Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold192
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: 2196177
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 12544 characters in sequence are not A, C, G, or T
File 11 of 14
Found at i:1649621 original size:158 final size:155
Alignment explanation
Indices: 1649326--1649765 Score: 490
Period size: 158 Copynumber: 2.8 Consensus size: 155
1649316 ATTCCTAAAT
* * * * *
1649326 TTTTCTTTCCAAAA-ATATCAAATTTTCATCTTGAGGATATTTCAACCCCGTTATTTTTAAGGGG
1 TTTTATTTCCAAAATAT-TAAAATTTTCATCTCG-GGATACTTCAACCCCGTTATTTCTAA-GGG
* ** *
1649390 ATACTCCAACCTCGCTTTTATTTCCAAAATATTAAATTCTTT-ATCTTAGGGATATTCCAACCCC
63 ATACTCCAACCCCATTTTTATTTCCAAAATATTAAATT-TTTCATC-TAGGGATACTCCAACCCC
** * * * *
1649454 GTCATTTTCGAGGGGATACTT-TAACTCTAC
126 ACCAATTTCGAGGGGATA-TTCCAACCCCAC
* * *
1649484 TTTTATTTCCAAAATATTAAAATTTTCATCTCAGGGATACTCCAACCCTGTTATTTCTAACGGCA
1 TTTTATTTCCAAAATATTAAAATTTTCATCTC-GGGATACTTCAACCCCGTTATTTCTAA-GGGA
* * * *
1649549 TACTCAAACCCCATTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGAATACTCTAACCCCAC
64 TACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTAGGG-ATACTCCAACCCCAC
1649614 CAATTTCGAGGGGATATTCCAACCCCAC
128 CAATTTCGAGGGGATATTCCAACCCCAC
* * * * *
1649642 ATTTATTTTCAAAATATTAAATTTTTCATCTCGGTGATACTTCAACCCCATTATTTCTGAGGAGA
1 TTTTATTTCCAAAATATTAAAATTTTCATCTCGG-GATACTTCAACCCCGTTATTTCTAAGG-GA
* *
1649707 TACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCATCTTGGGGATACTCCAA
64 TACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATC-TAGGGATACTCCAA
1649766 ACTCGTTTTT
Statistics
Matches: 238, Mismatches: 36, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
157 13 0.05
158 218 0.92
159 7 0.03
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (155 bp):
TTTTATTTCCAAAATATTAAAATTTTCATCTCGGGATACTTCAACCCCGTTATTTCTAAGGGATA
CTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTAGGGATACTCCAACCCCACCAA
TTTCGAGGGGATATTCCAACCCCAC
Found at i:1649760 original size:79 final size:79
Alignment explanation
Indices: 1649326--1649761 Score: 416
Period size: 79 Copynumber: 5.5 Consensus size: 79
1649316 ATTCCTAAAT
* * * * * * *
1649326 TTTTCTTTCCAAAA-ATATCAAATTTTCATCTTGAGGATATTTCAACCCCGTTATTTTTAAGGGG
1 TTTTATTTCCAAAATAT-TAAAATTTTCATCTCGGGGATACTTCAACCCCGTTATTTCTGAGGGG
* *
1649390 ATACTCCAACCTCGC
65 ATACTCCAACCCCAC
* ** *
1649405 TTTTATTTCCAAAATATT-AAATTCTTTATCTTAGGGATA-TTCCAACCCCGTCATTT-TCGAGG
1 TTTTATTTCCAAAATATTAAAATT-TTCATCTCGGGGATACTT-CAACCCCGTTATTTCT-GAGG
** * *
1649467 GGATACTTTAACTCTAC
63 GGATACTCCAACCCCAC
* * * * * *
1649484 TTTTATTTCCAAAATATTAAAATTTTCATCTCAGGGATACTCCAACCCTGTTATTTCTAACGGCA
1 TTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACTTCAACCCCGTTATTTCTGAGGGGA
* *
1649549 TACTCAAACCCCAT
66 TACTCCAACCCCAC
* * * ***
1649563 TTTTATTTTCAAAATATTAAATTTTTCATCTCGGGAATAC-TCTAACCCCACCAATTTC-GAGGG
1 TTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACTTC-AACCCC-GTTATTTCTGAGGG
*
1649626 GATATTCCAACCCCAC
64 GATACTCCAACCCCAC
* * * * * *
1649642 ATTTATTTTCAAAATATTAAATTTTTCATCTCGGTGATACTTCAACCCCATTATTTCTGAGGAGA
1 TTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACTTCAACCCCGTTATTTCTGAGGGGA
*
1649707 TACTCCAACCCCAT
66 TACTCCAACCCCAC
*
1649721 TTTTATTTCCAAAATATTAAAATTTTCATCTTGGGGATACT
1 TTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACT
1649762 CCAAACTCGT
Statistics
Matches: 292, Mismatches: 54, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
78 14 0.05
79 262 0.90
80 16 0.05
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (79 bp):
TTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACTTCAACCCCGTTATTTCTGAGGGGA
TACTCCAACCCCAC
Found at i:1649815 original size:50 final size:51
Alignment explanation
Indices: 1649705--1649815 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
1649695 TTTCTGAGGA
* * * *
1649705 GATACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCATCTTGGG
1 GATACTCCAAACTCGTTTTTATTTCCAAAATACTAAAATTTTCATCTTGGG
* * * *
1649756 GATACTCCAAACTCGTTTTTATTTGCAAAATGCTAAATTTTTCAT-TTTGG
1 GATACTCCAAACTCGTTTTTATTTCCAAAATACTAAAATTTTCATCTTGGG
*
1649806 GATATTCCAA
1 GATACTCCAA
1649816 CCCTATCAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
50 13 0.25
51 38 0.75
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.41
Consensus pattern (51 bp):
GATACTCCAAACTCGTTTTTATTTCCAAAATACTAAAATTTTCATCTTGGG
Found at i:1649867 original size:129 final size:130
Alignment explanation
Indices: 1649643--1649876 Score: 319
Period size: 129 Copynumber: 1.8 Consensus size: 130
1649633 CAACCCCACA
* * * * * *
1649643 TTTATTTTCAAAATATTAAATTTTTCATCTCGGTGATACTTCAACCCCATTATTTCTGAGGAGAT
1 TTTATTTGCAAAATACTAAATTTTTCATCTCGGTGATACTTCAACCCCATCAATTCTAAAGAGAT
1649708 ACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCATCTTGGGGATACTCCAAACTCGTT
66 ACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCATCTTGGGGATACTCCAAACTCGTT
* * * *
1649773 TTTATTTGCAAAATGCTAAATTTTTCATTTTGG-GATA-TTCCAACCCTATCAATTCTAAAGAGA
1 TTTATTTGCAAAATACTAAATTTTTCATCTCGGTGATACTT-CAACCCCATCAATTCTAAAGAGA
* ** *
1649836 TACTCTAATTCCATTTTTATTTCCAAAATATTAAATTTTTC
65 TACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTC
1649877 TTAGAGGTAC
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
128 2 0.02
129 59 0.66
130 28 0.31
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (130 bp):
TTTATTTGCAAAATACTAAATTTTTCATCTCGGTGATACTTCAACCCCATCAATTCTAAAGAGAT
ACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCATCTTGGGGATACTCCAAACTCGTT
Found at i:1653204 original size:20 final size:20
Alignment explanation
Indices: 1653176--1653214 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1653166 GGAAGATAGA
* *
1653176 GAAAGAAAGTTAGAAAAAAG
1 GAAAAAAAGATAGAAAAAAG
*
1653196 GAAAAAAAGATGGAAAAAA
1 GAAAAAAAGATAGAAAAAA
1653215 ATAAAGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (20 bp):
GAAAAAAAGATAGAAAAAAG
Found at i:1657655 original size:149 final size:149
Alignment explanation
Indices: 1657372--1657673 Score: 378
Period size: 149 Copynumber: 2.0 Consensus size: 149
1657362 TAGAAGTGGG
* *
1657372 TTTTATCTTTTTCAAGTCCTTTAGGATGACCAAGCACTTCTAAGTCGATGGTAGACCTTAGGGAT
1 TTTTAACTTTTTCAAGTCCTTTAGGATCACCAAGCACTTCTAAGTCGATGGTAGACCTTAGGGAT
* * * *
1657437 ATTTTAGCTTTTTTCACAAAACCTAGTCCTATAAAACTACCGAGTCCTCTTCTACGTCGAAGTTG
66 ATTTTAGCATTTTTCACAAAACCTAGTCATATAAAACTACCGAGTCCGCTTCTACGTCGAAGTTA
* *
1657502 TGAATTAGGAGTGGGTTTA
131 TGAATTAGAAGTGAGTTTA
* * * * * *
1657521 TTTTAACTTTTTCAAGTCTTTTAGGATCACCGAGTACTTCTAAGTTGATTGTAGACCTTGGGGAT
1 TTTTAACTTTTTCAAGTCCTTTAGGATCACCAAGCACTTCTAAGTCGATGGTAGACCTTAGGGAT
* * *
1657586 ATTTTAGCATTTTTCATC-AAACTTAGTCATATAAAACTACCTG-GTCCGCTTTTATG-CTGAAA
66 ATTTTAGCATTTTTCA-CAAAACCTAGTCATATAAAACTACC-GAGTCCGCTTCTACGTC-G-AA
*
1657648 G-TATGAATTAGAAGTGAGTTTG
127 GTTATGAATTAGAAGTGAGTTTA
1657670 TTTT
1 TTTT
1657674 TATCGTTTCT
Statistics
Matches: 131, Mismatches: 18, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
148 1 0.01
149 125 0.95
150 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (149 bp):
TTTTAACTTTTTCAAGTCCTTTAGGATCACCAAGCACTTCTAAGTCGATGGTAGACCTTAGGGAT
ATTTTAGCATTTTTCACAAAACCTAGTCATATAAAACTACCGAGTCCGCTTCTACGTCGAAGTTA
TGAATTAGAAGTGAGTTTA
Found at i:1662377 original size:13 final size:13
Alignment explanation
Indices: 1662359--1662383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1662349 ATAATGCACA
1662359 GTATCGATACATT
1 GTATCGATACATT
1662372 GTATCGATACAT
1 GTATCGATACAT
1662384 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1670854 original size:52 final size:51
Alignment explanation
Indices: 1670776--1670924 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
1670766 CGAAATATGA
*
1670776 AAATTTGCCTGCATGTATCAATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
1670828 AAATTTTCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
1670880 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1670925 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1670931 original size:13 final size:13
Alignment explanation
Indices: 1670913--1670937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1670903 CAAAGATCAG
1670913 TGTATCGATACAA
1 TGTATCGATACAA
1670926 TGTATCGATACA
1 TGTATCGATACA
1670938 TTTAAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1671018 original size:13 final size:13
Alignment explanation
Indices: 1671000--1671024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1670990 CAAAAAAAAA
1671000 TGTATCGATACAT
1 TGTATCGATACAT
1671013 TGTATCGATACA
1 TGTATCGATACA
1671025 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1674851 original size:13 final size:13
Alignment explanation
Indices: 1674833--1674858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1674823 TACACACAAG
1674833 ATGTATCGATACA
1 ATGTATCGATACA
1674846 ATGTATCGATACA
1 ATGTATCGATACA
1674859 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1674875 original size:33 final size:32
Alignment explanation
Indices: 1674815--1674878 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1674805 CTTAACTATT
*
1674815 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1674847 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1674879 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1676852 original size:67 final size:65
Alignment explanation
Indices: 1676756--1676967 Score: 194
Period size: 66 Copynumber: 3.2 Consensus size: 65
1676746 AAACTTGTCG
** * * **
1676756 TTTTCCAAATAGGTTGAGCTTTAGGATTAACATCAAGGTCTTTTTCATTTTAAAGTTGAACT-AC
1 TTTTCCAAATAGGTCAAGCCTTAGGATTAACATTAAGGTCTTTTTC-TTTTAAA-TCAAACTCA-
1676820 TCT
63 TCT
* ** * *
1676823 TTTTCCAAATAGGTCAAGCCTTAGTATTAATGTTAAGCTCTTATCTT-TTTCAAATCAAACTCAT
1 TTTTCCAAATAGGTCAAGCCTTAGGATTAACATTAAGGTCTT-T-TTCTTTTAAATCAAACTCAT
1676887 CT
64 CT
* * * * * *
1676889 TTTTCCAAATGGGTCAAGCCATGGGATTAACATTAAGGTCTTTTTCTTTTAATGTCAAACTCGTT
1 TTTTCCAAATAGGTCAAGCCTTAGGATTAACATTAAGGTCTTTTTCTTTTAA-ATCAAACTCATC
1676954 T
65 T
*
1676955 TTTTCAAAATAGG
1 TTTTCCAAATAGG
1676968 GCCAACCTTG
Statistics
Matches: 116, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
64 2 0.02
65 6 0.05
66 64 0.55
67 41 0.35
68 1 0.01
69 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (65 bp):
TTTTCCAAATAGGTCAAGCCTTAGGATTAACATTAAGGTCTTTTTCTTTTAAATCAAACTCATCT
Found at i:1679425 original size:2 final size:2
Alignment explanation
Indices: 1679418--1679445 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1679408 TTAGTTGTTC
1679418 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
1679446 CATAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1680395 original size:5 final size:5
Alignment explanation
Indices: 1680385--1680416 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1680375 GGTTAAAACC
*
1680385 ATATT ATATT ATATT ATGTT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT AT
1680417 GTTGCAAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:1680408 original size:15 final size:15
Alignment explanation
Indices: 1680388--1680419 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1680378 TAAAACCATA
1680388 TTATATTATATTATG
1 TTATATTATATTATG
1680403 TTATATTATATTATG
1 TTATATTATATTATG
1680418 TT
1 TT
1680420 GCAAAGCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATATTATATTATG
Found at i:1681058 original size:48 final size:48
Alignment explanation
Indices: 1680990--1681826 Score: 635
Period size: 48 Copynumber: 17.4 Consensus size: 48
1680980 ATCTCCTCCT
* * * * *
1680990 CCTTACTATTATAAGTCACCACCTCCGCCATCTTCATCACCACCACCT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
*
1681038 CCTTATTACTACAAGTCACCACCTCCACCATCTCCTAGTC-CC-CCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-A-TCACCACCACCA
* * * *
1681086 CCGTACTACTACAAGTCACCACCACCACCATCTCCTTCACCACCACCT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
* * * *
1681134 CCTTACTATTACAAGTCACCACCACCACCTTCACCAAGTC-CC-CCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-A-TCACCACCACCA
* * * *
1681182 CCATACTACTACAAGTCTCCACCTCCACCATCTCC-TCGTCCTCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATC-ACCACCACCA
* * * *
1681230 -CTGTACTACTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCT
1 CCT-TACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
* * * * * *
1681278 CCTTACTATTACAAGTCACCACCACCTCCTTCACC-T-AGTCCTCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCA--CCACCACCA
* * * * *
1681326 CCATATTACTACAACTCTCCACCTCCACCATCTCC-T-AGTCCTCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCA--CCACCACCA
* * *
1681374 CCGTACTACTACAAATCACCACCTCCACCATCTCCTAGT-TCC-CCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-A-TCACCACCACCA
* * *
1681422 CCATACTACTACAAGTCACCACCCCCACCATCTCCATCACCACCACCT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
* * * * * * * * *
1681470 CTTTATTATTACAAGTCGCCACCACCACCTTCACCTAGC-CCTCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-ATCACCACCACCA
* * * * * *
1681518 CCATACTACTACAAGTCACCACCCCCACCGTCTCCATCCCCGCCACCT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
* * * * * * * * *
1681566 CCTTATTATTACAATTCCCCACCTCAACCGTCACCTAGC-CCCCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-ATCACCACCACCA
* * * * * *
1681614 CCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
* * * * * * * *
1681662 GCTTATTATTACAAGTCCCCACCTCCACCTTCACCTAGC-CCCCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-ATCACCACCACCA
* * *
1681710 CCATACTACTACAAGTCACCACCTCCACCATCTCCTAGC-CCCCCACCA
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCC-ATCACCACCACCA
* * * *
1681758 CCATACTACTACAAGTCACCACCCCCACCGTCTCCATCACCACCACCT
1 CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
* * *
1681806 CCTTACGATTACAAGCCACCA
1 CCTTACTACTACAAGTCACCA
1681827 TATAACTACA
Statistics
Matches: 635, Mismatches: 129, Indels: 50
0.78 0.16 0.06
Matches are distributed among these distances:
45 2 0.00
46 4 0.01
47 15 0.02
48 592 0.93
49 17 0.03
50 4 0.01
51 1 0.00
ACGTcount: A:0.26, C:0.49, G:0.04, T:0.21
Consensus pattern (48 bp):
CCTTACTACTACAAGTCACCACCTCCACCATCTCCATCACCACCACCA
Found at i:1681128 original size:15 final size:15
Alignment explanation
Indices: 1681108--1681137 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1681098 AAGTCACCAC
*
1681108 CACCACCATCTCCTT
1 CACCACCACCTCCTT
1681123 CACCACCACCTCCTT
1 CACCACCACCTCCTT
1681138 ACTATTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (15 bp):
CACCACCACCTCCTT
Found at i:1681196 original size:144 final size:144
Alignment explanation
Indices: 1680987--1681792 Score: 786
Period size: 144 Copynumber: 5.6 Consensus size: 144
1680977 CCCATCTCCT
* * ** * * *
1680987 CCTCCTTACTATTATAAGTCACCACCTCCGCCATCTTC-A-TCACCACCACCTCCTTATTACTAC
1 CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTC-CC-CCACCACCATACTACTAC
*
1681050 AAGTCACCACCTCCACCATCTCCTAGTCCCCCACCACCGTACTACTACAAGTCACCACCACCACC
64 AAGTCACCACCTCCACCATCTCCTAGTCCCCCACCACCGTACTACTACAAGTCACCACCTCCACC
1681115 ATCTCCTTCACCACCA
129 ATCTCCTTCACCACCA
* * *
1681131 CCTCCTTACTATTACAAGTCACCACCACCACCTTCACCAAGTCCCCCACCACCATACTACTACAA
1 CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTCCCCCACCACCATACTACTACAA
* * * * *
1681196 GTCTCCACCTCCACCATCTCCTCGTCCTCCACCACTGTACTACTACAAATCACCACCTCCACCAT
66 GTCACCACCTCCACCATCTCCTAGTCCCCCACCACCGTACTACTACAAGTCACCACCTCCACCAT
* *
1681261 CTCCCTCACCACCT
131 CTCCTTCACCACCA
* * * * *
1681275 CCTCCTTACTATTACAAGTCACCACCACCTCCTTCACCTAGTCCTCCACCACCATATTACTACAA
1 CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTCCCCCACCACCATACTACTACAA
* * * *
1681340 CTCTCCACCTCCACCATCTCCTAGTCCTCCACCACCGTACTACTACAAATCACCACCTCCACCAT
66 GTCACCACCTCCACCATCTCCTAGTCCCCCACCACCGTACTACTACAAGTCACCACCTCCACCAT
*
1681405 CTCCTAGT-TCC-CCA
131 CTCCT--TCACCACCA
* * * * * * ** * *
1681419 CCACCATACTACTACAAGTCACCACCCCCACCATCTCC-A-TCACCACCACCTCTTTATTATTAC
1 CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTC-CC-CCACCACCATACTACTAC
* * * * * *
1681482 AAGTCGCCACCACCACCTTCACCTAG-CCCTCCACCACCATACTACTACAAGTCACCACCCCCAC
64 AAGTCACCACCTCCACCATCTCCTAGTCCC-CCACCACCGTACTACTACAAGTCACCACCTCCAC
* * * *
1681546 CGTCTCCATCCCCGCCA
128 CATCTCCTTCACCACCA
* * * * * *
1681563 CCTCCTTATTATTACAATTCCCCACCTCAACCGTCACCTAGCCCCCCACCACCATACTACTACAA
1 CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTCCCCCACCACCATACTACTACAA
* * * ** * * * *
1681628 TTCACCACCCCCACCGTCTCC-A-TCACCGCCACCTGCTTATTATTACAAGTCCCCACCTCCACC
66 GTCACCACCTCCACCATCTCCTAGTC-CC-CCACCACCGTACTACTACAAGTCACCACCTCCACC
* * * *
1681691 TTCACCTAGC-CCCCCA
129 ATCTCCT-TCACCACCA
* * * * *
1681707 CCACCATACTACTACAAGTCACCACCTCCACCATCTCCTAGCCCCCCACCACCATACTACTACAA
1 CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTCCCCCACCACCATACTACTACAA
* *
1681772 GTCACCACCCCCACCGTCTCC
66 GTCACCACCTCCACCATCTCC
1681793 ATCACCACCA
Statistics
Matches: 553, Mismatches: 95, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
142 3 0.01
143 8 0.01
144 529 0.96
145 9 0.02
146 4 0.01
ACGTcount: A:0.25, C:0.49, G:0.04, T:0.21
Consensus pattern (144 bp):
CCTCCTTACTATTACAAGTCACCACCTCCACCATCACCTAGTCCCCCACCACCATACTACTACAA
GTCACCACCTCCACCATCTCCTAGTCCCCCACCACCGTACTACTACAAGTCACCACCTCCACCAT
CTCCTTCACCACCA
Found at i:1681848 original size:162 final size:163
Alignment explanation
Indices: 1681671--1681982 Score: 518
Period size: 162 Copynumber: 1.9 Consensus size: 163
1681661 TGCTTATTAT
* *
1681671 TACAAGTCCCCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCTCC
1 TACAAGTCACCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCACC
*
1681736 ACCATCTCCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCGTCTCCAT-CACCA
66 ACCATCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCCACCA
1681800 CCACCTCCTTACGATTACAAGCCACCATATAAC
131 CCACCTCCTTACGATTACAAGCCACCATATAAC
* * *
1681833 TACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCACCACCATACTACTACAAGTCGCCACCACC
1 TACAAGTCACCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCACC
* * *
1681898 ACCTTCACCTAGCCCTCCACCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCCACCG
66 ACCATCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCCACCA
**
1681963 CCACCTCCTTATTATTACAA
131 CCACCTCCTTACGATTACAA
1681983 TTCCCCACCT
Statistics
Matches: 138, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
162 116 0.84
163 22 0.16
ACGTcount: A:0.27, C:0.49, G:0.05, T:0.19
Consensus pattern (163 bp):
TACAAGTCACCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCACC
ACCATCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCCACCA
CCACCTCCTTACGATTACAAGCCACCATATAAC
Found at i:1681885 original size:66 final size:66
Alignment explanation
Indices: 1681755--1681886 Score: 144
Period size: 66 Copynumber: 2.0 Consensus size: 66
1681745 TAGCCCCCCA
* * * *
1681755 CCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCACCACCACCTCCTTACGATTACAA
1 CCACCATACTACTACAAGTCACCACCCCCACCGTCACCATCACCACCACCACCATACGACTACAA
1681820 G
66 G
* * * *
1681821 CCACCATA-TAACTACAAGTCACCACCTCCTCCTTCACCTAGTC-CC-CCACCACCATACTACTA
1 CCACCATACT-ACTACAAGTCACCACCCCCACCGTCACC-A-TCACCACCACCACCATACGACTA
1681883 CAAG
63 CAAG
1681887 TCGCCACCAC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
65 1 0.02
66 49 0.89
67 3 0.05
68 2 0.04
ACGTcount: A:0.30, C:0.46, G:0.05, T:0.19
Consensus pattern (66 bp):
CCACCATACTACTACAAGTCACCACCCCCACCGTCACCATCACCACCACCACCATACGACTACAA
G
Found at i:1681921 original size:96 final size:95
Alignment explanation
Indices: 1681821--1682224 Score: 415
Period size: 96 Copynumber: 4.2 Consensus size: 95
1681811 CGATTACAAG
* * * * * *
1681821 CCACCATA-TAACTACAAGTCACCACCTCCTCCTTCACCTAGTC-CC-CCACCACCATACTACTA
1 CCACCATACT-ACTACAAGTCACCACCCCCACCGTCTCC-A-TCACCGCCACCACCTTACTATTA
* *
1681883 CAAGTCGCCACCACCACCTTCACCTAGCCCTCCA
63 CAAGTCACCACCTCCACCTTCACCTAGCCC-CCA
* *
1681917 CCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCCACCGCCACCTCCTTATTATTACA
1 CCACCATACTACTACAAGTCACCACCCCCACCGTCTCCAT-CACCGCCACCACCTTACTATTACA
* *
1681982 ATTCCCCACCTCCACCTTCACCTAGCCCCCCA
65 AGTCACCACCTCCACCTTCACCTAG-CCCCCA
* *
1682014 CCACCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCTA-CTTATTATTACA
1 CCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCACCGCCACC-ACCTTACTATTACA
*
1682078 AGTCACCACCTCCTCCTTCACCTAGTCCCCCA
65 AGTCACCACCTCCACCTTCACCTAG-CCCCCA
* * * * * * *
1682110 CCACCATACTACTACAAGTCACCACCTCCACCATCTCC-TCGTCCCCCACCGCCGTACTATTATA
1 CCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATC-ACCGCCACCACCTTACTATTACA
* * * *
1682174 AGTCACCACCGCCACCATCTCTCTCA-CCACCA
65 AGTCACCACCTCCACCTTCAC-CT-AGCCCCCA
* *
1682206 CCCCCATACTACTAAAAGT
1 CCACCATACTACTACAAGT
1682225 TTCTTTCCTA
Statistics
Matches: 265, Mismatches: 33, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
94 1 0.00
95 4 0.02
96 174 0.66
97 82 0.31
98 4 0.02
ACGTcount: A:0.26, C:0.49, G:0.05, T:0.21
Consensus pattern (95 bp):
CCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCACCGCCACCACCTTACTATTACAA
GTCACCACCTCCACCTTCACCTAGCCCCCA
Found at i:1681933 original size:114 final size:114
Alignment explanation
Indices: 1681707--1681940 Score: 301
Period size: 114 Copynumber: 2.1 Consensus size: 114
1681697 TAGCCCCCCA
*
1681707 CCACCATACTACTACAAGTCACCACCTCCACCATCTCCTAGCCCCCCACCACCATACTACTACAA
1 CCACCATACTACTACAAGTCACCACCTCCACCATCACCTAGCCCCCCACCACCATACTACTACAA
* * * * * *
1681772 GTCACCACCCCCACCGTCTCCATCACCACCACCTCCTTACGATTACAAG
66 GTCACCACCACCACCGTCACCAGCACCACCACCACCATACGACTACAAG
* * *
1681821 CCACCATA-TAACTACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCACCACCATACTACTACA
1 CCACCATACT-ACTACAAGTCACCACCTCCACCATCACCTAGCCCCCCACCACCATACTACTACA
* * * *
1681885 AGTCGCCACCACCACCTTCACCTAGC-CCTCCACCACCATACTACTACAAG
65 AGTCACCACCACCACCGTCACC-AGCACCACCACCACCATACGACTACAAG
*
1681935 TCACCA
1 CCACCA
1681941 CCCCCACCGT
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
113 1 0.01
114 100 0.97
115 2 0.02
ACGTcount: A:0.29, C:0.48, G:0.05, T:0.18
Consensus pattern (114 bp):
CCACCATACTACTACAAGTCACCACCTCCACCATCACCTAGCCCCCCACCACCATACTACTACAA
GTCACCACCACCACCGTCACCAGCACCACCACCACCATACGACTACAAG
Found at i:1682194 original size:48 final size:48
Alignment explanation
Indices: 1681821--1682189 Score: 356
Period size: 48 Copynumber: 7.7 Consensus size: 48
1681811 CGATTACAAG
*
1681821 CCACCATA-TAACTACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCA
1 CCACCATACT-ACTACAAGTCACCACCTCCACCTTCACCTAGTCCCCCA
* *
1681869 CCACCATACTACTACAAGTCGCCACCACCACCTTCACCTAG-CCCTCCA
1 CCACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGTCCC-CCA
* * *
1681917 CCACCATACTACTACAAGTCACCACCCCCACCGTCTCC-A-TCCACCGCCA
1 CCACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGT-C-CC-CCA
* * * * * * *
1681966 CCTCCTTATTATTACAATTCCCCACCTCCACCTTCACCTAGCCCCCCA
1 CCACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGTCCCCCA
* * * *
1682014 CCACCATACTACTACAATTCACCACCCCCACCGTCTCC-A-TCACCGCCA
1 CCACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGTC-CC-CCA
* * * *
1682062 CCTA-CTTATTATTACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCA
1 CC-ACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGTCCCCCA
* * *
1682110 CCACCATACTACTACAAGTCACCACCTCCACCATCTCCTCGTCCCCCA
1 CCACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGTCCCCCA
* * * * *
1682158 CCGCCGTACTATTATAAGTCACCACCGCCACC
1 CCACCATACTACTACAAGTCACCACCTCCACC
1682190 ATCTCTCTCA
Statistics
Matches: 261, Mismatches: 47, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
46 1 0.00
47 8 0.03
48 207 0.79
49 41 0.16
50 4 0.02
ACGTcount: A:0.25, C:0.49, G:0.05, T:0.20
Consensus pattern (48 bp):
CCACCATACTACTACAAGTCACCACCTCCACCTTCACCTAGTCCCCCA
Found at i:1682203 original size:403 final size:402
Alignment explanation
Indices: 1681479--1682207 Score: 1307
Period size: 403 Copynumber: 1.8 Consensus size: 402
1681469 TCTTTATTAT
1681479 TACAAGTCGCCACCACCACCTTCACCTAGCCCTCCACCACCATACTACTACAAGTCACCACCCCC
1 TACAAGTCGCCACCACCACCTTCACCTAGCCCTCCACCACCATACTACTACAAGTCACCACCCCC
1681544 ACCGTCTCCATCCCCGCCACCTCCTTATTATTACAATTCCCCACCTCAACCGTCACCTAGCCCCC
66 ACCGTCTCCATCCCCGCCACCTCCTTATTATTACAATTCCCCACCTCAACCGTCACCTAGCCCCC
*
1681609 CACCACCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCTGCTTATTATTAC
131 CACCACCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCTACTTATTATTAC
*
1681674 AAGTCCCCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCTCCACC
196 AAGTCACCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCTCCACC
*
1681739 ATCTCCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCGTCTCCATCACCACCAC
261 ATCTCCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCATCTCCATCACCACCAC
1681804 CTCCTTACGATTACAAGCCACCATATAACTACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCA
326 CTCCTTACGATTACAAGCCACCATATAACTACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCA
1681869 CCACCATACTAC
391 CCACCATACTAC
1681881 TACAAGTCGCCACCACCACCTTCACCTAGCCCTCCACCACCATACTACTACAAGTCACCACCCCC
1 TACAAGTCGCCACCACCACCTTCACCTAGCCCTCCACCACCATACTACTACAAGTCACCACCCCC
* *
1681946 ACCGTCTCCATCCACCGCCACCTCCTTATTATTACAATTCCCCACCTCCACCTTCACCTAGCCCC
66 ACCGTCTCCATCC-CCGCCACCTCCTTATTATTACAATTCCCCACCTCAACCGTCACCTAGCCCC
1682011 CCACCACCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCTACTTATTATTA
130 CCACCACCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCTACTTATTATTA
* *
1682076 CAAGTCACCACCTCCTCCTTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCCAC
195 CAAGTCACCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCTCCAC
* * * * * * *
1682141 CATCTCCTCGTCCCCCACCGCCGTACTATTATAAGTCACCACCGCCACCATCTCTC-TCACCACC
260 CATCTCCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCATCTC-CATCACCACC
1682205 ACC
324 ACC
1682208 CCCATACTAC
Statistics
Matches: 311, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
402 78 0.25
403 232 0.75
404 1 0.00
ACGTcount: A:0.25, C:0.50, G:0.05, T:0.20
Consensus pattern (402 bp):
TACAAGTCGCCACCACCACCTTCACCTAGCCCTCCACCACCATACTACTACAAGTCACCACCCCC
ACCGTCTCCATCCCCGCCACCTCCTTATTATTACAATTCCCCACCTCAACCGTCACCTAGCCCCC
CACCACCATACTACTACAATTCACCACCCCCACCGTCTCCATCACCGCCACCTACTTATTATTAC
AAGTCACCACCTCCACCTTCACCTAGCCCCCCACCACCATACTACTACAAGTCACCACCTCCACC
ATCTCCTAGCCCCCCACCACCATACTACTACAAGTCACCACCCCCACCATCTCCATCACCACCAC
CTCCTTACGATTACAAGCCACCATATAACTACAAGTCACCACCTCCTCCTTCACCTAGTCCCCCA
CCACCATACTAC
Found at i:1683546 original size:15 final size:17
Alignment explanation
Indices: 1683516--1683556 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1683506 ATTGATATTT
1683516 TAAATGTTTTATTAAA-A
1 TAAAT-TTTTATTAAACA
1683533 TAAATTTTTA-TAAACA
1 TAAATTTTTATTAAACA
*
1683549 TATATTTT
1 TAAATTTT
1683557 ACTGCCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAATTTTTATTAAACA
Found at i:1683971 original size:15 final size:15
Alignment explanation
Indices: 1683938--1683980 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1683928 TATTATATTT
1683938 TTAATTT-ATTTTTA
1 TTAATTTAATTTTTA
*
1683952 -AAATTTAATTTTTA
1 TTAATTTAATTTTTA
1683966 TTAATTTAATATTTT
1 TTAATTTAAT-TTTT
1683981 TTATTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 7 0.29
15 8 0.33
16 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATTTAATTTTTA
Found at i:1684079 original size:7 final size:7
Alignment explanation
Indices: 1684067--1684109 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1684057 TTATTAAAAT
1684067 TATATAA
1 TATATAA
1684074 TATATAA
1 TATATAA
*
1684081 AATATAA
1 TATATAA
*
1684088 AAT-TAA
1 TATATAA
*
1684094 TATATAT
1 TATATAA
1684101 TATATAA
1 TATATAA
1684108 TA
1 TA
1684110 GTAAAATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:1685620 original size:20 final size:21
Alignment explanation
Indices: 1685597--1685641 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1685587 ATATTATAAT
*
1685597 TTAAATTAATTT-TATAAATA
1 TTAAATTAATTTATACAAATA
1685617 TTAAA-TAATTTATACAAATA
1 TTAAATTAATTTATACAAATA
1685637 -TAAAT
1 TTAAAT
1685642 ATAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATTAATTTATACAAATA
Found at i:1685627 original size:19 final size:20
Alignment explanation
Indices: 1685597--1685642 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1685587 ATATTATAAT
*
1685597 TTAAATTAATTT-TATAAATA
1 TTAAA-TAATTTATACAAATA
1685617 TTAAATAATTTATACAAATA
1 TTAAATAATTTATACAAATA
1685637 -TAAATA
1 TTAAATA
1685643 TAAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAATAATTTATACAAATA
Found at i:1685628 original size:18 final size:18
Alignment explanation
Indices: 1685597--1685660 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
1685587 ATATTATAAT
1685597 TTAAATTAATTTTATAAATA
1 TTAAA-TAA-TTTATAAATA
1685617 TTAAATAATTTATACAA-A
1 TTAAATAATTTATA-AATA
**
1685635 TATAAATATAAATATAAATA
1 T-TAAATA-ATTTATAAATA
1685655 -TAAATA
1 TTAAATA
1685661 TAAATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 14 0.37
19 13 0.34
20 11 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAATAATTTATAAATA
Found at i:1685643 original size:6 final size:6
Alignment explanation
Indices: 1685609--1685667 Score: 73
Period size: 6 Copynumber: 9.5 Consensus size: 6
1685599 AAATTAATTT
** *
1685609 TATAAA TATTAAA TAATTTA TACAAA TATAAA TATAAA TATAAA TATAAA
1 TATAAA TA-TAAA T-ATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
1685659 TATAAA TAT
1 TATAAA TAT
1685668 TATTTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 36 0.80
7 8 0.18
8 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:1686463 original size:13 final size:12
Alignment explanation
Indices: 1686442--1686482 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
1686432 AAAGAAAAAA
1686442 TTAAAAAATAAT
1 TTAAAAAATAAT
1686454 TTATAAAAATAAT
1 TTA-AAAAATAAT
1686467 TGTAAATAAATAAT
1 T-TAAA-AAATAAT
1686481 TT
1 TT
1686483 GTATGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.12
13 13 0.50
14 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TTAAAAAATAAT
Found at i:1690235 original size:13 final size:13
Alignment explanation
Indices: 1690217--1690246 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1690207 CCATCAAAGG
1690217 AGAAAGATAACAC
1 AGAAAGATAACAC
1690230 AGAAAGATAACAC
1 AGAAAGATAACAC
1690243 AGAA
1 AGAA
1690247 GAAATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.13, G:0.17, T:0.07
Consensus pattern (13 bp):
AGAAAGATAACAC
Found at i:1691022 original size:2 final size:2
Alignment explanation
Indices: 1691015--1691043 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1691005 ACTTTCAATA
1691015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1691044 AAGATTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1696165 original size:153 final size:149
Alignment explanation
Indices: 1695905--1696191 Score: 367
Period size: 153 Copynumber: 1.9 Consensus size: 149
1695895 ACTATCATGC
** * * * * * *
1695905 CGAAGGTATATCTTAGGGGTATTTTGATAATTTTTTTAAAACTGCTTAGGTAGTCACCAAGTTAC
1 CGAAGGTATATCTTAAAGATATTTTGATAATTTTGTTAAAACAGCCTAGGTACTCACCAAGTCAC
* * * * *
1695970 TTTTACCCCGAAGGTATACGTTTAGGATAGGTTCATCTTTTTATAATATTTTTGTGTCCTTTATG
66 TTTTACCCCAAAGATATACGTTTAGGATAGGTTCATCTTTTTA-AATATTTTTATATCCTTTAAG
1696035 GTTACTGGTTGCTTTAATGT
130 GTTACTGGTTGCTTTAATGT
* *
1696055 CGAAGGTATATCTTAAAGATATTTTGGTAATTTTGTTAAAATCAAGTCCTAGGTACTCACCGAGT
1 CGAAGGTATATCTTAAAGATATTTTGATAATTTTGTTAAAA-C-AG-CCTAGGTACTCACCAAGT
* ** *
1696120 CGCTTTTATGCCAAAGATATACGTTTAGGATATGTTCATCTTTTTAAATATTTTTATATCCTTTA
63 CACTTTTACCCCAAAGATATACGTTTAGGATAGGTTCATCTTTTTAAATATTTTTATATCCTTTA
1696185 AGGTTAC
128 AGGTTAC
1696192 CAAGATACTT
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
150 36 0.31
151 1 0.01
152 24 0.21
153 54 0.47
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (149 bp):
CGAAGGTATATCTTAAAGATATTTTGATAATTTTGTTAAAACAGCCTAGGTACTCACCAAGTCAC
TTTTACCCCAAAGATATACGTTTAGGATAGGTTCATCTTTTTAAATATTTTTATATCCTTTAAGG
TTACTGGTTGCTTTAATGT
Found at i:1696240 original size:152 final size:150
Alignment explanation
Indices: 1695905--1696247 Score: 386
Period size: 152 Copynumber: 2.3 Consensus size: 150
1695895 ACTATCATGC
* * * * * *
1695905 CGAAGGTATATCTTAGGGGTATTTTGATAATTTTTTTAAAACTGCTTAGGTAGTCACCAAGTTAC
1 CGAAGGTATATCTTAGGAGTATTTTGGTAATTTTTTTAAAACAGCCTAGGTACTCACCAAGTCAC
* * * * *
1695970 TTTTACCCCGAAGGTATACGTTTAGGATAGGTTCATCTTTTTATAATATTTTTGTGTCCTTTATG
66 TTTTACCCCAAAGATATACGTTTAGGATAGGTTCATCTTTTTATAATATTTTTATATCCTTTAAG
** * *
1696035 GTTACTGGTTGCTTTAATGT
131 GTTACAAGATACTTTAATGT
* * *
1696055 CGAAGGTATATCTTA-AAGATATTTTGGTAATTTTGTTAAAATCAAGTCCTAGGTACTCACCGAG
1 CGAAGGTATATCTTAGGAG-TATTTTGGTAATTTTTTTAAAA-C-AG-CCTAGGTACTCACCAAG
* ** *
1696119 TCGCTTTTATGCCAAAGATATACGTTTAGGATATGTTCATCTTTTTA-AATATTTTTATATCCTT
62 TCACTTTTACCCCAAAGATATACGTTTAGGATAGGTTCATCTTTTTATAATATTTTTATATCCTT
*
1696183 TAAGGTTACCAAGATAC-TTCATGT
127 TAAGGTTA-CAAGATACTTTAATGT
* * *
1696207 TGAAGGTATACCTTAGGAGCATTTTGGTAATTTTTTTAAAA
1 CGAAGGTATATCTTAGGAGTATTTTGGTAATTTTTTTAAAA
1696248 AATTGACTCT
Statistics
Matches: 159, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
149 1 0.01
150 35 0.22
151 1 0.01
152 62 0.39
153 60 0.38
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (150 bp):
CGAAGGTATATCTTAGGAGTATTTTGGTAATTTTTTTAAAACAGCCTAGGTACTCACCAAGTCAC
TTTTACCCCAAAGATATACGTTTAGGATAGGTTCATCTTTTTATAATATTTTTATATCCTTTAAG
GTTACAAGATACTTTAATGT
Found at i:1697955 original size:20 final size:20
Alignment explanation
Indices: 1697930--1698096 Score: 102
Period size: 20 Copynumber: 8.8 Consensus size: 20
1697920 TTTTTACCTA
* *
1697930 AATGTATCGATACATTTTTC
1 AATGTATTGATACATTTATC
* *
1697950 AATGTATTGATACATGTATG
1 AATGTATTGATACATTTATC
1697970 AATGTATTGATACATTCTATC
1 AATGTATTGATACATT-TATC
*
1697991 --T-T-TT--TAC--CTA--
1 AATGTATTGATACATTTATC
* * *
1698001 GATGTATCGATACATTTTTC
1 AATGTATTGATACATTTATC
* * *
1698021 GATGTATCGATACATTTTTC
1 AATGTATTGATACATTTATC
* * *
1698041 AATGTATCGATACATGTATG
1 AATGTATTGATACATTTATC
* *
1698061 AATGTATCGATACATTTTTC
1 AATGTATTGATACATTTATC
*
1698081 AATGTATCGATACATT
1 AATGTATTGATACATT
1698097 CTGTCTTTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
12 3 0.03
13 1 0.01
14 1 0.01
15 3 0.03
16 3 0.03
17 2 0.02
18 2 0.02
19 1 0.01
20 100 0.84
21 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
AATGTATTGATACATTTATC
Found at i:1698045 original size:71 final size:71
Alignment explanation
Indices: 1697920--1698055 Score: 209
Period size: 71 Copynumber: 1.9 Consensus size: 71
1697910 AAAAGTCACA
* * *
1697920 TTTTTACCTAAATGTATCGATACATTTTTCAATGTATTGATACATGTATGAATGTATTGATACAT
1 TTTTTACCTAAATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
1697985 TCTATC
66 TCTATC
* * * *
1697991 TTTTTACCTAGATGTATCGATACATTTTTCGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TTTTTACCTAAATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
1698056 GTATGAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (71 bp):
TTTTTACCTAAATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
TCTATC
Found at i:1698050 original size:40 final size:40
Alignment explanation
Indices: 1698002--1698096 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1697992 TTTTACCTAG
*
1698002 ATGTATCGATACATTTTTCG-ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-GAATGTATCGATACATTTTTCA
*
1698042 ATGTATCGATACATGTATGAATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATGAATGTATCGATACATTTTTCA
1698082 ATGTATCGATACATT
1 ATGTATCGATACATT
1698097 CTGTCTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.02
40 50 0.98
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (40 bp):
ATGTATCGATACATTTATGAATGTATCGATACATTTTTCA
Found at i:1698119 original size:91 final size:95
Alignment explanation
Indices: 1697917--1698146 Score: 239
Period size: 91 Copynumber: 2.5 Consensus size: 95
1697907 TGAAAAAGTC
* * * *
1697917 ACATTTTTACCTAAATGTATCGATACATTTTTCAATGTATTGATACATGTATGAATGTATTGATA
1 ACATTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATA
** * * *
1697982 CATTCTATCTTTTTACCTAGATGTATCGAT
66 CATTCTATCAATGTACATACATGTATCGAT
1698012 ACATTTTT---C-GATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATA
1 ACATTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATA
* *
1698073 CATT-TTTCAATGTATCGATACAT-TCT-G-T
66 CATTCTATCAATGTA-C-ATACATGTATCGAT
**
1698101 -C-TTTTTACCCAGATGTATCGATACATTGAAT-AATGTATCGATACAT
1 ACATTTTTACCCAGATGTATCGATACATT-TTTCAATGTATCGATACAT
1698147 CTAGTTAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
87 5 0.04
88 1 0.01
89 1 0.01
90 8 0.07
91 87 0.76
92 5 0.04
95 8 0.07
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (95 bp):
ACATTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATA
CATTCTATCAATGTACATACATGTATCGAT
Found at i:1698137 original size:111 final size:111
Alignment explanation
Indices: 1697930--1698146 Score: 301
Period size: 111 Copynumber: 2.0 Consensus size: 111
1697920 TTTTTACCTA
* * * * *
1697930 AATGTATCGATACATTTTTCAATGTATTGATACATGTATGAATGTATTGATACATTCTATCTTTT
1 AATGTATCGATACATGTATCAATGTATCGATACATGTATCAATGTATCGATACATTCTATCTTTT
* ** *
1697995 TACCTAGATGTATCGATACATTTTTCGATGTATCGATACATTTTTC
66 TACCCAGATGTATCGATACATTAATCAATGTATCGATACATTTTTC
* * * *
1698041 AATGTATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTT
1 AATGTATCGATACATGTATCAATGTATCGATACATGTATCAATGTATCGATACATTCTATCTTTT
1698106 TACCCAGATGTATCGATACATTGAAT-AATGTATCGATACAT
66 TACCCAGATGTATCGATACATT-AATCAATGTATCGATACAT
1698147 CTAGTTAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 91 0.99
112 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (111 bp):
AATGTATCGATACATGTATCAATGTATCGATACATGTATCAATGTATCGATACATTCTATCTTTT
TACCCAGATGTATCGATACATTAATCAATGTATCGATACATTTTTC
Found at i:1700499 original size:18 final size:19
Alignment explanation
Indices: 1700479--1700547 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
1700469 TACCCAGATG
*
1700479 TATCGATACAT-TTCAATG
1 TATCGATACATCTTCAATA
* *
1700497 TATCGATACATGTATGAATA
1 TATCGATACATCT-TCAATA
* *
1700517 TATCAATACATTCTTTAATA
1 TATCGATACA-TCTTCAATA
1700537 TATCGATACAT
1 TATCGATACAT
1700548 TCTGTCTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
18 11 0.26
19 2 0.05
20 27 0.64
21 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
TATCGATACATCTTCAATA
Found at i:1702380 original size:6 final size:6
Alignment explanation
Indices: 1702369--1702403 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
1702359 ATTTTTTCAC
1702369 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TTTT
1702404 TAATTTCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:1702383 original size:18 final size:19
Alignment explanation
Indices: 1702362--1702402 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1702352 GCATAATATT
1702362 TTTTCACTTTTATTTTT-A
1 TTTTCACTTTTATTTTTAA
* *
1702380 TTTTTATTTTTATTTTTAA
1 TTTTCACTTTTATTTTTAA
1702399 TTTT
1 TTTT
1702403 TTAATTTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCACTTTTATTTTTAA
Found at i:1705101 original size:4 final size:4
Alignment explanation
Indices: 1705092--1705160 Score: 67
Period size: 4 Copynumber: 17.8 Consensus size: 4
1705082 ATTTGAAAAG
*
1705092 AATA AATAA AATA AAT- AAT- AATA AAAA TAAT- AATA AAT- AATA AATAA
1 AATA AAT-A AATA AATA AATA AATA AATA -AATA AATA AATA AATA AAT-A
1705139 AATA AATA AATA AAT- AATA AAT
1 AATA AATA AATA AATA AATA AAT
1705161 GTAAAAAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
3 15 0.27
4 31 0.55
5 10 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1705130 original size:31 final size:31
Alignment explanation
Indices: 1705093--1705160 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 31
1705083 TTTGAAAAGA
1705093 ATAAATAAAATAAAT-AAT-AATAA-AAATA
1 ATAAATAAAATAAATAAATAAATAATAAATA
1705121 AT-AATAAATAATAAATAAAATAAATAAATAAATA
1 ATAAAT-AA-AATAAAT-AAATAAAT-AATAAATA
1705155 ATAAAT
1 ATAAAT
1705161 GTAAAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
27 3 0.09
28 4 0.12
29 7 0.22
31 3 0.09
32 3 0.09
33 2 0.06
34 7 0.22
35 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (31 bp):
ATAAATAAAATAAATAAATAAATAATAAATA
Found at i:1705169 original size:24 final size:23
Alignment explanation
Indices: 1705095--1705174 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 23
1705085 TGAAAAGAAT
1705095 AAATAAAATAAATAAT-AATAAAA
1 AAAT-AAATAAATAATAAATAAAA
1705118 ATAAT-AATAAATAATAAATAAAA
1 A-AATAAATAAATAATAAATAAAA
*
1705141 TAAATAAATAAATAATAAATGTAAA
1 -AAATAAATAAATAATAAAT-AAAA
*
1705166 AAATGAATA
1 AAATAAATA
1705175 TTCGATGATG
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.20
23 11 0.22
24 26 0.52
25 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (23 bp):
AAATAAATAAATAATAAATAAAA
Found at i:1708411 original size:19 final size:19
Alignment explanation
Indices: 1708387--1708450 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
1708377 TAATTATAAT
1708387 ATAATTATATTATATAAAA
1 ATAATTATATTATATAAAA
* *
1708406 ATAATTAAATTATAATATCAA
1 ATAATTATATTAT-ATA-AAA
*
1708427 AT-ATTATATGATATAAAAA
1 ATAATTATATTATAT-AAAA
1708446 ATAAT
1 ATAAT
1708451 ATAAATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 18 0.50
20 14 0.39
21 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATTATATTATATAAAA
Found at i:1708475 original size:40 final size:37
Alignment explanation
Indices: 1708378--1708475 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 37
1708368 CGATAATTTT
1708378 AATTATAATATAAT-TATAT-TATATAAAAATAATTA
1 AATTATAATATAATATATATATATATAAAAATAATTA
1708413 AATTATAATATCAA-ATATTATATGATATAAAAAATAATATA
1 AATTATAATAT-AATATA-TATAT-ATAT-AAAAATAAT-TA
1708454 AA-TATAATATGAATATATATAT
1 AATTATAATAT-AATATATATAT
1708476 TAAAATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
35 11 0.20
36 4 0.07
37 3 0.06
38 1 0.02
39 4 0.07
40 24 0.44
41 7 0.13
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (37 bp):
AATTATAATATAATATATATATATATAAAAATAATTA
Found at i:1709160 original size:14 final size:16
Alignment explanation
Indices: 1709141--1709173 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1709131 ATTTGATTTC
1709141 AACCAAAA-AAAA-AA
1 AACCAAAACAAAACAA
1709155 AACCAAAACAAAACAA
1 AACCAAAACAAAACAA
1709171 AAC
1 AAC
1709174 ACTTTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (16 bp):
AACCAAAACAAAACAA
Found at i:1712245 original size:23 final size:23
Alignment explanation
Indices: 1712202--1712248 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1712192 ATATTAATAC
* *
1712202 TTTTTAATTTAATTTTTATAATT
1 TTTTTAATTTAATCTTAATAATT
*
1712225 TTTTTAATTTAGTCTTAATAATT
1 TTTTTAATTTAATCTTAATAATT
1712248 T
1 T
1712249 AATAAATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTTAATTTAATCTTAATAATT
Found at i:1713292 original size:32 final size:32
Alignment explanation
Indices: 1713252--1713359 Score: 162
Period size: 32 Copynumber: 3.4 Consensus size: 32
1713242 AGTATTAATC
*
1713252 ATAAATTTGATGAATATTAGATATAATTATTT
1 ATAAATTTGATAAATATTAGATATAATTATTT
*
1713284 ATAAATTTGATAAATATTAAATATAATTATTT
1 ATAAATTTGATAAATATTAGATATAATTATTT
* * *
1713316 TTAAATTCGATAAATATTAGACATAATTATTT
1 ATAAATTTGATAAATATTAGATATAATTATTT
*
1713348 TTAAATTTGATA
1 ATAAATTTGATA
1713360 TTCATTAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (32 bp):
ATAAATTTGATAAATATTAGATATAATTATTT
Found at i:1717273 original size:2 final size:2
Alignment explanation
Indices: 1717266--1717293 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1717256 ATCTCTGCTT
1717266 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
1717294 CATAAATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1717640 original size:3 final size:3
Alignment explanation
Indices: 1717629--1717666 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1717619 ATAAAAAAAT
1717629 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1717667 GTTGTGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1718053 original size:34 final size:34
Alignment explanation
Indices: 1717996--1718071 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
1717986 AAATATACAT
* *
1717996 TTTTAATATTTTAAATCATAATATTAT-TATAAAA
1 TTTTAATATTTTAAATCAAAATATCATAT-TAAAA
* *
1718030 TTTTAATATTTT-TATCGAAAATATCATATTAATA
1 TTTTAATATTTTAAATC-AAAATATCATATTAAAA
1718064 TTTTAATA
1 TTTTAATA
1718072 AATCCTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.08
34 32 0.89
35 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (34 bp):
TTTTAATATTTTAAATCAAAATATCATATTAAAA
Found at i:1732840 original size:1 final size:1
Alignment explanation
Indices: 1732834--1732895 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
1732824 ATGGCAATAG
* * ** * * * *
1732834 AAAAAAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAACACAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1732896 GTGAAGATTT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1732855 original size:13 final size:13
Alignment explanation
Indices: 1732834--1732895 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
1732824 ATGGCAATAG
1732834 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
1732847 AAAACAAAAAAAAG
1 AAAA-AAAAAAAAC
* *
1732861 GAAAAAGAAAAA-
1 AAAAAAAAAAAAC
* *
1732873 AAAAAAACACAAC
1 AAAAAAAAAAAAC
1732886 AAAAAAAAAA
1 AAAAAAAAAA
1732896 GTGAAGATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
12 8 0.21
13 19 0.50
14 11 0.29
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:1732857 original size:15 final size:14
Alignment explanation
Indices: 1732837--1732895 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 14
1732827 GCAATAGAAA
1732837 AAAAAAAAACAAAAC
1 AAAAAAAAA-AAAAC
*
1732852 AAAAAAAAGGAAAAAG
1 AAAAAAAA--AAAAAC
1732868 AAAAAAAAAAAACAC
1 AAAAAAAAAAAA-AC
1732883 AACAAAAAAAAAA
1 AA-AAAAAAAAAA
1732896 GTGAAGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.11
15 11 0.29
16 22 0.58
17 1 0.03
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:1737116 original size:171 final size:170
Alignment explanation
Indices: 1736826--1737168 Score: 569
Period size: 171 Copynumber: 2.0 Consensus size: 170
1736816 GGACAAAAAT
* *
1736826 AGCCTAAATAGTAAACTGCTCACTGGTTCCAAAGGTACCAAACAATGATGCTTTGAAAAATCATA
1 AGCCCAAATAGTAAACTGCTCACCGGTTCCAAAGGTACCAAACAATGATGCTTTGAAAAATCATA
* * *
1736891 ACTATTTAGTATCTCGTTGGAAATGCAATTCGAACCTTGTCAAGTGAAAAATATCAATAAATTCT
66 ACTATTTAGTATCTCGTTGGAAAGGCAATTAGAACCTCGTCAAGTGAAAAATATCAATAAATTCT
* *
1736956 AGAAAAATCATGTCTGATTTTAAAAATAATTTTTTGACTCA
131 AGAAAAATCATATCTGA-TTTAAAAATAATTTTTCGACTCA
* * * *
1736997 AGCCCAAATAGTAAACTGCTCACCGGTTCCAAAGGTGCCGAACAGTGATGTTTTGAAAAATCATA
1 AGCCCAAATAGTAAACTGCTCACCGGTTCCAAAGGTACCAAACAATGATGCTTTGAAAAATCATA
1737062 ACTATTTAGTATCTCGTTGGAAAGGCAATTAGAACCTCGTCAAGTGAAAAATATCAATAAATTCT
66 ACTATTTAGTATCTCGTTGGAAAGGCAATTAGAACCTCGTCAAGTGAAAAATATCAATAAATTCT
*
1737127 AGAAAAATCATATCTTATTTAAAAATAATTTTTCGACTCA
131 AGAAAAATCATATCTGATTTAAAAATAATTTTTCGACTCA
1737167 AG
1 AG
1737169 TTATAGTATT
Statistics
Matches: 160, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
170 24 0.15
171 136 0.85
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (170 bp):
AGCCCAAATAGTAAACTGCTCACCGGTTCCAAAGGTACCAAACAATGATGCTTTGAAAAATCATA
ACTATTTAGTATCTCGTTGGAAAGGCAATTAGAACCTCGTCAAGTGAAAAATATCAATAAATTCT
AGAAAAATCATATCTGATTTAAAAATAATTTTTCGACTCA
Found at i:1738917 original size:20 final size:20
Alignment explanation
Indices: 1738863--1738920 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1738853 TAAAAAACCT
**
1738863 AGAATGTATTGATAC-ATTG
1 AGAATGTATTGATACAATCC
* **
1738882 ATAATTGTATCAATACAATCC
1 AGAA-TGTATTGATACAATCC
1738903 AGAATGTATTGATACAAT
1 AGAATGTATTGATACAAT
1738921 TACTTGAGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
19 3 0.10
20 21 0.72
21 5 0.17
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
AGAATGTATTGATACAATCC
Found at i:1739021 original size:20 final size:21
Alignment explanation
Indices: 1738979--1739031 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1738969 ACTAAGGCTT
*
1738979 GTATCGATACAATCACACTAG
1 GTATCGATACCATCACACTAG
*
1739000 GTATCGATACCAT-ACCCTAG
1 GTATCGATACCATCACACTAG
*
1739020 GTATCAATACCA
1 GTATCGATACCA
1739032 AGCCTTCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (21 bp):
GTATCGATACCATCACACTAG
Found at i:1750007 original size:52 final size:52
Alignment explanation
Indices: 1749871--1750235 Score: 239
Period size: 51 Copynumber: 7.1 Consensus size: 52
1749861 CTAGCTAAGG
* * * * * * * *
1749871 TGGACTTAGGTTTCTATAAGGCTT-AGCCTTCCTATACTGGTGTC-GATTAGTG
1 TGGACTTTGGATTCTATAGGGCTTGA-CCTCCCTATACAGGTGCCAG-TTAATA
* * * * *
1749923 TGGAC-TTAGATTCTATA-GACTTGACCTTCCTATACAAGTGCCA-TGTAATG
1 TGGACTTTGGATTCTATAGGGCTTGACCTCCCTATACAGGTGCCAGT-TAATA
* * * * * *
1749973 TGGACTTTGGGTTTTATAGGGCTTGACCTCCCTATATAGGTG-TAGTTAGTG
1 TGGACTTTGGATTCTATAGGGCTTGACCTCCCTATACAGGTGCCAGTTAATA
** * * ** *
1750024 CAGA-TTTGGATTCTATAGGGCTTGACCTTCCTATGCAAATGCCAGTTACTA
1 TGGACTTTGGATTCTATAGGGCTTGACCTCCCTATACAGGTGCCAGTTAATA
* * * **
1750075 TAGA-TTTGGATTCTATAGGGTTTGACCTCCCTATACAGGTGCTAGTTACCA
1 TGGACTTTGGATTCTATAGGGCTTGACCTCCCTATACAGGTGCCAGTTAATA
* * * * *
1750126 TTGACTTTAGG-CTCTATAGGGCTTGACCTCCCTATACAGGTGCGAGCTAGTA
1 TGGACTTT-GGATTCTATAGGGCTTGACCTCCCTATACAGGTGCCAGTTAATA
* * * * *
1750178 TGGACTTT-GCTTTTATAAGGCTTGACCT-CCTAATATAGGTGCCAGTAAATA
1 TGGACTTTGGATTCTATAGGGCTTGACCTCCCT-ATACAGGTGCCAGTTAATA
1750229 TGGACTT
1 TGGACTT
1750236 CAAGTTCTAA
Statistics
Matches: 249, Mismatches: 53, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
49 1 0.00
50 62 0.25
51 114 0.46
52 70 0.28
53 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (52 bp):
TGGACTTTGGATTCTATAGGGCTTGACCTCCCTATACAGGTGCCAGTTAATA
Found at i:1750100 original size:101 final size:102
Alignment explanation
Indices: 1749931--1750122 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 102
1749921 TGTGGACTTA
* * * * *
1749931 GATTCTATAGACTTGACCTTCCTATACAAGTGCCATGTAATGTGGACTTTGGGTTTTATAGGGCT
1 GATTCTATAGACTTGACCTTCCTATACAAATGCCATGTAATATAGACTTTGGATTCTATAGGGCT
*
1749996 TGACCTCCCTATATAGGTG-TAGTTAGTGCAGATTTG
66 TGACCTCCCTATACAGGTGCTAGTTAGTGCAGATTTG
* * *
1750032 GATTCTATAGGGCTTGACCTTCCTATGCAAATGCCA-GTTACTATAGA-TTTGGATTCTATAGGG
1 GATTCTATA-GACTTGACCTTCCTATACAAATGCCATG-TAATATAGACTTTGGATTCTATAGGG
*
1750095 TTTGACCTCCCTATACAGGTGCTAGTTA
64 CTTGACCTCCCTATACAGGTGCTAGTTA
1750123 CCATTGACTT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
101 43 0.55
102 35 0.45
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (102 bp):
GATTCTATAGACTTGACCTTCCTATACAAATGCCATGTAATATAGACTTTGGATTCTATAGGGCT
TGACCTCCCTATACAGGTGCTAGTTAGTGCAGATTTG
Found at i:1750204 original size:51 final size:51
Alignment explanation
Indices: 1750086--1750207 Score: 138
Period size: 52 Copynumber: 2.4 Consensus size: 51
1750076 AGATTTGGAT
* * * * *
1750086 TCTATAGGGTTTGACCTCCCTATACAGGTGCTAGTTACCATTGACTTTAGGC
1 TCTATAAGGCTTGACCTCCCTATACAGGTGCGAGCTACCATGGACTTTA-GC
* **
1750138 TCTATAGGGCTTGACCTCCCTATACAGGTGCGAGCTAGTATGGACTTT-GC
1 TCTATAAGGCTTGACCTCCCTATACAGGTGCGAGCTACCATGGACTTTAGC
*
1750188 TTTTATAAGGCTTGACCTCC
1 -TCTATAAGGCTTGACCTCC
1750208 TAATATAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 2 0.03
51 17 0.28
52 42 0.69
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (51 bp):
TCTATAAGGCTTGACCTCCCTATACAGGTGCGAGCTACCATGGACTTTAGC
Found at i:1750218 original size:103 final size:101
Alignment explanation
Indices: 1749934--1750219 Score: 280
Period size: 103 Copynumber: 2.8 Consensus size: 101
1749924 GGACTTAGAT
* * *
1749934 TCTATA-GACTTGACCTTCCTATACAAGTGCCATGTAATGTGGACTTTGGGTTTTATAGGGCTTG
1 TCTATAGGGCTTGACCTTCCTATACAAGTGCCA-GTAATATGGACTTTGGATTTTATAGGGCTTG
* *
1749998 ACCTCCCTATATAGGTG-TAGTTAGTGCAGATTTGGAT
65 ACCTCCCTATATAGGTGCTAGTTAG-CCAGATTTGGAC
* * * * * *
1750035 TCTATAGGGCTTGACCTTCCTATGCAAATGCCAGTTACTATAGA-TTTGGATTCTATAGGGTTTG
1 TCTATAGGGCTTGACCTTCCTATACAAGTGCCAG-TAATATGGACTTTGGATTTTATAGGGCTTG
*
1750099 ACCTCCCTATACAGGTGCTAGTTA-CCATTGACTTTAGG-C
65 ACCTCCCTATATAGGTGCTAGTTAGCCA--GA-TTT-GGAC
* * * * * *
1750138 TCTATAGGGCTTGACCTCCCTATACAGGTGCGAGCTAGTATGGACTTT-GCTTTTATAAGGCTTG
1 TCTATAGGGCTTGACCTTCCTATACAAGTGCCAG-TAATATGGACTTTGGATTTTATAGGGCTTG
1750202 ACCT-CCTAATATAGGTGC
65 ACCTCCCT-ATATAGGTGC
1750220 CAGTAAATAT
Statistics
Matches: 151, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
100 2 0.01
101 40 0.26
102 40 0.26
103 64 0.42
104 5 0.03
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (101 bp):
TCTATAGGGCTTGACCTTCCTATACAAGTGCCAGTAATATGGACTTTGGATTTTATAGGGCTTGA
CCTCCCTATATAGGTGCTAGTTAGCCAGATTTGGAC
Found at i:1759666 original size:21 final size:21
Alignment explanation
Indices: 1759622--1759667 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1759612 TTTTTGCCAA
* * *
1759622 AATGTATTGATACATGCCCTT
1 AATGTATCGATACAAGCCCGT
*
1759643 AATGTATCGATACAAGGCCGT
1 AATGTATCGATACAAGCCCGT
1759664 AATG
1 AATG
1759668 GTCAAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
AATGTATCGATACAAGCCCGT
Found at i:1759727 original size:13 final size:13
Alignment explanation
Indices: 1759711--1759740 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1759701 ATACATTGTT
*
1759711 CATTGTATCGATA
1 CATTGTATCAATA
1759724 CATTGTATCAATA
1 CATTGTATCAATA
1759737 CATT
1 CATT
1759741 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:1759788 original size:20 final size:20
Alignment explanation
Indices: 1759773--1759862 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1759763 ATACATTTTG
*
1759773 CATTGTTTCGATACATTGCT
1 CATTGTATCGATACATTGCT
1759793 CATTGTATCGAT--A-----
1 CATTGTATCGATACATTGCT
*
1759806 CATTGTATCGATACATCGCT
1 CATTGTATCGATACATTGCT
*
1759826 CATTGTATCGATACATT-TT
1 CATTGTATCGATACATTGCT
*
1759845 ACAATGTATCGATACATT
1 -CATTGTATCGATACATT
1759863 CAGGCATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 12 0.21
15 1 0.02
18 1 0.02
19 1 0.02
20 43 0.74
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (20 bp):
CATTGTATCGATACATTGCT
Found at i:1759809 original size:13 final size:13
Alignment explanation
Indices: 1759793--1759821 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1759783 ATACATTGCT
1759793 CATTGTATCGATA
1 CATTGTATCGATA
1759806 CATTGTATCGATA
1 CATTGTATCGATA
1759819 CAT
1 CAT
1759822 CGCTCATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1759817 original size:33 final size:33
Alignment explanation
Indices: 1759773--1759842 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
1759763 ATACATTTTG
* *
1759773 CATTGTTTCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATCGCTCATTGTATCGATA
1759806 CATTGTATCGATACATCGCTCATTGTATCGATA
1 CATTGTATCGATACATCGCTCATTGTATCGATA
1759839 CATT
1 CATT
1759843 TTACAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATCGCTCATTGTATCGATA
Found at i:1762230 original size:51 final size:51
Alignment explanation
Indices: 1762168--1762333 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 51
1762158 TTTTCATCTC
** * * *
1762168 GGGATACTCCAATC-CCGATTCCATTTCCAAAACATCAATTTTTCTTAATTG
1 GGGATACTCCAA-CGCCGATTTTATTTCTAAAACACCAATTTTTCATAATTG
* * * * ** *
1762219 GGGATACTCCAACGTCGATTTTATTTCTAAAGCACCGATTTATCGCAATCG
1 GGGATACTCCAACGCCGATTTTATTTCTAAAACACCAATTTTTCATAATTG
*
1762270 GGGATACTCTAACGCCGATTTTACTTT-TAAAACACCAATTTTTCATAATTG
1 GGGATACTCCAACGCCGATTTTA-TTTCTAAAACACCAATTTTTCATAATTG
1762321 GGGATACTCCAAC
1 GGGATACTCCAAC
1762334 CCCGTTATTT
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
50 1 0.01
51 89 0.96
52 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACGCCGATTTTATTTCTAAAACACCAATTTTTCATAATTG
Found at i:1762353 original size:28 final size:28
Alignment explanation
Indices: 1762320--1762393 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
1762310 TTTCATAATT
**
1762320 GGGGATACTCCAACCCCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCAGA
* *
1762348 GGGGATACTCCAACCTCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
*
1762376 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
1762394 GCTTTATATC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAGA
Found at i:1762458 original size:109 final size:109
Alignment explanation
Indices: 1762311--1762549 Score: 315
Period size: 109 Copynumber: 2.2 Consensus size: 109
1762301 ACACCAATTT
* * *
1762311 TTCATAATTGGGGATACTCCAACCCCGTTATTTCATCGGGGATACTCCAA-CCTCGTTATTTCCG
1 TTCATAATCGGGGATACTCCAACCCAGTTATTTCATCGGGGATACTCCAATCC-CGTTAATTCCG
* *
1762375 AGGGGATACTCTAACCCCGGCTTTATATCTAAAAATATTATTTTC
65 AGGGGATACTCCAACCCCGACTTTATATCTAAAAATATTATTTTC
* *
1762420 TTCATAATCGGGGGTACTCCAACCTAGTTATTTCATCGGGGATACTCCAATCCCGTTAATTCCGA
1 TTCATAATCGGGGATACTCCAACCCAGTTATTTCATCGGGGATACTCCAATCCCGTTAATTCCGA
* * * **
1762485 GGGGATACTCCAACCGCGATTTTATTTCT-AAAATACCAATTTTC
66 GGGGATACTCCAACCCCGACTTTATATCTAAAAATA-TTATTTTC
*
1762529 --CACAATCGGGGATACTCCAAC
1 TTCATAATCGGGGATACTCCAAC
1762550 TCTGATTTTA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
107 19 0.17
108 6 0.05
109 87 0.76
110 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (109 bp):
TTCATAATCGGGGATACTCCAACCCAGTTATTTCATCGGGGATACTCCAATCCCGTTAATTCCGA
GGGGATACTCCAACCCCGACTTTATATCTAAAAATATTATTTTC
Found at i:1762477 original size:28 final size:28
Alignment explanation
Indices: 1762426--1762499 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
1762416 TTTCTTCATA
* *
1762426 ATCGGGGGTACTCCAACCTAGTTATTTC
1 ATCGGGGATACTCCAACCTAGTTAATTC
*
1762454 ATCGGGGATACTCCAATCC-CGTTAATTC
1 ATCGGGGATACTCCAA-CCTAGTTAATTC
***
1762482 CGAGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
1762500 GCGATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 2 0.05
28 35 0.90
29 2 0.05
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTAGTTAATTC
Found at i:1762545 original size:51 final size:50
Alignment explanation
Indices: 1762485--1762602 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 50
1762475 TTAATTCCGA
* *
1762485 GGGGATACTCCAACCGCGATTTTATTTCTAAAATACCAATTT-TCCACAATC
1 GGGGATACTCCAACC-CGATTTTATTTCCAAAACACCAATTTCT-CACAATC
*
1762536 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1762587 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1762603 CGTTATTTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 1 0.02
51 58 0.95
52 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.29
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:1762619 original size:79 final size:78
Alignment explanation
Indices: 1762535--1762765 Score: 273
Period size: 79 Copynumber: 2.9 Consensus size: 78
1762525 TTTCCACAAT
* * *
1762535 CGGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAA
1 CGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCGATTT-TCATAATCGGGGATACTCCAA
1762600 CCCCGTTATTTTCG
65 CCCCGTTATTTTCG
* * * * * ** *
1762614 CGGGGACACTCCAACCCCGATTTTATTTTCAAAATATCGATTTTCTATAATCAAGGATACTTCAA
1 CGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCGATTTTC-ATAATCGGGGATACTCCAA
*
1762679 CCCTGTTATTTTCG
65 CCCCGTTATTTTCG
* * * *
1762693 AGGGGATACTCCAACCCTGATTTTTATTTCTAGAACACCGATTTTCCATAATCGGGGATACTCTA
1 CGGGGATACTCCAACCCTGA-TTTTATTTCCAAAACACCGATTTT-CATAATCGGGGATACTCCA
*
1762758 GCCCCGTT
64 ACCCCGTT
1762766 GTTATCTCCA
Statistics
Matches: 123, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
78 2 0.02
79 81 0.66
80 39 0.32
81 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (78 bp):
CGGGGATACTCCAACCCTGATTTTATTTCCAAAACACCGATTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCG
Found at i:1769045 original size:62 final size:61
Alignment explanation
Indices: 1768920--1769187 Score: 367
Period size: 61 Copynumber: 4.4 Consensus size: 61
1768910 TTAGCCCTCT
* * * * * *
1768920 TAGTCCTCAAAAAGCAAGACGTCTTTTTCTTTTTAAAACCCAC-CTAAGTTGGTGGTACCTTC
1 TAGTCCTCAAAGAGCAGGACG-CCTTTTCCTTTTAAAGCCCACAC-AAGTTGGTGGCACCTTC
* * *
1768982 TAGTCCTCAAAGAGCAGGACACCTTTTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
* *
1769044 TAGTCCTCAAAGAGCAGGACGCATTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
1769105 CAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAATTGGTGGCACTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1769166 TAGTCCTCAAAGAGCAGGACGC
1 TAGTCCTCAAAGAGCAGGACGC
1769188 TCTCTTCTTT
Statistics
Matches: 182, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
61 107 0.59
62 75 0.41
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (61 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:1769163 original size:123 final size:122
Alignment explanation
Indices: 1768920--1769187 Score: 412
Period size: 123 Copynumber: 2.2 Consensus size: 122
1768910 TTAGCCCTCT
* * * * *
1768920 TAGTCCTCAAAAAGCAAGACGTCTTTTTCTTTTTAAAACCCACCTAAGTTGGTGGTACCTTCTAG
1 TAGTCCTCAAAGAGCAGGACG-CATTTTCTTTTTAAAACCCACCTAAGTTGGTGGCACCTTCCAG
*
1768985 TCCTCAAAGAGCAGGACACCTTTTCCTTCTAAAGCCCACACAAGTTGGTGGCACTTTTC
65 TCCTCAAAGAGCAGGACACCTTTTCCTTCTAAAGCCCACACAAATTGGTGGCAC-TTTC
*
1769044 TAGTCCTCAAAGAGCAGGACGCATTTTCTTTTTAAAGCCCACAC-AAGTTGGTGGCACCTTCCAG
1 TAGTCCTCAAAGAGCAGGACGCATTTTCTTTTTAAAACCCAC-CTAAGTTGGTGGCACCTTCCAG
** *
1769108 TCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAATTGGTGGCACTTTC
65 TCCTCAAAGAGCAGGACACCTTTTCCTTCTAAAGCCCACACAAATTGGTGGCACTTTC
1769166 TAGTCCTCAAAGAGCAGGACGC
1 TAGTCCTCAAAGAGCAGGACGC
1769188 TCTCTTCTTT
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
122 26 0.20
123 87 0.65
124 20 0.15
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (122 bp):
TAGTCCTCAAAGAGCAGGACGCATTTTCTTTTTAAAACCCACCTAAGTTGGTGGCACCTTCCAGT
CCTCAAAGAGCAGGACACCTTTTCCTTCTAAAGCCCACACAAATTGGTGGCACTTTC
Found at i:1769520 original size:61 final size:61
Alignment explanation
Indices: 1769226--1769585 Score: 492
Period size: 61 Copynumber: 5.9 Consensus size: 61
1769216 GAGCAGGATG
* *
1769226 CCTTTCAAAGCCCACACAAGTTGGTGGCACCCATC-AGTCCTCAAAGAGTAGGACGCCTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * *
1769287 CCTTTTAAAGCCCACACGAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACGCCTTCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * *
1769347 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAAGACGTCTTCG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * *
1769407 CCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * *
1769469 TCTTTTAAAGCCTACACAAATTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * *
1769530 CTTTTTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCAGGACGC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGC
1769586 TCTCTTCTTT
Statistics
Matches: 266, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
59 3 0.01
60 103 0.39
61 114 0.43
62 46 0.17
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (61 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
Found at i:1769726 original size:55 final size:55
Alignment explanation
Indices: 1769596--1769707 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
1769586 TCTCTTCTTT
* * *
1769596 CACCCTTTAGTCCTCAAAGAGTAAGACGCCTTTCAAAGCCCATACAAGTTGGTGG
1 CACCCTTCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
* *
1769651 CACCCTTCAGTCCTCAAAGAGTAGGACGTCTTTCACAGCCCACACAAGTTGGTGG
1 CACCCTTCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
1769706 CA
1 CA
1769708 TTTTCCAGTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
CACCCTTCAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:1769751 original size:149 final size:153
Alignment explanation
Indices: 1769469--1769868 Score: 461
Period size: 155 Copynumber: 2.6 Consensus size: 153
1769459 GACACCTTTT
* * *
1769469 TCTTTTAAAGCCTACACAAATTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTT
1 TCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACG----TTCTTT
* * *
1769534 TTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCAGGACGCTCTCTTCTTTCAC
62 TCAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCTATCTTCTTTCAC
*
1769599 CCTTTAGTCCTCAAAGAGTAAGACG-C
127 CCTTTAGTCCTCAAAGAGCAAGACGTC
* *
1769625 -CTTTCAAAGCCCATACAAGTTGGTGGCACCCTTC-AGTCCTCAAAGAGTAGGACG-TC-TTTCA
1 TCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAGGACGTTCTTTTCA
* * * * *
1769686 CAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGATGCTAT-TTCTTTTCGCCC
65 AAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCTATCTTC-TTTCACCC
* *
1769750 TTTAGTCCTCAAAGAGCAGGATGTTTTC
129 TTTAGTCCTCAAAGAGCAAGACG---TC
* *
1769778 TCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAGGACACATTTTCTT
1 TCTTT-CAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGG--AC--GTTCTT
*
1769843 TTTAAAGCCCACACAAGTTGGTGGCA
61 TTCAAAGCCCACACAAGTTGGTGGCA
1769869 CTTTTTAGTC
Statistics
Matches: 207, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
148 3 0.01
149 77 0.37
150 2 0.01
153 1 0.00
154 9 0.04
155 81 0.39
156 5 0.02
157 2 0.01
160 2 0.01
161 25 0.12
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (153 bp):
TCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGTTCTTTTCAA
AGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCTATCTTCTTTCACCCTT
TAGTCCTCAAAGAGCAAGACGTC
Found at i:1769757 original size:94 final size:96
Alignment explanation
Indices: 1769653--1769831 Score: 227
Period size: 100 Copynumber: 1.8 Consensus size: 96
1769643 GTTGGTGGCA
* * **
1769653 CCCTTCAGTCCTCAAAGAGTAGGACG-TCTTT-CACAGCCCACACAAGTTGGTGGCATTTTCCAG
1 CCCTTCAGTCCTCAAAGAGCAGGACGTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAG
* *
1769716 TCCTTAAAGAGCAGGATGCTATTTCTTTTCG
66 TCCTCAAAGAACAGGATGCTATTTCTTTTCG
* *
1769747 CCCTTTAGTCCTCAAAGAGCAGGATGTTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTT
1 CCCTTCAGTCCTCAAAGAGCAGGACG---T-TCTTTGCAAAGCCCACACAAGTTGGTGGCACCTT
*
1769812 CTAGTCCTCAAAGAACAGGA
62 CCAGTCCTCAAAGAACAGGA
1769832 CACATTTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
94 23 0.33
99 5 0.07
100 42 0.60
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (96 bp):
CCCTTCAGTCCTCAAAGAGCAGGACGTTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAG
TCCTCAAAGAACAGGATGCTATTTCTTTTCG
Found at i:1769901 original size:61 final size:61
Alignment explanation
Indices: 1769785--1769906 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
1769775 TTCTCTTTGC
* *
1769785 AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAGGACACATTTTCTTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAAGACACATTTTCCTTTT
* * * * *
1769846 AAAGCCCACACAAGTTGGTGGCACTTTTTAGTCTTCAAA-AAGCAAGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAA-CAAGACACATTTTCCTTTT
1769907 CTCATTTGTC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
60 2 0.04
61 51 0.96
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (61 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAACAAGACACATTTTCCTTTT
Found at i:1770012 original size:42 final size:43
Alignment explanation
Indices: 1769897--1770014 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 43
1769887 GCAAGACGCC
* *
1769897 TTTTCCTTTTCTCATTTGTCCTCAAAGAGCAGGACACACTTCA
1 TTTTCCTTTTCTCTTTTATCCTCAAAGAGCAGGACACACTTCA
* *
1769940 TTCCCTT-CTTTTCCCTTTTATCCTCAAAGAGCAGGACGCA-TTCTA
1 TT---TTCCTTTTCTCTTTTATCCTCAAAGAGCAGGACACACTTC-A
1769985 TTTTCCTTTT-TCTTTTATCCTCAAAGAGCA
1 TTTTCCTTTTCTCTTTTATCCTCAAAGAGCA
1770015 AGAAACATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
42 21 0.32
43 7 0.11
44 3 0.05
45 32 0.49
46 2 0.03
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (43 bp):
TTTTCCTTTTCTCTTTTATCCTCAAAGAGCAGGACACACTTCA
Found at i:1770036 original size:42 final size:41
Alignment explanation
Indices: 1769945--1770037 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
1769935 CTTCATTCCC
* * **
1769945 TTCTTTTCCCTTTTATCCTCAAAGAGCAGGACGCATTCTATT
1 TTCTTTT-TCTTTTATCCTCAAAGAGCAAGAAACATTCTATT
1769987 TTCCTTTTTCTTTTATCCTCAAAGAGCAAGAAACATTTCGT-TT
1 TT-CTTTTTCTTTTATCCTCAAAGAGCAAGAAACA-TTC-TATT
1770030 TTCTTTTT
1 TTCTTTTT
1770038 TCCTTTGTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
42 31 0.70
43 12 0.27
44 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (41 bp):
TTCTTTTTCTTTTATCCTCAAAGAGCAAGAAACATTCTATT
Found at i:1770805 original size:13 final size:13
Alignment explanation
Indices: 1770787--1770849 Score: 66
Period size: 13 Copynumber: 5.3 Consensus size: 13
1770777 ATACATTTTT
1770787 CATTGTATCAATA
1 CATTGTATCAATA
*
1770800 CATTGTATCGATA
1 CATTGTATCAATA
1770813 CA-T-TAT---T-
1 CATTGTATCAATA
*
1770820 CATTGTATCGATA
1 CATTGTATCAATA
1770833 CATTGTATCAATA
1 CATTGTATCAATA
1770846 CATT
1 CATT
1770850 CTAGGTTTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 3 0.07
11 3 0.07
12 2 0.05
13 30 0.71
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:1770814 original size:33 final size:33
Alignment explanation
Indices: 1770767--1770849 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
1770757 ATACATTGTT
* *
1770767 CATTATATCGATACATTTTTCATTGTATCAATA
1 CATTGTATCGATACATTATTCATTGTATCAATA
*
1770800 CATTGTATCGATACATTATTCATTGTATCGATA
1 CATTGTATCGATACATTATTCATTGTATCAATA
*
1770833 CATTGTATCAATACATT
1 CATTGTATCGATACATT
1770850 CTAGGTTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (33 bp):
CATTGTATCGATACATTATTCATTGTATCAATA
Found at i:1770825 original size:20 final size:20
Alignment explanation
Indices: 1770749--1770836 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
1770739 TTTTCACAAT
*
1770749 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTATTCA
* *
1770769 TTATATCGATACATTTTTCA
1 TTGTATCGATACATTATTCA
1770789 TTGTATC---A-A-TA--CA
1 TTGTATCGATACATTATTCA
1770802 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
1770822 TTGTATCGATACATT
1 TTGTATCGATACATT
1770837 GTATCAATAC
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.16
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
20 41 0.72
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1770919 original size:20 final size:20
Alignment explanation
Indices: 1770749--1770920 Score: 98
Period size: 20 Copynumber: 8.8 Consensus size: 20
1770739 TTTTCACAAT
1770749 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
* *
1770769 TTATATCGATACATTTTTCA
1 TTGTATCGATACATTGTTCA
*
1770789 TTGTATC---A-A---TACA
1 TTGTATCGATACATTGTTCA
*
1770802 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTGTTCA
1770822 TTGTATCGATACATTGTATCA
1 TTGTATCGATACATTGT-TCA
* ** ** *
1770843 ATACATTC--TAGGTT-TACCCA
1 TTGTA-TCGATACATTGT--TCA
*
1770863 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
1770884 TTGTATCGATACATTGCTT-A
1 TTGTATCGATACATTG-TTCA
1770904 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
1770921 ATCGATACAT
Statistics
Matches: 117, Mismatches: 19, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
13 10 0.09
16 2 0.02
17 2 0.02
19 2 0.02
20 82 0.70
21 10 0.09
22 9 0.08
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1770921 original size:13 final size:13
Alignment explanation
Indices: 1770903--1770930 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1770893 TACATTGCTT
1770903 ATTGTATCGATAC
1 ATTGTATCGATAC
1770916 ATTGTATCGATAC
1 ATTGTATCGATAC
1770929 AT
1 AT
1770931 CGCTCATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:1770924 original size:33 final size:33
Alignment explanation
Indices: 1770882--1770951 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
1770872 ATACATTTTG
* *
1770882 CATTGTATCGATACATTGCTTATTGTATCGATA
1 CATTGTATCGATACATCGCTCATTGTATCGATA
1770915 CATTGTATCGATACATCGCTCATTGTATCGATA
1 CATTGTATCGATACATCGCTCATTGTATCGATA
1770948 CATT
1 CATT
1770952 CAAGCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATCGCTCATTGTATCGATA
Found at i:1773345 original size:51 final size:51
Alignment explanation
Indices: 1773269--1773395 Score: 121
Period size: 51 Copynumber: 2.5 Consensus size: 51
1773259 TTCATCTCAG
** ** ** **
1773269 GGATACTCCAA-TCCCGATTCCATTTCCAAAACGTCAATTTTTCTTAATCGA
1 GGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTACCGCAATCGA
* * * *
1773320 GGATACTCCAACTCCGATTTTATTTCTAAAGCACCGATTTACCGCAATCGG
1 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTACCGCAATCGA
*
1773371 GGATACTCCAACTCTGATTTTATTT
1 GGATACTCCAACTCCGATTTTATTT
1773396 TTAACACCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
51 61 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTACCGCAATCGA
Found at i:1773451 original size:28 final size:28
Alignment explanation
Indices: 1773419--1773491 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
1773409 TTCACAATTG
1773419 GAGATACTCCAACCCCGTTATTTCCGAA
1 GAGATACTCCAACCCCGTTATTTCCGAA
1773447 GAGATACTCCAACCCCGTTATTTCCGAA
1 GAGATACTCCAACCCCGTTATTTCCGAA
*
1773475 GGGATACTCCAACCCCG
1 GAGATACTCCAACCCCG
1773492 ACTTTATATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.22
Consensus pattern (28 bp):
GAGATACTCCAACCCCGTTATTTCCGAA
Found at i:1773625 original size:109 final size:108
Alignment explanation
Indices: 1773369--1773626 Score: 280
Period size: 109 Copynumber: 2.4 Consensus size: 108
1773359 TACCGCAATC
* * *
1773369 GGGGATACTCCAACTCTGATTTTATTT-T-TAACACCAA--TTTTTCACAATTGGAGATACTCCA
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTTTCACAATTGGAGATACTCCA
1773430 ACCCCGTTATTTCCGAAGAGATACTCCAACCCCGTTATTTCCGA
66 ACCCCGTTATTTCCG-AGAGATACTCCAACCCCGTTATTTCCGA
* * * * ** *
1773474 AGGGATACTCCAACCCCGACTTTATATCTAAAAATA-TTATTTTTTTCATAATCATGG-G-TACT
1 GGGGATACTCCAACCCTGATTTTATTTCT-AAAATACCAATTTTTTTCACAAT--TGGAGATACT
* * * *
1773536 TCAACCTCGTTATTTCATCG-GAGATACTCCAATCCCGTTATTTCTGA
63 CCAACCCCGTTATTTC--CGAGAGATACTCCAACCCCGTTATTTCCGA
1773583 GGGGATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTT
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTT
1773627 CACAATCGGG
Statistics
Matches: 123, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
105 22 0.18
106 1 0.01
107 1 0.01
108 9 0.07
109 84 0.68
110 1 0.01
111 5 0.04
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (108 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTTTCACAATTGGAGATACTCCA
ACCCCGTTATTTCCGAGAGATACTCCAACCCCGTTATTTCCGA
Found at i:1773642 original size:51 final size:52
Alignment explanation
Indices: 1773587--1773700 Score: 151
Period size: 51 Copynumber: 2.2 Consensus size: 52
1773577 TTCTGAGGGG
* * *
1773587 ATACTCCAACCCT-GATTTTATTTCTAAAATACCAATTTTTCACAATCGGGA
1 ATACTCCAACCCTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGA
* * * *
1773638 ATACT-CAAACTTCGATTTTATTTCCAAAACACCAATTTCTCATAATCGGGG
1 ATACTCCAACCCTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGA
1773689 ATACTCCAACCC
1 ATACTCCAACCC
1773701 ATTATTTTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
50 5 0.10
51 43 0.83
52 4 0.08
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.32
Consensus pattern (52 bp):
ATACTCCAACCCTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGA
Found at i:1773733 original size:78 final size:77
Alignment explanation
Indices: 1773650--1773852 Score: 237
Period size: 78 Copynumber: 2.6 Consensus size: 77
1773640 ACTCAAACTT
*
1773650 CGATTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCAACCC-ATTATTTTCGCGG
1 CGATTTTATTTCCAAAACA-CAATTT-TCATAATCGGGGATACTCCAACCCTATTATTTTCGAGG
1773714 GGATACTCCAACCC
64 GGATACTCCAACCC
* * * * * * *
1773728 CGATTTTATTTTCAAAATATCGATTTTTTATAATCAGGGATACTTCAACCCTGTTATTTTCGAGG
1 CGATTTTATTTCCAAAACA-C-AATTTTCATAATCGGGGATACTCCAACCCTATTATTTTCGAGG
1773793 GGATACTCCAACCC
64 GGATACTCCAACCC
* * *
1773807 CGATTTTTATTTCTAGAACACAGATTTTCCATAATCGAGGATACTC
1 CGA-TTTTATTTCCAAAACACA-ATTTT-CATAATCGGGGATACTC
1773853 TAGCCCTGTT
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
78 40 0.39
79 37 0.36
80 25 0.25
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (77 bp):
CGATTTTATTTCCAAAACACAATTTTCATAATCGGGGATACTCCAACCCTATTATTTTCGAGGGG
ATACTCCAACCC
Found at i:1773860 original size:80 final size:79
Alignment explanation
Indices: 1773650--1773862 Score: 222
Period size: 79 Copynumber: 2.7 Consensus size: 79
1773640 ACTCAAACTT
* * * * * * *
1773650 CGATTTTATTTCCAAAACA-CCAATTTCTCATAATCGGGGATACTCCAACCC-ATTATTTTCGCG
1 CGATTTTATTTTCAAAACATCGATTTTC-CATAATCGAGGATACTCTAACCCTGTTATTTTCGAG
1773713 GGGATACTCCAACCC
65 GGGATACTCCAACCC
* **
1773728 CGATTTTATTTTCAAAATATCGATTTTTTATAATC-AGGGATACT-TCAACCCTGTTATTTTCGA
1 CGATTTTATTTTCAAAACATCGATTTTCCATAATCGA-GGATACTCT-AACCCTGTTATTTTCGA
1773791 GGGGATACTCCAACCC
64 GGGGATACTCCAACCC
* *
1773807 CGATTTT-TATTTCTAGAACA-CAGATTTTCCATAATCGAGGATACTCTAGCCCTGTT
1 CGATTTTAT-TTTC-AAAACATC-GATTTTCCATAATCGAGGATACTCTAACCCTGTT
1773863 GTTATCTTCA
Statistics
Matches: 111, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
78 36 0.32
79 42 0.38
80 31 0.28
81 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
CGATTTTATTTTCAAAACATCGATTTTCCATAATCGAGGATACTCTAACCCTGTTATTTTCGAGG
GGATACTCCAACCC
Found at i:1775260 original size:13 final size:13
Alignment explanation
Indices: 1775219--1775271 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1775209 TCGTTAGAAG
1775219 CAATGTATCGATA
1 CAATGTATCGATA
1775232 CAA--T-TC-AT-
1 CAATGTATCGATA
1775240 C-ATGTATCGATA
1 CAATGTATCGATA
*
1775252 CATTGTATCGATA
1 CAATGTATCGATA
1775265 CAATGTA
1 CAATGTA
1775272 CCATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1775264 original size:33 final size:33
Alignment explanation
Indices: 1775222--1775286 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1775212 TTAGAAGCAA
*
1775222 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
1775255 TGTATCGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
1775287 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:1775360 original size:19 final size:19
Alignment explanation
Indices: 1775316--1775370 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1775306 TTGCCAGTTT
***
1775316 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TAAA
1775336 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
*
1775355 CATGTACCGATACAAT
1 CATGTATCGATACAAT
1775371 GTATCGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:1775740 original size:19 final size:18
Alignment explanation
Indices: 1775717--1775782 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 18
1775707 TTTAAAAGTT
1775717 TTTATATTTTAAAAATAA
1 TTTATATTTTAAAAATAA
*
1775735 TTT-TATTTAAAAAATTTAA
1 TTTATATTTTAAAAA--TAA
1775754 TTTTATAATTTT-AAAATAA
1 -TTTAT-ATTTTAAAAATAA
*
1775773 TATATATTTT
1 TTTATATTTT
1775783 TTTATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
17 15 0.38
18 7 0.17
19 6 0.15
20 3 0.08
21 5 0.12
22 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTATATTTTAAAAATAA
Found at i:1775840 original size:14 final size:15
Alignment explanation
Indices: 1775823--1775870 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
1775813 ATTTTAAGAA
1775823 TTAAATATTATT-TT
1 TTAAATATTATTATT
* *
1775837 TTAAAAAATATTATT
1 TTAAATATTATTATT
1775852 TTAAATATT-TTATT
1 TTAAATATTATTATT
1775866 TTAAA
1 TTAAA
1775871 ATAAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAAATATTATTATT
Found at i:1776150 original size:22 final size:20
Alignment explanation
Indices: 1776116--1776167 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
1776106 AATATTTTTA
*
1776116 ATTTTGTTAAAAATTACATATTT
1 ATTTT-TTAAAAA-TA-AAATTT
1776139 ATTTTTTAAAAATAAAATTT
1 ATTTTTTAAAAATAAAATTT
1776159 ATATTTTTA
1 AT-TTTTTA
1776168 TATTTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 7 0.26
21 8 0.30
22 7 0.26
23 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTTTAAAAATAAAATTT
Found at i:1776796 original size:21 final size:20
Alignment explanation
Indices: 1776775--1776851 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1776765 GATGTTATAA
1776775 AAAATTATTATAAATATA-T
1 AAAATTATTATAAATATATT
*
1776794 -AAATTATTA-AAATTTATAT
1 AAAATTATTATAAATATAT-T
* *
1776813 AAAATAAATTATTAATATATT
1 AAAAT-TATTATAAATATATT
* *
1776834 AAAATTAATAAAAATATA
1 AAAATTATTATAAATATA
1776852 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
17 6 0.13
18 9 0.20
19 1 0.02
20 13 0.29
21 10 0.22
22 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTATTATAAATATATT
Found at i:1776799 original size:18 final size:17
Alignment explanation
Indices: 1776776--1776811 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1776766 ATGTTATAAA
1776776 AAATTATTATAAATATAT
1 AAATTATTA-AAATATAT
*
1776794 AAATTATTAAAATTTAT
1 AAATTATTAAAATATAT
1776811 A
1 A
1776812 TAAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATTAAAATATAT
Found at i:1776810 original size:28 final size:24
Alignment explanation
Indices: 1776769--1776827 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
1776759 TAATATGATG
*
1776769 TTATAAAAAATTATTATAAATATATAAA
1 TTATTAAAAATTA-TAT-AA-A-ATAAA
*
1776797 TTATTAAAATTTATATAAAATAAA
1 TTATTAAAAATTATATAAAATAAA
1776821 TTATTAA
1 TTATTAA
1776828 TATATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 12 0.41
25 1 0.03
26 2 0.07
27 3 0.10
28 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTATTAAAAATTATATAAAATAAA
Found at i:1776834 original size:32 final size:32
Alignment explanation
Indices: 1776784--1776866 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
1776774 AAAAATTATT
* *
1776784 ATAAATATATAAAT-TATTAAAATTTATATAAA
1 ATAAATATATTAATATATTAAAATTAATA-AAA
1776816 ATAAAT-TATTAATATATTAAAATTAATAAAA
1 ATAAATATATTAATATATTAAAATTAATAAAA
*
1776847 ATATAATATTTTAA-ATATTA
1 ATA-AATATATTAATATATTA
1776867 TTATAATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 12 0.27
32 28 0.62
33 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
ATAAATATATTAATATATTAAAATTAATAAAA
Found at i:1776861 original size:57 final size:58
Alignment explanation
Indices: 1776775--1776888 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 58
1776765 GATGTTATAA
* *
1776775 AAAATTATTATAAATATATAAATTATTAAA-ATT-TATATAAAATAAATTATTAATATATT
1 AAAATTA-TATAAAAATATAAATTATTAAATATTAT-TATAAAATAAA-TAATAATATATT
*
1776834 AAAATTA-ATAAAAATATAATATT-TTAAATATTATTATAATATAAATAATAATATA
1 AAAATTATATAAAAATATAA-ATTATTAAATATTATTATAAAATAAATAATAATATA
1776889 AATATCATGC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
57 25 0.51
58 16 0.33
59 8 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (58 bp):
AAAATTATATAAAAATATAAATTATTAAATATTATTATAAAATAAATAATAATATATT
Found at i:1777186 original size:53 final size:56
Alignment explanation
Indices: 1777129--1777243 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 56
1777119 ATTATTTATA
* *
1777129 TTTAAATTATATGTAT-TAATTTTATTAA-TTT-A-GTT-TTTAATATAAATATAACT
1 TTTAAATTATAT-TATATAATTTTAATAATTTTAATATTATTTAATATAAATATAA-T
* *
1777182 TTTAAATTTTATTTTATAATTTTAATAATTTTAATTATTATTTAATATAAATATAAT
1 TTTAAATTATATTATATAATTTTAATAATTTTAA-TATTATTTAATATAAATATAAT
1777239 TTTAA
1 TTTAA
1777244 TCACATATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
52 2 0.04
53 22 0.42
54 3 0.06
55 1 0.02
57 8 0.15
58 16 0.31
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (56 bp):
TTTAAATTATATTATATAATTTTAATAATTTTAATATTATTTAATATAAATATAAT
Found at i:1777858 original size:25 final size:25
Alignment explanation
Indices: 1777830--1777893 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
1777820 TAATTTTATA
*
1777830 ATAATAAAATTTATATATTTGTTAG
1 ATAATAAAATTTATATATTTATTAG
1777855 ATAATAAAATTTATATATTTATTAG
1 ATAATAAAATTTATATATTTATTAG
1777880 ATAATAAAATTTAT
1 ATAATAAAATTTAT
1777894 TCCCCAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
ATAATAAAATTTATATATTTATTAG
Found at i:1778373 original size:17 final size:17
Alignment explanation
Indices: 1778333--1778374 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1778323 TTTATTAAAT
* *
1778333 TTAATAAAAATAATATA
1 TTAATAAAAAAAATACA
1778350 TTAAATAAAAAAAATACA
1 TT-AATAAAAAAAATACA
1778368 TTAATAA
1 TTAATAA
1778375 TTAAATAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAATAAAAAAAATACA
Found at i:1778379 original size:21 final size:21
Alignment explanation
Indices: 1778333--1778379 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1778323 TTTATTAAAT
* *
1778333 TTAATAAAAATAATATATTAA
1 TTAAAAAAAATAATATAATAA
*
1778354 ATAAAAAAAATACAT-TAATAA
1 TTAAAAAAAATA-ATATAATAA
1778375 TTAAA
1 TTAAA
1778380 TAGTTCGTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAAAAAAATAATATAATAA
Found at i:1780235 original size:11 final size:12
Alignment explanation
Indices: 1780217--1780260 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
1780207 AATAAACCCT
1780217 ATTTTAAAACTA
1 ATTTTAAAACTA
1780229 A-TTTAAAACTA
1 ATTTTAAAACTA
1780240 ATTTTAAAACTA
1 ATTTTAAAACTA
1780252 ATTTTAAAA
1 ATTTTAAAA
1780261 TAAACCCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTTTAAAACTA
Found at i:1780373 original size:18 final size:17
Alignment explanation
Indices: 1780340--1780375 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1780330 AAAATAATAT
1780340 ATTAAAATAAATTTAAA
1 ATTAAAATAAATTTAAA
*
1780357 ATTAAATATATATTTAAA
1 ATTAAA-ATAAATTTAAA
1780375 A
1 A
1780376 ATACTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAATAAATTTAAA
Found at i:1780951 original size:53 final size:53
Alignment explanation
Indices: 1780847--1780951 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
1780837 TGTCTTCCAA
* * *
1780847 CATTTATTTTAGAATTAAAGGAGTAAAATTGTTAAGACATTGTAATTAAATTG
1 CATTTATTTTAGAATTAAAGGAGTAAAATTATTAAGACACTGTAATCAAATTG
* * *
1780900 CATTTATTTTA-AGTTAAAAGG-GTAAAAATTATTAATACACTGTAGTCAAATT
1 CATTTATTTTAGAATT-AAAGGAGT-AAAATTATTAAGACACTGTAATCAAATT
1780952 TTCAAAGAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
52 5 0.11
53 39 0.89
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (53 bp):
CATTTATTTTAGAATTAAAGGAGTAAAATTATTAAGACACTGTAATCAAATTG
Found at i:1781078 original size:29 final size:29
Alignment explanation
Indices: 1781044--1781105 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1781034 TTTAATATTA
** *
1781044 AATTTTATAATTTTATTTTTATTTGATTG
1 AATTTTATAATTAAATTTTGATTTGATTG
* * *
1781073 AATTTTGTTATTAAATTTTGATTTTATTG
1 AATTTTATAATTAAATTTTGATTTGATTG
1781102 AATT
1 AATT
1781106 AGCAACTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (29 bp):
AATTTTATAATTAAATTTTGATTTGATTG
Found at i:1782155 original size:19 final size:19
Alignment explanation
Indices: 1782133--1782175 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1782123 ATCGACAAAT
*
1782133 TTAATAAACT-TCGAAGATA
1 TTAATAAACTCT-AAAGATA
1782152 TTAATAAACTCTAAAGATA
1 TTAATAAACTCTAAAGATA
1782171 TTAAT
1 TTAAT
1782176 CTTATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (19 bp):
TTAATAAACTCTAAAGATA
Found at i:1782890 original size:60 final size:60
Alignment explanation
Indices: 1782795--1782914 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
1782785 TTAGAGAGAC
*
1782795 AGATGATAAAATATTATTAGACAATAGGAACAAAGTGGCTGCGGGAGCCATGAAACTGAAT
1 AGATGATAAAATATTATTAGACAATAGGAACAAAGTGG-TGCAGGAGCCATGAAACTGAAT
* *
1782856 AGATGAT-AAATATTATTGGACAATAGGAAGAAAGTGGTGCAGGAGCCATGAAACTGAAT
1 AGATGATAAAATATTATTAGACAATAGGAACAAAGTGGTGCAGGAGCCATGAAACTGAAT
1782915 TTTAGTGAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 21 0.38
60 28 0.50
61 7 0.12
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (60 bp):
AGATGATAAAATATTATTAGACAATAGGAACAAAGTGGTGCAGGAGCCATGAAACTGAAT
Found at i:1786489 original size:3 final size:3
Alignment explanation
Indices: 1786481--1786525 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1786471 ATTATACAAG
*
1786481 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1786526 GACACAGTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Done.