Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 88 of 322
Found at i:28435783 original size:47 final size:47
Alignment explanation
Indices: 28435705--28436112 Score: 618
Period size: 47 Copynumber: 8.6 Consensus size: 47
28435695 CCCTTCGGGA
* * * * * *
28435705 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28435752 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28435799 CTCATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28435846 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28435893 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28435942 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28435991 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28436038 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28436087 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
28436113 CACAATTATC
Statistics
Matches: 333, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
47 192 0.58
49 141 0.42
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28435939 original size:96 final size:97
Alignment explanation
Indices: 28435705--28436112 Score: 611
Period size: 96 Copynumber: 4.3 Consensus size: 97
28435695 CCCTTCGGGA
* * * * * * *
28435705 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC-ATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATA
28435767 CACTTTCACATTCATCACATCGGCCATTAGGC
66 CACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
28435799 CTCATCAC--ATATATACACTTTCACATTCATCACATCGACTATTAGGCCTTATTAC-ATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATA
28435861 CACTTTCACATTCATCACATCGGCCATTAGGC
66 CACTTTCACATTCATCACATCGGCCATTAGGC
28435893 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATAT
* *
28435958 ACACTTTCACATTCATCACATTGGCCATTCGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
28435991 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATAT
28436054 ACACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGGCCATTAGGC
28436087 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
28436113 CACAATTATC
Statistics
Matches: 287, Mismatches: 19, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
93 1 0.00
94 87 0.30
96 145 0.51
98 54 0.19
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (97 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATA
CACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28436711 original size:128 final size:128
Alignment explanation
Indices: 28436483--28436734 Score: 477
Period size: 128 Copynumber: 2.0 Consensus size: 128
28436473 TCACTTGCCC
*
28436483 TTAATTTTCCCTGAATATAGACTCGTATATCTTCCATCCATAAAATTTTCAGAATTTTAGGTTTG
1 TTAATTTTCCCTGAATATAGACTAGTATATCTTCCATCCATAAAATTTTCAGAATTTTAGGTTTG
* *
28436548 GCCAATAAATACCAGATTTTTCTTAAAGTTTCCCCTGTTTCACTGTTTGACTAATCTGATCCG
66 GCCAATAAATACCAGATTTTTCTTAAAGTTTCCCCTATTTCACTGTTTAACTAATCTGATCCG
28436611 TTAATTTTCCCTGAATATAGACTAGTATATCTTCCATCCATAAAATTTTCAGAATTTTAGGTTTG
1 TTAATTTTCCCTGAATATAGACTAGTATATCTTCCATCCATAAAATTTTCAGAATTTTAGGTTTG
28436676 GCCAATAAATACCAGATTTTTCTTAAAGTTTCCCCTATTTCACTGTTTAACTAATCTGA
66 GCCAATAAATACCAGATTTTTCTTAAAGTTTCCCCTATTTCACTGTTTAACTAATCTGA
28436735 CCACTCTTCA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 121 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (128 bp):
TTAATTTTCCCTGAATATAGACTAGTATATCTTCCATCCATAAAATTTTCAGAATTTTAGGTTTG
GCCAATAAATACCAGATTTTTCTTAAAGTTTCCCCTATTTCACTGTTTAACTAATCTGATCCG
Found at i:28440784 original size:40 final size:40
Alignment explanation
Indices: 28439801--28440757 Score: 1682
Period size: 40 Copynumber: 23.9 Consensus size: 40
28439791 CGAATACACG
* * * *
28439801 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * ** * *
28439841 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
28439881 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
28439921 TCACTAGCATGAATGCTCTTCGTGACTTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
28439961 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440001 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440041 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440081 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440121 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440161 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440201 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440241 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440281 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440321 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440361 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440401 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440441 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440481 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440521 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440561 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440601 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
28440641 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
28440681 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGTTATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * ** *
28440721 GTAACTCGCACAAATGC-CTTCGGGACTTAACCCGGAT
1 -TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
28440758 TTAGTAACTC
Statistics
Matches: 884, Mismatches: 32, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
40 872 0.99
41 12 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:28440816 original size:39 final size:39
Alignment explanation
Indices: 28439932--28440873 Score: 209
Period size: 40 Copynumber: 23.6 Consensus size: 39
28439922 CACTAGCATG
* * * * *
28439932 AATGCTCTTCGTGACTTAGCCCGGATATA-TCACTAGCACG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
* ** * * **
28439972 AATGCTCTTCGGAACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440012 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440052 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440092 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440132 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440172 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440212 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440252 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440292 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440332 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440372 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440412 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440452 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440492 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440532 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440572 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440612 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
** * * **
28440652 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATG
1 AATGC-CTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
*
28440692 AATGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
1 AATGC-CTTCGGGACTTAGCCCGATT-TAGTAACTCGCACA
* *
28440733 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
*
28440773 AATGCCTTCGGG-CTTAGCCCAGAATTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACA
* * * * *
28440812 AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCACA
*
28440853 AA-GCCTTCGAGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
28440874 GACATCATTC
Statistics
Matches: 867, Mismatches: 27, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
38 2 0.00
39 37 0.04
40 801 0.92
41 27 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCACA
Found at i:28440859 original size:79 final size:80
Alignment explanation
Indices: 28440652--28440872 Score: 209
Period size: 79 Copynumber: 2.8 Consensus size: 80
28440642 CACTAGCATG
* * * ** * *
28440652 AATGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATGAATGCTCTTCGGGACTTAGCCC-G
1 AATGC-CTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGC-CTTCGAGACTTAGCCCAG
**
28440715 GTTATAGTAACTCGCACA
64 AAT-TAGTAACTCGCACA
* * * *
28440733 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCG-GGCTTAGCCCAGAA
1 AATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGAGACTTAGCCCAGAA
28440797 TTAGTAACTCGCACA
66 TTAGTAACTCGCACA
** * *
28440812 AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGAGACTTAGCCC
1 AATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTCGAGACTTAGCCC
28440873 GGACATCATT
Statistics
Matches: 117, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.49
80 40 0.34
81 17 0.15
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGAGACTTAGCCCAGAA
TTAGTAACTCGCACA
Found at i:28444968 original size:50 final size:49
Alignment explanation
Indices: 28444908--28445008 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 49
28444898 TAAATGCCGA
28444908 AATTATTTAAGCAACTAAAGAAAATTCAAAACAACTTAAATAATTAAACT
1 AATTATTTAAGCAACTAAAGAAAATT-AAAACAACTTAAATAATTAAACT
* * * *
28444958 AATTATTTAAGCAACTAAAGACAATTATAACAACTTAATTAGTTAAACT
1 AATTATTTAAGCAACTAAAGAAAATTAAAACAACTTAAATAATTAAACT
28445007 AA
1 AA
28445009 AATAACCGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 22 0.47
50 25 0.53
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (49 bp):
AATTATTTAAGCAACTAAAGAAAATTAAAACAACTTAAATAATTAAACT
Found at i:28465551 original size:39 final size:40
Alignment explanation
Indices: 28465466--28465551 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
28465456 CGACTAAGAT
* * *
28465466 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGAATTTGTGCGAGTGACTATATCCGGGCTAAATC
28465506 CCGAAGGAATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGAATTTGTGCGAG-TGACTATATCCGGGCTAAATC
28465545 CCGAAGG
1 CCGAAGG
28465552 TACTTGGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 15 0.36
40 25 0.60
41 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGAATTTGTGCGAGTGACTATATCCGGGCTAAATC
Found at i:28467578 original size:26 final size:27
Alignment explanation
Indices: 28467538--28467617 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 27
28467528 TCTATTGCCT
*
28467538 TATTCAAAAAGAATTATTTTATTAAAAA
1 TATT-AAAAACAATTATTTTATTAAAAA
* **
28467566 TA-TAAAAATAATT-TACTATT-AAAA
1 TATTAAAAACAATTATTTTATTAAAAA
28467590 TATTAAAAACAACTTTTATTTTATTAAA
1 TATTAAAAACAA---TTATTTTATTAAA
28467618 TGAAACAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
24 6 0.15
25 13 0.32
26 9 0.22
27 1 0.03
28 4 0.10
29 5 0.12
30 2 0.05
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (27 bp):
TATTAAAAACAATTATTTTATTAAAAA
Found at i:28469568 original size:19 final size:18
Alignment explanation
Indices: 28469525--28469581 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
28469515 TTATGAATAC
28469525 AAATAAATATGATTTAAA
1 AAATAAATATGATTTAAA
28469543 AAATAAATGA-GATTTAAGA
1 AAATAAAT-ATGATTTAA-A
*
28469562 GAATAAA-AT-A-TTAAA
1 AAATAAATATGATTTAAA
28469577 AAATA
1 AAATA
28469582 TATAGTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
17 2 0.06
18 15 0.44
19 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (18 bp):
AAATAAATATGATTTAAA
Found at i:28472577 original size:21 final size:20
Alignment explanation
Indices: 28472548--28472587 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
28472538 TATGAGATTT
28472548 AATGATTGATGATAGATTATG
1 AATGATTGATGATAG-TTATG
*
28472569 AATGTTTGATGATAGTTAT
1 AATGATTGATGATAGTTAT
28472588 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
AATGATTGATGATAGTTATG
Found at i:28472595 original size:20 final size:21
Alignment explanation
Indices: 28472553--28472595 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28472543 GATTTAATGA
*
28472553 TTGATGATAGATTATGAATGT
1 TTGATGATAGATTATGAAAGT
28472574 TTGATGATAG-TTAT-ACAAGT
1 TTGATGATAGATTATGA-AAGT
28472594 TT
1 TT
28472596 TGTTAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATGAAAGT
Found at i:28475014 original size:20 final size:21
Alignment explanation
Indices: 28474989--28475042 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
28474979 TAGAATTTGT
28474989 TTTTGAAATTTTTATAAA-TA
1 TTTTGAAATTTTTATAAATTA
* *
28475009 TTTTGAAAATTTGA-AAATTA
1 TTTTGAAATTTTTATAAATTA
*
28475029 TTTTG-TATTTTTAT
1 TTTTGAAATTTTTAT
28475043 TGAAAGAGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTGAAATTTTTATAAATTA
Found at i:28476055 original size:27 final size:26
Alignment explanation
Indices: 28476000--28476060 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
28475990 ATTTTTCTTG
*
28476000 AAATTTTATTAGGGGTAAAATTGTAA
1 AAATTTTATTAGGGGTAAAATCGTAA
*
28476026 AAATTTTATT-GGGTAGTAAAATCGTCA
1 AAATTTTATTAGGG--GTAAAATCGTAA
28476053 AAATTTTA
1 AAATTTTA
28476061 CGAGAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 3 0.10
26 10 0.32
27 18 0.58
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.39
Consensus pattern (26 bp):
AAATTTTATTAGGGGTAAAATCGTAA
Found at i:28479150 original size:19 final size:19
Alignment explanation
Indices: 28479126--28479163 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28479116 TTTCATTGCC
28479126 TTAGTTCAGGGGTGCGATT
1 TTAGTTCAGGGGTGCGATT
28479145 TTAGTTCAGGGGTGCGATT
1 TTAGTTCAGGGGTGCGATT
28479164 GTTCTACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.37
Consensus pattern (19 bp):
TTAGTTCAGGGGTGCGATT
Found at i:28490809 original size:44 final size:44
Alignment explanation
Indices: 28490746--28490830 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
28490736 TTGATAGCAA
* * *
28490746 GAATGAGAAGTATAAACTCCTCGAACCACCATGATCATTCACAG
1 GAATGAGAAGTATAAACTCCTCAAACCACCATAACCATTCACAG
28490790 GAATGA-AGAGTATAAACTCCTCAAACCACCATAACCATTCA
1 GAATGAGA-AGTATAAACTCCTCAAACCACCATAACCATTCA
28490831 TTGGAGAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.03
44 36 0.97
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (44 bp):
GAATGAGAAGTATAAACTCCTCAAACCACCATAACCATTCACAG
Found at i:28491196 original size:55 final size:55
Alignment explanation
Indices: 28491088--28491197 Score: 136
Period size: 55 Copynumber: 2.0 Consensus size: 55
28491078 GTCGAGCCTA
*
28491088 CCAAAACAACACGGGCATGTGACACGCCCGTGTGGAAGAACCATGGGCGAACCTG
1 CCAAAACAACACGGGCATGTGACACGCCCGTGTGGAAGAACCATGGGCAAACCTG
* * *
28491143 CCAAAACAATACGGGCGT-TCGACACGCCCGTGT-G-AGACACCTATGGTCAAACCTG
1 CCAAAACAACACGGGCATGT-GACACGCCCGTGTGGAAGA-ACC-ATGGGCAAACCTG
28491198 TTAAAATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
53 3 0.06
54 5 0.10
55 40 0.83
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (55 bp):
CCAAAACAACACGGGCATGTGACACGCCCGTGTGGAAGAACCATGGGCAAACCTG
Found at i:28506729 original size:13 final size:13
Alignment explanation
Indices: 28506711--28506735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28506701 GAATCAGGAT
28506711 GTGTGAAAATTTC
1 GTGTGAAAATTTC
28506724 GTGTGAAAATTT
1 GTGTGAAAATTT
28506736 AATCGTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:28507926 original size:42 final size:44
Alignment explanation
Indices: 28507858--28507979 Score: 162
Period size: 43 Copynumber: 2.8 Consensus size: 44
28507848 CAAAAACTTA
*
28507858 TGATTTACGTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATT
1 TGATTTACATGTAAGACC-CTGTCTGGGACATTGGCATCGATATT
*
28507901 TGATTT-CATGTAAGACCCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTACATGTAAGACCCTGTCTGGGACATTGGCATCGATATT
* * *
28507944 TG-TTTACATGTAAGACCATGTCTAGGACGTTGGCAT
1 TGATTTACATGTAAGACCCTGTCTGGGACATTGGCAT
28507980 TGTACGAGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
41 1 0.01
42 31 0.44
43 38 0.54
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (44 bp):
TGATTTACATGTAAGACCCTGTCTGGGACATTGGCATCGATATT
Found at i:28512431 original size:25 final size:24
Alignment explanation
Indices: 28512415--28512484 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
28512405 CTCTTTTAAT
*
28512415 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTT-TGTA
28512440 AACTGGGGCAAAGCCCTTTTCTGTA
1 AACTGGGGCAAAGCCCTTTT-TGTA
*
28512465 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28512485 AGCACTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (24 bp):
AACTGGGGCAAAGCCCTTTTTGTA
Found at i:28513356 original size:27 final size:27
Alignment explanation
Indices: 28513295--28513371 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
28513285 GGCATATTCA
28513295 TCATTTTACCATACAGGGGTATTACGG
1 TCATTTTACCATACAGGGGTATTACGG
* *
28513322 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAGGGG-TATTACGG
* *
28513349 TCTTTTTACC-TATTAGGGGTATT
1 TCATTTTACCATA-CAGGGGTATT
28513372 TTAGTAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 3 0.07
27 38 0.90
28 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
TCATTTTACCATACAGGGGTATTACGG
Found at i:28513442 original size:27 final size:27
Alignment explanation
Indices: 28513412--28513463 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28513402 GTAAATCTAC
28513412 AAACCAAGGGTATTTC-AGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
28513439 AAACCAATGGTATTTCTATAATTTT
1 AAACCAAGGGTATTTCTATAATTTT
28513464 TAGAAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:28513524 original size:26 final size:27
Alignment explanation
Indices: 28513475--28513593 Score: 102
Period size: 27 Copynumber: 4.4 Consensus size: 27
28513465 AGAAAGTCAA
* * *
28513475 GGGTATTTTTGTAATTGTGT-AAATTAG
1 GGGTATTTTGGTAATT-TCTCAAACTAG
*
28513502 GGGTATTTTGGTAATTT-TCAAA-TTG
1 GGGTATTTTGGTAATTTCTCAAACTAG
* * *
28513527 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTCTCAAACTAG
* *
28513555 TGGTATTTTGATAATTT-TACAAACTAG
1 GGGTATTTTGGTAATTTCT-CAAACTAG
28513582 GGGTATTTTGGT
1 GGGTATTTTGGT
28513594 GATTCTACCC
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
25 3 0.04
26 20 0.27
27 50 0.68
28 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTCTCAAACTAG
Found at i:28513731 original size:27 final size:27
Alignment explanation
Indices: 28513629--28513720 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
28513619 GTAATTTCAC
* * *
28513629 AATCGAGGGTAAAA-CGATAATTTTGTA
1 AATCGAGGGTAAAATAG-TAATTCTATA
28513656 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTCTATA
* *
28513683 AATCAAGTGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTCTATA
28513710 AATCGAGGGTA
1 AATCGAGGGTA
28513721 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 56 0.98
28 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTCTATA
Found at i:28519612 original size:43 final size:44
Alignment explanation
Indices: 28519490--28519647 Score: 180
Period size: 43 Copynumber: 3.7 Consensus size: 44
28519480 ATGTGTTTTT
* * * * *
28519490 GTGTAAGACCACGTCTAGGATGTTGGCATCGACATATGATTTAC
1 GTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTTAC
*
28519534 GTGTAACACCATGTCTGGGACGTTGGCATCG-TATTTGATTT-C
1 GTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTTAC
* *
28519576 GTGTAAGACCCTGTTTGGGACAG-TGGCATCGATATTTG-TTTAC
1 GTGTAAGACCATGTCTGGGAC-GTTGGCATCGATATTTGATTTAC
* * *
28519619 ATGTAAGATCATGTCTAGGACGTTGGCAT
1 GTGTAAGACCATGTCTGGGACGTTGGCAT
28519648 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
42 31 0.32
43 38 0.40
44 27 0.28
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (44 bp):
GTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTTAC
Found at i:28522236 original size:87 final size:87
Alignment explanation
Indices: 28521880--28522227 Score: 678
Period size: 87 Copynumber: 4.0 Consensus size: 87
28521870 TCGAAGTTTC
28521880 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
1 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
28521945 TGAAAGAGTTGAAAGCAAAGTT
66 TGAAAGAGTTGAAAGCAAAGTT
28521967 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
1 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
28522032 TGAAAGAGTTGAAAGCAAAGTT
66 TGAAAGAGTTGAAAGCAAAGTT
28522054 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
1 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
28522119 TGAAAGAGTTGAAAGCAAAGTT
66 TGAAAGAGTTGAAAGCAAAGTT
* *
28522141 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACCGTAAAGAATGGCTCCCATAGAGT
1 CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
28522206 TGAAAGAGTTGAAAGCAAAGTT
66 TGAAAGAGTTGAAAGCAAAGTT
28522228 GCAAGAGTTG
Statistics
Matches: 259, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 259 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (87 bp):
CATTGAGTTAGTATCAGGAACATCACTGATATCGATAGCACTGTAAAGAATTGCTCCCATAGAGT
TGAAAGAGTTGAAAGCAAAGTT
Found at i:28524378 original size:40 final size:40
Alignment explanation
Indices: 28524304--28524442 Score: 203
Period size: 40 Copynumber: 3.5 Consensus size: 40
28524294 AACCCAAGTA
* *
28524304 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
28524343 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28524383 CCTTCGGGACTTAGCTCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
28524422 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
28524443 GTCATCCGAA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
39 35 0.38
40 55 0.60
41 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28530213 original size:42 final size:41
Alignment explanation
Indices: 28530155--28530318 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 41
28530145 TTAGGGTTAT
* *
28530155 TGAGATTACATGTAAGACCATATTTGGGATATGGCATCGATA
1 TGAGATT-CATGTAAGACCATATCTAGGATATGGCATCGATA
* * *
28530197 TGAGACTTCATATAAGACCATATCTAGGATATAGCATCGATG
1 TGAGA-TTCATGTAAGACCATATCTAGGATATGGCATCGATA
* * * *
28530239 TGAGATTTCGTGTAAGACCATAGCTAGGCTATTGACATCGATA
1 TGAGA-TTCATGTAAGACCATATCTAGGATA-TGGCATCGATA
* *
28530282 TGAGATCCCATGTAAGACCATATCTTGGATATGGCAT
1 TGAGAT-TCATGTAAGACCATATCTAGGATATGGCAT
28530319 TGGTATATTA
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 66 0.66
43 34 0.34
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (41 bp):
TGAGATTCATGTAAGACCATATCTAGGATATGGCATCGATA
Found at i:28532618 original size:20 final size:21
Alignment explanation
Indices: 28532593--28532632 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28532583 TCTTAGAAAC
*
28532593 AGGGC-ACGCGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
28532613 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
28532633 CCATTAGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.17, C:0.30, G:0.42, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:28536355 original size:20 final size:21
Alignment explanation
Indices: 28536329--28536395 Score: 95
Period size: 20 Copynumber: 3.3 Consensus size: 21
28536319 ATTTTGATAT
28536329 ACATGAT-TGATATGATATGC
1 ACATGATATGATATGATATGC
*
28536349 GCATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
*
28536369 ACATGATCT-ATATGATATGC
1 ACATGATATGATATGATATGC
28536389 ACATGAT
1 ACATGAT
28536396 GTATTCATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:28536510 original size:23 final size:24
Alignment explanation
Indices: 28536445--28536525 Score: 146
Period size: 24 Copynumber: 3.4 Consensus size: 24
28536435 GAGGAAGTAC
28536445 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28536469 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28536493 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28536516 AAAAGAGGCT
1 AAAAG-GGCT
28536526 AGGCCTCTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
23 18 0.32
24 38 0.68
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28544404 original size:20 final size:20
Alignment explanation
Indices: 28544379--28544445 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
28544369 ATTTTGATAT
28544379 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
28544399 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28544419 ACATGATCTGTATGATATGC
1 ACATGATATGTATGATATGC
28544439 ACATGAT
1 ACATGAT
28544446 GTATTCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28544406 original size:11 final size:11
Alignment explanation
Indices: 28544390--28544445 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
28544380 CATGATTGAT
28544390 ATGATATGCAC
1 ATGATATGCAC
*
28544401 ATGATATG--T
1 ATGATATGCAC
28544410 ATGATATGCAC
1 ATGATATGCAC
* *
28544421 ATGATCTG--T
1 ATGATATGCAC
28544430 ATGATATGCAC
1 ATGATATGCAC
28544441 ATGAT
1 ATGAT
28544446 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28544522 original size:24 final size:24
Alignment explanation
Indices: 28544495--28544575 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
28544485 GAGGAAGTAC
28544495 AAAAGGGCTTATGCCCAAGTTATT
1 AAAAGGGCTTATGCCCAAGTTATT
* *
28544519 AAAAGAGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCAAGTTATT
*
28544543 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCAAGTTATT
28544566 AAAAGAGGCT
1 AAAAG-GGCT
28544576 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 17 0.33
24 35 0.67
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCAAGTTATT
Found at i:28544588 original size:48 final size:48
Alignment explanation
Indices: 28544495--28544589 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 48
28544485 GAGGAAGTAC
* *
28544495 AAAAGGGCTTATGCCCAAGTTATTAAAAGAGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCAAGTTATTAAAAGAGCTTAGGCCCCAGTTATT
*
28544543 AAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCAAGTTATTAAAAGA-GCTTAGGCC-CCAGTTAT
28544590 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 23 0.55
48 19 0.45
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCAAGTTATTAAAAGAGCTTAGGCCCCAGTTATT
Found at i:28547823 original size:47 final size:47
Alignment explanation
Indices: 28547766--28548067 Score: 442
Period size: 47 Copynumber: 6.4 Consensus size: 47
28547756 ATTGATGTAC
* * *
28547766 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
28547813 AAGTATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * * *
28547860 AAGTGTATATATGTGATAGGGTCGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
28547907 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28547954 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
28548001 AAGTGTATATATGTGATAAGGTCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
28548048 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
28548068 TCCCGAAGGG
Statistics
Matches: 237, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 237 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:28550623 original size:28 final size:28
Alignment explanation
Indices: 28550583--28550641 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
28550573 TAATAATTTT
*
28550583 CATGCACTCATAAAATCATACTATAACA
1 CATGCACTCATAAAATCATACTACAACA
*
28550611 CATGCGCTCATAAAATCATACTACAACA
1 CATGCACTCATAAAATCATACTACAACA
28550639 CAT
1 CAT
28550642 AAAATAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (28 bp):
CATGCACTCATAAAATCATACTACAACA
Found at i:28554480 original size:40 final size:40
Alignment explanation
Indices: 28554436--28554697 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28554426 GCTCCTCGTT
* *
28554436 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
28554476 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28554516 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28554555 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28554594 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
28554633 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
28554674 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28554698 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:28557458 original size:93 final size:93
Alignment explanation
Indices: 28557299--28557483 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 93
28557289 ATAAAGTGAA
* * * *
28557299 CCGACTTAGTCAGTCTATCAACAACAACTCAAATCGCATCCTTCTTACTTGTTGACAATGGTAGT
1 CCGACTTAGTCAGCCTATCAACAACAACCCAAATCGCATCCTTCTTACTTGCTGACAATGGCAGT
*
28557364 CCGGACATAAAGTCCATTGTGACTCGAG
66 CCGGACACAAAGTCCATTGTGACTCGAG
28557392 CCGACTTAGTCAGCCTATCAACAACAACCCAAATCGCATCCTTCTTACTTGCTGACAATGGCAGT
1 CCGACTTAGTCAGCCTATCAACAACAACCCAAATCGCATCCTTCTTACTTGCTGACAATGGCAGT
28557457 CCGGACACAAAGTCCATTGTGACTCGA
66 CCGGACACAAAGTCCATTGTGACTCGA
28557484 TCCCATTTCC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (93 bp):
CCGACTTAGTCAGCCTATCAACAACAACCCAAATCGCATCCTTCTTACTTGCTGACAATGGCAGT
CCGGACACAAAGTCCATTGTGACTCGAG
Found at i:28563941 original size:40 final size:40
Alignment explanation
Indices: 28563897--28564158 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28563887 GCTCCTCGTT
* *
28563897 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
28563937 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28563977 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28564016 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
28564055 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
28564094 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
28564135 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28564159 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:28572132 original size:28 final size:28
Alignment explanation
Indices: 28572092--28572344 Score: 479
Period size: 28 Copynumber: 9.0 Consensus size: 28
28572082 CATAATGATT
28572092 TACATAATCAAACTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
28572120 TACATAATCAAACTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
28572148 TACATAATCAAACTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
28572176 TACATAATCAAACTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
28572204 TACATAATCAAACTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
28572232 TACATAATCAAACTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
*
28572260 TACATAATCAAATTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
*
28572288 TACATAATCAAGCTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
*
28572316 TACATAATCAAGCTCGCACACTTAGTGC
1 TACATAATCAAACTCGCACACTTAGTGC
28572344 T
1 T
28572345 GTACAATTTA
Statistics
Matches: 222, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 222 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (28 bp):
TACATAATCAAACTCGCACACTTAGTGC
Found at i:28578925 original size:29 final size:29
Alignment explanation
Indices: 28578619--28578911 Score: 414
Period size: 29 Copynumber: 10.2 Consensus size: 29
28578609 ACCCCTACAT
* *
28578619 ACATGCATATGGCCCACTAGGCCCAA-TC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* *
28578647 TCATTTATATGGCCCATCTA-GCCCAATTC
1 ACATTCATATGGCCCAT-TAGGCCCAATTC
*
28578676 ACATTCATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
28578705 ACATTCATATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
**
28578734 ACATTCATATGGCCCATCCGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
28578763 ACATTCATATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
**
28578792 ACATTCATATGGCCCATCCGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
*
28578821 ACATTCATATGGCCCATTAGACCCAA-TC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* * * *
28578849 TCATTTATATGGCTCATCCA-GCCCAATTC
1 ACATTCATATGGCCCAT-TAGGCCCAATTC
28578878 ACATTCATATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
28578907 ACATT
1 ACATT
28578912 TATGTGGGAT
Statistics
Matches: 233, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.18
29 191 0.82
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAATTC
Found at i:28587688 original size:24 final size:23
Alignment explanation
Indices: 28587653--28587697 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
28587643 ATCTCCTCGT
28587653 TTTTCTCCCTGATA-ACTCCCCAA
1 TTTTCTCCCTGA-ACACTCCCCAA
*
28587676 TTTTCTCTTCTGAACACTCCCC
1 TTTTCTC-CCTGAACACTCCCC
28587698 TTGGAGTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.18, C:0.40, G:0.04, T:0.38
Consensus pattern (23 bp):
TTTTCTCCCTGAACACTCCCCAA
Found at i:28594265 original size:29 final size:29
Alignment explanation
Indices: 28594194--28594374 Score: 183
Period size: 29 Copynumber: 6.3 Consensus size: 29
28594184 ACCCCTACAT
* * *
28594194 ACATGCATATGGCCCACTAGGCCCAA-TC
1 ACATTCATATGGCCCATTCGGCCCAATTC
*
28594222 TCA-TCTATATGGCCCATTCGGCCCAATTC
1 ACATTC-ATATGGCCCATTCGGCCCAATTC
* *
28594251 ACGTTCATATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTCGGCCCAATTC
* *
28594280 ATATTCATATGGCCCATCCGGCCCAATTC
1 ACATTCATATGGCCCATTCGGCCCAATTC
28594309 ACATTCATATGGCCCATTAC-GCCCAA-TC
1 ACATTCATATGGCCCATT-CGGCCCAATTC
* * * * * *
28594337 TCATTTATATGACTCATCCGGCCCAAATC
1 ACATTCATATGGCCCATTCGGCCCAATTC
28594366 ACATT-ATAT
1 ACATTCATAT
28594375 TTATGCTTAC
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
27 2 0.02
28 45 0.35
29 78 0.61
30 3 0.02
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCATTCGGCCCAATTC
Found at i:28594307 original size:58 final size:57
Alignment explanation
Indices: 28594194--28594374 Score: 249
Period size: 57 Copynumber: 3.2 Consensus size: 57
28594184 ACCCCTACAT
* * * *
28594194 ACATGCATATGGCCCACTAGGCCCAATCTCATCTATATGGCCCATTCGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTC
*
28594251 ACGTTCATATGGCCCATTAGGCCCAAT-TCATATTCATATGGCCCATCCGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATCTCAT-TT-ATATGGCCCATCCGGCCCAATTC
* * * *
28594309 ACATTCATATGGCCCATTACGCCCAATCTCATTTATATGACTCATCCGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTC
28594366 ACATT-ATAT
1 ACATTCATAT
28594375 TTATGCTTAC
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
56 8 0.07
57 50 0.45
58 49 0.44
59 4 0.04
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.28
Consensus pattern (57 bp):
ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTC
Found at i:28594477 original size:19 final size:18
Alignment explanation
Indices: 28594441--28594478 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
28594431 ATGGGCTCAA
28594441 TAGCCCTTCGGCCCCATT
1 TAGCCCTTCGGCCCCATT
28594459 TAGCCCATTCCGG-CCCATT
1 TAGCCC-TT-CGGCCCCATT
28594478 T
1 T
28594479 GGCCTATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.13, C:0.42, G:0.16, T:0.29
Consensus pattern (18 bp):
TAGCCCTTCGGCCCCATT
Found at i:28596756 original size:17 final size:17
Alignment explanation
Indices: 28596734--28596766 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28596724 TTCAATATTT
28596734 TTCCAATTATCTCACAA
1 TTCCAATTATCTCACAA
28596751 TTCCAATTATCTCACA
1 TTCCAATTATCTCACA
28596767 CATTTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TTCCAATTATCTCACAA
Found at i:28596869 original size:17 final size:17
Alignment explanation
Indices: 28596847--28596879 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28596837 TTCAATATTT
28596847 TTCCAATTATCTCACAA
1 TTCCAATTATCTCACAA
28596864 TTCCAATTATCTCACA
1 TTCCAATTATCTCACA
28596880 CATTTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TTCCAATTATCTCACAA
Found at i:28596900 original size:113 final size:113
Alignment explanation
Indices: 28596702--28596935 Score: 468
Period size: 113 Copynumber: 2.1 Consensus size: 113
28596692 TTTCAAAAGC
28596702 TTTCATGACAAAACCCTAGACTTTCAATATTTTTCCAATTATCTCACAATTCCAATTATCTCACA
1 TTTCATGACAAAACCCTAGACTTTCAATATTTTTCCAATTATCTCACAATTCCAATTATCTCACA
28596767 CATTTACAACCCATTTTATAAACTTTACAAAATGGTCCATTGAGGTGT
66 CATTTACAACCCATTTTATAAACTTTACAAAATGGTCCATTGAGGTGT
28596815 TTTCATGACAAAACCCTAGACTTTCAATATTTTTCCAATTATCTCACAATTCCAATTATCTCACA
1 TTTCATGACAAAACCCTAGACTTTCAATATTTTTCCAATTATCTCACAATTCCAATTATCTCACA
28596880 CATTTACAACCCATTTTATAAACTTTACAAAATGGTCCATTGAGGTGT
66 CATTTACAACCCATTTTATAAACTTTACAAAATGGTCCATTGAGGTGT
28596928 TTTCATGA
1 TTTCATGA
28596936 AAACTACTTC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 121 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (113 bp):
TTTCATGACAAAACCCTAGACTTTCAATATTTTTCCAATTATCTCACAATTCCAATTATCTCACA
CATTTACAACCCATTTTATAAACTTTACAAAATGGTCCATTGAGGTGT
Found at i:28602437 original size:42 final size:42
Alignment explanation
Indices: 28602346--28602442 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
28602336 CTAAGATTAA
* * *
28602346 GTGTAAGACCATATCCGGGATAAGGCATCAGTATGATACTTC
1 GTGTAAGACCATATCCGGGATAAGGCATCAATACGAGACTTC
* * * * * * *
28602388 ATATAAGACTATATCTGGGATATGGCATCAATGCGAGATTTC
1 GTGTAAGACCATATCCGGGATAAGGCATCAATACGAGACTTC
28602430 GTGTAAGACCATA
1 GTGTAAGACCATA
28602443 GTTGGGCTAT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCCGGGATAAGGCATCAATACGAGACTTC
Found at i:28605723 original size:27 final size:27
Alignment explanation
Indices: 28605651--28605751 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
28605641 CTTTACAACA
* * * * * *
28605651 TACTTTGAGTGGATTGTCATTTTGACA
1 TACTCTGAATGGATTGCCTTTTTGGCG
*
28605678 TACTCTGAATGAATTGCCTTTTTGGCG
1 TACTCTGAATGGATTGCCTTTTTGGCG
* *
28605705 TACTCTGAATGGATTGCCTTTATGGTG
1 TACTCTGAATGGATTGCCTTTTTGGCG
* *
28605732 TACTATGAATGGATTACCTT
1 TACTCTGAATGGATTGCCTT
28605752 ATGGCAAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (27 bp):
TACTCTGAATGGATTGCCTTTTTGGCG
Found at i:28605808 original size:18 final size:18
Alignment explanation
Indices: 28605785--28605820 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28605775 TTTGTGGTAT
28605785 TTTGTCATCTAGAAAACA
1 TTTGTCATCTAGAAAACA
28605803 TTTGTCATCTAGAAAACA
1 TTTGTCATCTAGAAAACA
28605821 ATGGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
TTTGTCATCTAGAAAACA
Found at i:28614699 original size:100 final size:100
Alignment explanation
Indices: 28614526--28614920 Score: 483
Period size: 100 Copynumber: 4.0 Consensus size: 100
28614516 ACACTATAGC
* * *
28614526 CGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGT
1 CGAA-CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCAGGT
*
28614589 ACACGTAGTAGCCTGCACTTAGTACTACACACGTGA
65 ACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * * *
28614625 TCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGG
1 -CGAA-CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCAGG
* *
28614688 TACACGTAGTAGCCTGCACTTAGTACTAGACACGTGA
64 TACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * * * *
28614725 CCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGT
1 -CGAACTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCAGGT
* * *
28614790 ACGCATAGTAGCCTGCACTTAGTACTACACATGCGA
65 ACACATAGTAGCCTGCACTTAGTACTACACACGTGA
* * * * * *
28614826 CCAATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTA
1 CGAACTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCAGGTA
*
28614891 CGCATAGTAGCCTGCACTTAGTACTACACA
66 CACATAGTAGCCTGCACTTAGTACTACACA
28614921 TGCGACCTCA
Statistics
Matches: 268, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
99 37 0.14
100 192 0.72
101 39 0.15
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (100 bp):
CGAACTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGATCCAAGTTATCAGGTA
CACATAGTAGCCTGCACTTAGTACTACACACGTGA
Found at i:28614771 original size:150 final size:149
Alignment explanation
Indices: 28614545--28614920 Score: 626
Period size: 150 Copynumber: 2.5 Consensus size: 149
28614535 CTGGTACGCA
* * *
28614545 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACGTAGTAGCCTGCACTTA
28614610 GTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCG
66 GTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCG
28614675 ACCAATTATCCGGTACACG
131 ACCAATTATCCGGTACACG
* ** * *
28614694 TAGTAGCCTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCAGGTACACGTAGTAGCCTGCACTT
28614759 AGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGC
65 AGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGC
28614824 GACCAATTATCCGGTACACG
130 GACCAATTATCCGGTACACG
* * *
28614844 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACGTAGTAGCCTGCACT
28614909 TAGTACTACACA
64 TAGTACTACACA
28614921 TGCGACCTCA
Statistics
Matches: 209, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
149 30 0.14
150 144 0.69
151 35 0.17
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (149 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACGTAGTAGCCTGCACTTA
GTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCG
ACCAATTATCCGGTACACG
Found at i:28619832 original size:43 final size:41
Alignment explanation
Indices: 28619732--28619854 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 41
28619722 AACTTATGTT
*
28619732 TTACGTGTAAGACCATGTCTGGAACATCGGCATCGTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAT-GGCATCGTATTTGA
* * *
28619774 TTTCGTGTAAAACCATGTCTGGGACAGTGGCATCGATATTTGG
1 TTACGTGTAAGACCATGTCTGGGACA-TGGCATCG-TATTTGA
* *
28619817 TTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TTACGTGTAAGACCATGTCTGGGACA-TGGCATCGTAT
28619855 GAGCTTTTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 33 0.47
43 37 0.53
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
TTACGTGTAAGACCATGTCTGGGACATGGCATCGTATTTGA
Found at i:28620591 original size:11 final size:10
Alignment explanation
Indices: 28620570--28620612 Score: 59
Period size: 11 Copynumber: 4.1 Consensus size: 10
28620560 TATTGAAACA
28620570 TATGATTTGG
1 TATGATTTGG
28620580 TATGATTTTGG
1 TATGA-TTTGG
*
28620591 TTTAGATTTGG
1 TAT-GATTTGG
28620602 TATGATTTGG
1 TATGATTTGG
28620612 T
1 T
28620613 TGGTGAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 13 0.45
11 14 0.48
12 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (10 bp):
TATGATTTGG
Found at i:28620598 original size:22 final size:21
Alignment explanation
Indices: 28620573--28620613 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
28620563 TGAAACATAT
28620573 GATTTGGTATGATTTTGGTTTA
1 GATTTGGTATGA-TTTGGTTTA
28620595 GATTTGGTATGATTTGGTT
1 GATTTGGTATGATTTGGTT
28620614 GGTGAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (21 bp):
GATTTGGTATGATTTGGTTTA
Found at i:28635514 original size:80 final size:79
Alignment explanation
Indices: 28635430--28635601 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
28635420 GGACTAAGAT
*
28635430 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
28635494 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
28635510 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
28635575 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
28635589 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28635602 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:28635581 original size:39 final size:39
Alignment explanation
Indices: 28635377--28635599 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
28635367 TTGAATGCTG
* * * * *
28635377 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
28635417 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
28635456 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
28635497 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
28635537 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
28635576 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28635600 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28635619 original size:79 final size:80
Alignment explanation
Indices: 28635457--28635634 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
28635447 AGATACAAAT
* * * *
28635457 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
28635522 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
28635537 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
28635601 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
28635616 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28635635 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:28641053 original size:91 final size:94
Alignment explanation
Indices: 28640952--28641121 Score: 231
Period size: 91 Copynumber: 1.8 Consensus size: 94
28640942 TATACATACT
* * *
28640952 GATGCATGTCCCAGACATGTCTTTCACTA-GCACAACTCT-TA-GCCGATG-CGTGTCCCAGACA
1 GATGCATGTCCCACACATGTCTTACACTAGGCAC-ACTCTCTACGCCGATGCCATGTCCCAGACA
*
28641013 CGTCTTACATTGGCTATCATCGTCGAGGCC
65 CGTCTTACACTGGCTATCATCGTCGAGGCC
* *
28641043 GATGCATGTCCCACACATGTCTTACACTAGTGCTCATTCTCTACGCCGATGCCATGTCCCAGACA
1 GATGCATGTCCCACACATGTCTTACACTAG-GCACACTCTCTACGCCGATGCCATGTCCCAGACA
*
28641108 TGTCTTACACTGGC
65 CGTCTTACACTGGC
28641122 ACACAAGTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
91 27 0.40
92 4 0.06
93 5 0.07
94 7 0.10
95 24 0.36
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (94 bp):
GATGCATGTCCCACACATGTCTTACACTAGGCACACTCTCTACGCCGATGCCATGTCCCAGACAC
GTCTTACACTGGCTATCATCGTCGAGGCC
Found at i:28641111 original size:48 final size:46
Alignment explanation
Indices: 28640952--28641118 Score: 164
Period size: 47 Copynumber: 3.6 Consensus size: 46
28640942 TATACATACT
* * *
28640952 GATGCATGTCCCAGACATGTCTTTCACTA-GCACA-ACTCTTA-GCC
1 GATGCATGTCCCAGACATGTCTTACACTAGGCTCATTCTC-TACGCC
* * * * *
28640996 GATGCGTGTCCCAGACACGTCTTACA-TTGGCT-ATCATCGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGGCTCAT--TC-TCTACGCC
*
28641043 GATGCATGTCCCACACATGTCTTACACTAGTGCTCATTCTCTACGCC
1 GATGCATGTCCCAGACATGTCTTACACTAG-GCTCATTCTCTACGCC
28641090 GATGCCATGTCCCAGACATGTCTTACACT
1 GATG-CATGTCCCAGACATGTCTTACACT
28641119 GGCACACAAG
Statistics
Matches: 99, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 2 0.02
44 25 0.25
46 2 0.02
47 38 0.38
48 27 0.27
49 3 0.03
50 2 0.02
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGGCTCATTCTCTACGCC
Found at i:28641127 original size:141 final size:142
Alignment explanation
Indices: 28640850--28641124 Score: 355
Period size: 139 Copynumber: 2.0 Consensus size: 142
28640840 GGGATATGTT
* * *
28640850 GCCGATGCCATGTCCCGGACATGGTCTTACATTGGCTATCATCATCGAGGCTGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATCGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
* * * *
28640915 AGACATGGTCTTATACTAGCTCTCGTCTATACATACTGATGCATGTCCCAGACATGTCTTTCACT
66 ACACATGGTCTTACACTAGCTCTCGTCTATACA-ACCGATGCATGTCCCAGACATGTCTTACACT
28640980 AGCACAACTCTTA
130 AGCACAACTCTTA
* *
28640993 GCCGATG-CGTGTCCCAGACA-CGTCTTACATTGGCTATCATCGTCGAGGCCGATG-CATGTCCC
1 GCCGATGCCATGTCCCAGACATCGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
* * *
28641055 ACACAT-GTCTTACACTAG-TGCTCATTCTCTAC-GCCGATGCCATGTCCCAGACATGTCTTACA
66 ACACATGGTCTTACACTAGCT-CTC-GTCTATACAACCGATG-CATGTCCCAGACATGTCTTACA
*
28641117 CTGGCACA
128 CTAGCACA
28641125 CAAGTAATCT
Statistics
Matches: 116, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
138 6 0.05
139 42 0.36
140 19 0.16
141 31 0.27
142 11 0.09
143 7 0.06
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.28
Consensus pattern (142 bp):
GCCGATGCCATGTCCCAGACATCGTCTTACATTGGCTATCATCATCGAGGCCGATGCCATGTCCC
ACACATGGTCTTACACTAGCTCTCGTCTATACAACCGATGCATGTCCCAGACATGTCTTACACTA
GCACAACTCTTA
Found at i:28644943 original size:40 final size:40
Alignment explanation
Indices: 28644888--28645218 Score: 608
Period size: 40 Copynumber: 8.3 Consensus size: 40
28644878 ATACTATGAT
28644888 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28644928 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28644968 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28645008 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28645048 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28645088 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28645128 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
* * * * * *
28645168 GGCATTTGTGCGAGTTGCTATACCCGGGTTAAGATCCGAA
1 GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
28645208 GGCAATTGTGC
1 GGCAATTGTGC
28645219 TTGTGGTTAT
Statistics
Matches: 284, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 284 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (40 bp):
GGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAA
Found at i:28657611 original size:38 final size:38
Alignment explanation
Indices: 28657569--28657646 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
28657559 ACATGGGGTA
*
28657569 CTGATTTCTGTTGTGTCGGATAGAGATCCGAGATTCAC
1 CTGATTTCTGTTGTGTCGGATAGAGATCCGAGAATCAC
*
28657607 CTGATTTCTGTTGTGTCTGATAGAGATCCGAGAATCAC
1 CTGATTTCTGTTGTGTCGGATAGAGATCCGAGAATCAC
28657645 CT
1 CT
28657647 CGCGATTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (38 bp):
CTGATTTCTGTTGTGTCGGATAGAGATCCGAGAATCAC
Found at i:28660373 original size:40 final size:40
Alignment explanation
Indices: 28660314--28660458 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
28660304 CATTTGAATG
* *
28660314 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* *
28660354 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* * * *
28660394 ATATCCGGGCTAAGACCCGAAGGCGTTTGTACGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
28660434 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
28660459 ATTGTGCTTG
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 90 0.97
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
Found at i:28660477 original size:80 final size:80
Alignment explanation
Indices: 28660314--28660485 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
28660304 CATTTGAATG
* * * * * *
28660314 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATACGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
28660379 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* * *
28660394 ATATCCGGGCTAAGACCCGAAGGCGTTTGTACGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATACGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
28660458 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
28660474 ATATCC-GGCTAA
1 ATATCCGGGCTAA
28660486 ATTCCGAAGA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 6 0.08
80 69 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATACGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:28663007 original size:37 final size:37
Alignment explanation
Indices: 28662947--28663024 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
28662937 TATTACGAAG
* * *
28662947 TCTTACCAGGACATAATCTCCACACGAAGTTATCGGA
1 TCTTACCAGGACAAAATCCCCACACGAAGTCATCGGA
* * *
28662984 TCTTACCCGGACAAAATCCCCACACGTAGTCATCGGG
1 TCTTACCAGGACAAAATCCCCACACGAAGTCATCGGA
28663021 TCTT
1 TCTT
28663025 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
TCTTACCAGGACAAAATCCCCACACGAAGTCATCGGA
Found at i:28663212 original size:47 final size:47
Alignment explanation
Indices: 28663143--28663271 Score: 179
Period size: 47 Copynumber: 2.7 Consensus size: 47
28663133 CCCTTTGGGA
* * * *
28663143 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
*
28663190 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* *
28663237 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATCCATCACAT
28663272 AGAATCCTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 1 0.01
47 72 0.99
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
Found at i:28669096 original size:30 final size:30
Alignment explanation
Indices: 28669031--28669097 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
28669021 TGTAAAAGAG
*
28669031 GTAAAAGTTAATTGATTTTGATTTAAAATA
1 GTAAAGGTTAATTGATTTTGATTTAAAATA
28669061 GTAAAGGTTAATTGATTTTGATTTAAAATA
1 GTAAAGGTTAATTGATTTTGATTTAAAATA
28669091 GTAAAGG
1 GTAAAGG
28669098 GACCAAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (30 bp):
GTAAAGGTTAATTGATTTTGATTTAAAATA
Found at i:28672704 original size:15 final size:16
Alignment explanation
Indices: 28672684--28672716 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28672674 CGTTTGAGTA
*
28672684 AAAAGAA-AAATAAAG
1 AAAAGAATAAAAAAAG
28672699 AAAAGAATAAAAAAAG
1 AAAAGAATAAAAAAAG
28672715 AA
1 AA
28672717 GAATGTGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAGAATAAAAAAAG
Found at i:28681442 original size:40 final size:40
Alignment explanation
Indices: 28681368--28682235 Score: 1544
Period size: 40 Copynumber: 21.6 Consensus size: 40
28681358 AACCCAAGTA
* * *
28681368 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAATTG
* * **
28681407 CCTTCGGGTCGTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
* *
28681447 CCTTCGGGACTTAGCCCGGATTTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
* * *
28681487 CCTTCGGGACTTAGCCTGGATTTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681527 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681567 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681607 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681647 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681687 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681727 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681767 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681807 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681847 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681887 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681927 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28681967 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28682007 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28682047 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28682087 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
28682127 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
* *
28682167 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAATTG
28682210 CCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGT
28682236 AACTTACATG
Statistics
Matches: 806, Mismatches: 16, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
39 12 0.01
40 761 0.94
41 1 0.00
43 32 0.04
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
Found at i:28689549 original size:40 final size:40
Alignment explanation
Indices: 28689475--28689615 Score: 180
Period size: 40 Copynumber: 3.6 Consensus size: 40
28689465 AACCCAAGTA
* *
28689475 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
28689514 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28689554 CCTTCGGGACTTAGCCCGAATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28689593 CCCTCGGGACTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28689616 CATCCGAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
39 34 0.38
40 54 0.61
41 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28694115 original size:12 final size:13
Alignment explanation
Indices: 28694098--28694126 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28694088 TGCCAAACTC
28694098 TACGTATGCAAG-
1 TACGTATGCAAGA
28694110 TACGTATGCAAGA
1 TACGTATGCAAGA
28694123 TACG
1 TACG
28694127 CTTCACACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (13 bp):
TACGTATGCAAGA
Found at i:28697444 original size:40 final size:40
Alignment explanation
Indices: 28697370--28697591 Score: 313
Period size: 40 Copynumber: 5.6 Consensus size: 40
28697360 AACCCAAGTA
* * *
28697370 CCTTCGGGATTTAG-CCAGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
28697409 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28697449 CCTTCGGGACTTAGCCCGGATTTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * *
28697489 CCTTCGGGACTTATCTCGGATTTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28697529 CCTTTGGGACTTAGCCCGGATATAGTCACTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28697569 CCTTCGGGACTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28697592 CATTCGAATA
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 12 0.07
40 151 0.92
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28705450 original size:28 final size:28
Alignment explanation
Indices: 28705419--28705496 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
28705409 TGTCTTATTT
*
28705419 TAATACAAGTTTTTAATATGTCATA-ACC
1 TAATACATGTTTTTAATATGTCATAGA-C
* * *
28705447 TAATACATGTTATTAATTTGTCCTAGAC
1 TAATACATGTTTTTAATATGTCATAGAC
* *
28705475 TAAAACATGTTTTTATTATGTC
1 TAATACATGTTTTTAATATGTC
28705497 CTAGCTACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (28 bp):
TAATACATGTTTTTAATATGTCATAGAC
Found at i:28708983 original size:10 final size:11
Alignment explanation
Indices: 28708958--28708985 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28708948 ATATTTGTAA
28708958 AAAAAATTCGT
1 AAAAAATTCGT
28708969 AAAAAATTCGT
1 AAAAAATTCGT
28708980 AAAAAA
1 AAAAAA
28708986 AGGTTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (11 bp):
AAAAAATTCGT
Found at i:28720457 original size:28 final size:28
Alignment explanation
Indices: 28720296--28720450 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
28720286 AACAGTACAG
* *
28720296 TGTGAGCCTTAGCCCAATACAGCAACAG
1 TGTGGGCCTTAGCCCAATACAGCAACAA
*
28720324 TATGGGCCTTAGCCCAATACAGCAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
**
28720352 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
* * * *
28720380 TATGGGCCTTAGCCCAAAATAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
28720408 TGTGGGCCTTAGCCCAATACAGCAACAA
1 TGTGGGCCTTAGCCCAATACAGCAACAA
28720436 TGTGGGCCTTAGCCC
1 TGTGGGCCTTAGCCC
28720451 TAAACAGTAT
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 113 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGCAACAA
Found at i:28720598 original size:26 final size:26
Alignment explanation
Indices: 28720567--28720673 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
28720557 AACACACCAA
*
28720567 TATCGCAGCAAAGCTACCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
*
28720593 AATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* * *
28720619 TATCACAGTAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* *
28720645 TATTGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
28720671 TAT
1 TAT
28720674 ACTTCCTCCA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:28721222 original size:108 final size:107
Alignment explanation
Indices: 28720819--28721526 Score: 560
Period size: 108 Copynumber: 6.6 Consensus size: 107
28720809 GGGGTATAAT
* * * * * * *
28720819 AGTCATTTTACCATATGGGGGTATTTTGGTTATTTTACCCTATCG-TGGTAATTCAGTCATTTTA
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCT-TCGAGGGTATTTCAGTCATTTTA
* * * *
28720883 CCCTATGGGGGTATTTCGATCATTTCACCCTTCGGGGGTATTTC
65 CCCT-TGAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
* * * * *
28720927 -GATCATTTCA-CCTTTCGGGGTATTTTGGTCATTTTACCCTAT-GAGGGTAATTCAGTCATCTT
1 AG-TCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCT-TCGAGGGTATTTCAGTCATTTT
* * * *
28720989 ACCCTATG-GGGATATTTCGGTTATTTCT-CCTTTCAG-GAGTATTTC
64 ACCCT-TGAGGG-TATTTCGATCATTT-TACCCTT-AGAGGGTATTTC
* * * * * * * **
28721034 AGTTATTTCACCCTTTGGGGGTATTTCGGCCATTTTACTCATCGATGGTATTTTGGTCATTTTAC
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
* *
28721099 CCTTTGAGGGCATTTCGATCATTTTACTCTGTAGA-GGTATTTC
66 CC-TTGAGGGTATTTCGATCATTTTACCCT-TAGAGGGTATTTC
* * * *
28721142 AGTCATTTTACCCTGTAGGGGTATTTCGATCATTTTACTCTTCGAGGGTATTTCAATCATTTTAC
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
* * ** *
28721207 CCTTCAGGGGTATTTCGGTCATTTTACATTTTGAGGGTATTTC
66 CCTTGA-GGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
* * * * * ** * * * *
28721250 GGTCATTTTACCCATCAAGGATATTTTAGTCATTTTACCCTTCGAGGGCATCTCAATTATTTTAC
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
* *
28721315 CCTTCGAGGGTATTTTGATCATTTTACCCTTTGAGGGTATTTC
66 CCTT-GAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
** * * * **
28721358 -GATCATTTTACCCTTTAAAGGTATTTCAGTCATTTTACCAATT-GAGGATATTTTGGTCATTTT
1 AG-TCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACC-CTTCGAGGGTATTTCAGTCATTTT
* * * *
28721421 ACCTTTCGAGGGCATTTCGATCATTTTACCCTTCGAGGGTATTTT
64 ACCCTT-GAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
* * * *
28721466 GGT-ATTTTACCCTGTAGGGGTATTTTGGTCATTTCA-CCTATC-AGGGGTATTTCAGTCATTT
1 AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCT-TCGA-GGGTATTTCAGTCATTT
28721527 GCCCACAAAT
Statistics
Matches: 485, Mismatches: 93, Indels: 45
0.78 0.15 0.07
Matches are distributed among these distances:
105 1 0.00
106 7 0.01
107 134 0.28
108 334 0.69
109 9 0.02
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (107 bp):
AGTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTAC
CCTTGAGGGTATTTCGATCATTTTACCCTTAGAGGGTATTTC
Found at i:28721274 original size:27 final size:27
Alignment explanation
Indices: 28720820--28721526 Score: 503
Period size: 27 Copynumber: 26.3 Consensus size: 27
28720810 GGGTATAATA
* * *
28720820 GTCATTTTACCATAT-GGGGGTATTTTG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * * *
28720847 GTTATTTTACCCTATCG-TGGTAATTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
28720874 GTCATTTTACCCTAT-GGGGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * *
28720901 ATCATTTCACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * *
28720928 ATCATTTCACCTTTCG-GGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
28720954 GTCATTTTACCCTAT-GAGGGTAATTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
28720981 GTCATCTTACCCTAT-G-GGGATATTTCG
1 GTCATTTTACCCT-TCGAGGG-TATTTCG
* * *
28721008 GTTATTTCT-CCTTTC-AGGAGTATTTCA
1 GTCATTT-TACCCTTCGAGG-GTATTTCG
* * * *
28721035 GTTATTTCACCCTTTGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * * *
28721062 GCCATTTTACTCATCGATGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
28721089 GTCATTTTACCCTTTGAGGGCATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * *
28721116 ATCATTTTACTCTGTAGA-GGTATTTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
28721143 GTCATTTTACCCTGTAG-GGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * *
28721170 ATCATTTTACTCTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
28721197 ATCATTTTACCCTTC-AGGGGTATTTCG
1 GTCATTTTACCCTTCGA-GGGTATTTCG
** *
28721224 GTCATTTTACATTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * **
28721251 GTCATTTTACCCATCAAGGATATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
28721278 GTCATTTTACCCTTCGAGGGCATCTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
28721305 ATTATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
28721332 ATCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* ** * *
28721359 ATCATTTTACCCTTTAAAGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
28721386 GTCATTTTACCAATT-GAGGATATTTTG
1 GTCATTTTACC-CTTCGAGGGTATTTCG
* *
28721413 GTCATTTTACCTTTCGAGGGCATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
28721440 ATCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
28721467 GT-ATTTTACCCTGTAG-GGGTATTTTG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* *
28721493 GTCATTTCA-CCTATC-AGGGGTATTTCA
1 GTCATTTTACCCT-TCGA-GGGTATTTCG
28721520 GTCATTT
1 GTCATTT
28721527 GCCCACAAAT
Statistics
Matches: 543, Mismatches: 114, Indels: 46
0.77 0.16 0.07
Matches are distributed among these distances:
26 57 0.10
27 475 0.87
28 11 0.02
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:28740666 original size:40 final size:39
Alignment explanation
Indices: 28740582--28740766 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
28740572 TTGAATGATG
* * * * *
28740582 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28740622 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
28740662 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
28740701 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTA-AA
*
28740742 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
28740767 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 36 0.29
40 77 0.62
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28740721 original size:79 final size:81
Alignment explanation
Indices: 28740582--28740766 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
28740572 TTGAATGATG
* *
28740582 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28740646 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28740661 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATC-CGAAGGCA
*
28740723 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28740741 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28740767 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 2 0.02
79 56 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28740788 original size:79 final size:78
Alignment explanation
Indices: 28740612--28740789 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 78
28740602 CTTTGTGCTA
* * *
28740612 AGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AGTGACTATATCCGG-TTAAGATCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCG
**
28740677 AAGGCATTTGTGCG
65 AAGGCATTTGAACG
* * * *
28740691 AGTTACTAAATCCGGGTTAAG-TCTCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 AGTGACTATATCC-GGTTAAGATC-CGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-C
28740754 CCGAAGGCATTTGAACG
62 CCGAAGGCATTTGAACG
28740771 AG-GAGCTATATCCGGTTAA
1 AGTGA-CTATATCCGGTTAA
28740790 ATTCCAAAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
78 4 0.05
79 52 0.63
80 27 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
AGTGACTATATCCGGTTAAGATCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGA
AGGCATTTGAACG
Found at i:28744900 original size:20 final size:20
Alignment explanation
Indices: 28744877--28744925 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
28744867 GGGTTAAGAT
28744877 TGAGCTGAATTGAGCACAAA
1 TGAGCTGAATTGAGCACAAA
* * * * *
28744897 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCACAAA
28744917 TGAGCTGAA
1 TGAGCTGAA
28744926 CTAAGTTAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCACAAA
Found at i:28745835 original size:33 final size:33
Alignment explanation
Indices: 28745789--28745860 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
28745779 TTTAGGAGGC
*
28745789 TTACCTTTAGGAGCAGGAAAATAAAGTTCGGTT
1 TTACCTTTAGGAGCAGGAAAACAAAGTTCGGTT
* * *
28745822 TTACCTTTTGGAGCAGGGAAGCAAAGTTCGGTT
1 TTACCTTTAGGAGCAGGAAAACAAAGTTCGGTT
28745855 TTACCT
1 TTACCT
28745861 GGCTCGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (33 bp):
TTACCTTTAGGAGCAGGAAAACAAAGTTCGGTT
Found at i:28746819 original size:18 final size:17
Alignment explanation
Indices: 28746766--28746811 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
28746756 TTTCTCACTC
*
28746766 TCATTTTCTTTTTCGATT
1 TCATGTTCTTTTTCG-TT
28746784 TCATGTTCTTTTTC-TT
1 TCATGTTCTTTTTCGTT
28746800 TCAT-TTCTTTTT
1 TCATGTTCTTTTT
28746812 TTCGTTTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
18 13 0.48
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (17 bp):
TCATGTTCTTTTTCGTT
Found at i:28747849 original size:17 final size:18
Alignment explanation
Indices: 28747829--28747875 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
28747819 TCACTTTTTT
28747829 TTCGAATTTTTTTTTA-C
1 TTCGAATTTTTTTTTATC
* *
28747846 TTCGTACTTTTTTTTATC
1 TTCGAATTTTTTTTTATC
*
28747864 CTC-AATTTTTTT
1 TTCGAATTTTTTT
28747876 CCTTTTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66
Consensus pattern (18 bp):
TTCGAATTTTTTTTTATC
Found at i:28764571 original size:53 final size:53
Alignment explanation
Indices: 28764508--28764613 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
28764498 AAACCTCTCT
28764508 AAATCTTAGACAATCCTTTATTCTCATTCTACTATATAGCCAATCACTCTTTC
1 AAATCTTAGACAATCCTTTATTCTCATTCTACTATATAGCCAATCACTCTTTC
*
28764561 AAATCTTAGACAATCCTTTATTCTCATTCTACTATATAGCCAATCTCTCTTTC
1 AAATCTTAGACAATCCTTTATTCTCATTCTACTATATAGCCAATCACTCTTTC
28764614 CTCTCGTTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.41
Consensus pattern (53 bp):
AAATCTTAGACAATCCTTTATTCTCATTCTACTATATAGCCAATCACTCTTTC
Found at i:28769188 original size:28 final size:28
Alignment explanation
Indices: 28769131--28769192 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
28769121 GGACAAAACA
* * *
28769131 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
28769159 AAGACATGATTTAAATATGTACCATGCT
1 AAGACATGATTTAAATATGTAACATACT
28769187 AAGACA
1 AAGACA
28769193 AAATAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:28774928 original size:50 final size:50
Alignment explanation
Indices: 28774848--28775029 Score: 203
Period size: 50 Copynumber: 3.7 Consensus size: 50
28774838 GGGAATAAGA
**
28774848 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * *
28774898 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * * * * *
28774948 TCCCATGTAAGACCATATCTAGGATATGGCATTGGTA--GTACAGGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC
*
28774996 ATCCCATGTAAGACCATGTCT-AGACATGGC-TTGG
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
28775030 GCATGTTATT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
47 4 0.04
48 11 0.10
49 23 0.20
50 76 0.67
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
Found at i:28775259 original size:20 final size:20
Alignment explanation
Indices: 28775234--28775282 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
28775224 TGAGTTATTT
28775234 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
28775254 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
28775274 AAG-AAGCAA
1 AAGTAAGCAA
28775283 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:28776513 original size:28 final size:28
Alignment explanation
Indices: 28776456--28776517 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
28776446 GGAAAAAACA
* * *
28776456 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
28776484 AAGACATGATTTAAATATGTAGCATGCT
1 AAGACATGATTTAAATATGTAACATACT
28776512 AAGACA
1 AAGACA
28776518 AAATAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:28787922 original size:20 final size:20
Alignment explanation
Indices: 28787897--28787951 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
28787887 CGTAAATTTA
28787897 ATCAAGCTAAAGTTGAACTC
1 ATCAAGCTAAAGTTGAACTC
* *
28787917 ATCAAGCT-GATTTGAACTC
1 ATCAAGCTAAAGTTGAACTC
** *
28787936 ATGGAGCTAAGGTTGA
1 ATCAAGCTAAAGTTGA
28787952 GTTGAGTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
ATCAAGCTAAAGTTGAACTC
Found at i:28789124 original size:46 final size:46
Alignment explanation
Indices: 28789071--28789164 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
28789061 CAAAGAAAAG
*
28789071 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
28789117 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
28789163 AC
1 AC
28789165 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:28792009 original size:18 final size:17
Alignment explanation
Indices: 28791988--28792022 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28791978 CCTCAATCTC
*
28791988 TTTTTCAATTTTCTTTTT
1 TTTTTCAA-ATTCTTTTT
28792006 TTTTTCAAATTCTTTTT
1 TTTTTCAAATTCTTTTT
28792023 CACTCTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCAAATTCTTTTT
Found at i:28794588 original size:46 final size:46
Alignment explanation
Indices: 28794536--28794623 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 46
28794526 AAAGACCTTG
28794536 ACCCACTATCAA-GAATGATAGGA-ACCTTGGTATATGATGAACCTCA
1 ACCCACTATCAATG-ATGATAGGACA-CTTGGTATATGATGAACCTCA
28794582 ACCCACTATCAATGATGATAGGACACTTGGTATATGATGAAC
1 ACCCACTATCAATGATGATAGGACACTTGGTATATGATGAAC
28794624 GCCACACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (46 bp):
ACCCACTATCAATGATGATAGGACACTTGGTATATGATGAACCTCA
Found at i:28797442 original size:27 final size:27
Alignment explanation
Indices: 28797412--28797470 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
28797402 CTTTCTCACA
*
28797412 TTTTTTTCAATCTCA-ATCTCGTTTTTC
1 TTTTTCTCAATCTCACATCT-GTTTTTC
* *
28797439 TTTTTCTCACTCTCACTATCTTTTTTTC
1 TTTTTCTCAATCTCAC-ATCTGTTTTTC
28797467 TTTT
1 TTTT
28797471 CTCGAGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 10 0.37
29 4 0.15
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTTCTCAATCTCACATCTGTTTTTC
Found at i:28798420 original size:15 final size:15
Alignment explanation
Indices: 28798400--28798428 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28798390 CTTTTTTTGG
28798400 TTTTTTTTTCACAAA
1 TTTTTTTTTCACAAA
28798415 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
28798429 CTTGATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTTTTCACAAA
Found at i:28798485 original size:12 final size:13
Alignment explanation
Indices: 28798468--28798496 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28798458 GGAAATAAAA
28798468 TTTTTTC-AAATT
1 TTTTTTCAAAATT
28798480 TTTTTTCAAAATT
1 TTTTTTCAAAATT
28798493 TTTT
1 TTTT
28798497 CGAAGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTCAAAATT
Found at i:28798867 original size:46 final size:46
Alignment explanation
Indices: 28798814--28798907 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 46
28798804 CAAAGAAAAG
28798814 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
28798860 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
28798906 AC
1 AC
28798908 GCCACACTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 46 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:28799931 original size:58 final size:58
Alignment explanation
Indices: 28799841--28799989 Score: 271
Period size: 58 Copynumber: 2.6 Consensus size: 58
28799831 TGGTTTTGAA
* * *
28799841 ATGCAAATTTAATTAACATGAGAGTTACATAATTAAACTAACTTGACTTAATTTAATG
1 ATGCAAACTTAACTAACATGAAAGTTACATAATTAAACTAACTTGACTTAATTTAATG
28799899 ATGCAAACTTAACTAACATGAAAGTTACATAATTAAACTAACTTGACTTAATTTAATG
1 ATGCAAACTTAACTAACATGAAAGTTACATAATTAAACTAACTTGACTTAATTTAATG
28799957 ATGCAAACTTAACTAACATGAAAGTTACATAAT
1 ATGCAAACTTAACTAACATGAAAGTTACATAAT
28799990 GCATGACTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 88 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (58 bp):
ATGCAAACTTAACTAACATGAAAGTTACATAATTAAACTAACTTGACTTAATTTAATG
Found at i:28811931 original size:2 final size:2
Alignment explanation
Indices: 28811926--28811992 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
28811916 ATTATAAATA
28811926 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
28811968 TG TG CG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
28811993 TAAAACATGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:28827742 original size:40 final size:40
Alignment explanation
Indices: 28827693--28827775 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
28827683 TTGAAATATT
28827693 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
1 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
28827733 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
1 GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
28827773 GGA
1 GGA
28827776 CATGCTGAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (40 bp):
GGAACACTATTTCCATTTACTGAAAGTATGTGATTATTGA
Found at i:28829490 original size:20 final size:21
Alignment explanation
Indices: 28829459--28829503 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
28829449 TTGGAAGCCA
28829459 TCTTTCGGTTAAAGAATGGTT
1 TCTTTCGGTTAAAGAATGGTT
28829480 TCTTT-GGTTAAAGAATGGTT
1 TCTTTCGGTTAAAGAATGGTT
28829500 TCTT
1 TCTT
28829504 CTCATCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (21 bp):
TCTTTCGGTTAAAGAATGGTT
Found at i:28830367 original size:31 final size:30
Alignment explanation
Indices: 28830329--28830389 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
28830319 AAGTCTCCTT
28830329 AGTACATCTTCATGCCACTTTACTCTTTCC
1 AGTACATCTTCATGCCACTTTACTCTTTCC
*
28830359 NAGTACATCTTCATGCCATTTTACTCTTTCC
1 -AGTACATCTTCATGCCACTTTACTCTTTCC
28830390 CATCTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.31, G:0.07, T:0.41
Consensus pattern (30 bp):
AGTACATCTTCATGCCACTTTACTCTTTCC
Found at i:28833835 original size:28 final size:28
Alignment explanation
Indices: 28833785--28833840 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
28833775 GTGATTGTAT
** *
28833785 AGTGTGGGCCTTAGCCCTTTACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAATAAC
*
28833813 AGTGTGGGTCTTAGCCCAATACAATAAC
1 AGTGTGGGCCTTAGCCCAATACAATAAC
28833841 CAGTACAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAATAAC
Found at i:28834196 original size:27 final size:26
Alignment explanation
Indices: 28834178--28834240 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
28834168 TATAATAGTT
*
28834178 ATTTTACCCTATGGGGGTATTCGATC
1 ATTTTACCCTATGGGGGTATTAGATC
* * *
28834204 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTA-TTAGATC
28834231 ATTTTACCCT
1 ATTTTACCCT
28834241 TCGAGATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (26 bp):
ATTTTACCCTATGGGGGTATTAGATC
Found at i:28834251 original size:27 final size:27
Alignment explanation
Indices: 28834178--28834451 Score: 270
Period size: 27 Copynumber: 10.2 Consensus size: 27
28834168 TATAATAGTT
* *
28834178 ATTTTACCCTAT-GGGGGTA-TTCGATC
1 ATTTTACCCT-TCGAGGGTATTTCGGTC
28834204 ATTTTACCCTAT-GAGGGTATTTCGGTC
1 ATTTTACCCT-TCGAGGGTATTTCGGTC
** **
28834231 ATTTTACCCTTCGAGATTATTTTTGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
** *
28834258 ATTTTACCAATCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* * **
28834285 ATTTTATCCATCGAGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
28834312 ATTTTACCCTTC-AGGGGTATTTCGGTC
1 ATTTTACCCTTCGA-GGGTATTTCGGTC
* * *
28834339 ATTTTACCCTTCGAGGATATTTTGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
** **
28834366 ATTTTATGCTTC-AGGGGTATTTTAGTC
1 ATTTTACCCTTCGA-GGGTATTTCGGTC
*
28834393 ATTTTACCCTTCGAGGGTATTTCAGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
**
28834420 ATTTTACCCTTCGAGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
28834447 ATTTT
1 ATTTT
28834452 CCCACGAATC
Statistics
Matches: 210, Mismatches: 32, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
26 21 0.10
27 187 0.89
28 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTC
Found at i:28834314 original size:81 final size:81
Alignment explanation
Indices: 28834178--28834451 Score: 324
Period size: 81 Copynumber: 3.4 Consensus size: 81
28834168 TATAATAGTT
* * *
28834178 ATTTTACCCTAT-GGGGGTA-TTCGATCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCC
1 ATTTTACCCT-TCGAGGGTATTTCGATCATTTTATCC-ATCGAGGGTATTTCAGTCATTTTACCC
** **
28834240 TTCGAGATTATTTTTGTC
64 TTCGAGGGTATTTCAGTC
** *
28834258 ATTTTACCAATCGAGGGTATTTCGATCATTTTATCCATCGAGGGTATTTCAATCATTTTACCCTT
1 ATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCATCGAGGGTATTTCAGTCATTTTACCCTT
*
28834323 C-AGGGGTATTTCGGTC
66 CGA-GGGTATTTCAGTC
* * * * *
28834339 ATTTTACCCTTCGAGGATATTTTGATCATTTTATGCTTC-AGGGGTATTTTAGTCATTTTACCCT
1 ATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCATCGA-GGGTATTTCAGTCATTTTACCCT
28834403 TCGAGGGTATTTCAGTC
65 TCGAGGGTATTTCAGTC
*
28834420 ATTTTACCCTTCGAGGGTATTTCAATCATTTT
1 ATTTTACCCTTCGAGGGTATTTCGATCATTTT
28834452 CCCACGAATC
Statistics
Matches: 166, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 18 0.11
81 146 0.88
82 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (81 bp):
ATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCATCGAGGGTATTTCAGTCATTTTACCCTT
CGAGGGTATTTCAGTC
Found at i:28835068 original size:34 final size:35
Alignment explanation
Indices: 28835029--28835101 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
28835019 AAAGAGGGAG
* * * *
28835029 AGAAAGGTAGTATTCGGCCA-AGAGAGAAGAAGAA
1 AGAAAGGCAATATTCGGCCACAAAGAAAAGAAGAA
*
28835063 AGAAAGGCAATATTCGGCCACAAAGAAAAGAGGAA
1 AGAAAGGCAATATTCGGCCACAAAGAAAAGAAGAA
28835098 AGAA
1 AGAA
28835102 CCAAAGGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.51, C:0.11, G:0.29, T:0.10
Consensus pattern (35 bp):
AGAAAGGCAATATTCGGCCACAAAGAAAAGAAGAA
Found at i:28837154 original size:20 final size:20
Alignment explanation
Indices: 28837129--28837183 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
28837119 TGTGGTTCAA
* *
28837129 CTCATTCGAGTTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
28837149 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
28837169 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
28837184 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:28840158 original size:5 final size:5
Alignment explanation
Indices: 28840148--28840174 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28840138 TACTTATTTA
28840148 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
28840175 TTGAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:28849752 original size:130 final size:130
Alignment explanation
Indices: 28849512--28849772 Score: 450
Period size: 130 Copynumber: 2.0 Consensus size: 130
28849502 CAACTCCAAA
* *
28849512 TATAGACATAGCACCTATTAGCCATGAACTCAAGGTACTTACCCGATCCGCTGTCCGTGATCGAC
1 TATAAACATAGCACCTATTAGCCATGAACTCAAGGTACTTACCCGATCCGCTGTCCGTGATCAAC
*
28849577 TCAATAACGTCGCACACTTAGTGTCCATAATGTTTCAAAAATATATAATAAGTCCGCACACTCAG
66 TCAATAACGTCGCACACTTAGTGTCCATAATGATTCAAAAATATATAATAAGTCCGCACACTCAG
*
28849642 TATAAACATAGCGCCTATTAGCCATGAACTCAAGGTACTTACCCGATCCGCTGTCCGTGATCAAC
1 TATAAACATAGCACCTATTAGCCATGAACTCAAGGTACTTACCCGATCCGCTGTCCGTGATCAAC
* * * *
28849707 TCAATAATGTCGCACACTTAGTGTCCATAGTGATTCAAAAGTATATATTAAGTCCGCACACTCAG
66 TCAATAACGTCGCACACTTAGTGTCCATAATGATTCAAAAATATATAATAAGTCCGCACACTCAG
28849772 T
1 T
28849773 GCTATATAAT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 123 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (130 bp):
TATAAACATAGCACCTATTAGCCATGAACTCAAGGTACTTACCCGATCCGCTGTCCGTGATCAAC
TCAATAACGTCGCACACTTAGTGTCCATAATGATTCAAAAATATATAATAAGTCCGCACACTCAG
Found at i:28849824 original size:28 final size:28
Alignment explanation
Indices: 28849761--28849938 Score: 225
Period size: 28 Copynumber: 6.4 Consensus size: 28
28849751 ATATTAAGTC
* *
28849761 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28849788 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28849816 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
28849844 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
28849872 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * * * *
28849899 CGCAGACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAA-TCAAACT
28849928 CGCACACTTAG
1 CGCACACTTAG
28849939 CGCCAATCTC
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
27 42 0.31
28 80 0.60
29 12 0.09
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:28856761 original size:77 final size:78
Alignment explanation
Indices: 28856628--28856776 Score: 282
Period size: 77 Copynumber: 1.9 Consensus size: 78
28856618 ATAATAAAGA
28856628 AATGGAAAAAAAAGAAAGAATGTGTGTGAGTGTTCCCCCCCCATTGCCGTGAGTTAAAGAAAAGA
1 AATGGAAAAAAAAGAAAGAATGTGTGTGAGTGTTCCCCCCCCATTGCCGTGAGTTAAAGAAAAGA
28856693 AAAAAAAAATTTT
66 AAAAAAAAATTTT
*
28856706 AATGGAAAAAAAAGAAAGAATGTGTGTGAGTGTT-CCCCCCCATTGCCGTGAGTTAAATAAAAGA
1 AATGGAAAAAAAAGAAAGAATGTGTGTGAGTGTTCCCCCCCCATTGCCGTGAGTTAAAGAAAAGA
28856770 AAAAAAA
66 AAAAAAA
28856777 TTTGTTCATC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 36 0.51
78 34 0.49
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (78 bp):
AATGGAAAAAAAAGAAAGAATGTGTGTGAGTGTTCCCCCCCCATTGCCGTGAGTTAAAGAAAAGA
AAAAAAAAATTTT
Found at i:28856834 original size:38 final size:38
Alignment explanation
Indices: 28856791--28856866 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
28856781 TTCATCCTTT
28856791 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
*
28856829 TTCATTTCTTTTGGCCGAAAATTCTAAGGAGGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
28856867 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:28857313 original size:40 final size:40
Alignment explanation
Indices: 28857219--28857363 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
28857209 TACTCGAATG
* *
28857219 ATATCCGGGCTAAGTCCCAAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* * *
28857260 ACATCCGGACTAAGAT-CCGAAGGCAGTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
28857300 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
28857340 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
28857364 CTTGTGCGAG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.69
41 26 0.29
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:28859260 original size:47 final size:46
Alignment explanation
Indices: 28859206--28859297 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 46
28859196 AATTTTCTTT
* *
28859206 AACTAAGTAACTTATCTGGAAATAATAAGGGCAAATTTAACAAGCTG
1 AACTAAGTAACTTATCCGGAAATAATAAGAGC-AATTTAACAAGCTG
*
28859253 AACTAAGTAACTTATCCGGAAATATTAAGAGCAATTTAACAAGCT
1 AACTAAGTAACTTATCCGGAAATAATAAGAGCAATTTAACAAGCT
28859298 TTAAATTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 13 0.31
47 29 0.69
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (46 bp):
AACTAAGTAACTTATCCGGAAATAATAAGAGCAATTTAACAAGCTG
Found at i:28861290 original size:15 final size:15
Alignment explanation
Indices: 28861270--28861299 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28861260 ACAGAACTGG
28861270 TACGGATTCAATATT
1 TACGGATTCAATATT
28861285 TACGGATTCAATATT
1 TACGGATTCAATATT
28861300 CTTTTCAGTC
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:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TACGGATTCAATATT
Done.