Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 5 of 362
Found at i:1705665 original size:9 final size:9
Alignment explanation
Indices: 1705614--1705686 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
1705604 AAAGCTATAA
1705614 TAATAATAG
1 TAATAATAG
1705623 TAAT--TA-
1 TAATAATAG
*
1705629 TAATAAAAG
1 TAATAATAG
*
1705638 TAATAATAA
1 TAATAATAG
1705647 T-A-AATA-
1 TAATAATAG
1705653 TAATAATAG
1 TAATAATAG
*
1705662 TAATATTAG
1 TAATAATAG
*
1705671 TGATAA-AG
1 TAATAATAG
1705679 -AATAATAG
1 TAATAATAG
1705687 ATATAAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
6 5 0.10
7 11 0.22
8 10 0.20
9 24 0.48
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.33
Consensus pattern (9 bp):
TAATAATAG
Found at i:1705970 original size:3 final size:3
Alignment explanation
Indices: 1705947--1705998 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
1705937 ATATGCATAT
* * *
1705947 ATA ATA AAA ATA TATA CTA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1705993 ATA ATA
1 ATA ATA
1705999 TTAAAATACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1706052 original size:143 final size:141
Alignment explanation
Indices: 1705876--1706291 Score: 504
Period size: 143 Copynumber: 2.9 Consensus size: 141
1705866 AAGGAAAGTG
* * **
1705876 TATAATATAATAATATTATTAAAATAAGGTAATTAAAATACTACTATATAAATTCATATATATAT
1 TATAACATAATAATAATATTAAAATAAAATAATTAAAATACTACTATATAAA-T-ATATATATAT
* *
1705941 GCATATATAATAAAAATATATACTAATAATAATAATAATAATAATAATAGTAATAATATTAAAAT
64 -CATATATAATAAAAACATATACTAATAATAATAATAATAATAATAATAGAAATAATATTAAAAT
*
1706006 AC-AAAAAATTAAA
128 ACAAAAAAAGTAAA
* *
1706019 TATAACATGATAATAATATTAAAATAAAATAATTAAAAAACAATACTATATATAAATATATATAT
1 TATAACATAATAATAATATTAAAATAAAATAATTAAAATAC--TAC--TATATAAATATATATAT
* * * * *
1706084 ATACATATATAAT-AAAACCTACACTAAT-AT--TATTAATAATAATACTAGAAATAATATCAAA
62 AT-CATATATAATAAAAACATATACTAATAATAATAATAATAATAATAATAGAAATAATATTAAA
1706145 ATACAAAAAAAAGTAAA
126 ATAC-AAAAAAAGTAAA
*
1706162 TATAACATAATAATAATATTAAAATAAAATAATTAAAAATAATACTATATAAATATATATATA-C
1 TATAACATAATAATAATATTAAAATAAAATAATT-AAAATACTACTATATAAATATATATATATC
* * *
1706226 ATATATAATAAAAACAT-TCACTAATATTAATAATAATAATGATAATAGGAAATAATAATAACAA
65 ATATATAATAAAAACATAT-ACTAATAATAATAATAATAATAATAATA-GAAATAATATTAA-AA
1706290 TA
127 TA
1706292 TATACTAATA
Statistics
Matches: 233, Mismatches: 26, Indels: 27
0.81 0.09 0.09
Matches are distributed among these distances:
138 10 0.04
139 12 0.05
140 19 0.08
141 31 0.13
142 17 0.07
143 91 0.39
144 21 0.09
145 23 0.10
146 1 0.00
147 8 0.03
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.32
Consensus pattern (141 bp):
TATAACATAATAATAATATTAAAATAAAATAATTAAAATACTACTATATAAATATATATATATCA
TATATAATAAAAACATATACTAATAATAATAATAATAATAATAATAGAAATAATATTAAAATACA
AAAAAAGTAAA
Found at i:1706174 original size:3 final size:3
Alignment explanation
Indices: 1706168--1706374 Score: 59
Period size: 3 Copynumber: 66.0 Consensus size: 3
1706158 TAAATATAAC
* * *
1706168 ATA ATA ATA ATA TTA A-A ATA A-A ATA ATTA AAA ATA ATA CTA TATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA -AT-A
* * * * *
1706214 ATA TATA TATA CATA TATA ATA AAA ACA TTCA CTA ATA TTA ATA ATA
1 ATA -ATA -ATA -ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * * *
1706261 ATA ATG ATA ATA GGA-A ATA ATA ATA ACA ATA TATA CTA ATA ACA GTA
1 ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * *
1706308 ATA AT- ATGA AAA ATA AGAA ATA ACA ATA GT- ATA A-A ATA ATA ATA
1 ATA ATA AT-A ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1706352 TATA CATGA A-A AAA ATA ATA ATA
1 -ATA -AT-A ATA ATA ATA ATA ATA
1706375 TAAATAATTG
Statistics
Matches: 149, Mismatches: 36, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
2 12 0.08
3 100 0.67
4 34 0.23
5 3 0.02
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1706351 original size:22 final size:21
Alignment explanation
Indices: 1706275--1706351 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
1706265 TGATAATAGG
1706275 AAATAATAATAACAATATATA
1 AAATAATAATAACAATATATA
* * * *
1706296 CTAATAACAGTAATAATATGA-A
1 -AAATAATAATAACAATAT-ATA
*
1706318 AAATAAGAAATAACAATAGTATA
1 AAATAA-TAATAACAATA-TATA
1706341 AAATAATAATA
1 AAATAATAATA
1706352 TATACATGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
21 5 0.12
22 28 0.67
23 9 0.21
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
AAATAATAATAACAATATATA
Found at i:1706417 original size:24 final size:24
Alignment explanation
Indices: 1706361--1706408 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1706351 ATATACATGA
*
1706361 AAAAAATAATAATATAAATAATTG
1 AAAAAATAATAAAATAAATAATTG
1706385 AAAAAATAATAAAATTAAATAATT
1 AAAAAATAATAAAA-TAAATAATT
1706409 TAACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAATAATAAAATAAATAATTG
Found at i:1713303 original size:3 final size:3
Alignment explanation
Indices: 1713297--1713352 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
1713287 TTTAGCCACT
*
1713297 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1713341 TTA TTA CTTA TT
1 TTA TTA -TTA TT
1713353 TGTTTATGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.08
3 39 0.81
4 5 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1713848 original size:16 final size:16
Alignment explanation
Indices: 1713829--1713859 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1713819 TACACCCATA
*
1713829 TATATGTACATATTTT
1 TATATATACATATTTT
1713845 TATATATACATATTT
1 TATATATACATATTT
1713860 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:1722849 original size:49 final size:49
Alignment explanation
Indices: 1722795--1722893 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
1722785 TAATGCAAGC
1722795 AATGCAAATAGAGAAGATCATATACAACAATAATTTTAACAGGTTAGTG
1 AATGCAAATAGAGAAGATCATATACAACAATAATTTTAACAGGTTAGTG
*
1722844 AATGCAAATAGAGAAGATTATATACAACAATAATTTTAACAGGTTAGTG
1 AATGCAAATAGAGAAGATCATATACAACAATAATTTTAACAGGTTAGTG
1722893 A
1 A
1722894 CTTGAATGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (49 bp):
AATGCAAATAGAGAAGATCATATACAACAATAATTTTAACAGGTTAGTG
Found at i:1725819 original size:109 final size:109
Alignment explanation
Indices: 1725628--1725870 Score: 450
Period size: 109 Copynumber: 2.2 Consensus size: 109
1725618 CTAGTATATA
* *
1725628 TATGTGGACCAAATTTATATAATTTGTAAATGAGGAGGGTTAATTTTATTAAATTGTTAAGAACT
1 TATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAATTGTTAAGAACT
*
1725693 AGGATCAAAATGATAAAATGTGTAATTGTCGATGACTAAATGTG
66 AGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTG
1725737 TATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAATTGTTAAGAACT
1 TATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAATTGTTAAGAACT
*
1725802 AGGATCAAAATGATAAAATGTGTAACTGTTGATGACTAAATGTG
66 AGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTG
1725846 TATGTGGACCAAATTTATATAATTT
1 TATGTGGACCAAATTTATATAATTT
1725871 GTGACTAAAT
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 130 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (109 bp):
TATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAATTGTTAAGAACT
AGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTG
Found at i:1725885 original size:38 final size:38
Alignment explanation
Indices: 1725834--1725908 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
1725824 TAACTGTTGA
1725834 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTG
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTG
1725872 TGACTAAATGTGTATGTGGACCAAATTTATATAATTT
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTT
1725909 CTAAATAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (38 bp):
TGACTAAATGTGTATGTGGACCAAATTTATATAATTTG
Found at i:1725992 original size:147 final size:147
Alignment explanation
Indices: 1725725--1726019 Score: 572
Period size: 147 Copynumber: 2.0 Consensus size: 147
1725715 TAATTGTCGA
1725725 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAA
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAA
*
1725790 TTGTTAAGAACTAGGATCAAAATGATAAAATGTGTAACTGTTGATGACTAAATGTGTATGTGGAC
66 TTGTTAAGAACTAGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTGTATGTGGAC
*
1725855 CAAATTTATATAATTTG
131 CAAATTTAAATAATTTG
1725872 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAA
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAA
1725937 TTGTTAAGAACTAGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTGTATGTGGAC
66 TTGTTAAGAACTAGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTGTATGTGGAC
1726002 CAAATTTAAATAATTTG
131 CAAATTTAAATAATTTG
1726019 T
1 T
1726020 AAATGAGGAG
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.36
Consensus pattern (147 bp):
TGACTAAATGTGTATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAA
TTGTTAAGAACTAGGATCAAAATGATAAAATGTGTAACTGTCGATGACTAAATGTGTATGTGGAC
CAAATTTAAATAATTTG
Found at i:1726101 original size:112 final size:109
Alignment explanation
Indices: 1725872--1726214 Score: 544
Period size: 109 Copynumber: 3.1 Consensus size: 109
1725862 ATATAATTTG
* *
1725872 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTCTAAATAAGGAGGGTTAATTTTATTAAA
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTGTAAATGAGGAGGGTTAATTTTATTAAA
*
1725937 TTGTTAAGAACTAGGATCAAAATGATAAAATGTGTAACTGTCGA
66 TTGTTAAGAACTAGGACCAAAATGATAAAATGTGTAACTGTCGA
*
1725981 TGACTAAATGTGTATGTGGACCAAATTTAAATAATTTGTAAATGAGGAGGGTTAATTTTATTATT
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTGTAAATGAGGAGGGTTAA--TT-TTATT
1726046 AAATTGTTAAGAACTAGGACCAAAATGATAAAATGTGTAACTGTCGA
63 AAATTGTTAAGAACTAGGACCAAAATGATAAAATGTGTAACTGTCGA
* *
1726093 TGACTAAATGTGTATGTGGACCAAATTTATATAATTAGTAAATGTGGAGGGTTAATTTTATTAAA
1 TGACTAAATGTGTATGTGGACCAAATTTATATAATTTGTAAATGAGGAGGGTTAATTTTATTAAA
* * * * *
1726158 TTATTAAGAATTTA-GACTAAAATGATAAAATGTGTAAGTGTTGA
66 TTGTTAAGAA-CTAGGACCAAAATGATAAAATGTGTAACTGTCGA
1726202 TGACTAAATGTGT
1 TGACTAAATGTGT
1726215 TAATATATCA
Statistics
Matches: 218, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
109 109 0.50
110 4 0.02
111 2 0.01
112 103 0.47
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (109 bp):
TGACTAAATGTGTATGTGGACCAAATTTATATAATTTGTAAATGAGGAGGGTTAATTTTATTAAA
TTGTTAAGAACTAGGACCAAAATGATAAAATGTGTAACTGTCGA
Found at i:1731466 original size:6 final size:6
Alignment explanation
Indices: 1731455--1731480 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1731445 ACTCGTATCA
1731455 TTATAT TTATAT TTATAT TTATAT TT
1 TTATAT TTATAT TTATAT TTATAT TT
1731481 GGATGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:1731665 original size:59 final size:59
Alignment explanation
Indices: 1731592--1731711 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
1731582 GGATTACTAG
*
1731592 TCGAACTAATCATGTCATCAATTCCAATTAATGGAAGAATCGATTTGGTTTGATTTGAA
1 TCGAACCAATCATGTCATCAATTCCAATTAATGGAAGAATCGATTTGGTTTGATTTGAA
*
1731651 TCGAACCAATCATGTCATCAATTCCAATTAATGGAAGAATTGATTTGGTTTGATTTGAA
1 TCGAACCAATCATGTCATCAATTCCAATTAATGGAAGAATCGATTTGGTTTGATTTGAA
1731710 TC
1 TC
1731712 AAAGTTTATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (59 bp):
TCGAACCAATCATGTCATCAATTCCAATTAATGGAAGAATCGATTTGGTTTGATTTGAA
Found at i:1740794 original size:94 final size:91
Alignment explanation
Indices: 1740657--1740921 Score: 275
Period size: 94 Copynumber: 2.9 Consensus size: 91
1740647 ATTTTTGTGT
* * * *
1740657 GCCAATGTAAGACATGTCTAGGATATGCATCGACCACATTATGATAGCTAGTGTAAGACCATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCG-CCACAGTATGATAGCTAGTGTAAGA-CATGTC
* *
1740722 TGGGACATGGCATCGGCATTGAGACGAGG
64 TGGGACAT-GCATCGGCATCGAGACGAGA
* * *
1740751 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAGTGTAAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GCCACAGTATGATAGCTAGTGTAAGACATGTCT
* * ****
1740816 AGGACATGCATCGGCCTCGAGATTTTA
65 GGGACATGCATCGGCATCGAGACGAGA
* * * *
1740843 GCCAGTGTCAGACATGTTTGGGACATGCGTCGGCTACGAG-ATG-T-GCTAGTGTAAGACATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GCCAC-AGTATGATAGCTAGTGTAAGACATGTC
*
1740905 TGGGACATGCATTGGCA
64 TGGGACATGCATCGGCA
1740922 CGGTTACATG
Statistics
Matches: 143, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
90 31 0.22
92 47 0.33
93 15 0.10
94 49 0.34
95 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (91 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGCCACAGTATGATAGCTAGTGTAAGACATGTCTG
GGACATGCATCGGCATCGAGACGAGA
Found at i:1740846 original size:46 final size:46
Alignment explanation
Indices: 1740657--1740916 Score: 233
Period size: 46 Copynumber: 5.7 Consensus size: 46
1740647 ATTTTTGTGT
* * * * * *
1740657 GCCAATGTAAGACATGTCTAGGATATGCATCGACCAC-ATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGATA
* * * * **
1740703 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGATA
* * * *
1740751 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG-ATGATA
* **
1740797 GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATTTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATA
* * *
1740843 GCCAGTGTCAGACATGTTTGGGACATGCGTCGG-CTACGAGATG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATA
*
1740887 GCTAGTGTAAGACATGTCTGGGACATGCAT
1 GCCAGTGTAAGACATGTCTGGGACATGCAT
1740917 TGGCACGGTT
Statistics
Matches: 174, Mismatches: 34, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
44 26 0.15
45 5 0.03
46 92 0.53
47 28 0.16
48 22 0.13
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATA
Found at i:1742116 original size:255 final size:256
Alignment explanation
Indices: 1741653--1742135 Score: 880
Period size: 255 Copynumber: 1.9 Consensus size: 256
1741643 AGGGGGGAAG
* *
1741653 AAATGTAACAGTCCGATTTTGGGCCTAGTCGGAATAGTGATTTTGGAACCACTGTTTCGAGGCCA
1 AAATGTAACAGTCCGATTTTGGGCCTAGTCGGAACAGTGATTTTGGAACCACTATTTCGAGGCCA
*
1741718 GAGAAAATTATTTTAGTATTATTTTATGTGTTATAATATAATTTTATAAGTGCATGTAAATTTTG
66 GAGAAAATTATTTTAGTATTATTTTATGTGTTATAATATAATTTTATAAGTACATGTAAATTTTG
1741783 GTAAGTTAATTTTAGCGATTTCTAGTCCAATTTCAAAAAAGGACTAAATCGCGTAAAAGATAAAA
131 GTAAGTTAATTTTAGCGATTTCTAGTCCAATTTCAAAAAAGGACTAAATCGCGTAAAAGATAAAA
*
1741848 GTTGTGTGTTAATGCCTAAATGTGTTAATAGACTAGAGAAATAAAATTGGAGGCATTTAGA
196 GTTGTGTGTTAATGCCTAAATATGTTAATAGACTAGAGAAATAAAATTGGAGGCATTTAGA
*
1741909 AAATGTAACAG-CCGATTTTGGGCCTAGTCGGAACAGTGGTTTTGGAACCACTA-TTCTGAGGCC
1 AAATGTAACAGTCCGATTTTGGGCCTAGTCGGAACAGTGATTTTGGAACCACTATTTC-GAGGCC
1741972 AGAGAAAATTATTTTAGTATTATTTTATGTGTTATAATATAATTTTATAAGTACATGTAAATTTT
65 AGAGAAAATTATTTTAGTATTATTTTATGTGTTATAATATAATTTTATAAGTACATGTAAATTTT
* *
1742037 GGTAAGTTAATTTTAGCGATTTCTAGTCCAATTTCGAAAAAGGACTAAATCGCGTAAAAGGTAAA
130 GGTAAGTTAATTTTAGCGATTTCTAGTCCAATTTCAAAAAAGGACTAAATCGCGTAAAAGATAAA
1742102 AGTTGTGTGTTAATGCCTAAATATGTTAATAGAC
195 AGTTGTGTGTTAATGCCTAAATATGTTAATAGAC
1742136 ACGGCCACGT
Statistics
Matches: 219, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
254 3 0.01
255 205 0.94
256 11 0.05
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (256 bp):
AAATGTAACAGTCCGATTTTGGGCCTAGTCGGAACAGTGATTTTGGAACCACTATTTCGAGGCCA
GAGAAAATTATTTTAGTATTATTTTATGTGTTATAATATAATTTTATAAGTACATGTAAATTTTG
GTAAGTTAATTTTAGCGATTTCTAGTCCAATTTCAAAAAAGGACTAAATCGCGTAAAAGATAAAA
GTTGTGTGTTAATGCCTAAATATGTTAATAGACTAGAGAAATAAAATTGGAGGCATTTAGA
Found at i:1754887 original size:21 final size:20
Alignment explanation
Indices: 1754863--1754903 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1754853 AATTCTTCTC
*
1754863 TTTTGCTTCTCTTTCCATCTA
1 TTTTGCTTCAC-TTCCATCTA
*
1754884 TTTTTCTTCACTTCCATCTA
1 TTTTGCTTCACTTCCATCTA
1754904 CTAGTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTGCTTCACTTCCATCTA
Found at i:1754963 original size:29 final size:29
Alignment explanation
Indices: 1754921--1754979 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1754911 CTTGCTTCTA
1754921 AATTGATGAACATACTCTCTAAAATCTTT
1 AATTGATGAACATACTCTCTAAAATCTTT
*
1754950 AATTGATGAACATACTCTCTAAGATCTTT
1 AATTGATGAACATACTCTCTAAAATCTTT
1754979 A
1 A
1754980 CTTTCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.37
Consensus pattern (29 bp):
AATTGATGAACATACTCTCTAAAATCTTT
Found at i:1756393 original size:34 final size:34
Alignment explanation
Indices: 1756355--1756437 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
1756345 AGAAAGAATC
1756355 TTACCTTAAAAAACATTATTTTTCACGCCATGCT
1 TTACCTTAAAAAACATTATTTTTCACGCCATGCT
* * * *
1756389 TTACCTTTAAAAGCATTGTTTTTCACGCTATGCT
1 TTACCTTAAAAAACATTATTTTTCACGCCATGCT
*
1756423 TT-TC-TAAAAAACATT
1 TTACCTTAAAAAACATT
1756438 TTCTTCTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 9 0.21
33 1 0.02
34 32 0.76
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (34 bp):
TTACCTTAAAAAACATTATTTTTCACGCCATGCT
Found at i:1759467 original size:114 final size:114
Alignment explanation
Indices: 1759320--1759586 Score: 426
Period size: 114 Copynumber: 2.3 Consensus size: 114
1759310 GGTTGTAATG
* **
1759320 AATTCCAATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATATTATTGGTTTTAATGTTAT
1 AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATATTATTACTTTTAATGTTAT
* * **
1759385 TAGGTAATGTTTTTAGAACCGGATCAATAGTCGAACCAGTCATGTCATC
66 TAGGTAATGTCTTCAGAACCAAATCAATAGTCGAACCAGTCATGTCATC
* * *
1759434 AATTTCAATTAATGGAGGAATTGGTTTGGTTTGATTTGATAATATTTTATTACTTTTTATGTTAT
1 AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATATTATTACTTTTAATGTTAT
* *
1759499 TAGGTAATGTCTTCAGAACCAAATTAATAGTTGAACCAGTCATGTCATC
66 TAGGTAATGTCTTCAGAACCAAATCAATAGTCGAACCAGTCATGTCATC
1759548 AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGA
1 AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGA
1759587 ATCAAAGTTT
Statistics
Matches: 140, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 140 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (114 bp):
AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATATTATTACTTTTAATGTTAT
TAGGTAATGTCTTCAGAACCAAATCAATAGTCGAACCAGTCATGTCATC
Found at i:1761080 original size:26 final size:26
Alignment explanation
Indices: 1761051--1761103 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1761041 TTTACAGTTT
*
1761051 TACCCTTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
1761077 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
1761103 T
1 T
1761104 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:1771089 original size:13 final size:13
Alignment explanation
Indices: 1771064--1771100 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1771054 TTACCATCTC
1771064 ATGAACATAATTGT
1 ATGAAC-TAATTGT
1771078 ATGAACTAATTGT
1 ATGAACTAATTGT
1771091 ATGAACTAAT
1 ATGAACTAAT
1771101 CGGACTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (13 bp):
ATGAACTAATTGT
Found at i:1771768 original size:23 final size:23
Alignment explanation
Indices: 1771742--1771789 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1771732 TATATCCATT
1771742 ATTAAATAAATTAAAAAT-ATTTA
1 ATTAAATAAA-TAAAAATCATTTA
**
1771765 ATTATTTAAATAAAAATCATTTA
1 ATTAAATAAATAAAAATCATTTA
1771788 AT
1 AT
1771790 AATTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTAAATAAATAAAAATCATTTA
Found at i:1771781 original size:22 final size:24
Alignment explanation
Indices: 1771748--1771796 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1771738 CATTATTAAA
*
1771748 TAAATTAAAAAT-ATTTAATTATT
1 TAAATTAAAAATCATTTAATAATT
1771771 TAAA-TAAAAATCATTTAATAATT
1 TAAATTAAAAATCATTTAATAATT
1771794 TAA
1 TAA
1771797 TGACTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAATTAAAAATCATTTAATAATT
Found at i:1779847 original size:21 final size:21
Alignment explanation
Indices: 1779821--1779861 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1779811 AGACAAGCGA
* *
1779821 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1779842 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1779862 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1782772 original size:27 final size:27
Alignment explanation
Indices: 1782742--1782825 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
1782732 ATTGGTTCTT
1782742 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
* * * * *
1782769 TGAAACAAGCACCA--CAAGCT-TG-GC
1 TGAAAC-TGCACAAGTCCATCTATGACC
1782793 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
1782820 TGAAAC
1 TGAAAC
1782826 AAGCACCACA
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 5 0.12
24 7 0.17
25 6 0.14
26 6 0.14
27 13 0.31
28 5 0.12
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (27 bp):
TGAAACTGCACAAGTCCATCTATGACC
Found at i:1782797 original size:51 final size:51
Alignment explanation
Indices: 1782742--1782845 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
1782732 ATTGGTTCTT
1782742 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
*
1782793 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAGGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1782844 TG
1 TG
1782846 GAGCTAAGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (51 bp):
TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
Found at i:1786508 original size:26 final size:26
Alignment explanation
Indices: 1786472--1786525 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1786462 TCTACACAGT
*
1786472 TCACATATTGAGCTTGTATATCGAGC
1 TCACACATTGAGCTTGTATATCGAGC
* *
1786498 TCACACATTGAGCTTGTGTATCGGGC
1 TCACACATTGAGCTTGTATATCGAGC
1786524 TC
1 TC
1786526 GCATGATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (26 bp):
TCACACATTGAGCTTGTATATCGAGC
Found at i:1792628 original size:406 final size:401
Alignment explanation
Indices: 1791856--1792614 Score: 903
Period size: 405 Copynumber: 1.9 Consensus size: 401
1791846 AATTTCAATG
* * * ** *
1791856 TTTCCGATATGAGCAGGTTCGCGAGGGCTTAATTTAAGCGTTCTTGAATATGATCATATCAGTTT
1 TTTCCGATACGACCAGGTTCGCAAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTT
* * *
1791921 CATGCTTAGAAAACTAGAGGAATCATGACAAATTGTTGAGTGAACAGAGTTTGAACAAGCTAGAA
66 CATGCTTAGAAAACTAGAGGAATCATGAAAAATAGTTGAGTGAACAGAGTTTGAACAAGCAAGAA
* * * *
1791986 CTAGTGAACTGAGACTGATTTCCCATTTGGCCTTGTGTGGCCAATCTTTTGAAAATCATATAGAA
131 CTAATGAACCGAGACTGATATCCCATTTGGCCTTGTGTGACCAATCTTTTGAAAATCATATAGAA
* * *
1792051 TCATTGAATGAGGATCAATTTTGATGTTTCCTGTATGATCATATGCACGAGGGCTTAATTTAAGC
196 TCATTGAATGAGGATCAA-TTTGATGCTTCCTGTATGATCATATGCACGAAGGCTTAAATTAAGC
* *** * *
1792116 GATCTTGAATATGATCGTATCAGTTTCATGGTTACTAGAGAAATCATTATAATCAGTCGATTGAA
260 GATCATGAATATGATCGTATCA---T-ATGAACACTAGAGAAATCATTATAATCAGTCAACTGAA
** * *
1792181 TTTAGTTTGAATAAGCTAGAACTAGTGAACTGAGACTGATTTCCAATTCTACCTTGTGTCATGTG
321 TAGAGTTTGAACAACCTAGAACTAGTGAACTGAGACTGATTTCCAATTCTACCTTGTGTCATGTG
1792246 TGACCAGAGGATGAAT
386 TGACCAGAGGATGAAT
* * **
1792262 TTTCCGATACGACCATGTTTGCAAGGGCTTAA-TTAAGCACTCGTGAATATGATTGTATCAGTTT
1 TTTCCGATACGACCAGGTTCGCAAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTT
* * * *
1792326 CATGCTTAGGAAACTAGAGGAATCCT-AAAAACTAGTTGATTGAATAGAGTTTGAACAAAGCAAG
66 CATGCTTAGAAAACTAGAGGAATCATGAAAAA-TAGTTGAGTGAACAGAGTTTGAAC-AAGCAAG
* ** *
1792390 AACTAATGACCCGAGACTGATATCTGATTCT-GCCTTGTGTGACCAATCTTTTGAAAA-CTGTAT
129 AACTAATGAACCGAGACTGATATCCCATT-TGGCCTTGTGTGACCAATCTTTTGAAAATC-ATAT
* * *
1792453 AGAATCATTGAATGAGGAT-GA-TTGATGCTT-CTGATATGATCATGTTCTCACGAAGGCTTAAA
192 AGAATCATTGAATGAGGATCAATTTGATGCTTCCTG-TATGATCAT-AT-GCACGAAGGCTTAAA
* * *
1792515 TTAAGCGCTCATGAATATGATCGTAT-A-A-GAACACTAGAGGAATCATTGACT-ATTAGT-AAC
254 TTAAGCGATCATGAATATGATCGTATCATATGAACACTAGAGAAATCATT-A-TAATCAGTCAAC
1792575 TGAATAGAGTTTGAACAACCTAGAACTAGTGGAACTGAGA
317 TGAATAGAGTTTGAACAACCTAGAACTAGT-GAACTGAGA
1792615 GCAATTTCTG
Statistics
Matches: 299, Mismatches: 44, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
398 42 0.14
399 16 0.05
400 1 0.00
402 3 0.01
403 17 0.06
404 6 0.02
405 110 0.37
406 103 0.34
407 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (401 bp):
TTTCCGATACGACCAGGTTCGCAAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTT
CATGCTTAGAAAACTAGAGGAATCATGAAAAATAGTTGAGTGAACAGAGTTTGAACAAGCAAGAA
CTAATGAACCGAGACTGATATCCCATTTGGCCTTGTGTGACCAATCTTTTGAAAATCATATAGAA
TCATTGAATGAGGATCAATTTGATGCTTCCTGTATGATCATATGCACGAAGGCTTAAATTAAGCG
ATCATGAATATGATCGTATCATATGAACACTAGAGAAATCATTATAATCAGTCAACTGAATAGAG
TTTGAACAACCTAGAACTAGTGAACTGAGACTGATTTCCAATTCTACCTTGTGTCATGTGTGACC
AGAGGATGAAT
Found at i:1797293 original size:26 final size:26
Alignment explanation
Indices: 1797257--1797309 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1797247 AAACTTGGTG
1797257 AAGAATTTTTAACAAGCTAATACCTA
1 AAGAATTTTTAACAAGCTAATACCTA
1797283 AAGAATTTTTAACAAGCTAATACCTA
1 AAGAATTTTTAACAAGCTAATACCTA
1797309 A
1 A
1797310 TGTAAGGCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (26 bp):
AAGAATTTTTAACAAGCTAATACCTA
Found at i:1797731 original size:11 final size:11
Alignment explanation
Indices: 1797716--1797748 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1797706 TTTCATTTTG
1797716 TTTTTTAATTTC
1 TTTTTT-ATTTC
1797728 TTTTTTATTTC
1 TTTTTTATTTC
1797739 TTTTTTATTT
1 TTTTTTATTT
1797749 TTGTTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTATTTC
Found at i:1806825 original size:29 final size:29
Alignment explanation
Indices: 1806783--1806838 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1806773 TTTTAAAATT
1806783 TAAAAAGTAAAAAGACTAAATTCCTAAAAA
1 TAAAAAGTAAAAAGACTAAATT-CTAAAAA
*
1806813 TAAAAA-TATAAAGACTAAATTCTAAA
1 TAAAAAGTAAAAAGACTAAATTCTAAA
1806839 TTTGTGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 14 0.56
30 6 0.24
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.23
Consensus pattern (29 bp):
TAAAAAGTAAAAAGACTAAATTCTAAAAA
Found at i:1808784 original size:18 final size:17
Alignment explanation
Indices: 1808761--1808800 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
1808751 GTATAATAAT
1808761 AAATAATA-TGATATATGA
1 AAATAATACT-ATATAT-A
1808779 AAATAATACTATATATA
1 AAATAATACTATATATA
1808796 AAATA
1 AAATA
1808801 TGTATACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 14 0.67
19 1 0.05
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATAATACTATATATA
Found at i:1808877 original size:20 final size:20
Alignment explanation
Indices: 1808811--1808877 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
1808801 TGTATACAAG
* *
1808811 AATAATAAAATATATGTACT
1 AATAATAAAATAAATGTAAT
* * *
1808831 AATATTAAAATAAATATAGT
1 AATAATAAAATAAATGTAAT
**
1808851 AGGAATAAAATAAATGTAAT
1 AATAATAAAATAAATGTAAT
1808871 AATAATA
1 AATAATA
1808878 TATACACAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.31
Consensus pattern (20 bp):
AATAATAAAATAAATGTAAT
Found at i:1809025 original size:13 final size:13
Alignment explanation
Indices: 1809007--1809048 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
1808997 ATAATATTAA
1809007 AATATATATACAT
1 AATATATATACAT
*
1809020 AATATATATATAT
1 AATATATATACAT
1809033 AACATATATATACAT
1 -A-ATATATATACAT
1809048 A
1 A
1809049 TACATTAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.48
14 2 0.08
15 11 0.44
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATATACAT
Found at i:1809028 original size:15 final size:15
Alignment explanation
Indices: 1809008--1809053 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1808998 TAATATTAAA
1809008 ATATATATACAT-A-
1 ATATATATACATAAC
*
1809021 ATATATATATATAAC
1 ATATATATACATAAC
1809036 ATATATATACATATAC
1 ATATATATACATA-AC
1809052 AT
1 AT
1809054 TAGCAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 12 0.43
16 4 0.14
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATATATACATAAC
Found at i:1809030 original size:17 final size:16
Alignment explanation
Indices: 1809008--1809053 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
1808998 TAATATTAAA
1809008 ATATATATACATAATAT
1 ATATATATACAT-ATAT
1809025 ATATATATAACATATAT
1 ATATATAT-ACATATAT
*
1809042 ATACATATACAT
1 ATATATATACAT
1809054 TAGCAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATATACATATAT
Found at i:1809191 original size:17 final size:19
Alignment explanation
Indices: 1809147--1809192 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
1809137 GAAATACTTA
1809147 ATATATAATATTTGAAATAT
1 ATATATAATA-TTGAAATAT
**
1809167 ATGCATAATA-T-AAATAT
1 ATATATAATATTGAAATAT
1809184 ATATATAAT
1 ATATATAAT
1809193 GTAGTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
20 8 0.36
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (19 bp):
ATATATAATATTGAAATAT
Found at i:1809359 original size:12 final size:12
Alignment explanation
Indices: 1809321--1809367 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1809311 TATTTAAAGT
*
1809321 ATACATAATGT-
1 ATACATAATATA
*
1809332 ATAAAT-ATATA
1 ATACATAATATA
1809343 TATACATAATATA
1 -ATACATAATATA
1809356 ATACATAATATA
1 ATACATAATATA
1809368 GACACATTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 3 0.10
11 5 0.17
12 17 0.57
13 5 0.17
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (12 bp):
ATACATAATATA
Found at i:1811345 original size:16 final size:17
Alignment explanation
Indices: 1811311--1811345 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1811301 TTGATTTTTG
*
1811311 AAAAGCATAAATTGAAA
1 AAAAACATAAATTGAAA
1811328 AAAAACATAAATTGAAA
1 AAAAACATAAATTGAAA
1811345 A
1 A
1811346 TACCTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (17 bp):
AAAAACATAAATTGAAA
Found at i:1811716 original size:183 final size:181
Alignment explanation
Indices: 1811185--1811769 Score: 885
Period size: 183 Copynumber: 3.2 Consensus size: 181
1811175 ACGTGAGCCA
* * * * * *
1811185 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-G-A-AAACAGAATTTGCAAAACAGATG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAATAGAAATTGAAAAACAAATT
* * *
1811247 TTGAAAATACCTTGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT
66 TTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTT
* * *
1811310 GAAAAGCATAAATTGAAAAAAAACATAAATTGAAAATACCTCAGCATG-CGAGCCG
131 GAAAAGCATAAATTG--AAAAAACAGAAATTGAAAATACCTCAGCGTGTC---CTG
*
1811365 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAGAATTAGAAATTGAAAAACGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGGAAGAAATAGAAATTGAAAAAC-AA
1811430 ATTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
63 ATTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTT
1811495 TTTTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
127 TTTTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
*
1811550 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAGAAATAGAAATTGAAAAACAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGG-AAGAAATAGAAATTGAAAAAC-AAA
*
1811615 TTTTGAAAATACATCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
64 TTTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT
1811680 TTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
129 TTGAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
*
1811733 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1811770 TTTTTTGAAA
Statistics
Matches: 375, Mismatches: 19, Indels: 19
0.91 0.05 0.05
Matches are distributed among these distances:
180 31 0.08
182 5 0.01
183 101 0.27
184 83 0.22
185 47 0.13
186 58 0.15
187 29 0.08
188 1 0.00
189 20 0.05
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (181 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAGAAATAGAAATTGAAAAACAAATT
TTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTT
GAAAAGCATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
Found at i:1812697 original size:44 final size:40
Alignment explanation
Indices: 1812635--1812738 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 40
1812625 CTTCATTAGA
*
1812635 ACGCCC-TTTCGGGTTTTCATCC-TAATCTTTTGTGTTAATCAAG
1 ACGCCCTTTTCGGGTTTTCATCCTTAATCATTT-T-TT--T-AAG
1812678 ACGCCCTTTTCGGGTTTTCA-CCTTAATCATTTTTTTAAG
1 ACGCCCTTTTCGGGTTTTCATCCTTAATCATTTTTTTAAG
*
1812717 ATGCCCTTTTCGGGTTTTCATC
1 ACGCCCTTTTCGGGTTTTCATC
1812739 TTGATTTGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
39 22 0.39
40 2 0.04
42 2 0.04
43 9 0.16
44 21 0.38
ACGTcount: A:0.16, C:0.24, G:0.15, T:0.44
Consensus pattern (40 bp):
ACGCCCTTTTCGGGTTTTCATCCTTAATCATTTTTTTAAG
Found at i:1814829 original size:32 final size:32
Alignment explanation
Indices: 1814793--1814856 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1814783 TGTATACATT
1814793 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1814825 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1814857 CGGTAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:1827377 original size:15 final size:14
Alignment explanation
Indices: 1827331--1827378 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1827321 AATATTGAAA
*
1827331 ATATATATACATA-
1 ATATATATATATAC
*
1827344 ATATATATATAAAAC
1 ATATATATAT-ATAC
1827359 ATATATGATATATAC
1 ATATAT-ATATATAC
1827374 ATATA
1 ATATA
1827379 CATTAGCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 14 0.48
16 4 0.14
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:1827660 original size:18 final size:19
Alignment explanation
Indices: 1827637--1827688 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1827627 AGTATATAAG
* *
1827637 ATATAATAT-TTAAAGTAT
1 ATATAATATATAAAAATAT
1827655 ATATAATATATAAAAATAT
1 ATATAATATATAAAAATAT
1827674 ATATACATAATATAA
1 ATATA-AT-ATATAA
1827689 TACATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.31
19 12 0.41
20 2 0.07
21 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
ATATAATATATAAAAATAT
Found at i:1827677 original size:12 final size:13
Alignment explanation
Indices: 1827652--1827706 Score: 64
Period size: 12 Copynumber: 4.5 Consensus size: 13
1827642 ATATTTAAAG
*
1827652 TATATATAATATA
1 TATACATAATATA
1827665 TA-A-A-AATATA
1 TATACATAATATA
1827675 TATACATAATATA
1 TATACATAATATA
1827688 -ATACATAATATA
1 TATACATAATATA
*
1827700 TACACAT
1 TATACAT
1827707 TAGAAATACT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 8 0.22
11 2 0.05
12 14 0.38
13 13 0.35
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (13 bp):
TATACATAATATA
Found at i:1827678 original size:23 final size:25
Alignment explanation
Indices: 1827652--1827706 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
1827642 ATATTTAAAG
*
1827652 TATATATAATAT-ATA-AAAATATA
1 TATACATAATATAATACAAAATATA
*
1827675 TATACATAATATAATACATAATATA
1 TATACATAATATAATACAAAATATA
*
1827700 TACACAT
1 TATACAT
1827707 TAGAAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 11 0.41
24 3 0.11
25 13 0.48
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (25 bp):
TATACATAATATAATACAAAATATA
Found at i:1827719 original size:23 final size:25
Alignment explanation
Indices: 1827669--1827720 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
1827659 AATATATAAA
* *
1827669 AATATATATACATAATATAATACAT
1 AATATATACACATAAGATAATACAT
*
1827694 AATATATACACATTAGA-AATAC-T
1 AATATATACACATAAGATAATACAT
1827717 AATA
1 AATA
1827721 ATTATTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 5 0.21
25 14 0.58
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (25 bp):
AATATATACACATAAGATAATACAT
Found at i:1827791 original size:3 final size:3
Alignment explanation
Indices: 1827785--1827833 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1827775 AACAACACAC
1827785 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1827833 A
1 A
1827834 TTAAAGTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1829645 original size:19 final size:19
Alignment explanation
Indices: 1829609--1829648 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1829599 CAGTAACAAT
**
1829609 AAAATAATGAAATGACAGC
1 AAAATAATGAAAAAACAGC
1829628 AAAATAATGAAAAAACAGC
1 AAAATAATGAAAAAACAGC
1829647 AA
1 AA
1829649 TATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAATAATGAAAAAACAGC
Found at i:1833823 original size:28 final size:28
Alignment explanation
Indices: 1833792--1833846 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1833782 CTGTCGATTC
*
1833792 AATAATAATTAAAT-AAATAATTATAAAA
1 AATAATAA-AAAATAAAATAATTATAAAA
*
1833820 AATAATAAAAAATAAAATATTTATAAA
1 AATAATAAAAAATAAAATAATTATAAA
1833847 TTTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAATAAAAAATAAAATAATTATAAAA
Found at i:1839254 original size:16 final size:16
Alignment explanation
Indices: 1839233--1839267 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1839223 TATATGTGGA
1839233 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
1839249 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
1839265 AAA
1 AAA
1839268 AAAACTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:1839438 original size:31 final size:31
Alignment explanation
Indices: 1839386--1839448 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1839376 CCTTAAATTT
* * *
1839386 ATTCATTGCATCTGTTAGAAAAATCAGATTG
1 ATTCATTACATCCGTTAGAAAAAGCAGATTG
*
1839417 ATTCATTACATCCGTTGGAAAAAGCAGATTG
1 ATTCATTACATCCGTTAGAAAAAGCAGATTG
1839448 A
1 A
1839449 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (31 bp):
ATTCATTACATCCGTTAGAAAAAGCAGATTG
Found at i:1842961 original size:21 final size:20
Alignment explanation
Indices: 1842937--1842975 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1842927 TATTGAAACT
*
1842937 AAAACTAATACTAATAATAGC
1 AAAACTAATA-AAATAATAGC
1842958 AAAACTAATAAAATAATA
1 AAAACTAATAAAATAATA
1842976 TAGTACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAACTAATAAAATAATAGC
Found at i:1843045 original size:24 final size:26
Alignment explanation
Indices: 1843018--1843065 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1843008 TATGAATACG
1843018 TACAT-ATAATATA-ATAT-TAAAATA
1 TACATAAT-ATATACATATATAAAATA
1843042 TACATAATATATACATATATAAAA
1 TACATAATATATACATATATAAAA
1843066 CATGTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
TACATAATATATACATATATAAAATA
Found at i:1843294 original size:22 final size:22
Alignment explanation
Indices: 1843268--1843327 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1843258 TACTCAATAT
1843268 ATAATATTTAAAATATATATA-C
1 ATAATA-TTAAAATATATATAGC
**
1843290 ATAATACAAAAATATATATAGC
1 ATAATATTAAAATATATATAGC
* *
1843312 GTAGTATTAAAATATA
1 ATAATATTAAAATATA
1843328 AACACAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
ATAATATTAAAATATATATAGC
Found at i:1843405 original size:14 final size:14
Alignment explanation
Indices: 1843386--1843432 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1843376 AATACTTCAC
*
1843386 AAATATATATATTA
1 AAATATATATAATA
*
1843400 AAATATACATAATA
1 AAATATATATAATA
*
1843414 ATATATATA-AATA
1 AAATATATATAATA
*
1843427 TAATAT
1 AAATAT
1843433 TAAAAGTACG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATATAATA
Found at i:1843457 original size:35 final size:36
Alignment explanation
Indices: 1843386--1843463 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
1843376 AATACTTCAC
* *
1843386 AAATATATATATTAAAATATACATAATAATATATAT
1 AAATATATATATTAAAATATACATAACAATAAATAT
* *
1843422 AAATATA-ATATTAAAA-GTACGTAACATATAAATAT
1 AAATATATATATTAAAATATACATAACA-ATAAATAT
*
1843457 ATATATA
1 AAATATA
1843464 CACATGGTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 7 0.19
35 22 0.61
36 7 0.19
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (36 bp):
AAATATATATATTAAAATATACATAACAATAAATAT
Found at i:1845567 original size:54 final size:54
Alignment explanation
Indices: 1845485--1845953 Score: 778
Period size: 54 Copynumber: 8.7 Consensus size: 54
1845475 ATGTGACCTG
** * * *
1845485 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTAAAAATAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
1845539 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
* * *
1845593 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATCAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
*
1845647 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
* *
1845701 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTAAAAAACAGAAATCAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
*
1845755 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAGCAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
* *
1845809 AGGCTCAACTCACCTCTCGCAATATGAGGTGATCTTTGAAAAACAGAAATCAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
** *
1845863 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAGTATAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
1845917 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTG
1845954 GAAACATGAA
Statistics
Matches: 391, Mismatches: 24, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
53 4 0.01
54 387 0.99
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAACAGAAATTAAA
Found at i:1846057 original size:75 final size:75
Alignment explanation
Indices: 1845969--1846208 Score: 227
Period size: 75 Copynumber: 3.0 Consensus size: 75
1845959 ATGAATTGAA
1845969 AAACAGAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAACAGAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1846034 GATTTTTTTG
66 GATTTTTTTG
* * * ** *
1846044 AAACATAAATTGAAAA-ACGGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCT
1 AAACAGAAATTGAAAATAC-----CTCAGCAT--GT--G-A-G-CC-GAGGCTCAACTCACCTCT
1846108 CGCAATATGAGTTGATTTTTTTG
53 CGCAATATGAGTTGATTTTTTTG
* * *
1846131 AAAAGCAGAATTTGAAAATACCTCAGC--GTG-TCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 -AAA-CAGAAATTGAAAATACCTCAGCATGTGAGC-CGAGGCTCAACTCACCTCTCGCAATATGA
1846193 GTTGATTTTTTTG
63 GTTGATTTTTTTG
1846206 AAA
1 AAA
1846209 AATAAATTAA
Statistics
Matches: 133, Mismatches: 15, Indels: 35
0.73 0.08 0.19
Matches are distributed among these distances:
74 5 0.04
75 57 0.43
79 5 0.04
81 2 0.02
83 1 0.01
84 1 0.01
85 3 0.02
86 2 0.02
87 41 0.31
88 3 0.02
89 11 0.08
90 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (75 bp):
AAACAGAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTG
Found at i:1846094 original size:87 final size:87
Alignment explanation
Indices: 1845917--1846133 Score: 359
Period size: 87 Copynumber: 2.5 Consensus size: 87
1845907 ATAAATTAAA
* *
1845917 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTGGAAACATGAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTGAAAAACAGAAATT
1845980 GAAAATACCTCAGCATGTGAGCCG
66 GAAAATACCTCAGCATGT--GCCG
*
1846004 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTGAAAAACGGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTGAAAAACAGAAATT
1846069 GAAAATACCTCAGCATGT-CCTG
66 GAAAATACCTCAGCATGTGCC-G
1846091 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
1846134 AGCAGAATTT
Statistics
Matches: 124, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
86 2 0.02
87 76 0.61
89 46 0.37
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (87 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTGAAAAACAGAAATT
GAAAATACCTCAGCATGTGCCG
Found at i:1846187 original size:162 final size:160
Alignment explanation
Indices: 1845964--1846542 Score: 735
Period size: 162 Copynumber: 3.5 Consensus size: 160
1845954 GAAACATGAA
* *
1845964 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--GTG-TCTGAGGCTCAACTCACCTCTCGCAATAT
* *
1846029 GAGTTGATTTTTTTGAAACATAAATTGAAAAACGGAAATTGAAAATACCTCAGCATGTCCTGAGG
63 GAGTTGATTTTTTTGAAAAATAAATTGAAAAACGGAAATTGAAAATACCTCAGCGTG-CCTGAGG
*
1846094 CTCAACTCACCTCTCGCAATATGAGTTGATTTTT
127 CTCAACTCACCTCTTGCAATATGAGTTGATTTTT
* *
1846128 TTGAAAAGCAGAATTTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTC-TGAGGCTCAACTCACCTCTCGCAATATGA
* * *
1846193 GTTGATTTTTTTGAAAAATAAATTAAAAAACGAAAATTGAAAATACTTCAGCGTGCCTCGAGGCT
65 GTTGATTTTTTTGAAAAATAAATTGAAAAACGGAAATTGAAAATACCTCAGCGTGCCT-GAGGCT
1846258 CAACTCACCTCTTGCAATATGAGTTGATTTTT
129 CAACTCACCTCTTGCAATATGAGTTGATTTTT
* * *
1846290 TTGAAAAACAAAAATTGAAAATACCCCTGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGA
* * * *
1846355 GTTGATTTTTTTTGAAAAATATAAATTGAAAAGCAGAAATCGAAAATACCTCAGCGTGACCCGAG
65 GTTGA-TTTTTTTG-AAAA-ATAAATTGAAAAACGGAAATTGAAAATACCTCAGCGTG-CCTGAG
*
1846420 GTTCAACTCACCTCTTGCAATATGAGTTGATTTTTTAAAAGCAT
126 GCTCAACTCACCTCTTGCAATATGAGTTGA--TTTT-------T
* * * *
1846464 AAATTGAAAAAACATAAATTGAAAATACCTTAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
1 ---TTG-AAAAACAGAAATTGAAAATACCTCAGCGTG-TCTGAGGCTCAACTCACCTCTCGCAAT
1846529 ATGAGTTGATTTTT
61 ATGAGTTGATTTTT
1846543 GAAAACATGA
Statistics
Matches: 365, Mismatches: 29, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
161 4 0.01
162 181 0.50
163 9 0.02
164 32 0.09
165 64 0.18
166 2 0.01
167 4 0.01
174 1 0.00
177 8 0.02
178 60 0.16
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (160 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTTGAAAAATAAATTGAAAAACGGAAATTGAAAATACCTCAGCGTGCCTGAGGCTCA
ACTCACCTCTTGCAATATGAGTTGATTTTT
Found at i:1846209 original size:75 final size:75
Alignment explanation
Indices: 1846053--1846386 Score: 298
Period size: 75 Copynumber: 4.3 Consensus size: 75
1846043 GAAACATAAA
* *
1846053 TTGAAAAACGGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1846118 GTTGATTTTT
66 GTTGATTTTT
* * *
1846128 TTGAAAAGCAGAATTTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1846193 GTTGATTTTT
66 GTTGATTTTT
* * ** *** * * *
1846203 TTG-AAAA-ATAAATT-AAAA-AACGAAAATTGAAAATACTTCAGCGTGCCTCGAGGCTCAACTC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTG----T-C--CTGAG-G-CTC-A-ACT-----C
*
1846264 ACCTCTTGCAATATGAGTTGATTTTT
50 ACCTCTCGCAATATGAGTTGATTTTT
* * *
1846290 TTGAAAAACAAAAATTGAAAATACCCCTGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1846355 GTTGATTTTTT
66 GTTGA-TTTTT
* *
1846366 TTGAAAAATATAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
1846387 GCAGAAATCG
Statistics
Matches: 205, Mismatches: 33, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
71 5 0.02
72 4 0.02
73 5 0.02
74 3 0.01
75 95 0.46
76 25 0.12
78 2 0.01
79 1 0.00
80 5 0.02
81 2 0.01
82 5 0.02
83 1 0.00
84 3 0.01
86 1 0.00
87 30 0.15
88 4 0.02
89 6 0.03
90 4 0.02
91 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTT
Found at i:1846443 original size:90 final size:89
Alignment explanation
Indices: 1846290--1846542 Score: 348
Period size: 88 Copynumber: 2.8 Consensus size: 89
1846280 GTTGATTTTT
* * * *
1846290 TTGAAAAACAAAAATTGAAAATACCCCTGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
*
1846355 GTTGATTTTTTTTGAAAAATATAAA
66 GTTGATTTTTTTT-AAAAACATAAA
* * * * *
1846380 TTGAAAAGCAGAAATCGAAAATACCTCAGCGTGACCCGAGGTTCAACTCACCTCTTGCAATATGA
1 TTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
*
1846445 GTTGA--TTTTTTAAAAGCATAAA
66 GTTGATTTTTTTTAAAAACATAAA
* * *
1846467 TTGAAAAAACATAAATTGAAAATACCTTAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTG-AAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
1846532 AGTTGATTTTT
65 AGTTGATTTTT
1846543 GAAAACATGA
Statistics
Matches: 142, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
87 12 0.08
88 66 0.46
90 64 0.45
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (89 bp):
TTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTTAAAAACATAAA
Found at i:1846488 original size:14 final size:15
Alignment explanation
Indices: 1846456--1846488 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1846446 TTGATTTTTT
*
1846456 AAAAGCATAAATTGA
1 AAAAACATAAATTGA
1846471 AAAAACATAAATTGA
1 AAAAACATAAATTGA
1846486 AAA
1 AAA
1846489 TACCTTAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.09, T:0.18
Consensus pattern (15 bp):
AAAAACATAAATTGA
Found at i:1863170 original size:31 final size:32
Alignment explanation
Indices: 1863111--1863172 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
1863101 AATAGCCTAA
*
1863111 TGACTTAAATAAAAAAATTTTAAATAGTTCAG
1 TGACTTAAATAAAAAAATTTCAAATAGTTCAG
* *
1863143 TGACTTAAAT-GAAAACTTTCAAATAGTTCA
1 TGACTTAAATAAAAAAATTTCAAATAGTTCA
1863173 ATAATCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34
Consensus pattern (32 bp):
TGACTTAAATAAAAAAATTTCAAATAGTTCAG
Found at i:1867693 original size:30 final size:29
Alignment explanation
Indices: 1867659--1867718 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
1867649 TGACCTACTA
1867659 ATCAACTTGTAACTTTTAAAAAATTCAATG
1 ATCAACTTGTAACTTTT-AAAAATTCAATG
* * *
1867689 ATCAATTTGTAACTTTTTAAAATTGAATG
1 ATCAACTTGTAACTTTTAAAAATTCAATG
1867718 A
1 A
1867719 CAAAATTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (29 bp):
ATCAACTTGTAACTTTTAAAAATTCAATG
Found at i:1867727 original size:29 final size:29
Alignment explanation
Indices: 1867659--1867738 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
1867649 TGACCTACTA
* *
1867659 ATCAACTTGTAACTTTTAAAAAATTCAATG
1 ATCAAATTGTAACTTTT-TAAAATTCAATG
* *
1867689 ATCAATTTGTAACTTTTTAAAATTGAATG
1 ATCAAATTGTAACTTTTTAAAATTCAATG
*
1867718 A-CAAAATTGTAAATTTATTAA
1 ATC-AAATTGTAACTTT-TTAA
1867739 TACTTGAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 1 0.02
29 22 0.51
30 20 0.47
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (29 bp):
ATCAAATTGTAACTTTTTAAAATTCAATG
Found at i:1870608 original size:3 final size:3
Alignment explanation
Indices: 1870600--1870624 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1870590 GAATTAATGT
1870600 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
1870625 AATGATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1870837 original size:6 final size:6
Alignment explanation
Indices: 1870826--1870851 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1870816 AAGCCATTTT
1870826 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
1870852 CATAGTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:1870949 original size:11 final size:11
Alignment explanation
Indices: 1870933--1870967 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1870923 ATAAGAATTG
*
1870933 TTTTTTTTTTA
1 TTTTTTATTTA
1870944 TTTTTTATTTA
1 TTTTTTATTTA
1870955 TTTTTTATTTA
1 TTTTTTATTTA
1870966 TT
1 TT
1870968 AAAACAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:1891764 original size:43 final size:42
Alignment explanation
Indices: 1891704--1891786 Score: 148
Period size: 43 Copynumber: 2.0 Consensus size: 42
1891694 TCCTAATTCA
1891704 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
*
1891746 GAAAATAGTTTCCCTTATTTTAATAAACTACTAAAACATAA
1 GAAAATAG-TTCCCTTATTCTAATAAACTACTAAAACATAA
1891787 ATAAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 8 0.21
43 31 0.79
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGG
Found at i:1895375 original size:18 final size:18
Alignment explanation
Indices: 1895352--1895394 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1895342 AATATGAATA
1895352 AAATTTATC-ACCTAAAT
1 AAATTTATCTACCTAAAT
1895369 AAGATTTATCTACCTAAAT
1 AA-ATTTATCTACCTAAAT
1895388 AAATTTA
1 AAATTTA
1895395 AAATATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 10 0.42
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (18 bp):
AAATTTATCTACCTAAAT
Found at i:1901195 original size:26 final size:26
Alignment explanation
Indices: 1901165--1901248 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 26
1901155 AACCTTCTGT
1901165 AGCCAAATAAGCTCACAAACACCTTG
1 AGCCAAATAAGCTCACAAACACCTTG
* *** *
1901191 AGCC--ATAACCTTGTATACACCTTCTG
1 AGCCAAATAAGCTCACAAACACC-T-TG
1901217 TAGCCAAATAAGCTCACAAACACCTTG
1 -AGCCAAATAAGCTCACAAACACCTTG
1901244 AGCCA
1 AGCCA
1901249 TAACCTTGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 12 0.28
25 1 0.02
26 11 0.26
27 6 0.14
28 1 0.02
29 12 0.28
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (26 bp):
AGCCAAATAAGCTCACAAACACCTTG
Found at i:1901219 original size:53 final size:53
Alignment explanation
Indices: 1901156--1901259 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
1901146 AACTCCTCCA
1901156 ACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTATAC
1 ACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTATAC
1901209 ACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
1 ACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTAT
1901260 TTTGCCTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.25
Consensus pattern (53 bp):
ACCTTCTGTAGCCAAATAAGCTCACAAACACCTTGAGCCATAACCTTGTATAC
Found at i:1901239 original size:29 final size:29
Alignment explanation
Indices: 1901156--1901242 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 29
1901146 AACTCCTCCA
1901156 ACCTTCTGTAGCCAAATAAGCTCACAAAC
1 ACCTTCTGTAGCCAAATAAGCTCACAAAC
* *** *
1901185 ACC-T-TG-AGCC--ATAACCTTGTATAC
1 ACCTTCTGTAGCCAAATAAGCTCACAAAC
1901209 ACCTTCTGTAGCCAAATAAGCTCACAAAC
1 ACCTTCTGTAGCCAAATAAGCTCACAAAC
1901238 ACCTT
1 ACCTT
1901243 GAGCCATAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
24 12 0.28
25 1 0.02
26 6 0.14
27 6 0.14
28 1 0.02
29 17 0.40
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.24
Consensus pattern (29 bp):
ACCTTCTGTAGCCAAATAAGCTCACAAAC
Found at i:1901757 original size:19 final size:18
Alignment explanation
Indices: 1901735--1901774 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1901725 TGAATAAAAC
1901735 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
1901754 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
1901772 TTA
1 TTA
1901775 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:1905460 original size:43 final size:44
Alignment explanation
Indices: 1905399--1905491 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
1905389 TCCTAATTAG
*
1905399 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
*
1905442 GAAAATAGTTCCGTTATTCTAATAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
1905486 -AAAATA
1 GAAAATA
1905492 TTTCTAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
Found at i:1905535 original size:19 final size:18
Alignment explanation
Indices: 1905513--1905552 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1905503 TGAATAAAAC
1905513 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
* *
1905532 TTATTTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
1905550 TTA
1 TTA
1905553 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:1906590 original size:66 final size:67
Alignment explanation
Indices: 1906484--1906616 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 67
1906474 GTGCTCGTGG
**
1906484 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCATCCACTCTTGG-ATAATAT
1 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
1906548 AT
66 AT
1906550 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
1 GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
1906615 AT
66 AT
1906617 TCATTTTTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 55 0.86
67 9 0.14
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (67 bp):
GTCTAACTTTTCAGCTTTCCGATCATGAACATAACAAATATATCCAAACACTCTTGGAATAATAT
AT
Found at i:1911719 original size:48 final size:48
Alignment explanation
Indices: 1911626--1912069 Score: 334
Period size: 48 Copynumber: 9.2 Consensus size: 48
1911616 AATTGGAGCA
* * ** * **
1911626 CCAATAGGTGCACCATCTCCCAGTGCATCAGCTGCAGTACCAGGCACT-
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCA-TG
* ** * **
1911674 CCAATAGGAGCACCAACTCCAAGTGCACCAGCTGCAACACAAGGCACA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* * * * * * * * **
1911722 CCAGTAGAAGCAGCACCTCCTGGGGAAGCAGCTGCAAAACAAGGCACA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* * * *
1911770 CCAATAGGAGCACCATCT-CTGGGTGCAACAGCTGCAACATCGGGCATG
1 CCAATAGGAGCACCACCTCCT-GGTGCACCAGCTGCAACACCAGGCATG
*** * * **
1911818 CCAATAGGAGCACCACCTCCTGACACAGCAGCTGCAACACCGGGCACA
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* *** *
1911866 CCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* ** *
1911914 ACAATAGGAGCACCACCTCCTGGCACACCAGCTGCAACAGCAGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* * * * * * *
1911962 GCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
* ** * * * *
1912010 GCAATAGGAGCACCACCTCCCAGTACATCAGTTGCAACACCAGACATG
1 CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
*
1912058 CCAATTGGAGCA
1 CCAATAGGAGCA
1912070 ACTCCTACCA
Statistics
Matches: 325, Mismatches: 68, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
47 2 0.01
48 321 0.99
49 2 0.01
ACGTcount: A:0.31, C:0.34, G:0.22, T:0.13
Consensus pattern (48 bp):
CCAATAGGAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCATG
Found at i:1912090 original size:144 final size:143
Alignment explanation
Indices: 1911792--1912127 Score: 307
Period size: 144 Copynumber: 2.3 Consensus size: 143
1911782 CCATCTCTGG
* *
1911792 GTGCAACAGCTGCAACATCGGGCATGCCAATAGGAGCACCACCTCCTGACACAGCAGCTGCAACA
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGACACAGCAGCTGCAACA
* * * *
1911857 CCGGGCACACCAGTAGGAGCACCACCTCCTGACACACCAACTGCAACACCAGGCATGACAATAGG
66 CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATAGG
* *
1911922 AGCACCACCTCCT
131 AGCAACACCTCCA
* * * * ** * *
1911935 G-GCACACCAGCTGCAACAGCAGGCATGGCAATAGGCGTACCATCTCCTGGTACATCAGCTGGAA
1 GTGCA-A-CAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGACACAGCAGCTGCAA
*** * * ** *
1911999 CACCAGGCATGGCAATAGGAGCACCACCTCCCAG-TACATCAGTTGCAACACCAGACATGCCAAT
64 CACCAGGCACACCAATAGGAGCACCACCT-CCAGACACACCAACTGCAACACCAGACATGACAAT
* *
1912063 TGGAGCAACTCCTACCA
128 AGGAGCAACACCT-CCA
* * * * ** * * *
1912080 GTGCAGCAGCTCCAGCAGCACGCACACCTATAGAAGCACCACCACCTG
1 GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTG
1912128 GCGCTCAAGC
Statistics
Matches: 149, Mismatches: 39, Indels: 9
0.76 0.20 0.05
Matches are distributed among these distances:
142 3 0.02
143 2 0.01
144 135 0.91
145 6 0.04
146 3 0.02
ACGTcount: A:0.30, C:0.35, G:0.21, T:0.13
Consensus pattern (143 bp):
GTGCAACAGCTGCAACAGCAGGCATGCCAATAGGAGCACCACCTCCTGACACAGCAGCTGCAACA
CCAGGCACACCAATAGGAGCACCACCTCCAGACACACCAACTGCAACACCAGACATGACAATAGG
AGCAACACCTCCA
Found at i:1912277 original size:39 final size:39
Alignment explanation
Indices: 1912205--1912299 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
1912195 AGGCATGGCG
*
1912205 ACAGGAGCACCACCTCCAGCAGCAAAGAAAGGCACAACA
1 ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
* * **
1912244 ACAGGAGCATCACCTCCAGCAG-AAACATCAGGCATGACA
1 ACAGGAGCACCACCTCCAGCAGCAAACA-AAGGCACAACA
* *
1912283 ACAAGAGCACCAACTCC
1 ACAGGAGCACCACCTCC
1912300 TGATGCACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.41, C:0.34, G:0.19, T:0.06
Consensus pattern (39 bp):
ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
Found at i:1912379 original size:48 final size:48
Alignment explanation
Indices: 1912288--1912441 Score: 137
Period size: 48 Copynumber: 3.2 Consensus size: 48
1912278 TGACAACAAG
* *
1912288 AGCACCAACTCCTGATGCACCAGATGCAACACCTGGCAAGCCAATAGA
1 AGCACCACCTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAGA
* * * * * * *
1912336 AGCACCACCTCCTGGTGCACCAGCTTCAAGACCAGGTACGCCAATAGG
1 AGCACCACCTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAGA
** * * * * * * * *
1912384 TTCACCACCTCCTGCTGCGCTAGCTGCAACAACAGGCATGCCAGTAGG
1 AGCACCACCTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAGA
1912432 AGCACCACCT
1 AGCACCACCT
1912442 ACCAGTGCAC
Statistics
Matches: 84, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 84 1.00
ACGTcount: A:0.29, C:0.36, G:0.21, T:0.15
Consensus pattern (48 bp):
AGCACCACCTCCTGATGCACCAGATGCAACACCAGGCAAGCCAATAGA
Found at i:1912661 original size:48 final size:48
Alignment explanation
Indices: 1912609--1912701 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
1912599 TCAACTCCTG
* *
1912609 GTGCACCAG-CAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTT
1 GTGCACCAGCCA-CAACACCAAGCACACCAATAGGAACACCACCTCTTT
* *
1912657 GTGCACCAGCCACAACACCAAGCACGCCAATAGGAGCACCACCTC
1 GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTC
1912702 CCAATGCACC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.95
49 2 0.05
ACGTcount: A:0.33, C:0.39, G:0.17, T:0.11
Consensus pattern (48 bp):
GTGCACCAGCCACAACACCAAGCACACCAATAGGAACACCACCTCTTT
Found at i:1912710 original size:48 final size:48
Alignment explanation
Indices: 1912610--1912750 Score: 122
Period size: 48 Copynumber: 2.9 Consensus size: 48
1912600 CAACTCCTGG
** * * ****
1912610 TGCACCAG-CAGCAACACCAAGCACATCAATAGGAACGCCACCTCTTTG
1 TGCACCAGCCA-CAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
1912658 TGCACCAGCCACAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
1 TGCACCAGCCACAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
** ** * * * *
1912706 TGCACCAGCTGCAACAGTAGGAAAGCCAATTGGAGCACCACCTCC
1 TGCACCAGCCACAACACCAAGCACGCCAATAGGAGCACCACCTCC
1912751 TGGTGCACAT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 74 0.97
49 2 0.03
ACGTcount: A:0.33, C:0.38, G:0.18, T:0.11
Consensus pattern (48 bp):
TGCACCAGCCACAACACCAAGCACGCCAATAGGAGCACCACCTCCCAA
Found at i:1920902 original size:26 final size:26
Alignment explanation
Indices: 1920866--1920923 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1920856 ATATGTTTGC
1920866 TTATTATATAAATATATTATATATTA
1 TTATTATATAAATATATTATATATTA
*
1920892 TTATTATATAAGTATATTATATATTA
1 TTATTATATAAATATATTATATATTA
1920918 TTATTA
1 TTATTA
1920924 AAAGTAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTATTATATAAATATATTATATATTA
Found at i:1920922 original size:13 final size:13
Alignment explanation
Indices: 1920866--1920923 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
1920856 ATATGTTTGC
*
1920866 TTATTATATA-AA
1 TTATTATATATTA
1920878 TATATTATATATTA
1 T-TATTATATATTA
*
1920892 TTATTATATAAGTA
1 TTATTATAT-ATTA
1920906 -TATTATATATTA
1 TTATTATATATTA
1920918 TTATTA
1 TTATTA
1920924 AAAGTAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 4 0.10
13 30 0.77
14 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TTATTATATATTA
Found at i:1920933 original size:29 final size:27
Alignment explanation
Indices: 1920866--1920934 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
1920856 ATATGTTTGC
*
1920866 TTATTATATAAA-TATATTATATATTA
1 TTATTAAATAAAGTATATTATATATTA
*
1920892 TTATTATAT-AAGTATATTATATATTA
1 TTATTAAATAAAGTATATTATATATTA
1920918 TTATTAAAAGTAAAGTA
1 TTATT-AAA-TAAAGTA
1920935 CATAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 2 0.05
26 28 0.74
27 2 0.05
28 1 0.03
29 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTATTAAATAAAGTATATTATATATTA
Found at i:1921486 original size:14 final size:14
Alignment explanation
Indices: 1921467--1921494 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1921457 CATTTTGCAC
1921467 TAAGACTGTTATGA
1 TAAGACTGTTATGA
1921481 TAAGACTGTTATGA
1 TAAGACTGTTATGA
1921495 ACAGCAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TAAGACTGTTATGA
Found at i:1925823 original size:32 final size:32
Alignment explanation
Indices: 1925771--1925842 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
1925761 TGGCAAACTC
*
1925771 AAATGACCCTAAACCAAAACAACCCGAACATG
1 AAATGACCCTAAACCAAAACAACACGAACATG
* *
1925803 AAATGACCC-AAACCCGAAACAACATGAACATG
1 AAATGACCCTAAA-CCAAAACAACACGAACATG
*
1925835 AATTGACC
1 AAATGACC
1925843 TGAATTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.49, C:0.29, G:0.11, T:0.11
Consensus pattern (32 bp):
AAATGACCCTAAACCAAAACAACACGAACATG
Found at i:1931024 original size:19 final size:19
Alignment explanation
Indices: 1931000--1931038 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1930990 AACAAAGAAG
1931000 ATAAAATTTTCTTTCAAAA
1 ATAAAATTTTCTTTCAAAA
1931019 ATAAAATTTTCTTTCAAAA
1 ATAAAATTTTCTTTCAAAA
1931038 A
1 A
1931039 CTCCCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAATTTTCTTTCAAAA
Found at i:1932580 original size:15 final size:15
Alignment explanation
Indices: 1932560--1932589 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1932550 TGCTTTGCGT
1932560 ACATTGAACCTTGAG
1 ACATTGAACCTTGAG
1932575 ACATTGAACCTTGAG
1 ACATTGAACCTTGAG
1932590 GGCTGCCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
ACATTGAACCTTGAG
Found at i:1933591 original size:16 final size:16
Alignment explanation
Indices: 1933560--1933593 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1933550 AGTTAGACCT
1933560 AAATTTTAAAATTTAA
1 AAATTTTAAAATTTAA
1933576 AAATTCTTAAAA-TTAA
1 AAATT-TTAAAATTTAA
1933592 AA
1 AA
1933594 TTACATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTTAAAATTTAA
Found at i:1934047 original size:6 final size:6
Alignment explanation
Indices: 1934013--1934059 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
1934003 ATTCGATTTA
*
1934013 ATTTTT ATATTTT -TTATTAT ATTTTT ATTTGT ATTTTT ATTTTT ATT
1 ATTTTT AT-TTTT ATT-TT-T ATTTTT ATTTTT ATTTTT ATTTTT ATT
1934060 GTAATATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 1 0.03
6 25 0.71
7 7 0.20
8 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:1934052 original size:20 final size:19
Alignment explanation
Indices: 1934009--1934058 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1933999 TTCGATTCGA
1934009 TTTA-ATTTTTATATTTTT
1 TTTATATTTTTATATTTTT
*
1934027 TATTATATTTTTAT-TTGTAT
1 T-TTATATTTTTATATT-TTT
1934047 TTT-TATTTTTAT
1 TTTATATTTTTAT
1934059 TGTAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 7 0.25
20 11 0.39
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTATATTTTTATATTTTT
Found at i:1937824 original size:39 final size:39
Alignment explanation
Indices: 1937775--1937854 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
1937765 AGCACTGGCA
* *
1937775 GTCATTGAATTTATACCGA-AGGCCTATCCATCATAACAT
1 GTCATAGAATTTATA-CGATAGGCCCATCCATCATAACAT
*
1937814 GTCATAGAATTTATACGATAGGCCCATGCATCATAACAT
1 GTCATAGAATTTATACGATAGGCCCATCCATCATAACAT
1937853 GT
1 GT
1937855 TTGCAATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 3 0.08
39 34 0.92
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (39 bp):
GTCATAGAATTTATACGATAGGCCCATCCATCATAACAT
Found at i:1939627 original size:20 final size:21
Alignment explanation
Indices: 1939604--1939649 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1939594 TAAAATTTGA
1939604 ATAATTATAAAAAAA-TAACT
1 ATAATTATAAAAAAACTAACT
* *
1939624 ATAAATCTAAAAAAACTAACT
1 ATAATTATAAAAAAACTAACT
1939645 -TAATT
1 ATAATT
1939650 TGAATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATTATAAAAAAACTAACT
Found at i:1944840 original size:14 final size:14
Alignment explanation
Indices: 1944816--1944854 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1944806 GAGTTTGATG
*
1944816 TTCATGATTTAAGA
1 TTCAAGATTTAAGA
*
1944830 TTCGAGATTTAAGA
1 TTCAAGATTTAAGA
1944844 TTCAAGATTTA
1 TTCAAGATTTA
1944855 GGATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (14 bp):
TTCAAGATTTAAGA
Found at i:1953231 original size:8 final size:8
Alignment explanation
Indices: 1953216--1953265 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
1953206 TCAACCAAAT
1953216 TTAA-AAA
1 TTAATAAA
1953223 TTAATAAA
1 TTAATAAA
1953231 TTAATAAA
1 TTAATAAA
1953239 --AA-AAA
1 TTAATAAA
*
1953244 TTGAAAAAA
1 TT-AATAAA
1953253 TTAATAAA
1 TTAATAAA
1953261 TTAAT
1 TTAAT
1953266 CAGTAGCTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 4 0.11
8 23 0.62
9 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (8 bp):
TTAATAAA
Found at i:1953243 original size:22 final size:22
Alignment explanation
Indices: 1953218--1953260 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1953208 AACCAAATTT
*
1953218 AAAAATT-AATAAATTAATAAA
1 AAAAATTGAAAAAATTAATAAA
1953239 AAAAATTGAAAAAATTAATAAA
1 AAAAATTGAAAAAATTAATAAA
1953261 TTAATCAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATTGAAAAAATTAATAAA
Found at i:1966405 original size:70 final size:70
Alignment explanation
Indices: 1966322--1966462 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
1966312 ATATCTTGAA
1966322 AAAGAATAGAGCTCAAATTTCTAATTTTCTTTCGGTCTAAGCCAACCAAGGTCTATGAATAGAGG
1 AAAGAATAGAGCTCAAATTTCTAATTTTCTTTCGGTCTAAGCCAACCAAGGTCTATGAATAGAGG
1966387 AACTG
66 AACTG
1966392 AAAGAATAGAGCTCAAATTTCTAATTTTCTTTCGGTCTAAGCCAACCAAGGTCTATGAATAGAGG
1 AAAGAATAGAGCTCAAATTTCTAATTTTCTTTCGGTCTAAGCCAACCAAGGTCTATGAATAGAGG
1966457 AACTG
66 AACTG
1966462 A
1 A
1966463 CAGGTACTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (70 bp):
AAAGAATAGAGCTCAAATTTCTAATTTTCTTTCGGTCTAAGCCAACCAAGGTCTATGAATAGAGG
AACTG
Found at i:1967078 original size:4 final size:4
Alignment explanation
Indices: 1967071--1967132 Score: 63
Period size: 4 Copynumber: 14.2 Consensus size: 4
1967061 AGAGAGAAGA
1967071 GGAG GGA- GGAGG GGAG GGAGG GGAG GGAGG GGAG GGAGG GGAG GGAGG
1 GGAG GGAG GGA-G GGAG GGA-G GGAG GGA-G GGAG GGA-G GGAG GGA-G
1967119 GGAG GGAAG GGAG G
1 GGAG GG-AG GGAG G
1967133 TAGAAAGCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.06
4 25 0.49
5 23 0.45
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:1967090 original size:9 final size:9
Alignment explanation
Indices: 1967074--1967132 Score: 102
Period size: 9 Copynumber: 6.7 Consensus size: 9
1967064 GAGAAGAGGA
1967074 GGGA-GGAG
1 GGGAGGGAG
1967082 GGGAGGGAG
1 GGGAGGGAG
1967091 GGGAGGGAG
1 GGGAGGGAG
1967100 GGGAGGGAG
1 GGGAGGGAG
1967109 GGGAGGGAG
1 GGGAGGGAG
*
1967118 GGGAGGGAA
1 GGGAGGGAG
1967127 GGGAGG
1 GGGAGG
1967133 TAGAAAGCTA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 4 0.08
9 45 0.92
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (9 bp):
GGGAGGGAG
Found at i:1967130 original size:5 final size:5
Alignment explanation
Indices: 1967078--1967129 Score: 67
Period size: 5 Copynumber: 11.2 Consensus size: 5
1967068 AGAGGAGGGA
1967078 GGAGG GGA-G GGAGG GGA-G GGAGG GGA-G GGAGG GGA-G GGAGG GGAGG
1 GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG
*
1967124 GAAGG G
1 GGAGG G
1967130 AGGTAGAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
4 16 0.38
5 26 0.62
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:1970736 original size:31 final size:31
Alignment explanation
Indices: 1970698--1970758 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1970688 GCAAGTTTGA
* *
1970698 AGGAATATAATGAATTGTATAATAAATAAAG
1 AGGAATATAATCAATTATATAATAAATAAAG
*
1970729 AGGAATATAATCAATTATATGATAAATAAA
1 AGGAATATAATCAATTATATAATAAATAAA
1970759 ATATCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.30
Consensus pattern (31 bp):
AGGAATATAATCAATTATATAATAAATAAAG
Found at i:1971522 original size:24 final size:22
Alignment explanation
Indices: 1971490--1971535 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1971480 TTATTACAAA
1971490 ATTTGTAAAAAATTGTAAAAAAAT
1 ATTTGT-AAAAATT-TAAAAAAAT
* *
1971514 ATTTTTAAAAGTTTAAAAAAAT
1 ATTTGTAAAAATTTAAAAAAAT
1971536 TATAAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTTGTAAAAATTTAAAAAAAT
Found at i:1971559 original size:15 final size:15
Alignment explanation
Indices: 1971531--1971566 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1971521 AAAGTTTAAA
1971531 AAAATTATAAAATTCT
1 AAAA-TATAAAATTCT
*
1971547 AAAATATATAATTCT
1 AAAATATAAAATTCT
1971562 AAAAT
1 AAAAT
1971567 TCTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATATAAAATTCT
Found at i:1971671 original size:21 final size:22
Alignment explanation
Indices: 1971624--1971672 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1971614 AGTTAAATAC
*
1971624 CTTTTTTATAACATTTTTTTAT
1 CTTTTTTATAACATTTTTTGAT
*
1971646 ATTTTTTAT-ACATTATTTTGA-
1 CTTTTTTATAACATT-TTTTGAT
1971667 CTTTTT
1 CTTTTT
1971673 ACAATTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.67
Consensus pattern (22 bp):
CTTTTTTATAACATTTTTTGAT
Found at i:1971672 original size:22 final size:22
Alignment explanation
Indices: 1971625--1971666 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1971615 GTTAAATACC
*
1971625 TTTTTTATAACATTTTTTTATA
1 TTTTTTATAACATTTTTTGATA
1971647 TTTTTTAT-ACATTATTTTGA
1 TTTTTTATAACATT-TTTTGA
1971667 CTTTTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTATAACATTTTTTGATA
Found at i:1973222 original size:19 final size:18
Alignment explanation
Indices: 1973195--1973238 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1973185 CTCTCACAAA
*
1973195 AAAAATTAAAATAATTTTT
1 AAAAATTAAAAT-ATTTAT
*
1973214 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
1973232 AAAAATT
1 AAAAATT
1973239 TCAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:1973239 original size:19 final size:19
Alignment explanation
Indices: 1973194--1973250 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1973184 TCTCTCACAA
*
1973194 AAAAAATTAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
1973213 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
1973232 AAAAATTTCAAAT-TTTAT
1 AAAAATTTAAAATATTTAT
1973250 A
1 A
1973251 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:1973550 original size:31 final size:31
Alignment explanation
Indices: 1973515--1973589 Score: 99
Period size: 26 Copynumber: 2.6 Consensus size: 31
1973505 AACTCAAATA
1973515 ATTTCACTTGATTCGATTCGACTCGAATTAC
1 ATTTCACTTGATTCGATTCGACTCGAATTAC
1973546 ATTTCAC-----TCGATTCGACTCGAATTAC
1 ATTTCACTTGATTCGATTCGACTCGAATTAC
1973572 ATTTCA-TTCGATTCGATT
1 ATTTCACTT-GATTCGATT
1973590 TAAAAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
26 25 0.66
31 13 0.34
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (31 bp):
ATTTCACTTGATTCGATTCGACTCGAATTAC
Found at i:1973556 original size:26 final size:26
Alignment explanation
Indices: 1973527--1973587 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1973517 TTCACTTGAT
1973527 TCGATTCGACTCGAATTACATTTCAC
1 TCGATTCGACTCGAATTACATTTCAC
*
1973553 TCGATTCGACTCGAATTACATTTCAT
1 TCGATTCGACTCGAATTACATTTCAC
1973579 TCGATTCGA
1 TCGATTCGA
1973588 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (26 bp):
TCGATTCGACTCGAATTACATTTCAC
Found at i:1974360 original size:53 final size:53
Alignment explanation
Indices: 1974302--1974402 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
1974292 ATAAATGTTA
*
1974302 AATCAACATTCATTCCAGAATAATAAACCCTAAATCTTAAACTATACCGAGCC
1 AATCAACATTCATTCCAGAATAATAAACCCTAAATCCTAAACTATACCGAGCC
* *
1974355 AATCAACATTCATTCGAGAATAATAAACCCTAAATCCTAAATTATACC
1 AATCAACATTCATTCCAGAATAATAAACCCTAAATCCTAAACTATACC
1974403 AAACTAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.26
Consensus pattern (53 bp):
AATCAACATTCATTCCAGAATAATAAACCCTAAATCCTAAACTATACCGAGCC
Found at i:1983199 original size:13 final size:13
Alignment explanation
Indices: 1983181--1983207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1983171 TGACATGCCC
1983181 CATGTACTTTATT
1 CATGTACTTTATT
1983194 CATGTACTTTATT
1 CATGTACTTTATT
1983207 C
1 C
1983208 TGACATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (13 bp):
CATGTACTTTATT
Found at i:2001948 original size:39 final size:39
Alignment explanation
Indices: 2001904--2001982 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
2001894 AAATACATAG
2001904 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
1 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
2001943 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
1 CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
2001982 C
1 C
2001983 TTTGCCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (39 bp):
CACCGATAAAGCTAGATATACAATTTGAAGGTATTGTTA
Found at i:2005664 original size:21 final size:22
Alignment explanation
Indices: 2005631--2005673 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2005621 ATTAAAATTG
2005631 TTAATACAATTAATCAAT-TTGT
1 TTAATACAATTAA-CAATGTTGT
*
2005653 TTAAT-CACTTAACAATGTTGT
1 TTAATACAATTAACAATGTTGT
2005674 AATTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATACAATTAACAATGTTGT
Done.