 AATATCCCTCTCTTTCAAGATTTAATCTTCCCTAAGTAACAGTGGAACAAGGCTGT-CTCGATTC
130 AAAATCCCTCTCTTTCAAGATTTAATCTTCCCTGAGTAACAGTGGAACAAGTCT-TCCTCGATTC
* * * *
1010885 AATCTTCCCTAAAGAACAATGAAATGAATCAACATTTCCAGATCTAATTTT-CCTTAAGAACAGC
194 AATCTTCCCTAAAGAACAATG-AATGAATCAACATTTTCATATCTGATTTTCCCTCAAGAACAGC
* * * * *
1010949 AGAACATATCCCTTTTTTCAAGAATTGATCTTCCCTGAGGAATAGTGGAACAAGTTTTCCTCGGT
258 AGAACATATCCCTTTTTTCAAGATTTGATCTTCCATGAGGAACAGTGGAACAAGTCTTCCTCGAT
* * * * * **
1011014 TCAATCTTCCCTGAAAAATAGTGGAATGAATCAACATTTCTAGAACTGATCTTCCCCCAATAAAA
323 TCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAATAAGC
* * * * * * * * *
1011079 AGTGGAATAGATCCCT-C-TTTTCCCATATTTGATCTTCCTTAAGGAACAGTGTAACAAGTCTGC
388 AGCGGAACAAATCCATCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGAAACAAGTCTGC
* * * * *
1011142 CTCTATTCAATATTTCCTGAAGAACAATGGAATGGATCAACATTTTCATATCTAATTTTTCCCTT
453 CTCAATTCAAT-CTTCCTGAAGAACAATGAAATGAATCAACATTTTCAGATCTAATTTTTCCCTT
*
1011207 AAGAAACAATGAAACATATT
517 AAGAAACAATGAAACATAAT
* * * * * * * *
1011227 CCTCTTTTTTCCAGATTTGAT-TTTTCCTATGGAACAGTGAAACAAGTCTGCCTCGATTTAAGCA
1 CCTCTTTTCTCCAGATTTGATCTTCTACGA-GGAACAGTGGAACAAGTCTGCCTCGATTCAATCT
* * * * *
1011291 TCCCTAAAGAACAGTGGAATGATTCAACGTCTCCAGATCTTATTTTACCTCAAGAA-AAGTGGAA
65 TCCCTAAAGAAAAGTGGAATGAATCAATGTCCCCAGATCTGATTTTACCTCAAGAAGAAGTGGAA
* ** * * *
1011355 TAGCTCCCTCTCTTTTAAGATTTGATCTTCCATGAGTAACAGTGGAACAAGTCTTCCTCGATTCA
130 AAAATCCCTCTCTTTCAAGATTTAATCTTCCCTGAGTAACAGTGGAACAAGTCTTCCTCGATTCA
* * *
1011420 ATCTTCCCAAAAGAACAATAGAACGAATCAAGATTTTCATATCTGATTTTCCCTCAAGAAGCAGC
195 ATCTTCCCTAAAGAACAAT-GAATGAATCAACATTTTCATATCTGATTTTCCCTCAAGAA-CAGC
* * *
1011485 AGAACATATCCCTTTTTTCAAGATTTGATATTCCATAAGGAACAGTGGAAAAAGTCTTCCTCGAT
258 AGAACATATCCCTTTTTTCAAGATTTGATCTTCCATGAGGAACAGTGGAACAAGTCTTCCTCGAT
** * *
1011550 TCAATCTTCCCTGAAGAGCAGTGGAATGAATCAACATTTCCAGATCTGGTTTTCTCTCAATAAGC
323 TCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAATAAGC
* *
1011615 AGCAGAACAAATCCATCCTTTTTTCCAGATTTGATATTCCCTGAGGAACAGTGAAACAAGTCTGC
388 AGCGGAACAAATCCATCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGAAACAAGTCTGC
* * * *
1011680 CTCGATTCAATCTTCCTTGAAGAACACTGAAATGAATCAATA-TTTCTAGATCTGA-TTTT-CC-
453 CTCAATTCAATCTTCC-TGAAGAACAATGAAATGAATCAACATTTTC-AGATCTAATTTTTCCCT
*
1011741 TAA-AAA-AGTAGCAAAACA-AAT
516 TAAGAAACAAT-G--AAACATAAT
* * * * *
1011762 CCATCTTTTCTCCAGATTTGATCTTCTACGAGGAATAATGGAACAAGTGTTCCTTGATTCAATCT
1 CC-TCTTTTCTCCAGATTTGATCTTCTACGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCT
* * * * *
1011827 TCCCTGAAGAATAGTGGAATGAATCAATGTCCCCAGATCTGAATTTACCTCAATAAGAAGCGGAA
65 TCCCTAAAGAAAAGTGGAATGAATCAATGTCCCCAGATCTGATTTTACCTCAAGAAGAAGTGGAA
* * * * * * * *
1011892 CAAATCCCTATCATTCAATATTTAATATTCCCTGAGTAATA-TGGAACAAGTATGCCTCGATTCA
130 AAAATCCCTCTCTTTCAAGATTTAATCTTCCCTGAGTAACAGTGGAACAAGTCTTCCTCGATTCA
* * *** * *
1011956 ATCTTCTCTATAGAATTGTGGAATGAATCAACA-TTTCTATATATGATTTTCCCTCAAGAATTAG
195 ATCTTCCCTAAAGAACAAT-GAATGAATCAACATTTTC-ATATCTGATTTTCCCTCAAGAA-CAG
* * ** * * *
1012020 CGGAACAGATCTATTTTCTTCCAGATTTGATCTTCCTTGAGGAACAGTGGAACAAGTCTACCTCG
257 CAGAACATATCCCTTTT-TTCAAGATTTGATCTTCCATGAGGAACAGTGGAACAAGTCTTCCTCG
* *
1012085 ATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGAA
321 ATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAATAA
** * * * *
1012150 GCAGCGGAACATGTCCTTCTTTTCTATTTTCCAGATTTGATCTTCCCCGAGGAACATTGAAACAA
386 GCAGCGGAACAAATCCATC----CTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGAAACAA
* * * * * ** * * *
1012215 GTCTACCTTAATTCAATCTTCCCTGAAGAATAGTGCAATGAATCAACATTCCCATATATGA-TTT
447 GTCTGCCTCAATTCAATCTT-CCTGAAGAACAATGAAATGAATCAACATTTTCAGATCTAATTTT
*
1012279 TCCCTTAAGAAGA-AAT-AGAGCAT-AT
511 TCCCTTAAGAA-ACAATGA-AACATAAT
* * * * ** * *
1012304 CCATCTTCTT-TCGAGATTTGATATTC-CCTGAGTAGTAGTGGAACAAGTCTACCTCTATTCAAT
1 CC-TCTT-TTCTCCAGATTTGATCTTCTAC-GAGGAACAGTGGAACAAGTCTGCCTCGATTCAAT
* *
1012367 CCTCCCTGAAGAAAAGTGGAATGAATCAA
63 CTTCCCTAAAGAAAAGTGGAATGAATCAA
1012396 CATTTCTCGA
Statistics
Matches: 966, Mismatches: 170, Indels: 58
0.81 0.14 0.05
Matches are distributed among these distances:
533 3 0.00
534 125 0.13
535 102 0.11
536 305 0.32
537 170 0.18
538 77 0.08
541 88 0.09
542 86 0.09
543 5 0.01
544 2 0.00
545 3 0.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (536 bp):
CCTCTTTTCTCCAGATTTGATCTTCTACGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCTT
CCCTAAAGAAAAGTGGAATGAATCAATGTCCCCAGATCTGATTTTACCTCAAGAAGAAGTGGAAA
AAATCCCTCTCTTTCAAGATTTAATCTTCCCTGAGTAACAGTGGAACAAGTCTTCCTCGATTCAA
TCTTCCCTAAAGAACAATGAATGAATCAACATTTTCATATCTGATTTTCCCTCAAGAACAGCAGA
ACATATCCCTTTTTTCAAGATTTGATCTTCCATGAGGAACAGTGGAACAAGTCTTCCTCGATTCA
ATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAATAAGCAGC
GGAACAAATCCATCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGAAACAAGTCTGCCTC
AATTCAATCTTCCTGAAGAACAATGAAATGAATCAACATTTTCAGATCTAATTTTTCCCTTAAGA
AACAATGAAACATAAT
Found at i:1034394 original size:84 final size:84
Alignment explanation
Indices: 1034265--1034467 Score: 268
Period size: 84 Copynumber: 2.4 Consensus size: 84
1034255 CACAAATTCA
* * *
1034265 TGTCATTGAAGCCACCGACATAAAT-ATTAGATGACGCGCAATTGTGCGTCATAAATCTATGACA
1 TGTCATTGAAGCC-CCGTCATAAATGA--AGATGACACACAATTGTGCGTCATAAATCTATGACA
1034329 CGCATTTATGACATT-CATTGCGC
63 CGCATTTATGAC-TTACATTGC-C
* * * *
1034352 -GTCATTGAAGACCCGTCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATGACACGC
1 TGTCATTGAAGCCCCGTCATAAATGAAGATGACACACAATTGTGCGTCATAAATCTATGACACGC
1034416 ATTTATGACTTACATTGCC
66 ATTTATGACTTACATTGCC
1034435 TGTCATTGAAGCCCACGTCATAAATGAAGATGA
1 TGTCATTGAAGCCC-CGTCATAAATGAAGATGA
1034468 TACATATTCG
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
83 3 0.03
84 61 0.59
85 28 0.27
86 12 0.12
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (84 bp):
TGTCATTGAAGCCCCGTCATAAATGAAGATGACACACAATTGTGCGTCATAAATCTATGACACGC
ATTTATGACTTACATTGCC
Found at i:1034510 original size:2 final size:2
Alignment explanation
Indices: 1034503--1034554 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1034493 TTTCGTAAAT
1034503 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
1034545 -A TA TA TA TA T
1 TA TA TA TA TA T
1034555 TGTAGATTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1037993 original size:62 final size:64
Alignment explanation
Indices: 1037888--1038013 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 64
1037878 GGATCTAAAC
1037888 AAAAGACAAAACCCAAATGCAAAATGAGCCATATCTTTCTCTTCCTTGTC-TGGTTTTCAAGGA
1 AAAAGACAAAACCCAAATGCAAAATGAGCCATATCTTTCTCTTCCTTGTCTTGGTTTTCAAGGA
*
1037951 AAAAGACAAAACCCAAATGC-AAATGAGCCATATCTTTCTCTTCCTTGTCTTGTTTTTCAAGGA
1 AAAAGACAAAACCCAAATGCAAAATGAGCCATATCTTTCTCTTCCTTGTCTTGGTTTTCAAGGA
1038014 TTTTCTGTCG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 29 0.48
63 32 0.52
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (64 bp):
AAAAGACAAAACCCAAATGCAAAATGAGCCATATCTTTCTCTTCCTTGTCTTGGTTTTCAAGGA
Found at i:1039327 original size:2 final size:2
Alignment explanation
Indices: 1039315--1039347 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1039305 TTTATTTAGT
1039315 TA TA TA T- 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
1039348 ATGTGTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1039530 original size:2 final size:2
Alignment explanation
Indices: 1039525--1039551 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1039515 TATATAACAT
1039525 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1039552 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1041926 original size:19 final size:18
Alignment explanation
Indices: 1041902--1041946 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
1041892 TTGCATTTGC
1041902 ATTTTATTTTCCGCACTGT
1 ATTTTATTTT-CGCACTGT
*
1041921 ATTTTACTTTTCGCATTGT
1 ATTTTA-TTTTCGCACTGT
1041940 ATTTTAT
1 ATTTTAT
1041947 CCATGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.58
Consensus pattern (18 bp):
ATTTTATTTTCGCACTGT
Found at i:1045660 original size:14 final size:14
Alignment explanation
Indices: 1045641--1045671 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1045631 GATTCTCATG
1045641 TATGTGTATATATA
1 TATGTGTATATATA
*
1045655 TATGTGTGTATATA
1 TATGTGTATATATA
1045669 TAT
1 TAT
1045672 ATATCCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (14 bp):
TATGTGTATATATA
Found at i:1045664 original size:16 final size:16
Alignment explanation
Indices: 1045643--1045673 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1045633 TTCTCATGTA
1045643 TGTGTATATATATATG
1 TGTGTATATATATATG
1045659 TGTGTATATATATAT
1 TGTGTATATATATAT
1045674 ATCCTCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (16 bp):
TGTGTATATATATATG
Found at i:1050718 original size:2 final size:2
Alignment explanation
Indices: 1050711--1050741 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1050701 TTTTATTTTC
1050711 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1050742 TACTAGTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1054262 original size:11 final size:11
Alignment explanation
Indices: 1054246--1054272 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1054236 AAAGGTGGCA
1054246 GAGTTTCATAG
1 GAGTTTCATAG
1054257 GAGTTTCATAG
1 GAGTTTCATAG
1054268 GAGTT
1 GAGTT
1054273 GGTGTTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (11 bp):
GAGTTTCATAG
Found at i:1056107 original size:18 final size:18
Alignment explanation
Indices: 1056084--1056127 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1056074 GATTGTTTTT
*
1056084 TAAAATAAAAGAT-TAGAA
1 TAAAATAAAAGATAAAG-A
1056102 TAAAATAAAAGATAAAGA
1 TAAAATAAAAGATAAAGA
1056120 TAAAATAA
1 TAAAATAA
1056128 TTAATAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
TAAAATAAAAGATAAAGA
Found at i:1056135 original size:43 final size:43
Alignment explanation
Indices: 1056086--1056178 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 43
1056076 TTGTTTTTTA
* *
1056086 AAATAAAAGATTAGAATAAAATAAAAGATAAAGATAAAATAAT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAAAAAT
* * ** *
1056129 TAATAAAAGATAAGGATGCAATAAAAGATAAGGATAAAAAAAT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAAAAAT
1056172 AAATAAA
1 AAATAAA
1056179 TTCAAGTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.68, C:0.01, G:0.12, T:0.19
Consensus pattern (43 bp):
AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAAAAAT
Found at i:1056946 original size:19 final size:20
Alignment explanation
Indices: 1056909--1056948 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1056899 AAAAACAAGG
*
1056909 AAAATATAATTTCTAAAAAT
1 AAAAGATAATTTCTAAAAAT
*
1056929 AAAAGATAA-TTCTTAAAAT
1 AAAAGATAATTTCTAAAAAT
1056948 A
1 A
1056949 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAGATAATTTCTAAAAAT
Found at i:1059690 original size:20 final size:21
Alignment explanation
Indices: 1059667--1059705 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1059657 ATGAAAAATA
1059667 TTTAAAT-AAAATTATATTAT
1 TTTAAATAAAAATTATATTAT
1059687 TTTAAATAAAAATTATATT
1 TTTAAATAAAAATTATATT
1059706 CATATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAATAAAAATTATATTAT
Found at i:1063934 original size:256 final size:251
Alignment explanation
Indices: 1063429--1063934 Score: 906
Period size: 256 Copynumber: 2.0 Consensus size: 251
1063419 ACTACAGTTT
1063429 CTCCAGTCCCGACAGATGATGCAACAGGCACTAACGCACGCTCTACAGATTCATAGGTTTCTTGG
1 CTCCAGTCCCGACAGATGATGCAACAGGCACTAACGCACGCTCTACAGATTCATAGGTTTCTTGG
1063494 GTAGTTCTTAGTTCCAAAAGGCTAAGCATATCACAATGAATTACAGCATAAAAATTAGAAAATGT
66 GTAGTTCTTAGTTCCAAAAGGCTAAGCATATCACAATGAATTACAGCATAAAAATTAGAAAATGT
1063559 GAAAACCAAAAGAAATGGATAAAAGGAACATAGTAGATCGTAGACTGCTGCGCGATAAAGACTTA
131 GAAAACCAAAAGAAATGGATAAAAGGAACATAGTAGATCGTAGACTGCTGCGCGATAAAGACTTA
1063624 AGAAGCACATACACAGAGTTGGGGACCAGGCTCGGCAGCACCGGTGGAGGTGGAGTACGAG
196 AGAAGCACATACACAGAGTTGGGGACCAGGCTCGGCAGCACC----G-GGTGGAGTACGAG
1063685 CTCCAGTCCCGACAGATGATGCAACAGGCACTAACGCACGCTCTACAGATTCATAGGTTTCTTGG
1 CTCCAGTCCCGACAGATGATGCAACAGGCACTAACGCACGCTCTACAGATTCATAGGTTTCTTGG
1063750 GTAGTTCTTAGTTCCAAAAGGCTAAGCAATATCTACAATATGAATTACAGCATAAAAATTAGAAA
66 GTAGTTCTTAGTTCCAAAAGGCTAAGC-ATATC-AC-A-ATGAATTACAGCATAAAAATTAGAAA
1063815 ATGTGAAAACCAAAAGAAAATGGATAAAAGGAACATAGTAGATCGTAGACTGCTGCGCGATAAAG
127 ATGTGAAAACCAAAAG-AAATGGATAAAAGGAACATAGTAGATCGTAGACTGCTGCGCGATAAAG
1063880 ACTTTAAGAAGCACATACACAGAGTTGGGGACCAGGCTCGGCAGCACC-GGTGGAG
191 AC-TTAAGAAGCACATACACAGAGTTGGGGACCAGGCTCGGCAGCACCGGGTGGAG
1063935 GTGGAGAGTA
Statistics
Matches: 244, Mismatches: 0, Indels: 12
0.95 0.00 0.05
Matches are distributed among these distances:
256 99 0.41
257 5 0.02
258 2 0.01
259 1 0.00
260 42 0.17
261 50 0.20
262 45 0.18
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (251 bp):
CTCCAGTCCCGACAGATGATGCAACAGGCACTAACGCACGCTCTACAGATTCATAGGTTTCTTGG
GTAGTTCTTAGTTCCAAAAGGCTAAGCATATCACAATGAATTACAGCATAAAAATTAGAAAATGT
GAAAACCAAAAGAAATGGATAAAAGGAACATAGTAGATCGTAGACTGCTGCGCGATAAAGACTTA
AGAAGCACATACACAGAGTTGGGGACCAGGCTCGGCAGCACCGGGTGGAGTACGAG
Found at i:1065275 original size:20 final size:20
Alignment explanation
Indices: 1065250--1065384 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1065240 AATTGGGAAA
1065250 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1065270 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1065290 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1065311 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1065331 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1065351 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1065371 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1065385 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1065316 original size:61 final size:61
Alignment explanation
Indices: 1065247--1065384 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
1065237 GCGAATTGGG
* * *
1065247 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
1065308 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
1065369 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1065385 TTTCAAAGCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1065580 original size:22 final size:22
Alignment explanation
Indices: 1065552--1065595 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1065542 CACTCTCTCA
1065552 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
1065574 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
1065596 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:1065602 original size:20 final size:21
Alignment explanation
Indices: 1065552--1065603 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1065542 CACTCTCTCA
1065552 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
1065573 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
1065595 -CTATCTCCA
1 CCCATCTCCA
1065604 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:1065909 original size:20 final size:20
Alignment explanation
Indices: 1065855--1065913 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1065845 TTGCGATTCT
**
1065855 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1065875 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1065895 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1065914 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1067267 original size:18 final size:18
Alignment explanation
Indices: 1067230--1067267 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1067220 TCCACTTCGG
* *
1067230 GAGCTATCACCTCGCTCA
1 GAGCTATCACCTCACCCA
1067248 GAGCTATCACCTCACCCA
1 GAGCTATCACCTCACCCA
1067266 GA
1 GA
1067268 CCCATCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.18
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:1067779 original size:20 final size:20
Alignment explanation
Indices: 1067754--1067830 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1067744 TTTGCAACAC
1067754 GAAATGACTATCGCAACGCG
1 GAAATGACTATCGCAACGCG
*
1067774 GAAATGGCTATCGCAACGCG
1 GAAATGACTATCGCAACGCG
* *
1067794 GAAATGGCTATCGCAATGC-
1 GAAATGACTATCGCAACGCG
**
1067813 GAAATGAAAATCGCAACG
1 GAAATGACTATCGCAACG
1067831 ACAAAAGCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 14 0.27
20 37 0.73
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (20 bp):
GAAATGACTATCGCAACGCG
Found at i:1067825 original size:19 final size:19
Alignment explanation
Indices: 1067803--1067898 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
1067793 GGAAATGGCT
1067803 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1067822 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1067836 AGCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
* *
1067854 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1067868 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1067887 ATCGCAATGCGA
1 ATCGCAATGCGA
1067899 TTTGTGTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 22
0.65 0.10 0.25
Matches are distributed among these distances:
14 18 0.32
15 1 0.02
16 6 0.11
17 2 0.04
18 9 0.16
19 21 0.37
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1067847 original size:33 final size:33
Alignment explanation
Indices: 1067805--1067893 Score: 144
Period size: 32 Copynumber: 2.7 Consensus size: 33
1067795 AAATGGCTAT
1067805 CGCAATGCGAAATGAAAATCGCAACGACAAAAG
1 CGCAATGCGAAATGAAAATCGCAACGACAAAAG
* *
1067838 CGCAATGCGAAATG-AAATCGTAACGACAAAAT
1 CGCAATGCGAAATGAAAATCGCAACGACAAAAG
*
1067870 CGCAACGCGAAATGAAAATCGCAA
1 CGCAATGCGAAATGAAAATCGCAA
1067894 TGCGATTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACGACAAAAG
Found at i:1067929 original size:14 final size:14
Alignment explanation
Indices: 1067910--1067986 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
1067900 TTGTGTTTCG
1067910 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1067924 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1067940 CGCATTGCGATTTTCATTT
1 CG--TTGCGA-TTT--TGT
1067959 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1067975 CGTTGCGATTTT
1 CGTTGCGATTTT
1067987 CATTTCGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 21 0.38
16 8 0.14
18 9 0.16
19 18 0.32
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1067939 original size:19 final size:18
Alignment explanation
Indices: 1067926--1068044 Score: 111
Period size: 19 Copynumber: 6.5 Consensus size: 18
1067916 GATTTTGTCG
1067926 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
1067944 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
*
1067963 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
1067977 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
**
1067996 TTGCGATAGCCATTTCCGCA
1 TTGCGAT-TTCATTT-CGCA
* *
1068016 TTGCGATAGTCATTTTCGCG
1 TTGCGAT-TTCA-TTTCGCA
1068036 TTGCGATTT
1 TTGCGATTT
1068045 TAAGTTTCGT
Statistics
Matches: 85, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
14 6 0.07
15 3 0.04
16 4 0.05
17 4 0.05
18 10 0.12
19 30 0.35
20 25 0.29
21 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:1067943 original size:51 final size:52
Alignment explanation
Indices: 1067888--1068022 Score: 184
Period size: 51 Copynumber: 2.6 Consensus size: 52
1067878 GAAATGAAAA
* * *
1067888 TCGCAATGCGATTTGT-GTTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTT-TCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1067939 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
***
1067991 TCGCATTGCGATAGCCATTTCCGCATTGCGAT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGAT
1068023 AGTCATTTTC
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 1 0.01
51 39 0.52
52 24 0.32
53 11 0.15
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:1068017 original size:20 final size:19
Alignment explanation
Indices: 1067987--1068042 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1067977 TTGCGATTTT
1067987 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
1068006 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
1068026 CATTTTCGCGTTGCGAT
1 CA-TTTCGCATTGCGAT
1068043 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1069925 original size:14 final size:14
Alignment explanation
Indices: 1069906--1069941 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1069896 ATTGTTTAAT
1069906 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1069920 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1069934 TGATTTGT
1 TGATTTGT
1069942 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1070129 original size:19 final size:19
Alignment explanation
Indices: 1070074--1070122 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1070064 ATCGCAACGA
1070074 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1070093 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1070112 GAAAATCGCAA
1 GAAAATCGCAA
1070123 CGAGAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1070141 original size:19 final size:18
Alignment explanation
Indices: 1070074--1070141 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
1070064 ATCGCAACGA
1070074 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGC-AAAT
1070093 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGC-AAAT
*
1070112 GAAAATCGCAA--C-GA-
1 GAAAATCGCAATGCAAAT
1070126 GAAAATCGCAATGCAA
1 GAAAATCGCAATGCAA
1070142 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 1 0.02
17 1 0.02
19 30 0.68
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (18 bp):
GAAAATCGCAATGCAAAT
Found at i:1070185 original size:20 final size:20
Alignment explanation
Indices: 1070160--1070213 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1070150 TCGCATTGCG
*
1070160 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
1070180 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
1070200 ATTTTCGCGTTGCG
1 ATTTTCGAGTTGCG
1070214 GTTTCCCCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:1070454 original size:20 final size:20
Alignment explanation
Indices: 1070429--1070520 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1070419 TTGAAGATGA
1070429 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1070449 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
1070469 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1070490 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
1070510 TTGCGATTTTC
1 TTGCGATTTTC
1070521 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1070549 original size:20 final size:21
Alignment explanation
Indices: 1070505--1070556 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1070495 ATAGTCAGTA
*
1070505 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1070526 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1070546 TCGCATTGCGA
1 TCGCATTGCGA
1070557 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1071487 original size:11 final size:11
Alignment explanation
Indices: 1071463--1071496 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
1071453 ATATAATCCT
1071463 GAAGAAGAAAAA
1 GAAGAAG-AAAA
1071475 GAAGAAGAAAA
1 GAAGAAGAAAA
1071486 GAAGAAGAAAA
1 GAAGAAGAAAA
1071497 AGTCCCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAAA
Found at i:1073807 original size:19 final size:19
Alignment explanation
Indices: 1073785--1073915 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1073775 GGAAATTACT
1073785 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1073804 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1073818 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1073837 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1073851 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1073870 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1073884 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1073903 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1073916 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1073827 original size:33 final size:33
Alignment explanation
Indices: 1073785--1073911 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1073775 GGAAATTACT
1073785 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1073818 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1073850 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1073884 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1073912 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1073892 original size:66 final size:66
Alignment explanation
Indices: 1073786--1073918 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1073776 GAAATTACTA
*
1073786 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1073851 T
66 T
*
1073852 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1073917 T
66 T
1073918 T
1 T
1073919 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1073964 original size:19 final size:19
Alignment explanation
Indices: 1073940--1073977 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1073930 GCAATTCTCT
1073940 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1073959 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1073978 TATTGTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1074126 original size:14 final size:14
Alignment explanation
Indices: 1074093--1074128 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1074083 CATCAATTAA
1074093 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1074107 AC-AATCACCTTTT
1 ACAAATCAACTTTT
1074120 ACAAATCAA
1 ACAAATCAA
1074129 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1075526 original size:21 final size:21
Alignment explanation
Indices: 1075496--1075661 Score: 77
Period size: 21 Copynumber: 7.9 Consensus size: 21
1075486 TGAATGGTGG
*
1075496 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTCAACGATGA
* * * * *
1075517 CAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* * *
1075538 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
1075559 TAGGGGCCTCTTCAACGAT-A
1 GAGGGGCCTCTTCAACGATGA
* * * **
1075579 GGAGTGGACTCTTGAGGGATGA
1 -GAGGGGCCTCTTCAACGATGA
* * * * *
1075601 CAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* *
1075622 GAGGGGACTC-TCAAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
1075643 TAGGGGCCTCTTCAACGAT
1 GAGGGGCCTCTTCAACGAT
1075662 AGGAGTGGAC
Statistics
Matches: 99, Mismatches: 40, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
20 8 0.08
21 81 0.82
22 10 0.10
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
GAGGGGCCTCTTCAACGATGA
Found at i:1075541 original size:42 final size:41
Alignment explanation
Indices: 1075482--1075687 Score: 182
Period size: 42 Copynumber: 4.9 Consensus size: 41
1075472 GTGAATCGGG
* *
1075482 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1075524 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1075566 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* *
1075608 CTCTTGAACGGTGGGAGGGGACTC-TCAAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1075650 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1075688 GCGAGTCAGG
Statistics
Matches: 130, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
41 10 0.08
42 108 0.83
43 12 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1075623 original size:84 final size:84
Alignment explanation
Indices: 1075512--1075687 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
1075502 CCTCTTCAAC
*
1075512 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCAAGGAATGATAGGGGCCTCTTCAACGA
1075577 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1075596 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCAAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCAAGGAATGATAGGGGCCTCTTCAACGA
1075661 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1075680 GATGACAG
1 GATGACAG
1075688 GCGAGTCAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCAAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1076082 original size:91 final size:90
Alignment explanation
Indices: 1075906--1076090 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1075896 ATTTCAAACT
*
1075906 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT---AAATAAACAGTTTAGC
*
1075971 AGAATTGGCAGCAATCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
1075999 TTCAACCAAAAGATAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1076063 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1076090 T
1 T
1076091 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1077744 original size:20 final size:19
Alignment explanation
Indices: 1077713--1077834 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
1077703 TCTTTTGGTT
1077713 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1077732 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1077753 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1077772 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1077786 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1077805 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1077819 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1077835 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.26
20 29 0.37
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1077795 original size:33 final size:33
Alignment explanation
Indices: 1077738--1077834 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
1077728 ACGAGATAAT
1077738 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1077772 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1077805 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
1077835 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1077875 original size:19 final size:19
Alignment explanation
Indices: 1077835--1077900 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
1077825 AAAATCGCAA
** *
1077835 TGCGATTTTGGTTTCACG-
1 TGCGATTTTTATTTCGCGT
1077853 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1077872 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
*
1077892 TGTGATTTT
1 TGCGATTTT
1077901 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 15 0.39
19 12 0.32
20 11 0.29
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1078504 original size:20 final size:20
Alignment explanation
Indices: 1078419--1078548 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
1078409 CGCTATGTAA
* * *
1078419 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* * *
1078439 ATCGCGTTGTGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1078459 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1078480 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1078500 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1078520 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1078540 ATCGCATTG
1 ATCGCATTG
1078549 TGATTTTCCC
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.03
20 78 0.82
21 12 0.13
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1078571 original size:81 final size:81
Alignment explanation
Indices: 1078419--1078573 Score: 177
Period size: 81 Copynumber: 1.9 Consensus size: 81
1078409 CGCTATGTAA
* * * * * ** *
1078419 ATCGCGTTGCGAAAGTCAGAATCGCGTTGTGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
1078484 CATTGCGATAGTAAGT
66 CATTGCGATAGTAAGT
* * * *
1078500 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGTGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
*
1078564 GCGTTGCGAT
65 GCATTGCGAT
1078574 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
81 58 0.97
82 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
CATTGCGATAGTAAGT
Found at i:1078663 original size:21 final size:21
Alignment explanation
Indices: 1078623--1078663 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1078613 ACTGTAGACC
**
1078623 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1078644 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1078664 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1082482 original size:3 final size:3
Alignment explanation
Indices: 1082474--1082521 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
1082464 ACATTTTTAA
*
1082474 TAT TAT TAT TAT TAAT TAT AAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
1082521 T
1 T
1082522 TTAAGGCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1082497 original size:13 final size:12
Alignment explanation
Indices: 1082474--1082521 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
1082464 ACATTTTTAA
1082474 TATTATTATTAT
1 TATTATTATTAT
*
1082486 TAATTATAATTATT
1 T-ATTATTATTA-T
1082500 TATTATTATTAT
1 TATTATTATTAT
1082512 TATTATTATT
1 TATTATTATT
1082522 TTAAGGCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 12 0.38
13 18 0.56
14 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTATTATTAT
Found at i:1082625 original size:12 final size:12
Alignment explanation
Indices: 1082593--1082627 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1082583 AATGACCTAA
1082593 CAAGCCCAGAACC
1 CAAGCCCA-AACC
1082606 CGAAGCCCAAACC
1 C-AAGCCCAAACC
1082619 CAAGCCCAA
1 CAAGCCCAA
1082628 TACTAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 6 0.29
14 7 0.33
ACGTcount: A:0.40, C:0.46, G:0.14, T:0.00
Consensus pattern (12 bp):
CAAGCCCAAACC
Found at i:1082900 original size:3 final size:3
Alignment explanation
Indices: 1082892--1082942 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
1082882 ACGTTTTTAA
* *
1082892 TAT TAT TAT TAT TAT TGT TAT TAT TAAT TAT AAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT
1082939 TAT T
1 TAT T
1082943 TTCAGGCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1085270 original size:131 final size:131
Alignment explanation
Indices: 1085117--1085484 Score: 551
Period size: 131 Copynumber: 2.8 Consensus size: 131
1085107 TCGACATTGA
* * * * *
1085117 AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGAATACTTTAAGGCATGAGATGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* *
1085182 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTAAATTTTAAGAC
1085247 G
131 G
* * * ** * *
1085248 TAATAGTGATATCTCTTCATTTCGATTGAAGTAATAGATGGTTGCTTTAAGGCATGAAAGGTAAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* * *
1085313 TTATTCTCTATTGGAAATCATTAGATATTATCATTTT-TACTCGAATCAATATTAAATTTTAAGA
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCT-CTCGAATCAATATTAAATTTTAAGA
1085377 CG
130 CG
*
1085379 AAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
1085444 TTATTCTCGATTGGAAATAATTAG-TATTATCGTTTTCTCTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTC
1085485 TTAGAATTAT
Statistics
Matches: 207, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
130 15 0.07
131 192 0.93
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTAAATTTTAAGAC
G
Found at i:1087229 original size:5 final size:5
Alignment explanation
Indices: 1087221--1087256 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1087211 ACTAAACTAC
* *
1087221 ATGCT ATGCA ATGCA ATGCA ATACA ATGCA ATGCA A
1 ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA A
1087257 AGTACCTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (5 bp):
ATGCA
Found at i:1098743 original size:45 final size:45
Alignment explanation
Indices: 1098675--1098908 Score: 398
Period size: 45 Copynumber: 5.2 Consensus size: 45
1098665 TGAATAAAAT
1098675 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
*
1098720 AATGCATATGGGTGCATTCTTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
*
1098765 AATGCATATGGGTGCATTCTTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
* *
1098810 AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAATTTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
*
1098855 AATGCATATGGGTGCATTATTGGCATGAAATGATG-CTATAATTGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTC-ATAATTG-A
1098901 AATGCATA
1 AATGCATA
1098909 ATGATGCATT
Statistics
Matches: 181, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
44 1 0.01
45 171 0.94
46 9 0.05
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
Found at i:1105007 original size:41 final size:41
Alignment explanation
Indices: 1104949--1105042 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
1104939 AATGTCAAAA
*
1104949 TGGTATCGATACTAAAAAGGACTATTGATACCATAGTATGG
1 TGGTATCGATACAAAAAAGGACTATTGATACCATAGTATGG
*
1104990 TGGTATCGATACAAAAAAGGAGTATTGATACCATAGTATGG
1 TGGTATCGATACAAAAAAGGACTATTGATACCATAGTATGG
*
1105031 TAGTATCGATAC
1 TGGTATCGATAC
1105043 TGAGAGAAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (41 bp):
TGGTATCGATACAAAAAAGGACTATTGATACCATAGTATGG
Found at i:1105036 original size:22 final size:22
Alignment explanation
Indices: 1104975--1105042 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
1104965 AAGGACTATT
*
1104975 GATACCATAGTATGGTGGTATC
1 GATACCATAGTATGGTAGTATC
** * *
1104997 GATA-CA-AAAAAGG-AGTATT
1 GATACCATAGTATGGTAGTATC
1105016 GATACCATAGTATGGTAGTATC
1 GATACCATAGTATGGTAGTATC
1105038 GATAC
1 GATAC
1105043 TGAGAGAAGG
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
19 8 0.24
20 6 0.18
21 6 0.18
22 14 0.41
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (22 bp):
GATACCATAGTATGGTAGTATC
Found at i:1105607 original size:22 final size:22
Alignment explanation
Indices: 1105582--1105652 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1105572 TGGGTGTATT
1105582 ATTGGCATGAAAGGATTCCATA
1 ATTGGCATGAAAGGATTCCATA
* * * *
1105604 ATTGGAATGAATATGG-GTGCATT
1 ATTGGCATGAA-A-GGATTCCATA
* *
1105627 CTTGGCATGAAAGGATACCATA
1 ATTGGCATGAAAGGATTCCATA
1105649 ATTG
1 ATTG
1105653 AAATGCATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
23 14 0.40
24 2 0.06
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (22 bp):
ATTGGCATGAAAGGATTCCATA
Found at i:1105633 original size:45 final size:45
Alignment explanation
Indices: 1105564--1105809 Score: 359
Period size: 45 Copynumber: 5.4 Consensus size: 45
1105554 TGAATAAAAT
* * *
1105564 AATGCATATGGGTGTATTATTGGCATGAAAGGATTCCATAATTGG
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* * *
1105609 AATGAATATGGGTGCATTCTTGGCATGAAAGGATACCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* *
1105654 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAATTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* * *
1105699 AATGCATATGGGTGAATTATTGGCATGAACGGATGCCATAATTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
*
1105744 AATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAATTGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTG-A
1105790 AATGCATAAT-GGTGCATTAT
1 AATGCAT-ATGGGTGCATTAT
1105810 AAGTATGAAT
Statistics
Matches: 182, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
45 162 0.89
46 18 0.10
47 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
Found at i:1106450 original size:3 final size:3
Alignment explanation
Indices: 1106430--1106495 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
1106420 GCTTAAAAAA
* *
1106430 TAT TAT ATAT TA- TAT TAT TAT GAT TAT TAT TAT TAT GAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1106475 TAT TAT TAT TAT CAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1106496 TCATTTTTGG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1116516 original size:91 final size:91
Alignment explanation
Indices: 1116387--1116561 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 91
1116377 AGGAGGTGGA
* * * *
1116387 TCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAG-GAGAAGAAGTTCAC
1 TCAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCAA-CAAGAGAAAAGAAGTTCAC
1116451 AACGAGAAGAACTTGTTCAACCTTAGC
65 AACGAGAAGAACTTGTTCAACCTTAGC
* *
1116478 TCAATATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCAACAAGAGAAAAGAAGTTCATA
1 TCAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCAACAAGAGAAAAGAAGTTCACA
*
1116543 ATGAGAAGAACTTGTTCAA
66 ACGAGAAGAACTTGTTCAA
1116562 TCCAACACTT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
90 3 0.04
91 73 0.96
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (91 bp):
TCAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCAACAAGAGAAAAGAAGTTCACA
ACGAGAAGAACTTGTTCAACCTTAGC
Found at i:1116748 original size:3 final size:3
Alignment explanation
Indices: 1116717--1116774 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
1116707 GCTTAAAAAA
*
1116717 TAT TAT ATAT TA- TAG TAT TA- TATT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
1116761 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
1116775 AAATTTTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
2 6 0.12
3 38 0.78
4 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1116758 original size:23 final size:23
Alignment explanation
Indices: 1116717--1116774 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 23
1116707 GCTTAAAAAA
*
1116717 TATTATATATTA-TAGTATTATA-
1 TATTAT-TATTATTATTATTATAG
1116739 T-TTATTATTATTATT-TTAT--
1 TATTATTATTATTATTATTATAG
1116758 TATTATTATTATTATTA
1 TATTATTATTATTATTA
1116775 AAATTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 23 0.72
21 7 0.22
22 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTATTATTATTATTATTATAG
Found at i:1116761 original size:17 final size:17
Alignment explanation
Indices: 1116717--1116772 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1116707 GCTTAAAAAA
*
1116717 TATTATA-TATTA-TAG
1 TATTATATTATTATTAT
1116732 TATTATATTTATTATTAT
1 TATTATA-TTATTATTAT
*
1116750 TATTTTATTATTATTAT
1 TATTATATTATTATTAT
1116767 TATTAT
1 TATTAT
1116773 TAAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.20
17 20 0.57
18 8 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTATATTATTATTAT
Found at i:1116780 original size:26 final size:26
Alignment explanation
Indices: 1116732--1116791 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1116722 TATATTATAG
**
1116732 TATTATATTTATTATTATTATTTTAT
1 TATTATATTTATTATTAAAATTTTAT
1116758 TATTAT-TATTATTATTAAAATTTTA-
1 TATTATAT-TTATTATTAAAATTTTAT
1116783 T-TTATATTT
1 TATTATATTT
1116792 TTGACAGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 6 0.20
25 3 0.10
26 21 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTATATTTATTATTAAAATTTTAT
Found at i:1116783 original size:20 final size:19
Alignment explanation
Indices: 1116739--1116784 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1116729 TAGTATTATA
**
1116739 TTTATTATTATTATTTTAT
1 TTTATTATTATTATTAAAT
1116758 TATTATTATTATTATTAAAAT
1 T-TTATTATTATTATT-AAAT
1116779 TTTATT
1 TTTATT
1116785 TATATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTATTATTATTAAAT
Found at i:1118513 original size:32 final size:31
Alignment explanation
Indices: 1118448--1118513 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
1118438 TCATTTTTAG
* *
1118448 TTTTAAATTTTTATTTGTACTATTTTGGTAT
1 TTTTAAATTTTTATTTGTACTATTTTAGCAT
* * *
1118479 TTTTAAAATTTTTATTTTTATTGTTTTAGCAT
1 TTTT-AAATTTTTATTTGTACTATTTTAGCAT
1118511 TTT
1 TTT
1118514 AACTTTACGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (31 bp):
TTTTAAATTTTTATTTGTACTATTTTAGCAT
Found at i:1119792 original size:3 final size:3
Alignment explanation
Indices: 1119784--1119829 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
1119774 TTTCATCCCG
*
1119784 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
1119830 ATATGTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1119845 original size:31 final size:30
Alignment explanation
Indices: 1119785--1119846 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
1119775 TTCATCCCGT
1119785 ATTATTATTATTATTATTACTATTATTATTA
1 ATTATTATTATTATTATTA-TATTATTATTA
*
1119816 ATTATTATTATTATATATGT-TATTTTTATTA
1 ATTATTATTATTAT-TAT-TATATTATTATTA
1119847 CAGGCTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 24 0.86
32 3 0.11
33 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (30 bp):
ATTATTATTATTATTATTATATTATTATTA
Found at i:1122245 original size:131 final size:130
Alignment explanation
Indices: 1121933--1122416 Score: 661
Period size: 131 Copynumber: 3.7 Consensus size: 130
1121923 GTAATAACTT
* * * *
1121933 TTCATTTC-AGTTGGCGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGG
1 TTCATTTCGA-TTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGG
* * *
1121997 AAATAATTTGATATTATCGTTTTCTCTCGAATCAATATTGACTTTTAAGAC--AGAATAGCATAT
65 AAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGACGGATAAT-G-ATAT
1122060 CTC
128 CTC
**
1122063 TTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTATATTGGA
1 TTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGA
* * * * * *
1122128 AATCATTAGATATTAGC-TTTCTCTCTCGAATTAATATTTATTTTTAAGATGGATTAATGATATC
66 AATAATTAGATATTATCGTTT-TCTCTCGAATCAATATTGAATTTTAAGACGGA-TAATGATATC
1122192 TC
129 TC
1122194 TTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGA
* * * * *
1122259 AATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGACGGGATAGTGACATCT
66 AATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGAC-GGATAATGATATCT
1122324 C
130 C
* * * *
1122325 TTCATTTCGATTGGAGAAATAAATGATTGCTTTAAGGTATGAGAGATTATTTATTCTTGATTGGA
1 TTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGA
*
1122390 AATAATTAGATATTATCGTTTTTTCTC
66 AATAATTAGATATTATCGTTTTCTCTC
1122417 TTAAAATTAT
Statistics
Matches: 315, Mismatches: 32, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
129 3 0.01
130 96 0.30
131 205 0.65
132 8 0.03
133 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (130 bp):
TTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGA
AATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGACGGATAATGATATCTC
Found at i:1123254 original size:23 final size:23
Alignment explanation
Indices: 1123228--1123273 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1123218 CATTGAAGTG
*
1123228 CCACGTAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* * *
1123251 CCACATAGCATTGTTCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
1123274 ATGTCCTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:1123307 original size:36 final size:36
Alignment explanation
Indices: 1123237--1123309 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1123227 GCCACGTAGA
* *
1123237 AATGTCCCGAAGGACCACATAGCATTGTTCCGAAGG
1 AATGTCCCGAAGGACCACATAGAATTGATCCGAAGG
* *
1123273 AATGTCCTGAAGGACCACGTAGAATT-ATCACGAAGG
1 AATGTCCCGAAGGACCACATAGAATTGATC-CGAAGG
1123309 A
1 A
1123310 CCGCGTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (36 bp):
AATGTCCCGAAGGACCACATAGAATTGATCCGAAGG
Found at i:1123439 original size:28 final size:28
Alignment explanation
Indices: 1123407--1123476 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
1123397 GCATAGCTTT
*
1123407 TATCATATAGACATTGTCATGTACGTTA
1 TATCACATAGACATTGTCATGTACGTTA
* *
1123435 TATCACATAGACATTGTCATGTAGGTTG
1 TATCACATAGACATTGTCATGTACGTTA
1123463 TATCACATAGACAT
1 TATCACATAGACAT
1123477 GTATTAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (28 bp):
TATCACATAGACATTGTCATGTACGTTA
Found at i:1132171 original size:7 final size:6
Alignment explanation
Indices: 1132156--1132243 Score: 60
Period size: 6 Copynumber: 14.5 Consensus size: 6
1132146 TCGCTTGAAG
* *
1132156 AAAGAA AAATGAA AAATAA AGAA-AA AAAGTA AAAG-A AAAGAA AAA-AA
1 AAAGAA AAA-GAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
1132203 AATGAA AAATGAA AAATG-A AAA-AA AAAGAAA CAAAGAA AAA
1 AAAGAA AAA-GAA AAA-GAA AAAGAA AAAG-AA -AAAGAA AAA
1132244 AAGAATAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
5 15 0.22
6 29 0.43
7 20 0.29
8 4 0.06
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:1132189 original size:19 final size:20
Alignment explanation
Indices: 1132153--1132245 Score: 68
Period size: 20 Copynumber: 4.5 Consensus size: 20
1132143 ACTTCGCTTG
1132153 AAGAAAGAAAAATGAAAA-ATA
1 AAGAAA-AAAAATGAAAAGA-A
*
1132174 AAGAAAAAAAGT-AAAAGAA
1 AAGAAAAAAAATGAAAAGAA
1132193 AAGAAAAAAAAATGAAAAATGAAA
1 AAG-AAAAAAAATG-AAAA-G-AA
* *
1132217 AATGAAAAAAAAAG-AAA-CA
1 AA-GAAAAAAAATGAAAAGAA
1132236 AAGAAAAAAA
1 AAGAAAAAAA
1132246 GAATAAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
18 8 0.13
19 11 0.18
20 14 0.23
21 6 0.10
22 7 0.11
23 1 0.02
24 13 0.21
25 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (20 bp):
AAGAAAAAAAATGAAAAGAA
Found at i:1132217 original size:16 final size:15
Alignment explanation
Indices: 1132176--1132257 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 15
1132166 GAAAAATAAA
*
1132176 GAAAAAAAGTAAAA-
1 GAAAAAAAGAAAAAT
*
1132190 GAAAAGAAAAAAAAAT
1 GAAAA-AAAGAAAAAT
*
1132206 G-AAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
*
1132220 GAAAAAAAAAGAAACAAA
1 G--AAAAAAAGAAA-AAT
1132238 GAAAAAAAGAATAAAT
1 GAAAAAAAGAA-AAAT
1132254 -AAAA
1 GAAAA
1132258 TGGGGTTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
14 14 0.26
15 14 0.26
16 13 0.24
17 10 0.19
18 3 0.06
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:1132218 original size:54 final size:53
Alignment explanation
Indices: 1132151--1132259 Score: 143
Period size: 54 Copynumber: 2.0 Consensus size: 53
1132141 GTACTTCGCT
*
1132151 TGAAGAAAGAAAAATGAAAAATAAAGAAAAAAAGTAAAAGAAAAGAA-AAA-AAAA
1 TGAAGAAAGAAAAATGAAAAAAAAAGAAAAAAAG--AAA-AAAAGAATAAATAAAA
*
1132205 TGAA-AAATGAAAAATGAAAAAAAAAGAAACAAAGAAAAAAAGAATAAATAAAA
1 TGAAGAAA-GAAAAATGAAAAAAAAAGAAAAAAAGAAAAAAAGAATAAATAAAA
1132258 TG
1 TG
1132260 GGGTTTAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
51 7 0.14
52 6 0.12
53 9 0.18
54 28 0.56
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.09
Consensus pattern (53 bp):
TGAAGAAAGAAAAATGAAAAAAAAAGAAAAAAAGAAAAAAAGAATAAATAAAA
Found at i:1132230 original size:40 final size:38
Alignment explanation
Indices: 1132153--1132257 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 38
1132143 ACTTCGCTTG
*
1132153 AAGAAAGAAAAATGAAAAATAAAGAAAAAAAGTAAAAGAA
1 AAGAAAAAAAAATGAAAAATAAA-AAAAAAAG-AAAAGAA
1132193 AAGAAAAAAAAATGAAAAATGAAAAATGAAAAA-AAAAGAA
1 AAGAAAAAAAAATGAAAAAT-AAAAA--AAAAAGAAAAGAA
1132233 ACA-AAGAAAAAAA-GAATAAATAAAA
1 A-AGAA-AAAAAAATGAA-AAATAAAA
1132258 TGGGGTTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
40 38 0.66
41 15 0.26
42 5 0.09
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (38 bp):
AAGAAAAAAAAATGAAAAATAAAAAAAAAAGAAAAGAA
Found at i:1133821 original size:134 final size:134
Alignment explanation
Indices: 1133491--1134053 Score: 627
Period size: 134 Copynumber: 4.2 Consensus size: 134
1133481 GTCGAACTCA
* * * * ** * * *
1133491 ATTCAATCTTTCTTGAAGAACACTGGAATGAATCAACGTTTCCATATCTGGTTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCACCAAATCTGATTTTCACTCAAGAA
* * * * * * *
1133556 GTAGTTGAACACATACCCCTCCCTTTCAAGACTTGATCTTCCCTGAGTAACAGTGGAACAATTCT
66 GAAGATGAACA-A-ATCCCTCTCTTTCAAGATTTGATCTTCTCTGAGTAACAGTGGAACAAGTCT
*
1133621 ACCTC-
129 GCCTCG
* * *
1133626 ATTCAATCTTCCCTGAATAACAGTGGAATGAATCAACGTCACCAGATCTGATTTT-ACCTCAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCACCAAATCTGATTTTCA-CTCAAGA
* * * * *
1133690 AAAAGATAAACATATCCCTATTTTTCAAGATTTGATCTTCTCTGAGTAACAGTGGAACAAGTCTG
65 AGAAGATGAACAAATCCCTCTCTTTCAAGATTTGATCTTCTCTGAGTAACAGTGGAACAAGTCTG
1133755 CCTCG
130 CCTCG
* * * * * *
1133760 ATTCAATATTCCCTGAAGAATAGTGGAATGAACCAGCATCCCCATATCTGATTTTCACTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCACCAAATCTGATTTTCACTCAAGAA
*
1133825 GAAGCA-GAACAAATCCATCTCTTTCAAGATTTGATCTT-TCCTGAGTAACAGTGGAACAAGTCT
66 GAAG-ATGAACAAATCCCTCTCTTTCAAGATTTGATCTTCT-CTGAGTAACAGTGGAACAAGTCT
1133888 GCCTCG
129 GCCTCG
* * * ** *
1133894 ATTCAATCTTCCCTAAAGAACAATGTAATGAATCAACATTTCCAAATTTGATTCTTC-CTCAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCACCAAATCTGATT-TTCACTCAAGA
* * *
1133958 AGAAG-TGGAACAGATCCCTCTCTTTCTAGATTTGATCTTC-CATGAGTAACAGTGGAATAAGTC
65 AGAAGAT-GAACAAATCCCTCTCTTTCAAGATTTGATCTTCTC-TGAGTAACAGTGGAACAAGTC
*
1134021 TGCCTCA
128 TGCCTCG
1134028 ATTCAATCTTCCCTGAAGAACAGTGG
1 ATTCAATCTTCCCTGAAGAACAGTGG
1134054 TATTAGTTAT
Statistics
Matches: 363, Mismatches: 55, Indels: 21
0.83 0.13 0.05
Matches are distributed among these distances:
133 50 0.14
134 246 0.68
135 67 0.18
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCACCAAATCTGATTTTCACTCAAGAA
GAAGATGAACAAATCCCTCTCTTTCAAGATTTGATCTTCTCTGAGTAACAGTGGAACAAGTCTGC
CTCG
Found at i:1133991 original size:268 final size:269
Alignment explanation
Indices: 1133487--1134053 Score: 703
Period size: 268 Copynumber: 2.1 Consensus size: 269
1133477 GCGAGTCGAA
* * * * * * * ** * *
1133487 CTCAATTCAATCTTTCTTGAAGAACACTGGAATGAATCAACGTTTCCATATCTGGTTTTCCCTCA
1 CTCAATTCAATATTCCCTGAAGAACAGTGGAATGAACCAGCATCCCCATATCTGATTTTCACTCA
* ** *
1133552 AGAAGTAGTTGAACACATACCCCTCCCTTTCAAGACTTGATCTTCCCTGAGTAACAGTGGAACAA
66 AGAAGAAGCAGAACACATACCCATCCCTTTCAAGACTTGATCTTCCCTGAGTAACAGTGGAACAA
* * * * * *
1133617 TTCTACCTCATTCAATCTTCCCTGAATAACAGTGGAATGAATCAACGTCACCAGATCTGATTTTA
131 GTCTACCTCATTCAATCTTCCCTAAAGAACAATGGAATGAATCAACATCACCAAATCTGATTTTA
* *
1133682 CCTCAAGAAAAAGATAAACATATCCCTATTTTTCAAGATTTGATCTTCTC-TGAGTAACAGTGGA
196 CCTCAAGAAAAAGATAAACAGATCCCTATCTTTCAAGATTTGATCTTC-CATGAGTAACAGTGGA
1133746 ACAAGTCTGC
260 ACAAGTCTGC
* *
1133756 CTCGATTCAATATTCCCTGAAGAATAGTGGAATGAACCAGCATCCCCATATCTGATTTTCACTCA
1 CTCAATTCAATATTCCCTGAAGAACAGTGGAATGAACCAGCATCCCCATATCTGATTTTCACTCA
* * * *
1133821 AGAAGAAGCAGAACA-A-ATCCATCTCTTTCAAGATTTGATCTTTCCTGAGTAACAGTGGAACAA
66 AGAAGAAGCAGAACACATACCCATCCCTTTCAAGACTTGATCTTCCCTGAGTAACAGTGGAACAA
* * ** *
1133884 GTCTGCCTCGATTCAATCTTCCCTAAAGAACAATGTAATGAATCAACATTTCCAAATTTGATTCT
131 GTCTACCTC-ATTCAATCTTCCCTAAAGAACAATGGAATGAATCAACATCACCAAATCTGATT-T
* * * *
1133949 T-CCTCAAGAAGAAG-TGGAACAGATCCCTCTCTTTCTAGATTTGATCTTCCATGAGTAACAGTG
194 TACCTCAAGAAAAAGAT-AAACAGATCCCTATCTTTCAAGATTTGATCTTCCATGAGTAACAGTG
*
1134012 GAATAAGTCTGC
258 GAACAAGTCTGC
*
1134024 CTCAATTCAATCTTCCCTGAAGAACAGTGG
1 CTCAATTCAATATTCCCTGAAGAACAGTGG
1134054 TATTAGTTAT
Statistics
Matches: 252, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
267 51 0.20
268 135 0.54
269 66 0.26
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (269 bp):
CTCAATTCAATATTCCCTGAAGAACAGTGGAATGAACCAGCATCCCCATATCTGATTTTCACTCA
AGAAGAAGCAGAACACATACCCATCCCTTTCAAGACTTGATCTTCCCTGAGTAACAGTGGAACAA
GTCTACCTCATTCAATCTTCCCTAAAGAACAATGGAATGAATCAACATCACCAAATCTGATTTTA
CCTCAAGAAAAAGATAAACAGATCCCTATCTTTCAAGATTTGATCTTCCATGAGTAACAGTGGAA
CAAGTCTGC
Found at i:1137621 original size:20 final size:19
Alignment explanation
Indices: 1137584--1137622 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1137574 GATTAAATTT
**
1137584 GACTAAATTACAGTATATG
1 GACTAAATTACAACATATG
1137603 GACTAAATCTACAACATATG
1 GACTAAAT-TACAACATATG
1137623 TGTTGTGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (19 bp):
GACTAAATTACAACATATG
Found at i:1138188 original size:41 final size:41
Alignment explanation
Indices: 1138131--1138209 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
1138121 TAAGATCCAG
1138131 AAAATGAGAGCCCAAGCAATCGCTCAAGGTTCTCCCCACAC
1 AAAATGAGAGCCCAAGCAATCGCTCAAGGTTCTCCCCACAC
1138172 AAAATGAGAGCCCAAGCAATCGCTCAAGGTTCTCCCCA
1 AAAATGAGAGCCCAAGCAATCGCTCAAGGTTCTCCCCA
1138210 TATTAGCTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.33, G:0.18, T:0.15
Consensus pattern (41 bp):
AAAATGAGAGCCCAAGCAATCGCTCAAGGTTCTCCCCACAC
Found at i:1138798 original size:14 final size:14
Alignment explanation
Indices: 1138779--1138805 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1138769 TGTCTTTCCC
1138779 TAAAAATCAAAACT
1 TAAAAATCAAAACT
1138793 TAAAAATCAAAAC
1 TAAAAATCAAAAC
1138806 CTCTTCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAAATCAAAACT
Found at i:1145800 original size:18 final size:19
Alignment explanation
Indices: 1145777--1145814 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1145767 AAAAATAATT
*
1145777 AATAAACCAAATAA-AAAA
1 AATAAAACAAATAACAAAA
*
1145795 AATAAAATAAATAACAAAA
1 AATAAAACAAATAACAAAA
1145814 A
1 A
1145815 CAATAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (19 bp):
AATAAAACAAATAACAAAA
Found at i:1146174 original size:126 final size:123
Alignment explanation
Indices: 1146022--1146474 Score: 544
Period size: 119 Copynumber: 3.8 Consensus size: 123
1146012 AAAATCAGCG
* *
1146022 GTTAGCAGAGTCCGAACTATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAAGCCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCAGATCGGGTCACCACAAAGCCGAAT
1146087 CAAATATTAGAAATAATAAATAAATAAATAAAAGTTAGAATGCAATAAAATAAAAGTCAGTA
66 CAAATATTAG--A-AATAAATAAATAAATAAAAGTTA-AATGCAATAAAATAAAAGTCAGTA
* *
1146149 GTTAG-AGAGTCCGAACCATAATAATGCGGATCATACCCCAGATTGGGTCACCACAAGGCCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCAGATCGGGTCACCACAAAGCCGAAT
*
1146213 GAAATATTAGAAATAAATAAATAAAT-AAA--TAAAT--AAT-AAATAAAAGT---TA
66 CAAATATTAGAAATAAATAAATAAATAAAAGTTAAATGCAATAAAATAAAAGTCAGTA
* * * * *
1146262 G-TAGTAGAGTCTGAACCATAATAATGCAGATCACACCCCAAATCGGGTCACCACAAAGCCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCAGATCGGGTCACCACAAAGCCGAAT
* *
1146326 CAAATATTAG----AAAT-AATAAATAAAAGTTAGAATGCAATAAAATAAATGCCAGTA
66 CAAATATTAGAAATAAATAAATAAATAAAAGTTA-AATGCAATAAAATAAAAGTCAGTA
* * * * * *
1146380 GTTAGTAGAGTCTGAACCATAATAATGCGGATCATACCTCGGATCGGGTCACCACAAGGTCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCAGATCGGGTCACCACAAAGCCGAAT
* *
1146445 CGAATATTA-AAAAATAATAAAATAAATAAA
66 CAAATATTAGAAATA-AAT-AAATAAATAAA
1146475 TAACAATAAT
Statistics
Matches: 285, Mismatches: 22, Indels: 40
0.82 0.06 0.12
Matches are distributed among these distances:
108 7 0.02
109 7 0.02
111 2 0.01
112 6 0.02
113 65 0.23
114 3 0.01
115 8 0.03
116 10 0.04
117 3 0.01
118 3 0.01
119 67 0.24
120 2 0.01
122 4 0.01
123 18 0.06
124 1 0.00
125 10 0.04
126 64 0.22
127 5 0.02
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (123 bp):
GTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCAGATCGGGTCACCACAAAGCCGAAT
CAAATATTAGAAATAAATAAATAAATAAAAGTTAAATGCAATAAAATAAAAGTCAGTA
Found at i:1146232 original size:4 final size:4
Alignment explanation
Indices: 1146223--1146256 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1146213 GAAATATTAG
1146223 AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1146257 AGTTAGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1146687 original size:33 final size:33
Alignment explanation
Indices: 1146645--1146712 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1146635 CAAAAGGACT
1146645 AGAATACAAGGGGTTATACATGATTTACCCAAA
1 AGAATACAAGGGGTTATACATGATTTACCCAAA
1146678 AGAATACAAGGGGTTATACATGATTTACCCAAA
1 AGAATACAAGGGGTTATACATGATTTACCCAAA
1146711 AG
1 AG
1146713 CACTAAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (33 bp):
AGAATACAAGGGGTTATACATGATTTACCCAAA
Found at i:1147670 original size:44 final size:44
Alignment explanation
Indices: 1147620--1147712 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
1147610 TTAATCCACA
* * * * *
1147620 TCCTTTTGTGATGGAATTGAACATAATGTT-AGTGTTGATCTACC
1 TCCTTTTGTGATAGAATCGAACAAAATGTTGA-TGTTGATCCAAC
*
1147664 TCCTTTTGTGATAGAATCGAGCAAAATGTTGATGTTGATCCAAC
1 TCCTTTTGTGATAGAATCGAACAAAATGTTGATGTTGATCCAAC
1147708 TCCTT
1 TCCTT
1147713 ATACGATGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (44 bp):
TCCTTTTGTGATAGAATCGAACAAAATGTTGATGTTGATCCAAC
Found at i:1147809 original size:130 final size:132
Alignment explanation
Indices: 1147651--1147957 Score: 388
Period size: 130 Copynumber: 2.3 Consensus size: 132
1147641 CATAATGTTA
* * *
1147651 GTGTTGATCTACCTCCTTTTGTGATAGAATCGAGCAAAATGTTGAT-GTTGATCCAACTCCTTAT
1 GTGTTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAATGTTGATACTT-ATCCAACTCCATAT
** * * *
1147715 ACGATGGATTTGAATGAAATGAAAATTTCAATCCACCTCCTT-TGTGATAGAATCAAACGAGATG
65 ACGATGGATTTGAACAAAATAAAAATGTCAATCCACCTCCTTCTGTGATAGAATCAAACGAGATA
1147779 TC-
130 TCG
*
1147781 GTGTTGATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAT-TTGATACTTATCCAACTCCATAT
1 GTGTTGATCTACCTCCTTCTGTGATAGAATCGAGC-AAAATGTTGATACTTATCCAACTCCATAT
* * * * * * *
1147845 GCGATGGATTTGAGCAAAATAAAAATGTCGATCCACCTCTTTCTGTGATAGAATCGAATGATATA
65 ACGATGGATTTGAACAAAATAAAAATGTCAATCCACCTCCTTCTGTGATAGAATCAAACGAGATA
1147910 TCG
130 TCG
* * * *
1147913 GTGCTGATCTACCTCTTTCTATGATAGAATCGAGCAAAAAGTTGA
1 GTGTTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAATGTTGA
1147958 ACAATCTCTT
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
130 85 0.56
131 31 0.21
132 35 0.23
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (132 bp):
GTGTTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAATGTTGATACTTATCCAACTCCATATA
CGATGGATTTGAACAAAATAAAAATGTCAATCCACCTCCTTCTGTGATAGAATCAAACGAGATAT
CG
Found at i:1148060 original size:20 final size:21
Alignment explanation
Indices: 1148035--1148092 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
1148025 AGATTGAACA
*
1148035 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTG
*
1148056 A-TTC-TCTC-TAATCGAA-TG
1 AGTTCTTCTCATTAT-GAACTG
1148074 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
1148093 CCTTCCATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 10 0.34
21 4 0.14
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (21 bp):
AGTTCTTCTCATTATGAACTG
Found at i:1148439 original size:21 final size:21
Alignment explanation
Indices: 1148410--1148467 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1148400 TTCAAGGGAA
* * * *
1148410 TTGTCTCAAGGTAGACAAACT
1 TTGTTTCAAGGGAAACAAAAT
1148431 TTGTTTCAAGGGAAACAAAAT
1 TTGTTTCAAGGGAAACAAAAT
1148452 TTGTTTCAAGGGAAAC
1 TTGTTTCAAGGGAAAC
1148468 TGTCTCAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (21 bp):
TTGTTTCAAGGGAAACAAAAT
Found at i:1148485 original size:36 final size:35
Alignment explanation
Indices: 1148445--1148565 Score: 116
Period size: 37 Copynumber: 3.6 Consensus size: 35
1148435 TTCAAGGGAA
*
1148445 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 ACAAAATTCGTTTCAAGGGAAACTGTCTC-AGAGAG
*
1148481 ACAAAATTCGTTTTCAAGGGAAACAGAT-TCA-A-AG
1 ACAAAATTCG-TTTCAAGGGAAACTG-TCTCAGAGAG
*
1148515 -----ATTGGTGTTCAAGGG-AACTGTCTCAGAGAG
1 ACAAAATTCGT-TTCAAGGGAAACTGTCTCAGAGAG
1148545 ACAAAATTCGTTTCAAGGGAA
1 ACAAAATTCGTTTCAAGGGAA
1148566 CGATGTCAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
27 1 0.01
28 8 0.12
29 13 0.19
30 2 0.03
34 10 0.15
35 7 0.10
36 10 0.15
37 16 0.24
38 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (35 bp):
ACAAAATTCGTTTCAAGGGAAACTGTCTCAGAGAG
Found at i:1148610 original size:64 final size:64
Alignment explanation
Indices: 1148453--1148754 Score: 277
Period size: 64 Copynumber: 4.8 Consensus size: 64
1148443 AAACAAAATT
* *
1148453 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTTCAAGGGAAACAGATTCAAAGATT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGAGACAAAATTCG-TTTCAAGGGAAACAGATTCAAAGTTT
1148518 G
64 G
* *
1148519 -GTGTTCAAGGGAACTGTCTC-AGAGAGACAAAATTCGTTTCAAGGG-AAC-GATGTCAAACGTT
1 TGT-TTCAAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAGAT-TCAAA-GTT
1148580 TG
63 TG
* * * * * *
1148582 TGTTTCAAGAGAAATTTCTCAAGGGAGACTAAATTTGTTTTAAGGGAAACAGATTCAAAGATTGG
1 TGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAGATTCAAAG-TTTG
* * * **
1148647 TGTTTCAAGAGAAATTGTCTCAAGAGAGCCAAAATTATGTTTCAAGAGACTCAG--TC----TTT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGAGACAAAATT-CGTTTCAAGGGAAACAGATTCAAAGTTT
1148706 -
64 G
* * *
1148706 TGTTTCGAAGA-AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
1 TGTTTC-AAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAA
1148755 ATATCTCAAA
Statistics
Matches: 202, Mismatches: 23, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
57 12 0.06
58 20 0.10
59 8 0.04
60 6 0.03
61 3 0.01
62 8 0.04
63 27 0.13
64 40 0.20
65 35 0.17
66 30 0.15
67 13 0.06
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (64 bp):
TGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAGATTCAAAGTTTG
Found at i:1148657 original size:65 final size:65
Alignment explanation
Indices: 1148453--1148682 Score: 290
Period size: 64 Copynumber: 3.5 Consensus size: 65
1148443 AAACAAAATT
*
1148453 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTTCAAGGGAAACAGATTCAAAGATT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGAGACAAAATTCGTTTT-AAGGGAAACAGATTCAAAGATT
1148518 GG
64 GG
* * *
1148520 TG-TTCAAGGGAACTGTCTC-AGAGAGACAAAATTCGTTTCAAGGG-AAC-GATGTCAAACG-TT
1 TGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACAGAT-TCAAA-GATT
*
1148580 TG
64 GG
* * * *
1148582 TGTTTCAAGAGAAATTTCTCAAGGGAGACTAAATTTGTTTTAAGGGAAACAGATTCAAAGATTGG
1 TGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACAGATTCAAAGATTGG
*
1148647 TGTTTCAAGAGAAATTGTCTCAAGAGAGCCAAAATT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGAGACAAAATT
1148683 ATGTTTCAAG
Statistics
Matches: 140, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
61 3 0.02
62 13 0.09
63 20 0.14
64 41 0.29
65 31 0.22
66 30 0.21
67 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACAGATTCAAAGATTGG
Found at i:1148808 original size:21 final size:21
Alignment explanation
Indices: 1148774--1148814 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1148764 AGTCTATCAA
* *
1148774 TTTTGTTTCCAGTGAAACAAT
1 TTTTGATTCAAGTGAAACAAT
1148795 TTTTGATTCAAGTGAAACAA
1 TTTTGATTCAAGTGAAACAA
1148815 ATTCGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (21 bp):
TTTTGATTCAAGTGAAACAAT
Found at i:1148911 original size:35 final size:36
Alignment explanation
Indices: 1148843--1148915 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 36
1148833 AAAGGAAAAA
1148843 TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
1 TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
*
1148879 TGCCTCAAGTGAGACG-AAATTGTTTTGAAAGAAAG
1 TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
1148914 TG
1 TG
1148916 TCTCGAGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 20 0.56
36 16 0.44
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (36 bp):
TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
Found at i:1149143 original size:36 final size:36
Alignment explanation
Indices: 1149103--1149183 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
1149093 AAAGGAAAAA
1149103 TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
1 TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
*
1149139 TGCCTCAAGTGAGACGAAAATTGTTTTGAAAGAAAG
1 TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
*
1149175 TGTCTCAAG
1 TGCCTCAAG
1149184 CTAGATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (36 bp):
TGCCTCAAGTGAGACGAAAATCGTTTTGAAAGAAAG
Found at i:1150370 original size:11 final size:11
Alignment explanation
Indices: 1150354--1150496 Score: 95
Period size: 11 Copynumber: 12.9 Consensus size: 11
1150344 GCTTTTTATC
1150354 CTTTTTCTTTG
1 CTTTTTCTTTG
*
1150365 CTTTTTCTTTT
1 CTTTTTCTTTG
*
1150376 TTTTTCTCTTTG
1 CTTTT-TCTTTG
1150388 CTTTTTTCTTTG
1 C-TTTTTCTTTG
1150400 CTTTTTCTTTCTTAG
1 CTTTTTC--T-TT-G
* *
1150415 CTTTTTTATTTA
1 C-TTTTTCTTTG
*
1150427 CTTTTTTCTTTT
1 C-TTTTTCTTTG
*
1150439 CTTTTTCTTTT
1 CTTTTTCTTTG
1150450 C-TTTTC-TT-
1 CTTTTTCTTTG
1150458 -TTTTTCTTTG
1 CTTTTTCTTTG
1150468 C-TTTTCTTT-
1 CTTTTTCTTTG
1150477 CTTTTTTCTTT-
1 C-TTTTTCTTTG
1150488 C-TTTTCTTT
1 CTTTTTCTTT
1150497 TTTGTTTTTT
Statistics
Matches: 111, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
8 5 0.05
9 13 0.12
10 13 0.12
11 40 0.36
12 23 0.21
13 7 0.06
14 3 0.03
15 2 0.02
16 5 0.05
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.77
Consensus pattern (11 bp):
CTTTTTCTTTG
Found at i:1150375 original size:5 final size:5
Alignment explanation
Indices: 1150356--1150510 Score: 77
Period size: 5 Copynumber: 29.4 Consensus size: 5
1150346 TTTTTATCCT
* * *
1150356 TTTTC TTTGC TTTTTC TTTTT TTTTC TCTTTGC TTTTTTC TTTGC TTTT-
1 TTTTC TTTTC -TTTTC TTTTC TTTTC T-TTT-C --TTTTC TTTTC TTTTC
** *
1150405 TCTTTC TTAGC TTTTT TATTTAC TTTTTTC TTTTC TTTTTC TTTTC TTTTC
1 T-TTTC TTTTC TTTTC T-TTT-C -TT-TTC TTTTC -TTTTC TTTTC TTTTC
* * *
1150456 -TTT- TTTTC TTTGC TTTTC -TTTC TTTTT TCTTTC TTTTC TTTT- TTGTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TT-TTC
1150504 TTTTC TT
1 TTTTC TT
1150511 AGCTTTGATT
Statistics
Matches: 115, Mismatches: 17, Indels: 36
0.68 0.10 0.21
Matches are distributed among these distances:
4 13 0.11
5 67 0.58
6 24 0.21
7 4 0.03
8 6 0.05
9 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:1150403 original size:29 final size:28
Alignment explanation
Indices: 1150368--1150507 Score: 99
Period size: 27 Copynumber: 5.3 Consensus size: 28
1150358 TTCTTTGCTT
1150368 TTTCTTTTTTTTTCTCTTTGCTTTTTTC
1 TTTCTTTTTTTTTCTCTTTGCTTTTTTC
* * *
1150396 TTTGC-TTTTTCTT-TCTTAGCTTTTTTA
1 TTT-CTTTTTTTTTCTCTTTGCTTTTTTC
1150423 TTTAC---TTTTTTCT-TTT-C-TTTTTC
1 TTT-CTTTTTTTTTCTCTTTGCTTTTTTC
*
1150446 TTTTCTTTTCTTTTTTTCTTTGC--TTTTC
1 -TTTCTTTT-TTTTTCTCTTTGCTTTTTTC
*
1150474 TTTCTTTTTTCTTTCT-TTT-CTTTTTTG
1 TTTCTTTTTT-TTTCTCTTTGCTTTTTTC
1150501 TTT-TTTT
1 TTTCTTTT
1150508 CTTAGCTTTG
Statistics
Matches: 90, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
23 6 0.07
24 4 0.04
25 8 0.09
26 11 0.12
27 41 0.46
28 18 0.20
29 2 0.02
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (28 bp):
TTTCTTTTTTTTTCTCTTTGCTTTTTTC
Found at i:1150418 original size:50 final size:47
Alignment explanation
Indices: 1150355--1150516 Score: 136
Period size: 50 Copynumber: 3.3 Consensus size: 47
1150345 CTTTTTATCC
*
1150355 TTTTTCTTTGCTTTTTCTTTTTTTTTCTCTTTGCTTTTTTCTTTGCTTT
1 TTTTTCTTAGCTTTTTCTTTTTTTTT-TCTTT-CTTTTTTCTTTGCTTT
*
1150404 TTCTTTCTTAGCTTTTT-TATTTACTTTTTTCTTT-TCTTTTTCTTTTCTTTTCTT
1 TT-TTTCTTAGCTTTTTCT-TTT--TTTTTTCTTTCT-TTTTTCTTTGC---T-TT
* * *
1150458 TTTTTCTTTGC-TTTTCTTTCTTTTTTCTTTCTTTTCTTTTTTG--TT
1 TTTTTCTTAGCTTTTTCTTTTTTTTTTCTTTCTTTT-TTCTTTGCTTT
1150503 TTTTTCTTAGCTTT
1 TTTTTCTTAGCTTT
1150517 GATTTGATCT
Statistics
Matches: 93, Mismatches: 7, Indels: 29
0.72 0.05 0.22
Matches are distributed among these distances:
45 12 0.13
46 2 0.02
49 4 0.04
50 39 0.42
51 11 0.12
52 11 0.12
53 10 0.11
54 4 0.04
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.77
Consensus pattern (47 bp):
TTTTTCTTAGCTTTTTCTTTTTTTTTTCTTTCTTTTTTCTTTGCTTT
Found at i:1150431 original size:39 final size:39
Alignment explanation
Indices: 1150355--1150499 Score: 160
Period size: 39 Copynumber: 3.8 Consensus size: 39
1150345 CTTTTTATCC
*
1150355 TTTTTCTTTGCTTTTTC--T-TTTT-TTTTCTCTTTGCT
1 TTTTTCTTTGCTTTTTCTTTCTTTTCTTTTTTCTTTGCT
** * *
1150390 TTTTTCTTTGCTTTTTCTTTCTTAGCTTTTTTATTTACT
1 TTTTTCTTTGCTTTTTCTTTCTTTTCTTTTTTCTTTGCT
*
1150429 TTTTTCTTTTCTTTTTCTTTTCTTTTCTTTTTTTCTTTGC-
1 TTTTTCTTTGCTTTTTC-TTTCTTTTC-TTTTTTCTTTGCT
1150469 -TTTTCTTT-CTTTTTTCTTTCTTTTCTTTTTT
1 TTTTTCTTTGC-TTTTTCTTTCTTTTCTTTTTT
1150500 GTTTTTTTCT
Statistics
Matches: 93, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
35 17 0.18
37 7 0.08
38 12 0.13
39 40 0.43
40 7 0.08
41 10 0.11
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (39 bp):
TTTTTCTTTGCTTTTTCTTTCTTTTCTTTTTTCTTTGCT
Found at i:1150505 original size:45 final size:45
Alignment explanation
Indices: 1150382--1150516 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
1150372 TTTTTTTTTC
* * * *
1150382 TCTTTGCTTTTTTCTTTGCTTTTTCTTTCTTAGCTTTTTTATTTAC-TT
1 TCTTT-CTTTTTTCTTT-C-TTTTCTTT-TTTGTTTTTTTCTTTGCTTT
*
1150430 T-TTTCTTTTCTT-TTTCTTTTC--TTTTCTTTTTTTCTTTGCTTT
1 TCTTTCTTTT-TTCTTTCTTTTCTTTTTTGTTTTTTTCTTTGCTTT
*
1150472 TCTTTCTTTTTTCTTTCTTTTCTTTTTTGTTTTTTTCTTAGCTTT
1 TCTTTCTTTTTTCTTTCTTTTCTTTTTTGTTTTTTTCTTTGCTTT
1150517 GATTTGATCT
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
41 12 0.16
42 6 0.08
43 17 0.23
44 5 0.07
45 20 0.27
46 8 0.11
47 5 0.07
48 1 0.01
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.76
Consensus pattern (45 bp):
TCTTTCTTTTTTCTTTCTTTTCTTTTTTGTTTTTTTCTTTGCTTT
Found at i:1150506 original size:74 final size:76
Alignment explanation
Indices: 1150367--1150510 Score: 179
Period size: 78 Copynumber: 1.9 Consensus size: 76
1150357 TTTCTTTGCT
*
1150367 TTTTCTTTTTTTTTCTCTTTGCTTTTTTCTTTGCTTTTTCTTTCTTAGCTTTTTTATTTACTTTT
1 TTTTCTTTTTTTTTCTCTTTGC-TTTTTCTTTGCTTTTTCTTTCTTA--TTCTTTATTTACTTTT
1150432 TTCTTTTCTTTTTC
63 TTCTTTTCTTTTTC
* **
1150446 TTTTCTTTTCTTTTTTTCTTTGC-TTTTCTTT-CTTTTTTCTTTCTT-TTCTTT-TTTGTTTTTT
1 TTTTCTTTT-TTTTTCTCTTTGCTTTTTCTTTGC-TTTTTCTTTCTTATTCTTTATTTACTTTTT
1150507 TCTT
64 TCTT
1150511 AGCTTTGATT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
74 12 0.20
75 5 0.08
77 1 0.02
78 20 0.34
79 9 0.15
80 12 0.20
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.78
Consensus pattern (76 bp):
TTTTCTTTTTTTTTCTCTTTGCTTTTTCTTTGCTTTTTCTTTCTTATTCTTTATTTACTTTTTTC
TTTTCTTTTTC
Found at i:1158788 original size:20 final size:20
Alignment explanation
Indices: 1158763--1158948 Score: 152
Period size: 20 Copynumber: 9.4 Consensus size: 20
1158753 TCAGTTTCTT
1158763 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1158783 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** * * *
1158803 T--CATTGCGATTTTTTA-AA
1 TCGCAACGCGA-TTCTGACTA
*** *
1158821 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAACGCGA--TTCTGACTA
* *
1158844 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTGACTA
1158864 TCGCAACGCGA---TGACTA
1 TCGCAACGCGATTCTGACTA
*
1158881 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1158901 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1158921 TCGCAATGCGATGCTGACTA
1 TCGCAACGCGATTCTGACTA
1158941 T-GCAACGC
1 TCGCAACGC
1158949 AATGCGATTT
Statistics
Matches: 137, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
17 16 0.12
18 7 0.05
19 11 0.08
20 82 0.60
21 7 0.05
22 13 0.09
23 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1158882 original size:37 final size:38
Alignment explanation
Indices: 1158839--1158948 Score: 143
Period size: 37 Copynumber: 2.9 Consensus size: 38
1158829 GCGATTTTCC
*
1158839 GACTATCGCAATGCGATTATGACTATCGCAACGCGA-T
1 GACTATCGCAATGCGATTCTGACTATCGCAACGCGATT
* * *
1158876 GACTATCGCAACGAGATTCTGACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTCTGACTATCGCAACGCGA-T-T
*
1158916 GACTATCGCAATGCGATGCTGACTAT-GCAACGC
1 GACTATCGCAATGCGATTCTGACTATCGCAACGC
1158949 AATGCGATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 32 0.52
39 6 0.10
40 24 0.39
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (38 bp):
GACTATCGCAATGCGATTCTGACTATCGCAACGCGATT
Found at i:1158988 original size:55 final size:56
Alignment explanation
Indices: 1158919--1159041 Score: 221
Period size: 56 Copynumber: 2.2 Consensus size: 56
1158909 CGATTCTGAC
**
1158919 TATCGCAATGCGATGCTGACTAT-GCAACGCAATGCGATTTTCAAAGTACCATTAT
1 TATCGCAACACGATGCTGACTATCGCAACGCAATGCGATTTTCAAAGTACCATTAT
1158974 TATCGCAACACGATGCTGACTATCGCAACGCAATGCGATTTTCAAAGTACCATTAT
1 TATCGCAACACGATGCTGACTATCGCAACGCAATGCGATTTTCAAAGTACCATTAT
1159030 TATCGCAACACG
1 TATCGCAACACG
1159042 TATTTTTTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
55 21 0.32
56 44 0.68
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (56 bp):
TATCGCAACACGATGCTGACTATCGCAACGCAATGCGATTTTCAAAGTACCATTAT
Done.