Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005546.1 Hibiscus syriacus cultivar Beakdansim tig00012840_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: 1755203
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1650627 original size:2 final size:2
Alignment explanation
Indices: 1650622--1650676 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1650612 GTATACATAC
1650622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1650664 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1650677 GGGTTAGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1650809 original size:26 final size:26
Alignment explanation
Indices: 1650773--1650826 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1650763 TTGACTCCTT
1650773 GTTTCTTTTTCAGTGAATATCTTCTC
1 GTTTCTTTTTCAGTGAATATCTTCTC
1650799 GTTTCTTTTTCAGTGAATATCTTCTC
1 GTTTCTTTTTCAGTGAATATCTTCTC
1650825 GT
1 GT
1650827 ATTTTACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.54
Consensus pattern (26 bp):
GTTTCTTTTTCAGTGAATATCTTCTC
Found at i:1650840 original size:24 final size:26
Alignment explanation
Indices: 1650773--1650834 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1650763 TTGACTCCTT
**
1650773 GTTTCTTTTTCAGTGAATATCTTCTC
1 GTTTCTTACTCAGTGAATATCTTCTC
**
1650799 GTTTCTTTTTCAGTGAATATCTTCTC
1 GTTTCTTACTCAGTGAATATCTTCTC
1650825 GTATT-TTACT
1 GT-TTCTTACT
1650835 ATGAATCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 31 0.94
27 2 0.06
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (26 bp):
GTTTCTTACTCAGTGAATATCTTCTC
Found at i:1651169 original size:2 final size:2
Alignment explanation
Indices: 1651162--1651191 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1651152 ATCATATCCC
1651162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1651192 CTCACATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1668564 original size:18 final size:18
Alignment explanation
Indices: 1668538--1668572 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1668528 TTTCTCCATC
*
1668538 ATGAATCCATTTGTTTCT
1 ATGAATCCATATGTTTCT
*
1668556 ATGATTCCATATGTTTC
1 ATGAATCCATATGTTTC
1668573 ATAGTAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (18 bp):
ATGAATCCATATGTTTCT
Found at i:1674777 original size:229 final size:228
Alignment explanation
Indices: 1674372--1674858 Score: 875
Period size: 229 Copynumber: 2.1 Consensus size: 228
1674362 GTAAATTATC
* * *
1674372 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
1674437 TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
1674502 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1674567 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTCAAAAAAGTATA
*
1674600 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
* *
1674665 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
1674730 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
*
1674795 GAAACATAAATTACATAACTTTCAAAGAAGTATA
195 GAAACATAAATTACATAACTTTCAAAAAAGTATA
1674829 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
1674859 AAAAGTAGGT
Statistics
Matches: 248, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
228 36 0.15
229 212 0.85
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:1675160 original size:20 final size:19
Alignment explanation
Indices: 1675137--1675183 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1675127 CGATATACCA
1675137 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1675157 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1675177 GGTAAAA
1 GGTAAAA
1675184 CGTTACCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1675271 original size:181 final size:182
Alignment explanation
Indices: 1674925--1675397 Score: 680
Period size: 181 Copynumber: 2.6 Consensus size: 182
1674915 GATCCAAATT
* * * *
1674925 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
1674989 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
1675054 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
1675107 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
1675172 AAACCGGTAAAACGTTACCAGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
1675236 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * * * *
1675288 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCAGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
1675353 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
1675398 CGTAAGTACG
Statistics
Matches: 261, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
181 165 0.63
182 96 0.37
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:1677624 original size:21 final size:21
Alignment explanation
Indices: 1677597--1677661 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1677587 AAGACAATCA
*
1677597 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
1677618 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1677639 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1677660 AG
1 AG
1677662 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1677737 original size:33 final size:33
Alignment explanation
Indices: 1677695--1677760 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1677685 AAATAGATGG
*
1677695 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1677728 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1677761 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1679580 original size:19 final size:19
Alignment explanation
Indices: 1679556--1679604 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1679546 AATGTAGGGT
1679556 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1679575 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1679594 TATTTTTGTAT
1 TAATTTTGTAT
1679605 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1680180 original size:199 final size:199
Alignment explanation
Indices: 1679713--1681270 Score: 2911
Period size: 199 Copynumber: 7.8 Consensus size: 199
1679703 GGCAAATTTA
* * *
1679713 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
* * * * *
1679778 TATAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAA
1679843 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATGGAAAACAGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATGGAAAACAGG
1679908 GTGCAC
194 GTGCAC
*
1679914 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1679979 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
* *
1680044 TAATGTGTCGACACTAATATAGTTTATGTCGATATTTTTTTTCCATAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1680109 GCAC
196 GCAC
1680113 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1680178 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
1680243 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1680308 GCAC
196 GCAC
1680312 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1680377 GTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
1680442 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1680507 GCAC
196 GCAC
1680511 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1680576 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
1680641 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1680706 GCAC
196 GCAC
1680710 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1680775 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
1680840 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1680905 GCAC
196 GCAC
1680909 CCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
1680973 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
1681038 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1681103 GCAC
196 GCAC
1681107 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
1681172 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
1681237 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
1681271 CTAATTAATA
Statistics
Matches: 1333, Mismatches: 23, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
198 196 0.15
199 982 0.74
200 109 0.08
201 46 0.03
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
GCAC
Found at i:1682754 original size:6 final size:6
Alignment explanation
Indices: 1682730--1682803 Score: 58
Period size: 6 Copynumber: 12.3 Consensus size: 6
1682720 AGCGGTCGCA
* * * * * *
1682730 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * *
1682778 GGCGAT GAAGAT GATGAT GATGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
1682804 TGAAGATGAT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:1682765 original size:3 final size:3
Alignment explanation
Indices: 1682745--1682816 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
1682735 TGAAGCTGAC
* * * * * ** *
1682745 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
1682793 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
1682817 CCAAACAAGT
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:1682784 original size:36 final size:36
Alignment explanation
Indices: 1682733--1682803 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1682723 GGTCGCAGAA
1682733 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
* *
1682769 GATGAAGCTGGCGATGAAGATGATGATGATGATGA
1 GATGAAGCTGACGATGAAGATGACGATGATGATGA
1682804 TGAAGATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGATGATGATGAC
Found at i:1682802 original size:18 final size:18
Alignment explanation
Indices: 1682730--1682816 Score: 81
Period size: 18 Copynumber: 5.0 Consensus size: 18
1682720 AGCGGTCGCA
* *
1682730 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
1682748 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * **
1682766 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGATGAT
1682784 GAAGAT---GATGATGAT
1 GAAGATGAAGATGATGAT
*
1682799 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
1682817 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
15 11 0.21
18 42 0.79
ACGTcount: A:0.37, C:0.07, G:0.34, T:0.22
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:1682816 original size:12 final size:12
Alignment explanation
Indices: 1682733--1682803 Score: 88
Period size: 12 Copynumber: 5.9 Consensus size: 12
1682723 GGTCGCAGAA
*
1682733 GATGAAGCTGAC
1 GATGAAGATGAC
1682745 GATGAAGATGAC
1 GATGAAGATGAC
*
1682757 GATGATGATGAC
1 GATGAAGATGAC
* *
1682769 GATGAAGCTGGC
1 GATGAAGATGAC
*
1682781 GATGAAGATGAT
1 GATGAAGATGAC
*
1682793 GATGATGATGA
1 GATGAAGATGA
1682804 TGAAGATGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1684690 original size:182 final size:181
Alignment explanation
Indices: 1684284--1684766 Score: 826
Period size: 182 Copynumber: 2.7 Consensus size: 181
1684274 TTCAACATAT
* *
1684284 TATAAATATATGGTTTT-TGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTGT
1 TATAAATATACGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGT
* *
1684348 CGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTTA
66 CGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATTTA
*
1684413 CACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 CACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
1684465 TATAAATATATCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATA-CGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
1684530 TCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACA-TT
65 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATTT
*
1684594 ACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGG
129 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
* *
1684647 TATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATA-CGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1684712 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGT
65 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
1684767 GTCGGTAATT
Statistics
Matches: 287, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
181 10 0.03
182 173 0.60
183 101 0.35
184 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (181 bp):
TATAAATATACGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGT
CGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTTAC
ACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:1687220 original size:25 final size:25
Alignment explanation
Indices: 1687192--1687256 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1687182 TTATAATTAA
1687192 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1687217 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1687242 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1687257 TCTTTGAGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1687633 original size:23 final size:23
Alignment explanation
Indices: 1687602--1687674 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
1687592 ATAGGTAAAC
*
1687602 ATATGATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1687625 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1687648 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1687671 ATAT
1 ATAT
1687675 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 43 0.96
24 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1687699 original size:46 final size:45
Alignment explanation
Indices: 1687602--1687699 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
1687592 ATAGGTAAAC
* * *
1687602 ATATGATGTAATAGGTAGTGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGTGCTTATAT-ATGTAATAGCTATCCTTT
* *
1687648 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGTGCTTATATATGT-AA-TAGCTATCCTTT
*
1687694 TTATAA
1 ATATAA
1687700 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGTGCTTATATATGTAATAGCTATCCTTT
Found at i:1688123 original size:18 final size:18
Alignment explanation
Indices: 1688102--1688138 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1688092 GTAATTGGAG
1688102 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1688120 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1688138 T
1 T
1688139 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1688146 original size:24 final size:24
Alignment explanation
Indices: 1688094--1688140 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1688084 TTTCATATGT
* *
1688094 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1688118 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1688141 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1688480 original size:38 final size:39
Alignment explanation
Indices: 1688397--1688482 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1688387 TCCGATGCTC
*
1688397 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
1688436 ATCAAAATCCAAATCTCATATGATGCCAAGC-AAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1688474 ATCAAAATC
1 ATCAAAATC
1688483 TACAACTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 16 0.36
39 29 0.64
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1688935 original size:23 final size:23
Alignment explanation
Indices: 1688904--1688976 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1688894 ATAGGTAAAC
*
1688904 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
1688927 ATATAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1688950 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1688973 ATAT
1 ATAT
1688977 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1689181 original size:30 final size:29
Alignment explanation
Indices: 1689122--1689188 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1689112 GTTACGATAT
* *
1689122 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
1689152 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
1689182 ATTTTTT
1 ATATTTT
1689189 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:1689483 original size:22 final size:23
Alignment explanation
Indices: 1689448--1689490 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1689438 TATTGTACTT
**
1689448 TATAATATTTCCGGT-TAAATAA
1 TATAATATAACCGGTATAAATAA
1689470 TATAATATAACCGGTATAAAT
1 TATAATATAACCGGTATAAAT
1689491 TTTAACCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
TATAATATAACCGGTATAAATAA
Found at i:1690921 original size:23 final size:23
Alignment explanation
Indices: 1690886--1690958 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1690876 ATACTTTACA
*
1690886 ATATAAGCGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
1690909 ATATAAGTACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* * * *
1690932 ATATAACCGCTACTTATTACATC
1 ATATAAGCACTACCTATTACATT
1690955 ATAT
1 ATAT
1690959 TTTTATCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:1693589 original size:12 final size:12
Alignment explanation
Indices: 1693562--1693619 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1693552 ATTTGGATCA
* *
1693562 TCATCATCATCA
1 TCATCGTCATCT
*
1693574 TCATCGTCATTT
1 TCATCGTCATCT
*
1693586 TCATCGTTATCT
1 TCATCGTCATCT
*
1693598 TCATCGTCAGCT
1 TCATCGTCATCT
*
1693610 TCATCTTCAT
1 TCATCGTCAT
1693620 TGACCGCTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:1695166 original size:20 final size:19
Alignment explanation
Indices: 1695120--1695166 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1695110 TCCGGTAGCG
1695120 TTTTACCGGTTTCATCATT
1 TTTTACCGGTTTCATCATT
* *
1695139 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTCATCAT-T
1695160 TTTTACC
1 TTTTACC
1695167 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGTTTCATCATT
Found at i:1695282 original size:182 final size:181
Alignment explanation
Indices: 1694966--1695376 Score: 637
Period size: 182 Copynumber: 2.3 Consensus size: 181
1694956 CGTTTTACTT
1694966 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTTAAAGTATCGACAC
1 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACA-TTTTTTTAAAGTATCGACAC
* * * *
1695031 TTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTTGATCCTTATATAAATTATCG
65 TTTATAGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAGTACCG
* * * **
1695096 ACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCG
130 ACACTTTAAATATATCCGGTACCGCTTTACCGGTTTCATCATTTCAATACCG
*
1695148 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGATACT
1 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACT
* *
1695213 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATTAAAGTACCG
66 TTATAGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGTCGATCCTTATA-TAAAGTACCG
* *
1695278 ACACTTTAAATATATCCGGTACCGCTTTACCGGTTTTATCATTTCAATACTG
130 ACACTTTAAATATATCCGGTACCGCTTTACCGGTTTCATCATTTCAATACCG
* * *
1695330 GTTTTGTCATAGTTTTACATG-T-TATCGTTGTGGATCGATACATTTTT
1 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
1695377 AATTTGGATT
Statistics
Matches: 211, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
180 25 0.12
181 71 0.34
182 115 0.55
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACT
TTATAGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAGTACCGA
CACTTTAAATATATCCGGTACCGCTTTACCGGTTTCATCATTTCAATACCG
Found at i:1698212 original size:72 final size:71
Alignment explanation
Indices: 1698070--1698204 Score: 189
Period size: 71 Copynumber: 1.9 Consensus size: 71
1698060 ATACCTAAGT
* * * *
1698070 CATAGGTACCGATACCCTTATGTTGATTTTGGCTCGAGAAAAACAGAATGTCAAATGGGTACCAA
1 CATAGGTACCGACACCCTTATGTTAATTTTGGCTCAAGAAAAACAGAATGCCAAATGGGTACCAA
1698135 GACCCC
66 GACCCC
* * * *
1698141 CATAGGTATCGACACCCTTGTGTTAATTTTGGCTACAAGAAAAATAGAATGCCTAATGGGTACC
1 CATAGGTACCGACACCCTTATGTTAATTTTGGCT-CAAGAAAAACAGAATGCCAAATGGGTACC
1698205 GATACCCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
71 30 0.55
72 25 0.45
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (71 bp):
CATAGGTACCGACACCCTTATGTTAATTTTGGCTCAAGAAAAACAGAATGCCAAATGGGTACCAA
GACCCC
Found at i:1698233 original size:18 final size:19
Alignment explanation
Indices: 1698199--1698234 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1698189 ATGCCTAATG
*
1698199 GGTACCGATACCCCTTAGA
1 GGTAACGATACCCCTTAGA
1698218 GGTAACGATA-CCCTTAG
1 GGTAACGATACCCCTTAG
1698235 TCGTTTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (19 bp):
GGTAACGATACCCCTTAGA
Found at i:1700155 original size:21 final size:21
Alignment explanation
Indices: 1700131--1700172 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1700121 TATGAGAAAT
*
1700131 TATTTTGAAATACAAAAATGA
1 TATTTTAAAATACAAAAATGA
**
1700152 TATTTTAAAATTGAAAAATGA
1 TATTTTAAAATACAAAAATGA
1700173 AAATGATCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (21 bp):
TATTTTAAAATACAAAAATGA
Found at i:1704014 original size:21 final size:21
Alignment explanation
Indices: 1703988--1704039 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1703978 TGTGCAACAT
*
1703988 GTATCGATACCCCCTTTATAG
1 GTATCGATACCCCCTTGATAG
*
1704009 GTATCGATACCCCCTTGCTAG
1 GTATCGATACCCCCTTGATAG
1704030 GTATCGATAC
1 GTATCGATAC
1704040 TCCTTCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (21 bp):
GTATCGATACCCCCTTGATAG
Found at i:1704587 original size:12 final size:13
Alignment explanation
Indices: 1704558--1704590 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1704548 TATATATGAT
*
1704558 TTTTCAAACATTG
1 TTTTCAAACATAG
1704571 TTTTCAAA-ATAG
1 TTTTCAAACATAG
1704583 TTTTCAAA
1 TTTTCAAA
1704591 GTTTGCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:1706811 original size:72 final size:72
Alignment explanation
Indices: 1706668--1706801 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 72
1706658 ATACCTAAGT
* * * * *
1706668 CATAGGTACCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAACAAAATGTCAAATGGGTACCA
1 CATAGGTACCGACACCCTTATGTTAATTTTGGCTACAAGAAAAACAAAATGCCAAATGGGTACCA
1706733 AGACCCC
66 AGACCCC
* * * * *
1706740 CATAGGTATCGACACCCTTGTGTTAATTTTGGCTACAAGAAAAATAGAATGCCTAATGGGTA
1 CATAGGTACCGACACCCTTATGTTAATTTTGGCTACAAGAAAAACAAAATGCCAAATGGGTA
1706802 TCGATACCCC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (72 bp):
CATAGGTACCGACACCCTTATGTTAATTTTGGCTACAAGAAAAACAAAATGCCAAATGGGTACCA
AGACCCC
Found at i:1715969 original size:17 final size:17
Alignment explanation
Indices: 1715947--1715979 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1715937 CATGTTCCTG
1715947 AAAATGAAAAAAAATGT
1 AAAATGAAAAAAAATGT
*
1715964 AAAATGATAAAAAATG
1 AAAATGAAAAAAAATG
1715980 AAATTGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGAAAAAAAATGT
Found at i:1718578 original size:20 final size:20
Alignment explanation
Indices: 1718541--1718578 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1718531 TTTATATAAC
1718541 ATATTAGGGTATCTCGATTT
1 ATATTAGGGTATCTCGATTT
*
1718561 ATATTTGGG-ATCTACGAT
1 ATATTAGGGTATCT-CGAT
1718579 ATTTTCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (20 bp):
ATATTAGGGTATCTCGATTT
Found at i:1719731 original size:12 final size:12
Alignment explanation
Indices: 1719714--1719764 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1719704 TTCAAAGAGG
1719714 TTTTATATTTAA
1 TTTTATATTTAA
1719726 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1719738 TTTGAT-TTTAA
1 TTTTATATTTAA
1719749 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1719761 TTTT
1 TTTT
1719765 TAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1719845 original size:64 final size:64
Alignment explanation
Indices: 1719744--1719881 Score: 251
Period size: 64 Copynumber: 2.2 Consensus size: 64
1719734 TATATTTGAT
1719744 TTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATCATAGATA
1 TTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATCATAGATA
*
1719808 -TTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1 TTTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAATTTTTTAATATTATATCATAGATA
1719872 TTTAATTTTA
1 TTTAATTTTA
1719882 TATCATATAT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
63 16 0.23
64 46 0.65
65 9 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (64 bp):
TTTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAATATTATATCATAGATA
Found at i:1719875 original size:21 final size:21
Alignment explanation
Indices: 1719851--1719894 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1719841 ATATTAATTT
*
1719851 TTTAATATTATATTATAGATA
1 TTTAATATTATATCATAGATA
* *
1719872 TTTAATTTTATATCATATATA
1 TTTAATATTATATCATAGATA
1719893 TT
1 TT
1719895 ATTTTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAATATTATATCATAGATA
Found at i:1722202 original size:3 final size:3
Alignment explanation
Indices: 1722194--1722221 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1722184 TTACTACCAC
1722194 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1722222 TCGAAAGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1723352 original size:60 final size:60
Alignment explanation
Indices: 1723227--1723353 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
1723217 AAAAGTGTCA
* * **
1723227 ATTTAAAAGTTTGGTGACCAATTTAGAATGAAGATCATAGTTTGGGGATAAAACTGAAAT
1 ATTTAAAAGTTTGGTGACCAATCTAAAATGAAGATCATAGTTTAAGGATAAAACTGAAAT
* * * *
1723287 ATTTAAAAGTTTGAG-GACTAATCTAAAATGATAG-TCATAGTTTAAGGATGAAATTGGAAT
1 ATTTAAAAGTTTG-GTGACCAATCTAAAATGA-AGATCATAGTTTAAGGATAAAACTGAAAT
*
1723347 GTTTAAA
1 ATTTAAA
1723354 GATTTAGGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 53 0.95
61 3 0.05
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (60 bp):
ATTTAAAAGTTTGGTGACCAATCTAAAATGAAGATCATAGTTTAAGGATAAAACTGAAAT
Found at i:1725622 original size:20 final size:19
Alignment explanation
Indices: 1725586--1725638 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1725576 TCATTGAATC
**
1725586 AGTATCGATACTGAAGGGA
1 AGTATCGATACCAAAGGGA
1725605 GAGTATCGATACCAAAGGGA
1 -AGTATCGATACCAAAGGGA
*
1725625 AGGTATCAATACCA
1 A-GTATCGATACCA
1725639 TTAAAAACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:1725684 original size:19 final size:19
Alignment explanation
Indices: 1725660--1725731 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
1725650 ATGCAAAAAT
1725660 GGTATCGATACCATAGTAG
1 GGTATCGATACCATAGTAG
*
1725679 GGTATCGGTACCATAGTATG
1 GGTATCGATACCATAGTA-G
* *
1725699 GTAGTATCGATACTATGGTAG
1 G--GTATCGATACCATAGTAG
1725720 TGGTATCGATAC
1 -GGTATCGATAC
1725732 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
19 17 0.38
20 12 0.27
21 1 0.02
22 15 0.33
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:1726910 original size:21 final size:22
Alignment explanation
Indices: 1726883--1726950 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 22
1726873 TCAATATAAG
1726883 GGGTATCGGTACCTTTGGGATA
1 GGGTATCGGTACCTTTGGGATA
* *
1726905 -GGTATCGGTACCTCTTTGTATA
1 GGGTATCGGTACCT-TTGGGATA
*
1726927 GGAGTATCGGTACCCTATGGGATA
1 GG-GTATCGGTA-CCTTTGGGATA
1726951 TTCGTACCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 13 0.35
22 6 0.16
23 1 0.03
24 14 0.38
25 3 0.08
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (22 bp):
GGGTATCGGTACCTTTGGGATA
Found at i:1727322 original size:13 final size:13
Alignment explanation
Indices: 1727304--1727335 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1727294 TAAGATTTTC
1727304 TTGAAAAATCATT
1 TTGAAAAATCATT
1727317 TTG-AAAATCATT
1 TTGAAAAATCATT
1727329 TTGAAAA
1 TTGAAAA
1727336 TTACTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (13 bp):
TTGAAAAATCATT
Found at i:1727325 original size:12 final size:12
Alignment explanation
Indices: 1727308--1727336 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1727298 ATTTTCTTGA
1727308 AAAATCATTTTG
1 AAAATCATTTTG
1727320 AAAATCATTTTG
1 AAAATCATTTTG
1727332 AAAAT
1 AAAAT
1727337 TACTCCCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (12 bp):
AAAATCATTTTG
Found at i:1729555 original size:20 final size:20
Alignment explanation
Indices: 1729530--1729578 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1729520 GAATGTTTTT
1729530 AGGTTTTGGCAAAATAATGA
1 AGGTTTTGGCAAAATAATGA
1729550 AGGTTTTGGCAAAATAATGA
1 AGGTTTTGGCAAAATAATGA
*
1729570 AGATTTTGG
1 AGGTTTTGG
1729579 GGATTTAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (20 bp):
AGGTTTTGGCAAAATAATGA
Found at i:1729628 original size:20 final size:22
Alignment explanation
Indices: 1729603--1729660 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
1729593 AACCTGACAT
* *
1729603 GGGGTATCGGTACCCA-TC-AA
1 GGGGTATCGATACACATTCAAA
1729623 GGGGTATCGATACACATTCAAA
1 GGGGTATCGATACACATTCAAA
1729645 GAGGGTATCGATACAC
1 G-GGGTATCGATACAC
1729661 GTTGAAGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 3 0.09
23 14 0.42
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (22 bp):
GGGGTATCGATACACATTCAAA
Found at i:1735995 original size:28 final size:28
Alignment explanation
Indices: 1735963--1736050 Score: 67
Period size: 28 Copynumber: 3.2 Consensus size: 28
1735953 TATATGTGTA
1735963 AATTTAAGAAATTCATACTAAGTGGATG
1 AATTTAAGAAATTCATACTAAGTGGATG
** * * * *
1735991 AATTTCCG-TATGGGCACTA-TATGT-G-TA
1 AATTTAAGAAAT--TCA-TACTAAGTGGATG
1736018 AATTTAAGAAATTCATACTAAGTGGATG
1 AATTTAAGAAATTCATACTAAGTGGATG
1736046 AATTT
1 AATTT
1736051 CTGTATGGGC
Statistics
Matches: 41, Mismatches: 12, Indels: 14
0.61 0.18 0.21
Matches are distributed among these distances:
25 2 0.05
26 6 0.15
27 10 0.24
28 15 0.37
29 6 0.15
30 2 0.05
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (28 bp):
AATTTAAGAAATTCATACTAAGTGGATG
Found at i:1736003 original size:55 final size:56
Alignment explanation
Indices: 1735838--1736207 Score: 550
Period size: 55 Copynumber: 6.7 Consensus size: 56
1735828 TTCTCAACAA
1735838 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* * *
1735894 CACTATATGTGTAAAACTTAAAAAATTCATACTAAATGGATGAATTTCCATATGGG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
*
1735950 CACTATATGTGT-AAATTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* *
1736005 CACTATATGTGT-AAATTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* * **
1736060 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTAGATGGATTTTTGTAT-GG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* * * *
1736115 CAATATATATGTAAAACTGAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* * * *
1736171 CACTATATATGCAAAAC-TAGGAAATTTATACTAAGTG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTG
1736208 TAGAAATATA
Statistics
Matches: 289, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
55 171 0.59
56 118 0.41
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (56 bp):
CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
Found at i:1736081 original size:111 final size:112
Alignment explanation
Indices: 1735838--1736207 Score: 559
Period size: 111 Copynumber: 3.3 Consensus size: 112
1735828 TTCTCAACAA
1735838 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
* * **
1735903 TGTAAAACTTAAAAAATTCATACTAAATGGATGAATTTCCATATGGG
66 TGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
*
1735950 CACTATATGTGT-AAATTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
*
1736014 TGT-AAATTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
66 TGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
* * ** * *
1736060 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTAGATGGATTTTTGTAT-GGCAATATATA
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
*
1736124 TGTAAAACTGAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
66 TGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
* * * *
1736171 CACTATATATGCAAAAC-TAGGAAATTTATACTAAGTG
1 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTG
1736208 TAGAAATATA
Statistics
Matches: 236, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
110 79 0.33
111 145 0.61
112 12 0.05
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (112 bp):
CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
TGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
Found at i:1736140 original size:166 final size:166
Alignment explanation
Indices: 1735838--1736207 Score: 544
Period size: 166 Copynumber: 2.2 Consensus size: 166
1735828 TTCTCAACAA
1735838 CACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
1 CACTATATGTGTAAAA-TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATG
* * * * *
1735903 TGTAAAACTTAAAAAATTCATACTAAATGGATGAATTTCCATATGGGCACTATATGTGTAAATTT
65 TGTAAAACTTAAAAAATTCATACTAAATAGATGAATTTCCATATGGGCAATATATATGTAAACTG
1735968 AAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
130 AAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* *
1736005 CACTATATGTGTAAATTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTATATGT
1 CACTATATGTGTAAAATTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGT
* * * ***
1736070 GTAAAACTTAAGAAATTCATACTAAGTAGATGGATTTTTGTAT-GGCAATATATATGTAAAACTG
66 GTAAAACTTAAAAAATTCATACTAAATAGATGAATTTCCATATGGGCAATATATATGT-AAACTG
*
1736134 AAGAAATTCATACTAAGTGGATGAATTTCTGTATGGG
130 AAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
* * * * *
1736171 CACTATATATGCAAAACTAGGAAATTTATACTAAGTG
1 CACTATATGTGTAAAATTAAGAAATTCATACTAAGTG
1736208 TAGAAATATA
Statistics
Matches: 182, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
165 12 0.07
166 155 0.85
167 15 0.08
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (166 bp):
CACTATATGTGTAAAATTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGT
GTAAAACTTAAAAAATTCATACTAAATAGATGAATTTCCATATGGGCAATATATATGTAAACTGA
AGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
Found at i:1742437 original size:19 final size:20
Alignment explanation
Indices: 1742413--1742484 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 20
1742403 ATGCAAAAAT
*
1742413 GGTATCGATACCATATTA-G
1 GGTATCGATACCATAGTAGG
1742432 GGTATC-AGTACCATAGTATGG
1 GGTATCGA-TACCATAGTA-GG
* *
1742453 TAGTATCGATACCATGGTAGG
1 -GGTATCGATACCATAGTAGG
1742474 GGTATCGATAC
1 GGTATCGATAC
1742485 TGAGAAGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 1 0.02
19 15 0.34
20 10 0.23
21 3 0.07
22 14 0.32
23 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:1742465 original size:22 final size:19
Alignment explanation
Indices: 1742413--1742484 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 19
1742403 ATGCAAAAAT
*
1742413 GGTATCGATACCATATTAG
1 GGTATCGATACCATAGTAG
1742432 GGTATC-AGTACCATAGTATG
1 GGTATCGA-TACCATAGTA-G
*
1742452 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCATAGTA-G
1742474 GGTATCGATAC
1 GGTATCGATAC
1742485 TGAGAAGCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.02
19 15 0.33
20 12 0.27
22 16 0.36
23 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:1743025 original size:55 final size:56
Alignment explanation
Indices: 1742807--1743195 Score: 525
Period size: 56 Copynumber: 7.0 Consensus size: 56
1742797 ATTACCAAAT
*
1742807 GGCACTA-AGTGTGCAAAATCTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
1 GGCACTATA-TGTGTAAAA-CTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
* *
1742864 GGCACTATATGTGTAAAAGTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
1 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
* *
1742920 GGCACTACATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATA
1 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
* * * *
1742976 GGCACTATATGTGT-AAATTTAATAAATTCATATTAAGTCGATGAATTTCCGTATG
1 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
* **
1743031 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGGATTTTTGTAT-
1 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
* * *
1743086 GGCACTATATGTGTAAACCTGAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
1 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
* * * * * * * *
1743142 AGCACTATATGTGCAAAAC-TAGGAAATTTATGCTAAGTGTATAAATTTTCGTAT
1 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT
1743196 TGGTAGCAGG
Statistics
Matches: 294, Mismatches: 35, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
55 128 0.44
56 150 0.51
57 15 0.05
58 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (56 bp):
GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATG
Found at i:1743056 original size:111 final size:110
Alignment explanation
Indices: 1742807--1743195 Score: 530
Period size: 111 Copynumber: 3.5 Consensus size: 110
1742797 ATTACCAAAT
1742807 GGCACTA-AGTGTGCAAAATCTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTA
1 GGCACTATA-TGTGCAAAA-CTTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT-GGCACTA
*
1742871 TATGTGTAAAAGTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
63 TATGTGT-AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
* *
1742920 GGCACTACATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATAGGCACTATA
1 GGCACTATATGTGCAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT-GGCACTATA
* * * * *
1742985 TGTGTAAATTTAATAAATTCATATTAAGTCGATGAATTTCCGTATG
65 TGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
* * **
1743031 GGCACTATATGTGTAAAACTTAAGAAATTCATACTAAGTGGATGGATTTTTGTATGGCACTATAT
1 GGCACTATATGTGCAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCACTATAT
*
1743096 GTGTAAACCTGAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
66 GTGTAAA-CTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
* * * * * * *
1743142 AGCACTATATGTGCAAAAC-TAGGAAATTTATGCTAAGTGTATAAATTTTCGTAT
1 GGCACTATATGTGCAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT
1743196 TGGTAGCAGG
Statistics
Matches: 248, Mismatches: 26, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
110 45 0.18
111 136 0.55
112 51 0.21
113 15 0.06
114 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (110 bp):
GGCACTATATGTGCAAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCACTATAT
GTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATG
Found at i:1744203 original size:226 final size:226
Alignment explanation
Indices: 1743723--1744161 Score: 639
Period size: 226 Copynumber: 1.9 Consensus size: 226
1743713 GTTACAATTG
* ** * *
1743723 GAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGTGCCTTTT
1 GAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCACATTGT
* * * *
1743788 TAAAGATGACGGGGCTTTGGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTTATTA
66 TAAAGATGACGGGGCCTTAGAAATCCAACAATAACAAAATAGGTTAATTACTTAATTTGTTATCA
* * *
1743853 GTATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATAGAGCCTTAGAA
131 GTATTATCAACATATTAGGTAACACCTAAAATATTAACAAAATTTAAGCTGATAGAGCCTTAGAA
1743918 ATCCAACGATAACATAACCAGTTAATTACTA
196 ATCCAACGATAACATAACCAGTTAATTACTA
* * *
1743949 GAAACATTATCAAGCATAATAACATATTAGGTAGCTCTTATGTAACGTAATAGGTAGCACATTGT
1 GAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCACATTGT
* * **
1744014 TAAAGTTGATGGGGCCTTAGAAATCTGACAATAACAAAATAGGTTAATTACTTAATTTGTTATCA
66 TAAAGATGACGGGGCCTTAGAAATCCAACAATAACAAAATAGGTTAATTACTTAATTTGTTATCA
* * * * *
1744079 GTATTATCAACAT-TTTGGTAA-AGCCTAAGATATTAAGAAAATTTAAGCTGATGGAGCCTTAGG
131 GTATTATCAACATATTAGGTAACA-CCTAAAATATTAACAAAATTTAAGCTGATAGAGCCTTAGA
1744142 AATCCAACGATAACATAACC
195 AATCCAACGATAACATAACC
1744162 GATTTATTAC
Statistics
Matches: 190, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
224 1 0.01
225 60 0.32
226 129 0.68
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (226 bp):
GAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCACATTGT
TAAAGATGACGGGGCCTTAGAAATCCAACAATAACAAAATAGGTTAATTACTTAATTTGTTATCA
GTATTATCAACATATTAGGTAACACCTAAAATATTAACAAAATTTAAGCTGATAGAGCCTTAGAA
ATCCAACGATAACATAACCAGTTAATTACTA
Found at i:1744333 original size:2 final size:2
Alignment explanation
Indices: 1744328--1744370 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1744318 TATATATATA
*
1744328 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1744370 T
1 T
1744371 ATATGTATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:1748635 original size:165 final size:165
Alignment explanation
Indices: 1748368--1748690 Score: 407
Period size: 165 Copynumber: 2.0 Consensus size: 165
1748358 TCTTTTAAAA
* * * *
1748368 GTATCGATAATATGATACATATACTTATAAAAGTACCGATACCTTCAACATATTCGGTAACGCTT
1 GTATCGATAATATGACACATATACTTATAAAAATACCGATACCTTCAACATATCCGATAACGCTT
* * * *
1748433 TACCGGTTTTTCCATATTCAAACTAGTTTTGTCATATTTTAACCTATTATATTATCATGTATCGA
66 TACCGGTTTGTCCATATTCAAACGAGTTTTGTCATATTTTAACATATTATATTATCATGTATCAA
* *
1748498 TACATGTTTCTAAAGTATTGATAATTTAGAAACAT
131 TACATGTTTATAAAGTATCGATAATTTAGAAACAT
* ** * *
1748533 GTATCGATAATATGACACATATACTTATAAAAATATCGATATTTTCAACATATCCGATAGCTCTT
1 GTATCGATAATATGACACATATACTTATAAAAATACCGATACCTTCAACATATCCGATAACGCTT
* * * * * * *
1748598 TACTGGATTTGT-CATATTGAAACCGA-TTTTTTCATATTTTAACATGTTATTTTGTTATGTATC
66 TACCGG-TTTGTCCATATTCAAA-CGAGTTTTGTCATATTTTAACATATTATATTATCATGTATC
*
1748661 AATACATGTTTATAAAGTATCGATACTTTA
129 AATACATGTTTATAAAGTATCGATAATTTA
1748691 CATGCACTAT
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
165 127 0.95
166 6 0.05
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (165 bp):
GTATCGATAATATGACACATATACTTATAAAAATACCGATACCTTCAACATATCCGATAACGCTT
TACCGGTTTGTCCATATTCAAACGAGTTTTGTCATATTTTAACATATTATATTATCATGTATCAA
TACATGTTTATAAAGTATCGATAATTTAGAAACAT
Found at i:1748862 original size:194 final size:194
Alignment explanation
Indices: 1748533--1748961 Score: 653
Period size: 194 Copynumber: 2.2 Consensus size: 194
1748523 TTAGAAACAT
*
1748533 GTATCGATAATATGACACATATACTTATAAAAATATCGATATTTTCAACATATCCGATAGCTCTT
1 GTATCGATAATATGATACATATACTTATAAAAATATCGATATTTTCAACATATCCGATAGCTCTT
* * *
1748598 TACTGGATTTGTCATATTGAAACCGATTTTTTCATATTTTAACATGTTATTTTGTTATGTATCAA
66 TACTGGATTTGTCATATGGAAACCGATTTTCTCATATTTTAACATGTTATGTTGTTATGTATCAA
* *
1748663 TACATGTTTATAAAGTATCGATACTTTACATGCACTATTATTGCAATTCTTTTAAATTTCTAAA
131 TACATGTTTATAAAGTATCGATACTTTACAGGCACTATTATTGCAATTCTTTTAAATTCCTAAA
* * * *
1748727 GTATCGATAATATAATACATATACTTATAAAAGTATCGATATTTTCAACATATCCGGTAGTTCTT
1 GTATCGATAATATGATACATATACTTATAAAAATATCGATATTTTCAACATATCCGATAGCTCTT
* * *
1748792 TATTGGTTTTGTCATATGGAAACC-AGTTTTCTCATATTTTAACCTGTTATGTTGTTATGTATCA
66 TACTGGATTTGTCATATGGAAACCGA-TTTTCTCATATTTTAACATGTTATGTTGTTATGTATCA
* * * **
1748856 ATACATGTTTCTAAAGTCTCGATACTTTATAGGCGTTATTATTGCAATTCTTTTAAATTCCTAAA
130 ATACATGTTTATAAAGTATCGATACTTTACAGGCACTATTATTGCAATTCTTTTAAATTCCTAAA
* * *
1748921 GTATCGATAATTTGATGCATATACTTAGAAAAATATCGATA
1 GTATCGATAATATGATACATATACTTATAAAAATATCGATA
1748962 CAAAATTCAA
Statistics
Matches: 211, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
193 1 0.00
194 210 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (194 bp):
GTATCGATAATATGATACATATACTTATAAAAATATCGATATTTTCAACATATCCGATAGCTCTT
TACTGGATTTGTCATATGGAAACCGATTTTCTCATATTTTAACATGTTATGTTGTTATGTATCAA
TACATGTTTATAAAGTATCGATACTTTACAGGCACTATTATTGCAATTCTTTTAAATTCCTAAA
Found at i:1754276 original size:22 final size:22
Alignment explanation
Indices: 1754238--1754280 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1754228 GGGATTTTTA
*
1754238 TTTTTATATTGTCAAAATATAT
1 TTTTTATATTATCAAAATATAT
1754260 TTTTTA-ATTATCAAAAATATA
1 TTTTTATATTATC-AAAATATA
1754281 AAAGTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTATATTATCAAAATATAT
Done.