Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1532
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1715538
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 192937 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:873281 original size:2 final size:2
Alignment explanation
Indices: 873274--873323 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
873264 TAACATCAGA
873274 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
873316 CT CT CT CT
1 CT CT CT CT
873324 GTAATGAGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:875222 original size:4 final size:4
Alignment explanation
Indices: 875213--875291 Score: 158
Period size: 4 Copynumber: 19.8 Consensus size: 4
875203 AAGTTTCCTT
875213 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
875261 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
875292 TAGTATCTAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:875329 original size:4 final size:4
Alignment explanation
Indices: 875322--875371 Score: 75
Period size: 4 Copynumber: 12.5 Consensus size: 4
875312 CGATCGATCG
*
875322 ATCC ATCC ATCC ATCC ATCC ATCC AT-C AACTC ATCC ATCC ATCC ATCC
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATC-C ATCC ATCC ATCC ATCC
875370 AT
1 AT
875372 GTATCTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 2 0.05
4 37 0.88
5 3 0.07
ACGTcount: A:0.28, C:0.46, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:876876 original size:2 final size:2
Alignment explanation
Indices: 876869--876902 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
876859 GGATTATAAA
*
876869 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
876903 ATATATTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:890778 original size:22 final size:22
Alignment explanation
Indices: 890753--890816 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
890743 TAAGGATGAC
890753 CAGGAACAGTAACTCTTGGTCT
1 CAGGAACAGTAACTCTTGGTCT
**
890775 CAGGAACAGTAACTCTTCATCT
1 CAGGAACAGTAACTCTTGGTCT
*
890797 CAGGAACAGTAACTCCTGGT
1 CAGGAACAGTAACTCTTGGT
890817 GCCAAGAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (22 bp):
CAGGAACAGTAACTCTTGGTCT
Found at i:902082 original size:13 final size:13
Alignment explanation
Indices: 902064--902088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
902054 AATGAGAGAG
902064 AGTGAGAGAGGAA
1 AGTGAGAGAGGAA
902077 AGTGAGAGAGGA
1 AGTGAGAGAGGA
902089 GAGAGGCAGG
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:0.44, C:0.00, G:0.48, T:0.08
Consensus pattern (13 bp):
AGTGAGAGAGGAA
Found at i:910780 original size:20 final size:20
Alignment explanation
Indices: 910757--910795 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
910747 TTTGTGTGTT
910757 TGTTTA-TTCTGAGTGTTGAA
1 TGTTTACTT-TGAGTGTTGAA
910777 TGTTTACTTTGAGTGTTGA
1 TGTTTACTTTGAGTGTTGA
910796 CAGCGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.18, C:0.05, G:0.26, T:0.51
Consensus pattern (20 bp):
TGTTTACTTTGAGTGTTGAA
Found at i:921600 original size:13 final size:13
Alignment explanation
Indices: 921582--921615 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
921572 AGGGACCATG
921582 AACAAATACAGTA
1 AACAAATACAGTA
*
921595 AACAAAAACAGTA
1 AACAAATACAGTA
921608 AACAAATA
1 AACAAATA
921616 TGATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.12
Consensus pattern (13 bp):
AACAAATACAGTA
Found at i:925758 original size:16 final size:15
Alignment explanation
Indices: 925722--925758 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
925712 CCGGTGGATG
925722 CTGGAGAAGTCGTAT
1 CTGGAGAAGTCGTAT
925737 CATGGAGAAGTCGTACT
1 C-TGGAGAAGTCGTA-T
925754 CTGGA
1 CTGGA
925759 AAAATCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24
Consensus pattern (15 bp):
CTGGAGAAGTCGTAT
Found at i:928272 original size:13 final size:13
Alignment explanation
Indices: 928254--928278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
928244 TGATTTATAT
928254 ACTATAACCAGGC
1 ACTATAACCAGGC
928267 ACTATAACCAGG
1 ACTATAACCAGG
928279 ATGTGCACAT
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:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (13 bp):
ACTATAACCAGGC
Found at i:928908 original size:21 final size:21
Alignment explanation
Indices: 928829--928907 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
928819 CATTTCAATT
928829 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
*
928850 TCTCATAGCATACCATACAAA
1 TCTCATAGCATAGCATACAAA
*
928871 TCTCATAGCATATCATTA-AAA
1 TCTCATAGCATAGCA-TACAAA
* *
928892 TCGCATACCATAGCAT
1 TCTCATAGCATAGCAT
928908 TGCATTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 49 0.94
22 2 0.04
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:929431 original size:21 final size:21
Alignment explanation
Indices: 929415--929458 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
929405 TGCCCATCAT
*
929415 CAGGGTCTGTACACCCATAAC
1 CAGGGTCAGTACACCCATAAC
* *
929436 CAGGGTCAGTATACCCATTAC
1 CAGGGTCAGTACACCCATAAC
929457 CA
1 CA
929459 TAGTTTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (21 bp):
CAGGGTCAGTACACCCATAAC
Found at i:929554 original size:105 final size:105
Alignment explanation
Indices: 929372--929590 Score: 294
Period size: 105 Copynumber: 2.1 Consensus size: 105
929362 ACAAGGGTCC
* * *
929372 CCAGGGTCAGAGTACGTATCACCAGAGTCTGTGTGCCCATCATCAGGGTCTGTACACCCATAACC
1 CCAGGGTCAGAGTACGTATCACCAGAGTCTGTGTGCCCATAAACAGGGTATGTACACCCATAACC
** * * * * *
929437 AGGGTCAGTATACCCATTACCATAGTTTCCATACCTATCA
66 AAAGTCAGTATACCCATCACCAGAGTCTCAATACCTATAA
* * * *
929477 CCAGGGTCAGAGTACGTATCACCATATTCTGTGTGCTCATAAACAGGGTATGTACACCTATAACC
1 CCAGGGTCAGAGTACGTATCACCAGAGTCTGTGTGCCCATAAACAGGGTATGTACACCCATAACC
*
929542 AAAGTCAGTATACCCATCACCAGGGTCTCAATACCTATAA
66 AAAGTCAGTATACCCATCACCAGAGTCTCAATACCTATAA
*
929582 CAAGGGTCA
1 CCAGGGTCA
929591 TTATACCCAT
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (105 bp):
CCAGGGTCAGAGTACGTATCACCAGAGTCTGTGTGCCCATAAACAGGGTATGTACACCCATAACC
AAAGTCAGTATACCCATCACCAGAGTCTCAATACCTATAA
Found at i:929575 original size:21 final size:21
Alignment explanation
Indices: 929520--930239 Score: 212
Period size: 21 Copynumber: 34.4 Consensus size: 21
929510 TGCTCATAAA
* * *
929520 CAGGGTATGTACACCTATAAC
1 CAGGGTCTGTATACCTATCAC
** * *
929541 CAAAGTCAGTATACCCATCAC
1 CAGGGTCTGTATACCTATCAC
** *
929562 CAGGGTCTCAATACCTATAAC
1 CAGGGTCTGTATACCTATCAC
* *
929583 AAGGGTCAT-TATACCCATCAC
1 CAGGGTC-TGTATACCTATCAC
* * * *
929604 CAGGGTCTGTACACCCATAAT
1 CAGGGTCTGTATACCTATCAC
929625 CAGGGTCAT-TATACCTATCAC
1 CAGGGTC-TGTATACCTATCAC
* *
929646 CAGGGTCTCTATACCTAACAC
1 CAGGGTCTGTATACCTATCAC
* * *
929667 AAGGGTCAG-AGTACGTATCAC
1 CAGGGTCTGTA-TACCTATCAC
* * *
929688 CAGAGTCTGTGTGCCTATCAC
1 CAGGGTCTGTATACCTATCAC
* * * * *
929709 TAGAGTCTGTACACCCATAAC
1 CAGGGTCTGTATACCTATCAC
** * *
929730 CAAAGTCAGTATACCCATCAC
1 CAGGGTCTGTATACCTATCAC
**
929751 CAGGGTCTCAATACCTATCAC
1 CAGGGTCTGTATACCTATCAC
* ** *
929772 CAGGGTCAT-CATAGAATTTCAC
1 CAGGGTC-TGTATA-CCTATCAC
* * * * * *
929794 TAGAGTCTGTGTGCCCAACAC
1 CAGGGTCTGTATACCTATCAC
* * *
929815 CGGGGTCTGAAAACCTAT-ATC
1 CAGGGTCTGTATACCTATCA-C
*
929836 CAGGGTCAGTATATCC-ATCAC
1 CAGGGTCTGTATA-CCTATCAC
* **
929857 AAGGGTCTCAATACCTATCAC
1 CAGGGTCTGTATACCTATCAC
* * *
929878 CAGAGTCACG-AGTACATATCAC
1 CAGGGTC-TGTA-TACCTATCAC
* * * *
929900 CAGAGTCTGTGTGCATATCAC
1 CAGGGTCTGTATACCTATCAC
* * * *
929921 CTGGGTCAGTTTACAC-ATAAC
1 CAGGGTCTGTATAC-CTATCAC
* *
929942 CAGGGTCAGTATACCCATCAC
1 CAGGGTCTGTATACCTATCAC
** *
929963 CAGGGTCTACATACCAATCAC
1 CAGGGTCTGTATACCTATCAC
** * *
929984 CAGGGTAAGTGTACGTATCAC
1 CAGGGTCTGTATACCTATCAC
** * * *
930005 CACAGTCTGTATGCCCATAAC
1 CAGGGTCTGTATACCTATCAC
*
930026 CAGGGTCT-TAATACCTAGCAC
1 CAGGGTCTGT-ATACCTATCAC
* ** * *
930047 CAGAGTAAGTGTACGTATCAC
1 CAGGGTCTGTATACCTATCAC
** * *
930068 CAGAATCTGTGT--GT-TCAC
1 CAGGGTCTGTATACCTATCAC
* *
930086 TAGGGTCTGTACACAC-AT-AGC
1 CAGGGTCTGTATAC-CTATCA-C
* * *
930107 CAGGGTCAGTATACCCAACAC
1 CAGGGTCTGTATACCTATCAC
** *
930128 CAGGG-CTCCATACCTATTAC
1 CAGGGTCTGTATACCTATCAC
* * *
930148 TAGGGTCAG-AGTACGTATCAC
1 CAGGGTCTGTA-TACCTATCAC
* * * * *
930169 TAGAGTCTGTGTGCCCATCAC
1 CAGGGTCTGTATACCTATCAC
* * * *
930190 CAGGATCTGTACACCCATAAC
1 CAGGGTCTGTATACCTATCAC
* * *
930211 CATGGTCAGTATACCCATCAC
1 CAGGGTCTGTATACCTATCAC
930232 CAGGGTCT
1 CAGGGTCT
930240 CCATTATACC
Statistics
Matches: 489, Mismatches: 180, Indels: 60
0.67 0.25 0.08
Matches are distributed among these distances:
18 11 0.02
19 2 0.00
20 24 0.05
21 417 0.85
22 35 0.07
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (21 bp):
CAGGGTCTGTATACCTATCAC
Found at i:929854 original size:106 final size:104
Alignment explanation
Indices: 929599--930033 Score: 419
Period size: 106 Copynumber: 4.1 Consensus size: 104
929589 CATTATACCC
* * * * * *
929599 ATCACCAGGGTCTGTACACCCATAATCAGGGTCATTATACCTATCACCAGGGTCTCTATACCTAA
1 ATCACCAGGGTCTGTA-AACCATAACCAGGGTCAGTATACCCATCACCAGGGTCTCAATACCTAT
* *
929664 CACAAGGGTCAGAGTACG-TATCACCAGAGTCTGTGTGCCT
65 CACCAGGGTCACAGTA-GATATCACCAGAGTCTGTGTGCCT
* * * **
929704 ATCACTAGAGTCTGTACACCCATAACCAAAGTCAGTATACCCATCACCAGGGTCTCAATACCTAT
1 ATCACCAGGGTCTGTA-AACCATAACCAGGGTCAGTATACCCATCACCAGGGTCTCAATACCTAT
* * *
929769 CACCAGGGTCATCA-TAGAATTTCACTAGAGTCTGTGTGCCC
65 CACCAGGGTCA-CAGTAG-ATATCACCAGAGTCTGTGTGCCT
* * * * * *
929810 AACACCGGGGTCTGAAAACCTATATCCAGGGTCAGTATATCCATCACAAGGGTCTCAATACCTAT
1 ATCACCAGGGTCTGTAAACC-ATAACCAGGGTCAGTATACCCATCACCAGGGTCTCAATACCTAT
* * *
929875 CACCAGAGTCACGAGTACATATCACCAGAGTCTGTGTGCAT
65 CACCAGGGTCAC-AGTAGATATCACCAGAGTCTGTGTGCCT
* * ** *
929916 ATCACCTGGGTCAGTTTACACATAACCAGGGTCAGTATACCCATCACCAGGGTCT-ACATACCAA
1 ATCACCAGGGTCTGTAAAC-CATAACCAGGGTCAGTATACCCATCACCAGGGTCTCA-ATACCTA
* ** * * *
929980 TCACCAGGGTAAGTGTACG-TATCACCACAGTCTGTATGCCC
64 TCACCAGGGTCACAGTA-GATATCACCAGAGTCTGTGTGCCT
*
930021 ATAACCAGGGTCT
1 ATCACCAGGGTCT
930034 TAATACCTAG
Statistics
Matches: 268, Mismatches: 53, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
104 1 0.00
105 104 0.39
106 160 0.60
107 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (104 bp):
ATCACCAGGGTCTGTAAACCATAACCAGGGTCAGTATACCCATCACCAGGGTCTCAATACCTATC
ACCAGGGTCACAGTAGATATCACCAGAGTCTGTGTGCCT
Found at i:930292 original size:108 final size:105
Alignment explanation
Indices: 930089--930401 Score: 319
Period size: 108 Copynumber: 3.0 Consensus size: 105
930079 TGTTCACTAG
* * * *
930089 GGTCTGTACACACATAGCCAGGGTCAGTATACCCAACACCAGGG-CTCCATACCTATTACTAGGG
1 GGTCTGTACACCCATAACCAAGGTCAGTATACCCATCACCAGGGTCTCCATACCTATTACTAGGG
930153 TCAGAGTACGTATCACTAGAGTCTGTGTGCCCATCACCA-
66 TCAGAGTACGTATCACTAGAGTCTGTGTGCCCATCACCAT
* *
930192 GGATCTGTACACCCATAACCATGGTCAGTATACCCATCACCAGGGTCTCCATTATACCTTTTACT
1 GG-TCTGTACACCCATAACCAAGGTCAGTATACCCATCACCAGGGTCTCC---ATACCTATTACT
* * * * *
930257 AGTGTCAGTGTTCGTAGT-ACTAGGGTCTGTTTGCCCATCACCAT
62 AGGGTCAGAGTACGTA-TCACTAGAGTCTGTGTGCCCATCACCAT
* * * * ** * *
930301 GGTCTGTGCATCCATTACCAAGGTCAGTTTACCCATCACCAGGGTCTTAATACCTATCACCAGGG
1 GGTCTGTACACCCATAACCAAGGTCAGTATACCCATCACCAGGGTCTCCATACCTATTACTAGGG
** ** * *
930366 AT-AGTTTACAAATCAATAGGGTCTGTGTGCCCATCA
66 -TCAGAGTACGTATCACTAGAGTCTGTGTGCCCATCA
930402 TTAGGGTCAG
Statistics
Matches: 174, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
103 2 0.01
104 39 0.22
105 42 0.24
106 1 0.01
108 87 0.50
109 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (105 bp):
GGTCTGTACACCCATAACCAAGGTCAGTATACCCATCACCAGGGTCTCCATACCTATTACTAGGG
TCAGAGTACGTATCACTAGAGTCTGTGTGCCCATCACCAT
Found at i:930304 original size:21 final size:21
Alignment explanation
Indices: 930280--930347 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
930270 GTAGTACTAG
*
930280 GGTCTGTTTGCCCATCACCAT
1 GGTCTGTTTGCCCATCACCAA
*
930301 GGTCTG--TGCATCCATTACCAA
1 GGTCTGTTTGC--CCATCACCAA
* * *
930322 GGTCAGTTTACCCATCACCAG
1 GGTCTGTTTGCCCATCACCAA
930343 GGTCT
1 GGTCT
930348 TAATACCTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 3 0.08
21 31 0.86
23 2 0.06
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (21 bp):
GGTCTGTTTGCCCATCACCAA
Found at i:930931 original size:23 final size:21
Alignment explanation
Indices: 930885--930970 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
930875 TGTGTGCTCT
930885 TCACCAGGGTCAGTATACCTA
1 TCACCAGGGTCAGTATACCTA
*
930906 TCACCGGGGTCAGTATATATCC-A
1 TCACCAGGGTCAG--TATA-CCTA
* * * *
930929 TCACCAGGGTTACTTTACTTA
1 TCACCAGGGTCAGTATACCTA
*
930950 TCAACAGGGTCAGTATTACCT
1 TCACCAGGGTCAGTA-TACCT
930971 TATTTAGGCA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.02
21 27 0.55
22 4 0.08
23 15 0.31
24 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (21 bp):
TCACCAGGGTCAGTATACCTA
Found at i:931298 original size:21 final size:21
Alignment explanation
Indices: 931181--931756 Score: 202
Period size: 21 Copynumber: 27.7 Consensus size: 21
931171 ACGTACTCTT
* * **
931181 ACCCTGGTGATAGTTATGGAG
1 ACCCTGGTGATGGGTATACAG
* *
931202 ATCCTGGTGATGGGTATACTG
1 ACCCTGGTGATGGGTATACAG
* * * ** *
931223 GCCCTGATTATGGGTGCAAAG
1 ACCCTGGTGATGGGTATACAG
**
931244 ACGTTGGTGATGGGTATACAG
1 ACCCTGGTGATGGGTATACAG
*
931265 ACCCTGG-GTATGGGTGTTA-AG
1 ACCCTGGTG-ATGGGT-ATACAG
* * *
931286 ACCCTGGTGATGGGCACACAA
1 ACCCTGGTGATGGGTATACAG
* *
931307 ACTCTAGTGATGGGTATA-AG
1 ACCCTGGTGATGGGTATACAG
* ** *
931327 ACCCTGGTGATAGGTATTGAC
1 ACCCTGGTGATGGGTATACAG
* * *
931348 ACTCTTGTGAT---T-TAGAG
1 ACCCTGGTGATGGGTATACAG
* ** * *
931365 ACCCTGGTGTTACGTAAACTG
1 ACCCTGGTGATGGGTATACAG
* * *
931386 ACCCTGGTTATGAGTGTACAG
1 ACCCTGGTGATGGGTATACAG
* * * * *
931407 ACCTTGGTGTTGGGCACACAA
1 ACCCTGGTGATGGGTATACAG
* * *
931428 ACTCTAGTGATGGGTTTA-ATG
1 ACCCTGGTGATGGGTATACA-G
* ** **
931449 ACCCTGTTGATAAGTATTGAG
1 ACCCTGGTGATGGGTATACAG
* * *
931470 AACCTGGTAATGGGTATACTG
1 ACCCTGGTGATGGGTATACAG
** * *
931491 ACTTTGGTTATGGGTGTACAG
1 ACCCTGGTGATGGGTATACAG
* * * *
931512 ACCCTGGTTATGAGCACACAG
1 ACCCTGGTGATGGGTATACAG
* ** *
931533 ACTCTGGTGATACGTACT-CTG
1 ACCCTGGTGATGGGTA-TACAG
* **
931554 ACCCTGGTGATAGGTATGGAG
1 ACCCTGGTGATGGGTATACAG
* *
931575 ATCCTGGTGATGGGTATACTG
1 ACCCTGGTGATGGGTATACAG
* *
931596 ACCC-GGTTATGGGTGTACAG
1 ACCCTGGTGATGGGTATACAG
* * *
931616 AACCTGGTGATGGGTACACAA
1 ACCCTGGTGATGGGTATACAG
* ** *
931637 ACTCTAATGATGGCTATA-ATG
1 ACCCTGGTGATGGGTATACA-G
* * **
931658 ACCTTGGTGATAGGTATTGAG
1 ACCCTGGTGATGGGTATACAG
*
931679 ACCCTGGTGATGGGTATACTG
1 ACCCTGGTGATGGGTATACAG
** * * *
931700 ACTTTGGTTATTGGTGTACAG
1 ACCCTGGTGATGGGTATACAG
* * *
931721 ACCCTGGTGATAGGCACACAG
1 ACCCTGGTGATGGGTATACAG
* *
931742 ACCTTGGTGAGGGGT
1 ACCCTGGTGATGGGT
931757 TATGGATAGA
Statistics
Matches: 379, Mismatches: 160, Indels: 32
0.66 0.28 0.06
Matches are distributed among these distances:
17 11 0.03
18 1 0.00
20 37 0.10
21 325 0.86
22 5 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (21 bp):
ACCCTGGTGATGGGTATACAG
Found at i:933539 original size:19 final size:20
Alignment explanation
Indices: 933477--933595 Score: 71
Period size: 19 Copynumber: 5.7 Consensus size: 20
933467 TTAAAACAGA
*
933477 TTAAATTCGTCATAACGAATT
1 TTAAATTCGTTATAACGAA-T
* * *
933498 CTTAAAATTTGTTATTACAAAT
1 -TT-AAATTCGTTATAACGAAT
933520 TT-AATTCGTTATAACGAAT
1 TTAAATTCGTTATAACGAAT
* *
933539 TCAAAAATTCGTTATAGCG-AT
1 T--TAAATTCGTTATAACGAAT
* * *
933560 TTGAATTCGTTTTAACAAAT
1 TTAAATTCGTTATAACGAAT
*
933580 TCAAGAATTCGTTATA
1 T-TA-AATTCGTTATA
933596 TCAAATTCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
19 26 0.36
20 3 0.04
21 5 0.07
22 26 0.36
23 13 0.18
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
TTAAATTCGTTATAACGAAT
Found at i:933551 original size:22 final size:22
Alignment explanation
Indices: 933479--933609 Score: 85
Period size: 22 Copynumber: 6.2 Consensus size: 22
933469 AAAACAGATT
* * *
933479 AAATTCGTCATAACGAATTCTTA
1 AAATTCGTTATAACAAATTC-AA
* *
933502 AAATTTGTTATTACAAATT---
1 AAATTCGTTATAACAAATTCAA
* *
933521 TAATTCGTTATAACGAATTCAA
1 AAATTCGTTATAACAAATTCAA
* * *
933543 AAATTCGTTATAGC-GATT--T
1 AAATTCGTTATAACAAATTCAA
* *
933562 GAATTCGTTTTAACAAATTCAA
1 AAATTCGTTATAACAAATTCAA
* *
933584 GAATTCGTTATATCAAATTCAA
1 AAATTCGTTATAACAAATTCAA
933606 AAAT
1 AAAT
933610 ATTTTTGATA
Statistics
Matches: 82, Mismatches: 20, Indels: 13
0.71 0.17 0.11
Matches are distributed among these distances:
19 26 0.32
20 3 0.04
21 3 0.04
22 35 0.43
23 15 0.18
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATTCGTTATAACAAATTCAA
Found at i:933567 original size:41 final size:40
Alignment explanation
Indices: 933480--933602 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 40
933470 AAACAGATTA
* * *
933480 AATTCGTCATAACGAATTCTTAAAATTTGTTATTACAAATTT
1 AATTCGTTATAACGAATTC-AAAAATTCGTTA-TACAAATTT
*
933522 AATTCGTTATAACGAATTCAAAAATTCGTTATAGC-GATTT
1 AATTCGTTATAACGAATTCAAAAATTCGTTATA-CAAATTT
* * *
933562 GAATTCGTTTTAACAAATTCAAGAATTCGTTATATCAAATT
1 -AATTCGTTATAACGAATTCAAAAATTCGTTATA-CAAATT
933603 CAAAAATATT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 6 0.09
41 42 0.61
42 21 0.30
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (40 bp):
AATTCGTTATAACGAATTCAAAAATTCGTTATACAAATTT
Found at i:937805 original size:2 final size:2
Alignment explanation
Indices: 937798--937843 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
937788 TGAAATTTGG
937798 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
937840 CT CT
1 CT CT
937844 GGTTATACCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:938281 original size:13 final size:13
Alignment explanation
Indices: 938263--938287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
938253 TATCATATAC
938263 TGTATGTAAAACA
1 TGTATGTAAAACA
938276 TGTATGTAAAAC
1 TGTATGTAAAAC
938288 CTTCAATAGT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATGTAAAACA
Found at i:946729 original size:2 final size:2
Alignment explanation
Indices: 946722--946778 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
946712 TAAAACATTT
946722 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
946764 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
946779 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:957021 original size:21 final size:21
Alignment explanation
Indices: 956979--957021 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
956969 AGATCCTAAA
*
956979 ATAGAGGAAGAAATAGCGGTC
1 ATAGAGGAAGAAATAGCAGTC
*
957000 ATAGAGGTAATAAA-AGCAGTC
1 ATAGAGG-AAGAAATAGCAGTC
957021 A
1 A
957022 ACCCTCTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (21 bp):
ATAGAGGAAGAAATAGCAGTC
Found at i:963154 original size:20 final size:20
Alignment explanation
Indices: 963129--963192 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
963119 AGGGGCATGC
963129 ACAGGGGTATACAGTGGCTT
1 ACAGGGGTATACAGTGGCTT
*
963149 ACAGGGG-ATGACAGTGGCGT
1 ACAGGGGTAT-ACAGTGGCTT
* *
963169 ACAGGCGGT-GACAGGGGCTT
1 ACAGG-GGTATACAGTGGCTT
963189 ACAG
1 ACAG
963193 TGGCACACAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.17
Consensus pattern (20 bp):
ACAGGGGTATACAGTGGCTT
Found at i:963255 original size:42 final size:43
Alignment explanation
Indices: 963199--963280 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
963189 ACAGTGGCAC
* *
963199 ACAGGGGCTGTGTACAGGGGCGCACAGGGGATG-ACAGGGTAT
1 ACAGGGGCTCTGTACAGGGGCACACAGGGGATGTACAGGGTAT
*
963241 ACAGGGGCTCTGTACAGTGGCACACAGGGGATGTACAGGG
1 ACAGGGGCTCTGTACAGGGGCACACAGGGGATGTACAGGG
963281 GATGACAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.24, C:0.18, G:0.43, T:0.15
Consensus pattern (43 bp):
ACAGGGGCTCTGTACAGGGGCACACAGGGGATGTACAGGGTAT
Found at i:963267 original size:23 final size:23
Alignment explanation
Indices: 963188--963278 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 23
963178 GACAGGGGCT
*
963188 TACAGTGGCACACAGGGGCTGTG
1 TACAGTGGCACACAGGGGCTATG
* *
963211 TACAGGGGCGCACAGGGG--ATG
1 TACAGTGGCACACAGGGGCTATG
* * *
963232 -ACAG-GGTATACAGGGGCTCTG
1 TACAGTGGCACACAGGGGCTATG
963253 TACAGTGGCACACAGGGG--ATG
1 TACAGTGGCACACAGGGGCTATG
963274 TACAG
1 TACAG
963279 GGGATGACAG
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
19 9 0.17
20 4 0.07
21 11 0.20
22 4 0.07
23 26 0.48
ACGTcount: A:0.25, C:0.20, G:0.40, T:0.15
Consensus pattern (23 bp):
TACAGTGGCACACAGGGGCTATG
Found at i:963280 original size:11 final size:10
Alignment explanation
Indices: 963264--963324 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
963254 ACAGTGGCAC
963264 ACAGGGGATG
1 ACAGGGGATG
963274 TACAGGGGATG
1 -ACAGGGGATG
** **
963285 ACAGTGAAAAC
1 ACAG-GGGATG
*
963296 ACAGGGGGTG
1 ACAGGGGATG
*
963306 ACAGGGGAAG
1 ACAGGGGATG
963316 ACAGGGGAT
1 ACAGGGGAT
963325 TTTCATACGG
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.34, C:0.11, G:0.44, T:0.10
Consensus pattern (10 bp):
ACAGGGGATG
Found at i:966024 original size:437 final size:432
Alignment explanation
Indices: 965236--966145 Score: 1240
Period size: 437 Copynumber: 2.1 Consensus size: 432
965226 AAGTCTTCGT
* * * *
965236 AGCCCTTTTGGCCTCTTATTTGAGGGGTCA-CTCCTTTTTTCTTGATATCAAATGAAAGGTCTTG
1 AGCCCTTTTGGCC-CTTATTTGAGGGGCCAGC-CCCTTTTTATTGATATCAAATAAAAGGTCTTG
* * *
965300 TAAATATAAACATATTTTGTTCTACATGTATTCACGAATTGTTGACCGTTCTAGAGATATCCGAA
64 TAAATATAAACACATTTTGTTCAACAAGTATTCACGAATTGTTGACCGTTCTAGAGATATCCGAA
* * * *
965365 CAATTGTGTTTTGAGGCCGACCCAACTCCTTACCAGGGCCACCAACATAAATGTTTTAGATACCA
129 CAAATGTGTTTTGAGGCCGACCCAAATCCTTACCAGGGCCACCAACAAAAATGTTTTAGAGACCA
965430 TATCGTTAAGAACATTATTTTAAGCATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCTTT
194 TATCGTTAAGAACATTATTTTAAGCATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCTTT
* ** * * *
965495 TCTAGATATTAATGATCAAAGTTTTTGACATATGGCCCCTTGAAACCCCTAATTACGTATCATAT
259 TCTAGATATTAATGATCAAAATTTCGGACATATGGCCCCGTGAAACCCCTAATGACGTAACATAT
* *
965560 GACATATGTATGGTACCGTATAGATAAACAGATGTACAATGAACATTTTTGGTTCTATAATTGAT
324 GACATATGCATGGTACCGTATAGATAAAAAGATGTACAATGAACATTTTTGGTTCTATAATTGAT
* * *
965625 AACAAATTATTTTTCAGTTAAGAGTTATTATAAAAAGAATTTAC
389 AACAAATTATTTTTCAGTAAAGAGTAATTACAAAAAGAATTTAC
*
965669 AGCCCTCTTGGTCCCTTATTTGAGGGGCCAGCCCCTTTTTATTGATATCAAATAAAAGGTCTTGT
1 AGCCCTTTTGG-CCCTTATTTGAGGGGCCAGCCCCTTTTTATTGATATCAAATAAAAGGTCTTGT
* * *
965734 AAATATAAACGCATTTTGTTCAACAAGTGTTCA-GAAATTGTTGACCGTTCTTA-AGATATCTGA
65 AAATATAAACACATTTTGTTCAACAAGTATTCACG-AATTGTTGACCGTTC-TAGAGATATCCGA
* * *
965797 ACAAATGTGTTTTAGGGGCCGACCCTTAAAATCCTTA-CTGGGACCACCAACAAAAATTTTTTAG
128 ACAAATGTGTTTT-GAGGCCGACCC---AAATCCTTACCAGGG-CCACCAACAAAAATGTTTTAG
* * * *
965861 GGAGCATATTGTTAAGAACATTATTTTGAGCATTTTTTGTTCTATAATGCTTATCAAAATATTTC
188 AGACCATATCGTTAAGAACATTATTTTAAGCATTTTTTGTTCTATAATGCTTATCAAAATATTTC
* *
965926 TCCTTTTCTAGATATTTAA-GATCAAAATTTCGGACTTTTGGCCCCGT-AAAGCCCCTAATGACG
253 TCCTTTTCTAGATA-TTAATGATCAAAATTTCGGACATATGGCCCCGTGAAA-CCCCTAATGACG
* * * *
965989 TAACATATGACTTA-GACATGGTACTGTTTAGATAAAAAGATGTATAATGAACATTTTTGGTTCT
316 TAACATATGACATATG-CATGGTACCGTATAGATAAAAAGATGTACAATGAACATTTTTGGTTCT
* * * *
966053 ATAATTGATAACAAATTATTTTTCAGTAAAGAGTAATTGCAAAAATACTTTAG
380 ATAATTGATAACAAATTATTTTTCAGTAAAGAGTAATTACAAAAAGAATTTAC
* *
966106 AGCCGTTTTGGCCCCTAATTTGAGGGGCCAGCCCCTTTTT
1 AGCCCTTTTGG-CCCTTATTTGAGGGGCCAGCCCCTTTTT
966146 TCTGAAATCA
Statistics
Matches: 418, Mismatches: 47, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
432 1 0.00
433 119 0.28
434 15 0.04
436 8 0.02
437 271 0.65
438 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (432 bp):
AGCCCTTTTGGCCCTTATTTGAGGGGCCAGCCCCTTTTTATTGATATCAAATAAAAGGTCTTGTA
AATATAAACACATTTTGTTCAACAAGTATTCACGAATTGTTGACCGTTCTAGAGATATCCGAACA
AATGTGTTTTGAGGCCGACCCAAATCCTTACCAGGGCCACCAACAAAAATGTTTTAGAGACCATA
TCGTTAAGAACATTATTTTAAGCATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCTTTTC
TAGATATTAATGATCAAAATTTCGGACATATGGCCCCGTGAAACCCCTAATGACGTAACATATGA
CATATGCATGGTACCGTATAGATAAAAAGATGTACAATGAACATTTTTGGTTCTATAATTGATAA
CAAATTATTTTTCAGTAAAGAGTAATTACAAAAAGAATTTAC
Found at i:966769 original size:30 final size:30
Alignment explanation
Indices: 966730--966793 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
966720 AAAAGATGAA
966730 AAAATCGAAT-ATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAGGTACGACTTAAC
*
966759 AAAATACGAATGATTTTAGGTACGACTTAAC
1 AAAAT-CGAATGATTCTAGGTACGACTTAAC
966790 AAAA
1 AAAA
966794 ACCTTTTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.16
30 6 0.19
31 20 0.65
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (30 bp):
AAAATCGAATGATTCTAGGTACGACTTAAC
Found at i:967576 original size:31 final size:32
Alignment explanation
Indices: 967534--967601 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
967524 AAAAAGATGA
* *
967534 AAAAAATCGAATTATTCCT-GGTACGACTTAAC
1 AAAAAATCGAATGATT-CTACGTACGACTTAAC
*
967566 AAAAAA-CGAATGATTTTACGTACGACTTAAC
1 AAAAAATCGAATGATTCTACGTACGACTTAAC
967597 AAAAA
1 AAAAA
967602 CCTTTCTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 25 0.78
32 6 0.19
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (32 bp):
AAAAAATCGAATGATTCTACGTACGACTTAAC
Found at i:969588 original size:437 final size:436
Alignment explanation
Indices: 968717--969594 Score: 1330
Period size: 437 Copynumber: 2.0 Consensus size: 436
968707 ATAAGACTGT
* * * *
968717 TCTTGTCAATTCAAACACATTTTGTTCCACAAGTGATAGAAATTCTGTACCGTTCTCGAGATATC
1 TCTTGTCAATTCAAACACATTTTGTTCAACAACTAATACAAATTCTGTACCGTTCTCGAGATATC
** * * * *
968782 TTTTGGGGGTCATTTTAGGGGCCGACCCTGAAACTCCTTTTAGGGTCCGCATAACAAAGAAATTA
66 TTGAGAGGGTCATTTTAGGGGCCGACCCTGAAACTCCCTTTAAGGACCGCATAACAAAGAAATTA
* *
968847 TGGTTGCATATTGTTAAGCTCAATATTTTGAGCATCTTCTGTTCAATATTGCTCTTCTAAATTGT
131 TGGTTGCATATTGTTAAACTCAATATTTTGAGCATCTTCTGTTCAATATTGCTCTTCAAAATTGT
* *
968912 CCTCCATTTTGATATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTAAAATTCCCTAATAACG
196 CCTCCATTTTGAGATATTAAGCATCAAAGTTTTGGACTTCTGGCCCCTAAAATTCCCTAATAACG
* * * *
968977 TAACATAGGAGTAAATGATTGCCATGTACAGATGAATACCGTTAGAATGAACATAATTGCTTCTA
261 TAACATAGGAGTAAATGATTGCAATGTACAGATGAATACCGTTAAAATAAACAAAATTGCTTCTA
*
969042 TAATGTATCACAAAATATTTCACAGTAAAAAGTTATTATCAAAAGACTTAAGAGCCCCCTCAGCC
326 TAATGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTAAGAGCCCCCTCAGCC
*
969107 CCTTATTTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATGAAAGC
391 CCTTATTTGAAGGGCCAGCCCCTTTTTCATGATGTCAAATGAAAGC
** *
969153 TCTTGTCAATTCAAACATTTTTTGTTCAACAACTAATTACAAATTTTGTACCGTTCTCGAGATAT
1 TCTTGTCAATTCAAACACATTTTGTTCAACAACTAA-TACAAATTCTGTACCGTTCTCGAGATAT
* * *
969218 CTTGAGAGGGTCGTTTTAGGGGCCGACCCTGTAACTCCCTTTAAGGACCGCATATCAAAGAAATT
65 CTTGAGAGGGTCATTTTAGGGGCCGACCCTGAAACTCCCTTTAAGGACCGCATAACAAAGAAATT
* * *
969283 ATGGTTG-ATTATTGTTAAACTCAATATTTTGAGCATCTTTTGTTCGATATTGCTTTTCAAAATT
130 ATGGTTGCA-TATTGTTAAACTCAATATTTTGAGCATCTTCTGTTCAATATTGCTCTTCAAAATT
*
969347 TTCCTCCATTTTGAGATATTAAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAA-TCCCTAACT
194 GTCCTCCATTTTGAGATATTAAGCATCAAAGTTTTGGACTTCTGGCCCC-TAAAATTCCCTAA-T
* * * * *
969411 -ATGTAACATAGGAGTAAATGATTGTAATGTATAGTTGAATACCTTTAAAATAAACAAAATTGCT
257 AACGTAACATAGGAGTAAATGATTGCAATGTACAGATGAATACCGTTAAAATAAACAAAATTGCT
* * * *
969475 TCTATAATGTATCACAAAATATTTCACAGTAAAAGGTTATCATTAAAAGACTTTAGAGCCCCTTC
322 TCTATAATGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTAAGAGCCCCCTC
* *
969540 AGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCTTGATGTCACATGAAAGC
387 AGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCATGATGTCAAATGAAAGC
969590 TCTTG
1 TCTTG
969595 ACTTTATAAA
Statistics
Matches: 397, Mismatches: 41, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
436 32 0.08
437 359 0.90
438 6 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (436 bp):
TCTTGTCAATTCAAACACATTTTGTTCAACAACTAATACAAATTCTGTACCGTTCTCGAGATATC
TTGAGAGGGTCATTTTAGGGGCCGACCCTGAAACTCCCTTTAAGGACCGCATAACAAAGAAATTA
TGGTTGCATATTGTTAAACTCAATATTTTGAGCATCTTCTGTTCAATATTGCTCTTCAAAATTGT
CCTCCATTTTGAGATATTAAGCATCAAAGTTTTGGACTTCTGGCCCCTAAAATTCCCTAATAACG
TAACATAGGAGTAAATGATTGCAATGTACAGATGAATACCGTTAAAATAAACAAAATTGCTTCTA
TAATGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTAAGAGCCCCCTCAGCC
CCTTATTTGAAGGGCCAGCCCCTTTTTCATGATGTCAAATGAAAGC
Found at i:970124 original size:57 final size:58
Alignment explanation
Indices: 970063--970207 Score: 238
Period size: 59 Copynumber: 2.5 Consensus size: 58
970053 AAAACAATAA
*
970063 GGTCTTCCGTTGGAAACGGAAGACCTTAAT-GAAAAAGAAACAATAGAATAACAAGAG
1 GGTCTTCCGTTGGAAACGGAAGACCCTAATAGAAAAAGAAACAATAGAATAACAAGAG
*
970120 GGTCTTCCGTTGGAAACGGAAGACCCTAATAAGGAAAAGAAACAATAGAATAACAAGAG
1 GGTCTTCCGTTGGAAACGGAAGACCCTAAT-AGAAAAAGAAACAATAGAATAACAAGAG
**
970179 GGTCTTCCGCCGGAAACGGAAGACCCTAA
1 GGTCTTCCGTTGGAAACGGAAGACCCTAA
970208 ATATTATCAG
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
57 29 0.35
59 53 0.65
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (58 bp):
GGTCTTCCGTTGGAAACGGAAGACCCTAATAGAAAAAGAAACAATAGAATAACAAGAG
Found at i:997481 original size:4 final size:4
Alignment explanation
Indices: 997472--997543 Score: 99
Period size: 4 Copynumber: 18.0 Consensus size: 4
997462 ATTCAAGTGT
* * * * *
997472 TCTC TCTC TCTG TCTG TCTC TGTC TGTC TGTC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
997520 TCTC TCTC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC
997544 ACCTGCAGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (4 bp):
TCTC
Found at i:997493 original size:10 final size:10
Alignment explanation
Indices: 997472--997543 Score: 99
Period size: 10 Copynumber: 7.2 Consensus size: 10
997462 ATTCAAGTGT
997472 TCTCTCTCTC
1 TCTCTCTCTC
* *
997482 TGTCTGTCTC
1 TCTCTCTCTC
* * *
997492 TGTCTGTCTG
1 TCTCTCTCTC
997502 TCTCTCTCTC
1 TCTCTCTCTC
997512 TCTCTCTCTC
1 TCTCTCTCTC
997522 TCTCTCTCTC
1 TCTCTCTCTC
997532 TCTCTCTCTC
1 TCTCTCTCTC
997542 TC
1 TC
997544 ACCTGCAGAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 56 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:997497 original size:14 final size:14
Alignment explanation
Indices: 997472--997543 Score: 99
Period size: 14 Copynumber: 5.1 Consensus size: 14
997462 ATTCAAGTGT
*
997472 TCTCTCTCTCTGTC
1 TCTCTCTCTCTCTC
* * *
997486 TGTCTCTGTCTGTC
1 TCTCTCTCTCTCTC
*
997500 TGTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
997514 TCTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
997528 TCTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
997542 TC
1 TC
997544 ACCTGCAGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 53 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (14 bp):
TCTCTCTCTCTCTC
Found at i:1000410 original size:12 final size:13
Alignment explanation
Indices: 1000385--1000409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1000375 ATTTTAAAGC
1000385 AAAATTATTTTTT
1 AAAATTATTTTTT
1000398 AAAATTATTTTT
1 AAAATTATTTTT
1000410 AGCTAACGCT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:1002052 original size:20 final size:20
Alignment explanation
Indices: 1002015--1002052 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1002005 CTGTATGCTT
*
1002015 AATTTGTATTGATTTGAAGA
1 AATTTGTATTGATGTGAAGA
1002035 AATTTGTTATT-ATGTGAA
1 AATTTG-TATTGATGTGAA
1002053 ATTGGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
AATTTGTATTGATGTGAAGA
Found at i:1004801 original size:9 final size:9
Alignment explanation
Indices: 1004783--1004817 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1004773 CTCCCCCCAA
1004783 TATATATAT
1 TATATATAT
*
1004792 TATCTATAT
1 TATATATAT
*
1004801 TATATATTT
1 TATATATAT
1004810 TATATATA
1 TATATATA
1004818 CTGCACACTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATATAT
Found at i:1033872 original size:11 final size:11
Alignment explanation
Indices: 1033856--1033895 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1033846 TAAGCAAGTC
1033856 CTTAAAGGTGG
1 CTTAAAGGTGG
1033867 CTTAAAGGTGG
1 CTTAAAGGTGG
* *
1033878 CGTAAAGCTGG
1 CTTAAAGGTGG
1033889 CTTAAAG
1 CTTAAAG
1033896 AATATACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1033993 original size:22 final size:21
Alignment explanation
Indices: 1033965--1034016 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1033955 TGTCCAAACT
1033965 TCTTTAAGTCACCTTTAAGCCA
1 TCTTTAAGTCACCTTTAAG-CA
* ***
1033987 TCTTTAAGCCGGTTTTAAGCA
1 TCTTTAAGTCACCTTTAAGCA
1034008 TCTTTAAGT
1 TCTTTAAGT
1034017 GGCATTTACG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (21 bp):
TCTTTAAGTCACCTTTAAGCA
Found at i:1034401 original size:2 final size:2
Alignment explanation
Indices: 1034394--1034437 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1034384 ATCGTTGAAA
1034394 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1034436 TC
1 TC
1034438 AGTTCATCCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1034853 original size:112 final size:112
Alignment explanation
Indices: 1034656--1035106 Score: 778
Period size: 112 Copynumber: 4.0 Consensus size: 112
1034646 TAGTTTTGTT
* *
1034656 CGTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTTAGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
* *
1034721 AGAATGTACAAGATATACACAACAGTTATGTCGTGTGCCCAGGGGCA
66 AGAATGTACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
*
1034768 CGTTTGTGTATATCTGATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
* *
1034833 AGAATGTACAAGATATACACAACAGTCGTGTCGTGTGCCCCGGTGCA
66 AGAATGTACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
*
1034880 CGTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTGT-AGAAAACCCCTGGAACTAACA
1 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACT-TAAGAAAACCCCTGGAACTAACA
1034944 CAGAATGTACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
65 CAGAATGTACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
* *
1034992 CGTTTGTGTATATTTGATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
1 CGTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
* *
1035057 AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 AGAATGTACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
1035104 CGT
1 CGT
1035107 CAGGGTTTCT
Statistics
Matches: 321, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
111 1 0.00
112 319 0.99
113 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (112 bp):
CGTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAC
AGAATGTACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCA
Found at i:1036092 original size:11 final size:11
Alignment explanation
Indices: 1036076--1036140 Score: 103
Period size: 11 Copynumber: 5.9 Consensus size: 11
1036066 AAACTTTTAA
1036076 TGGCTTAAAGG
1 TGGCTTAAAGG
1036087 TGGCTTAAAGG
1 TGGCTTAAAGG
*
1036098 TGGCATAAAGG
1 TGGCTTAAAGG
*
1036109 TAGCTTAAAGG
1 TGGCTTAAAGG
*
1036120 TAGCTTAAAGG
1 TGGCTTAAAGG
1036131 TGGCTTAAAG
1 TGGCTTAAAG
1036141 AAGTTTGGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 50 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.26
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:1036306 original size:11 final size:11
Alignment explanation
Indices: 1036290--1036328 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1036280 TAAAGATCGT
1036290 CTTTAAGCTAC
1 CTTTAAGCTAC
*
1036301 CTTTAAAC-AC
1 CTTTAAGCTAC
*
1036311 CTTTAAGCTAT
1 CTTTAAGCTAC
1036322 CTTTAAG
1 CTTTAAG
1036329 GTGAACTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:1058838 original size:15 final size:16
Alignment explanation
Indices: 1058818--1058860 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1058808 CCACCTATTC
1058818 TGTTTCGC-CCTGAGA
1 TGTTTCGCACCTGAGA
* *
1058833 TGTTTCTCACCT-CGA
1 TGTTTCGCACCTGAGA
1058848 TGTTTCGCACCTG
1 TGTTTCGCACCTG
1058861 CCTCGGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.37
Consensus pattern (16 bp):
TGTTTCGCACCTGAGA
Found at i:1060251 original size:15 final size:15
Alignment explanation
Indices: 1060226--1060268 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1060216 TGCACTGAGG
1060226 CAGGCGCGAAACATC-
1 CAGG-GCGAAACATCT
*
1060241 GAGGTGCGAAACATCT
1 CAGG-GCGAAACATCT
1060257 CAGGGCGAAACA
1 CAGGGCGAAACA
1060269 GAATATGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.35, C:0.26, G:0.30, T:0.09
Consensus pattern (15 bp):
CAGGGCGAAACATCT
Found at i:1060874 original size:37 final size:37
Alignment explanation
Indices: 1060814--1060886 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
1060804 CCATCGTGCC
* * *
1060814 TTGGCTGATCAAAGTAACCTACTGGAGTTATTTCGAT
1 TTGGCTGATCAAAGAAACATACTGGAGTTATATCGAT
* *
1060851 TTGGCTGATCAATGAAACATACTGGGGTTATATCGA
1 TTGGCTGATCAAAGAAACATACTGGAGTTATATCGA
1060887 CTTAATAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGGCTGATCAAAGAAACATACTGGAGTTATATCGAT
Found at i:1069498 original size:2 final size:2
Alignment explanation
Indices: 1069491--1069548 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
1069481 AAAAATGCAC
1069491 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1069532 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
1069549 ACAACTGATT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1072609 original size:45 final size:45
Alignment explanation
Indices: 1072558--1072647 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
1072548 CGTGTAATGC
* * *
1072558 ATTGTCTTCAGTGATAAAGGTATGGTGATACGGTGCAACAGTATT
1 ATTGTCTGCAGTGATAAAGATATGGTGACACGGTGCAACAGTATT
* *
1072603 ATTGTCTGCAGTGATACAGATATGGTGACACGGTGCAACATTATT
1 ATTGTCTGCAGTGATAAAGATATGGTGACACGGTGCAACAGTATT
1072648 TGTTATTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (45 bp):
ATTGTCTGCAGTGATAAAGATATGGTGACACGGTGCAACAGTATT
Found at i:1079634 original size:63 final size:65
Alignment explanation
Indices: 1079493--1079628 Score: 195
Period size: 64 Copynumber: 2.1 Consensus size: 65
1079483 AACATGAGTT
*
1079493 GAAACTTGACTCGAGCCAAATATGACGATATATACCTGAGGTTAAACAGCAGGAAAACACCAATA
1 GAAACTTGACTCGAGCCAAATATGACGATATATACCTGAGGTTAAACAGCAGGAAAACACCAAAA
* * * **
1079558 GAAGCTTGACTCGAGCCAAA-A-GACGTTCTATACCTGAGGTTAAAACTTCAGGAAAACACCAAA
1 GAAACTTGACTCGAGCCAAATATGACGATATATACCTGAGGTT-AAACAGCAGGAAAACACCAAA
1079621 A
65 A
1079622 GAAACTT
1 GAAACTT
1079629 TCTCGAATCA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 18 0.29
64 26 0.41
65 19 0.30
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (65 bp):
GAAACTTGACTCGAGCCAAATATGACGATATATACCTGAGGTTAAACAGCAGGAAAACACCAAAA
Found at i:1079645 original size:63 final size:63
Alignment explanation
Indices: 1079493--1079645 Score: 173
Period size: 63 Copynumber: 2.4 Consensus size: 63
1079483 AACATGAGTT
* * * *
1079493 GAAACTTGACTCGAGCCAAATATGACGATATATACCTGAGGTTAAACAGCAGGAAAACACCAATA
1 GAAACTTGACTCGAACCAAA-A-GACGTTCTATACCTGAGGTTAAACAGCAGGAAAACACCAAAA
* * **
1079558 GAAGCTTGACTCGAGCCAAAAGACGTTCTATACCTGAGGTTAAAACTTCAGGAAAACACCAAAA
1 GAAACTTGACTCGAACCAAAAGACGTTCTATACCTGAGGTT-AAACAGCAGGAAAACACCAAAA
* * *
1079622 GAAACTT-TCTCGAATCAAGAGACG
1 GAAACTTGACTCGAACCAAAAGACG
1079646 CTGAAAATGA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 31 0.41
64 26 0.34
65 19 0.25
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (63 bp):
GAAACTTGACTCGAACCAAAAGACGTTCTATACCTGAGGTTAAACAGCAGGAAAACACCAAAA
Found at i:1085964 original size:2 final size:2
Alignment explanation
Indices: 1085957--1085982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1085947 CAGATTTTAA
1085957 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1085983 CAATTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1088684 original size:12 final size:13
Alignment explanation
Indices: 1088667--1088725 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
1088657 ACGTTGTAAT
1088667 CATGTTTTTA-AA
1 CATGTTTTTAGAA
1088679 CATGTTTTGTA-AA
1 CATGTTTT-TAGAA
*
1088692 CAT-TTCTTAGAA
1 CATGTTTTTAGAA
*
1088704 -ATGTTTATAGAA
1 CATGTTTTTAGAA
*
1088716 AATGTTTTTA
1 CATGTTTTTA
1088726 TAACGTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 4 0.10
12 20 0.51
13 15 0.38
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (13 bp):
CATGTTTTTAGAA
Found at i:1088693 original size:13 final size:13
Alignment explanation
Indices: 1088660--1088694 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1088650 CAGATTTACG
*
1088660 TTGTAATCATGTT
1 TTGTAAACATGTT
1088673 TT-TAAACATGTT
1 TTGTAAACATGTT
1088685 TTGTAAACAT
1 TTGTAAACAT
1088695 TTCTTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (13 bp):
TTGTAAACATGTT
Found at i:1088750 original size:95 final size:95
Alignment explanation
Indices: 1088587--1088793 Score: 281
Period size: 95 Copynumber: 2.2 Consensus size: 95
1088577 TCTTTCAAAC
* * * *
1088587 GTTTTGTTAACATTTCTTGGAAATGTTTTTAGAAACTCTTATTATAACGTAACAAAAACTACACA
1 GTTTTGTTAACATTTCTTAGAAATGTTTATAGAAAATCTTATTATAACGTAACAAAAACCACACA
* * * * *
1088652 GATTTACGTTGTAATCATGTTTTTAAACAT
66 GATTCACGTTGTAATAACGTTTTCAAAAAT
* * * *
1088682 GTTTTGTAAACATTTCTTAGAAATGTTTATAGAAAATGTTTTTATAACGTAA-AAATCACCACAC
1 GTTTTGTTAACATTTCTTAGAAATGTTTATAGAAAATCTTATTATAACGTAACAAA-AACCACAC
1088746 AGATTCACGTTGTAATAACGTTTTCAAAAAT
65 AGATTCACGTTGTAATAACGTTTTCAAAAAT
1088777 GTTTTGTTAACATTTCT
1 GTTTTGTTAACATTTCT
1088794 ACAATGTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 3 0.03
95 94 0.97
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (95 bp):
GTTTTGTTAACATTTCTTAGAAATGTTTATAGAAAATCTTATTATAACGTAACAAAAACCACACA
GATTCACGTTGTAATAACGTTTTCAAAAAT
Found at i:1094633 original size:32 final size:32
Alignment explanation
Indices: 1094587--1094662 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1094577 ATTGACCCGG
*
1094587 GTTGAAAATCGACCCGGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGTCATTTTTCAAC
*
1094619 GTTGAATATTGACCCGGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGTCATTTTTCAAC
1094651 GTTGAAAATTGA
1 GTTGAAAATTGA
1094663 GACCAAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (32 bp):
GTTGAAAATTGACCCGGGGGTCATTTTTCAAC
Found at i:1097554 original size:197 final size:196
Alignment explanation
Indices: 1097219--1097599 Score: 753
Period size: 197 Copynumber: 1.9 Consensus size: 196
1097209 AACTAAAATA
1097219 ATAAATCCTGTGACATATACAAATATTCTTTAAAACATATATTTTTTAAGAAATATATAGATATC
1 ATAAATCCTGTGACATATACAAATATTCTTTAAAACATATATTTTTTAAGAAATATATAGATATC
1097284 ACACAAAACAGCAATTATACGCGAAAAGTTTATTATGAATAAAATAGTTATTACATATTTAAAGG
66 ACACAAAACAGCAATTATACGCGAAAAGTTTATTATGAATAAAATAGTTATTACATATTTAAAGG
1097349 GATAATATGTAAATTAAAAAATATTCATTTATAAAGTTTCATTTTTAACACCCCCCCCCCCCCCC
131 GATAATATGTAAATTAAAAAATATTCATTTATAAAGTTTCATTTTTAACACCCCCCCCCCCCCCC
1097414 C
196 C
1097415 NATAAATCCTGTGACATATACAAATATTCTTTAAAACATATATTTTTTAAGAAATATATAGATAT
1 -ATAAATCCTGTGACATATACAAATATTCTTTAAAACATATATTTTTTAAGAAATATATAGATAT
1097480 CACACAAAACAGCAATTATACGCGAAAAGTTTATTATGAATAAAATAGTTATTACATATTTAAAG
65 CACACAAAACAGCAATTATACGCGAAAAGTTTATTATGAATAAAATAGTTATTACATATTTAAAG
1097545 GGATAATATGTAAATTAAAAAATATTCATTTATAAAGTTTCATTTTTAACACCCC
130 GGATAATATGTAAATTAAAAAATATTCATTTATAAAGTTTCATTTTTAACACCCC
1097600 NGATCAAAAT
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 184 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (196 bp):
ATAAATCCTGTGACATATACAAATATTCTTTAAAACATATATTTTTTAAGAAATATATAGATATC
ACACAAAACAGCAATTATACGCGAAAAGTTTATTATGAATAAAATAGTTATTACATATTTAAAGG
GATAATATGTAAATTAAAAAATATTCATTTATAAAGTTTCATTTTTAACACCCCCCCCCCCCCCC
C
Found at i:1098019 original size:16 final size:16
Alignment explanation
Indices: 1097994--1098025 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1097984 TATACGGGAC
1097994 ATACTAAAGACCTGAA
1 ATACTAAAGACCTGAA
*
1098010 ATACTTAAGACCTGAA
1 ATACTAAAGACCTGAA
1098026 TGTCATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (16 bp):
ATACTAAAGACCTGAA
Found at i:1114894 original size:350 final size:353
Alignment explanation
Indices: 1114237--1114926 Score: 1034
Period size: 350 Copynumber: 2.0 Consensus size: 353
1114227 ATCATGGAAA
* * * * *
1114237 TTCAATAAAATTCTTCTAGTCTATCCTAATAAGGTCTGGAATAAGATCTGGCTTATGCATGTACA
1 TTCAATAAAATGCTTCTAGTCTATCCTAATAAGGTCTGAAATAACATCTGGCATATGCATGCACA
* *
1114302 AAATGTAAAACAGTTATGACACTATAAAAATTCAACTCGATTTTACTTTTCATAAAAAGGAAACA
66 AAATGTAAAACAGTTATGACACTATAAAAATTCAACTCAATTTTACTTATCATAAAAAGGAAACA
** * * *
1114367 AAGTAACATGATTTTTTTTCTCAAAAATGTCTTATCTAGTATGGTTTGTTTATTCCTTGCATCAA
131 AAGTAACACCATTATTTTACTCAAAAATGTCTTATCAAGTATGGTTTGTTTATTCCTTGCATCAA
1114432 TAGAAAACTGACAGGGAAGCCTCACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACC
196 TAGAAAACTGACAGGGAAGCCTCACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACC
1114497 ACCTTTCTCTTACTTGGGTATCAAGATCTACAACTTACTGCCAGCAAAGCCCTTTCAAAATACTC
261 ACCTTTCTCTTACTTGGGTATCAAGATCTACAACTTACTGCCAGCAAAGCCCTTTCAAAATACTC
1114562 TCT-CAGTGTCTCCTGCTTAAAATTCACT
326 T-TGCAGTGTCTCCTGCTTAAAATTCACT
*
1114590 TTCAATAAAAATGCTTCTAGTCTATCCTATTAAGGTCTGAAATAACA-CATGGCATATGCATGCA
1 TTCAAT-AAAATGCTTCTAGTCTATCCTAATAAGGTCTGAAATAACATC-TGGCATATGCATGCA
* *
1114654 CAGAATGTAAAACAGTTATGACACTATAAATATTCAACTCAATTTTACTTATCATAAAAA-GAAA
64 CAAAATGTAAAACAGTTATGACACTATAAAAATTCAACTCAATTTTACTTATCATAAAAAGGAAA
* ** ** * * *
1114718 -ACAGTTGC-CCATTATTTTACTCGGAAATGTCTTATCAAGTCTTGTTTGTTTATT-CTTGCATG
129 CAAAGTAACACCATTATTTTACTCAAAAATGTCTTATCAAGTATGGTTTGTTTATTCCTTGCATC
** *
1114780 TGTA-AGAAACTGACAGGGAAGCCTCACTCGCCTACAAGCAAGAGCAAAAGGATCGGTCTGAGAC
194 AATAGA-AAACTGACAGGGAAGCCTCACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGAC
*
1114844 ACCACCTTTCTCTTACTTGGGTATCAAGATCTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATA
258 ACCACCTTTCTCTTACTTGGGTATCAAGATCTACAACTTACTGCCAGCAAAGCCCTTTCAAAATA
* *
1114909 GTCTTGCATTGTCTCCTG
323 CTCTTGCAGTGTCTCCTG
1114927 TATATTTTGA
Statistics
Matches: 304, Mismatches: 29, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
349 2 0.01
350 144 0.47
351 37 0.12
352 5 0.02
353 11 0.04
354 105 0.35
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (353 bp):
TTCAATAAAATGCTTCTAGTCTATCCTAATAAGGTCTGAAATAACATCTGGCATATGCATGCACA
AAATGTAAAACAGTTATGACACTATAAAAATTCAACTCAATTTTACTTATCATAAAAAGGAAACA
AAGTAACACCATTATTTTACTCAAAAATGTCTTATCAAGTATGGTTTGTTTATTCCTTGCATCAA
TAGAAAACTGACAGGGAAGCCTCACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACC
ACCTTTCTCTTACTTGGGTATCAAGATCTACAACTTACTGCCAGCAAAGCCCTTTCAAAATACTC
TTGCAGTGTCTCCTGCTTAAAATTCACT
Found at i:1115623 original size:15 final size:16
Alignment explanation
Indices: 1115592--1115624 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1115582 ATTGATGAAC
*
1115592 ATAAAAAAATTCAACA
1 ATAAAAAAATACAACA
1115608 ATAAAAAAATAC-ACA
1 ATAAAAAAATACAACA
1115623 AT
1 AT
1115625 GAATAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
ATAAAAAAATACAACA
Found at i:1126556 original size:21 final size:21
Alignment explanation
Indices: 1126532--1126594 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1126522 GTGAAACGTA
1126532 TGCAACCAATGCGAGAGCTCG
1 TGCAACCAATGCGAGAGCTCG
* *
1126553 TGCAACGTAA-GCGAGGGCTCG
1 TGCAAC-CAATGCGAGAGCTCG
**
1126574 TGCAACGTATGCGAGAGCTCG
1 TGCAACCAATGCGAGAGCTCG
1126595 CGCGAAGCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.16
Consensus pattern (21 bp):
TGCAACCAATGCGAGAGCTCG
Found at i:1144273 original size:2 final size:2
Alignment explanation
Indices: 1144266--1144324 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1144256 GATTCTGAGA
1144266 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1144308 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1144325 TAACTTTAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1145385 original size:168 final size:168
Alignment explanation
Indices: 1145023--1145598 Score: 782
Period size: 168 Copynumber: 3.4 Consensus size: 168
1145013 CCCCTCATGT
* * ** *
1145023 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGTAAAGGAG-ATTGTGGATATCA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGG-GCCTCATGGACATCA
* * ** ** * * * *
1145086 TAACCATGTATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAAATTTT-TAAGATTTAA
64 TAACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA
* * *
1145150 AACAGTTTTACT-TTATGGTCATATTGGCCCCACCCTAGAG
129 TACATTTTTACTATT-TGGCCATATTGGCCCCACCCTAGAG
* * **
1145190 CCTGAACACCTAACAAAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATA
*
1145255 ACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGATGAAGATTTTCTAAGATTTAATA
66 ACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
1145320 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
131 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* *
1145358 CCTGAACCCCTGACCCAGTGGTCATGAATTTCACAATTTTAGTAGAGGGCTTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATA
* *
1145423 ATCATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAAGAAGATTTTCTAAGATTTAATA
66 ACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
* *
1145488 CATTTTTACTATATGGCCATATTGGCCCCACTCTAGAG
131 CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
* * * * * *
1145526 CCAGAACCCCTTACCCAGGGGCCATAAATTTCACAGTTTTGGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATA
1145591 ACCATGCA
66 ACCATGCA
1145599 ACCAGTTTTT
Statistics
Matches: 362, Mismatches: 43, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
166 1 0.00
167 90 0.25
168 269 0.74
169 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (168 bp):
CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATA
ACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA
CATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
Found at i:1152032 original size:28 final size:28
Alignment explanation
Indices: 1152000--1152056 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1151990 TCTTTCGGTC
1152000 ACTTAAACGGAGAGATAGAAGGAAAGAG
1 ACTTAAACGGAGAGATAGAAGGAAAGAG
1152028 ACTTAAACGGAGAGATAGAAGGAAAGAG
1 ACTTAAACGGAGAGATAGAAGGAAAGAG
1152056 A
1 A
1152057 GATGCTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.32, T:0.11
Consensus pattern (28 bp):
ACTTAAACGGAGAGATAGAAGGAAAGAG
Found at i:1168255 original size:22 final size:22
Alignment explanation
Indices: 1168230--1168271 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1168220 GCTGATAACG
*
1168230 CGATGGTGGGATAGCAATGACA
1 CGATGGTGCGATAGCAATGACA
1168252 CGATGGTGCGATAGCAATGA
1 CGATGGTGCGATAGCAATGA
1168272 TGCGTTGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.36, T:0.19
Consensus pattern (22 bp):
CGATGGTGCGATAGCAATGACA
Found at i:1169158 original size:22 final size:21
Alignment explanation
Indices: 1169133--1169173 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
1169123 GAGCATCGCA
1169133 TCATCGCTATCGCACCATCGTG
1 TCATCGCTATCGCA-CATCGTG
1169155 TCATCGCTATCGCACATCG
1 TCATCGCTATCGCACATCG
1169174 CTATCACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.27
Consensus pattern (21 bp):
TCATCGCTATCGCACATCGTG
Found at i:1169174 original size:13 final size:13
Alignment explanation
Indices: 1169156--1169186 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1169146 ACCATCGTGT
*
1169156 CATCGCTATCGCA
1 CATCGCTATCACA
1169169 CATCGCTATCACA
1 CATCGCTATCACA
1169182 CATCG
1 CATCG
1169187 AGTTATCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.23
Consensus pattern (13 bp):
CATCGCTATCACA
Found at i:1169195 original size:34 final size:36
Alignment explanation
Indices: 1169127--1169206 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 36
1169117 GCGATAGAGC
* *
1169127 ATCGCATCATCGCTATCGCACCATCGTGTCATCGCT
1 ATCGCATCATCGCTATCACACCATCGAGTCATCGCT
*
1169163 ATCGCA-CATCGCTATCACA-CATCGAGTTATCGCT
1 ATCGCATCATCGCTATCACACCATCGAGTCATCGCT
*
1169197 ATCGTATCAT
1 ATCGCATCAT
1169207 TGGATCATCG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
34 18 0.46
35 15 0.38
36 6 0.15
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (36 bp):
ATCGCATCATCGCTATCACACCATCGAGTCATCGCT
Found at i:1172615 original size:2 final size:2
Alignment explanation
Indices: 1172608--1172693 Score: 145
Period size: 2 Copynumber: 43.0 Consensus size: 2
1172598 GAAAGGCTAT
* **
1172608 GA GA GA GA GA AA GA GA GA GA CC GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1172650 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1172692 GA
1 GA
1172694 NNNNNNNNNN
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1183069 original size:223 final size:222
Alignment explanation
Indices: 1182682--1183111 Score: 824
Period size: 223 Copynumber: 1.9 Consensus size: 222
1182672 GCAAGACATG
1182682 TTCAATAAAATAAATTAAAGAGTGCAAAAAAAAGTTGAAATACACAGACTTTTTTTTATAAATCC
1 TTCAATAAAATAAATTAAAGAGTGCAAAAAAAAGTTGAAATACACAGACTTTTTTTTATAAATCC
*
1182747 TACTAATACATGTTAGTTTGACACGAGTATTTGTGCGTTTCAGGACAGTGTTTGAATGGCAAAAA
66 TACTAATACATGTTAGTTTGACACGAGTATTTGTGCGTTTCAGGACAGTGCTTGAATGGCAAAAA
*
1182812 ACCATCAGATTAACTTTTAAGTTTGATAGATGATTTCTTCAACATTTTTTACGTAAACTTAAATT
131 ACCATCAGATTAACTTTTAAGTTTGATAGATGATTTCTTCAACATTTTTCACGTAAACTTAAATT
1182877 TAAAAAAGAAAATTTTTAAATTAAAGC
196 TAAAAAAGAAAATTTTTAAATTAAAGC
1182904 TTCAATAAAATAAATTAAAGAGTGCAAAAAAAAGTTGAAATACACAGACATTTTTTTTATAAATC
1 TTCAATAAAATAAATTAAAGAGTGCAAAAAAAAGTTGAAATACACAGAC-TTTTTTTTATAAATC
1182969 CTACTAATACATGTTAGTTTGACACGAGTATTTGTGCGTTTCAGGACAGTGCTTGAATGGCAAAA
65 CTACTAATACATGTTAGTTTGACACGAGTATTTGTGCGTTTCAGGACAGTGCTTGAATGGCAAAA
*
1183034 AACCATCAGATTAACTTTTAAGTTTGATCGATGATTTCTTCAACATTTTTCACGTAAACTTAAAT
130 AACCATCAGATTAACTTTTAAGTTTGATAGATGATTTCTTCAACATTTTTCACGTAAACTTAAAT
1183099 TTAAAAAAGAAAA
195 TTAAAAAAGAAAA
1183112 ATTTCTAATA
Statistics
Matches: 204, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
222 49 0.24
223 155 0.76
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (222 bp):
TTCAATAAAATAAATTAAAGAGTGCAAAAAAAAGTTGAAATACACAGACTTTTTTTTATAAATCC
TACTAATACATGTTAGTTTGACACGAGTATTTGTGCGTTTCAGGACAGTGCTTGAATGGCAAAAA
ACCATCAGATTAACTTTTAAGTTTGATAGATGATTTCTTCAACATTTTTCACGTAAACTTAAATT
TAAAAAAGAAAATTTTTAAATTAAAGC
Found at i:1183558 original size:21 final size:21
Alignment explanation
Indices: 1183531--1183607 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
1183521 CGGTTCGTTA
1183531 CGCTTTGTGAACGGTACGGTT
1 CGCTTTGTGAACGGTACGGTT
*
1183552 CGTTTTGTGAACGGTACGGTT
1 CGCTTTGTGAACGGTACGGTT
*
1183573 CGCTTTGTGAACGGTACGGTA
1 CGCTTTGTGAACGGTACGGTT
*
1183594 CGCTTTATGAACGG
1 CGCTTTGTGAACGG
1183608 AACAGTTCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.32
Consensus pattern (21 bp):
CGCTTTGTGAACGGTACGGTT
Found at i:1183629 original size:42 final size:42
Alignment explanation
Indices: 1183531--1183632 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
1183521 CGGTTCGTTA
* * * * *
1183531 CGCTTTGTGAACGGTACGGTTCGTTTTGTGAACGGTACGGTT
1 CGCTTTGTGAACGGTACGGTACGCTTTATGAACGGAACAGTT
1183573 CGCTTTGTGAACGGTACGGTACGCTTTATGAACGGAACAGTT
1 CGCTTTGTGAACGGTACGGTACGCTTTATGAACGGAACAGTT
* *
1183615 CTCTTCT-TGCACGGTACG
1 CGCTT-TGTGAACGGTACG
1183633 CTTTGCTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
42 51 0.98
43 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (42 bp):
CGCTTTGTGAACGGTACGGTACGCTTTATGAACGGAACAGTT
Found at i:1184122 original size:15 final size:15
Alignment explanation
Indices: 1184102--1184133 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1184092 TCCTAGTGAA
1184102 TAGACGATGTAAAAT
1 TAGACGATGTAAAAT
1184117 TAGACGATGTAAAAT
1 TAGACGATGTAAAAT
1184132 TA
1 TA
1184134 CACGCAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAGACGATGTAAAAT
Found at i:1190464 original size:168 final size:166
Alignment explanation
Indices: 1190060--1190696 Score: 751
Period size: 168 Copynumber: 3.8 Consensus size: 166
1190050 AGTTGCATAG
* *
1190060 TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGGCCCCTGGGTCAGGGGTTCTG
1 TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCAT-GACCCTGGGTCAGGGGTTCTG
* * *
1190125 GCTCTAGAGTCGGGCCAATATGGCCATATAGTAAAAATGTATCAAATCTTAGAAAATCGTCTTCT
65 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAATCGTCTTCT
* *
1190190 CTACTACCATATATA-TTGTGAAAACTAAATGCATGA
130 CTACTACCATATATATTTTTAAAAACTAAATGCATGA
* ** * * *
1190226 TTATGATGTCCATGAAGCCAGCTACCTAAATTGTGAAATTCATGACCCATTGGTCAGGGGTTCCG
1 TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCC-TGGGTCAGGGGTTCTG
* **
1190291 GCTCTAGGGTGGGGCCAATATGGCCATATAGTCAAAATGTATTAAATCTTAGAAAATTTTC-TCT
65 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAATCGTCTTC-
* *
1190355 TCTACTCCCATATATATTTATTAAAAACTAAATGCATTA
129 TCTACTACCATATATATTT-TTAAAAACTAAATGCATGA
* * * * *
1190394 TTATGAAGTCCATGAGGCCCTCTACTAGAATTGTGAAATCCATGGACTCTGGGTCAGGGGTTCTG
1 TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCAT-GACCCTGGGTCAGGGGTTCTG
* * * * * * * * * * *
1190459 GCTCTAAGGCGGGACCAACATGGCCATATTGTATAAATGTATTTAATTTTAGAAAATGAGGC-CC
65 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAAT-CGTCTTC
* * *
1190523 TCTACTACCATATATGTTTGTTAAAAACTAAATGCCTGG
129 TCTACTACCATATATATTT-TTAAAAACTAAATGCATGA
* * ** * *
1190562 TTATAAAGTCCATGAAGCCCTCAACCAAAATTGTGAAATTCATGACCCCTTTG-CTATGGGTTCA
1 TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGA-CCCTGGGTC-AGGGGTTCT
* * *
1190626 GGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTTTTAAATCTTAAAAAATCTTCTTC
64 GGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAATCGTCTTC
1190691 TCTACT
129 TCTACT
1190697 CCAACACATG
Statistics
Matches: 391, Mismatches: 71, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
165 6 0.02
166 124 0.32
167 6 0.02
168 249 0.64
169 6 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (166 bp):
TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCTGGGTCAGGGGTTCTGG
CTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAATCGTCTTCTC
TACTACCATATATATTTTTAAAAACTAAATGCATGA
Found at i:1190698 original size:336 final size:334
Alignment explanation
Indices: 1190060--1190698 Score: 881
Period size: 336 Copynumber: 1.9 Consensus size: 334
1190050 AGTTGCATAG
* * *
1190060 TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGGCCCCTGGGTCAGGGGTTCTG
1 TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATCCATGGACCCTGGGTCAGGGGTTCTG
* * * * *
1190125 GCTCTAGAGTCGGGCCAATATGGCCATATAGTAAAAATGTATCAAATCTTAGAAAATCGTCTTCT
66 GCTCTAGAGGCGGGCCAACATGGCCATATAGTAAAAATGTATCAAATCTTAGAAAATAGGCTCCT
* * * * *
1190190 CTACTACCATATATATTGTGAAAACTAAATGCATGATTATGATGTCCATGAAGCCAGCTACCTAA
131 CTACTACCATATATATTGTAAAAACTAAATGCATGATTATAAAGTCCATGAAGCCAGCAACCAAA
* *
1190255 ATTGTGAAATTCATGACCCATTGGTCAGGGGTTCCGGCTCTAGGGTGGGGCCAATATGGCCATAT
196 ATTGTGAAATTCATGACCCATTGCTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATAT
* * *
1190320 AGTCAAAATGTATTAAATCTTAGAAAATTTTCTCTTCTACTCCCATATATATTTATTAAAAACTA
261 AGTAAAAATGTATTAAATCTTAAAAAATCTTCTCTTCTACTCCCATATATATTTATTAAAAACTA
1190385 AATGCATTA
326 AATGCATTA
* * * *
1190394 TTATGAAGTCCATGAGGCCCTCTACTAGAATTGTGAAATCCATGGACTCTGGGTCAGGGGTTCTG
1 TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATCCATGGACCCTGGGTCAGGGGTTCTG
* * ** *
1190459 GCTCTA-AGGCGGGACCAACATGGCCATATTGTATAAATGTATTTAATTTTAGAAAATGAGGC-C
66 GCTCTAGAGGCGGG-CCAACATGGCCATATAGTAAAAATGTATCAAATCTTAGAAAAT-AGGCTC
* * * **
1190522 CTCTACTACCATATATGTTTGTTAAAAACTAAATGCCTGGTTATAAAGTCCATGAAGCCCTCAAC
129 CTCTACTACCATATAT-ATTG-TAAAAACTAAATGCATGATTATAAAGTCCATGAAGCCAGCAAC
* *
1190587 CAAAATTGTGAAATTCATGACCCCTTTGCT-ATGGGTTCAGGCTCTAGGGTGGGGCCAATATGGC
192 CAAAATTGTGAAATTCATGA-CCCATTGCTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGC
*
1190651 CATATAGTAAAAATGTTTTAAATCTTAAAAAATCTTCT-TCTCTACTCC
256 CATATAGTAAAAATGTATTAAATCTTAAAAAATCTTCTCT-TCTACTCC
1190699 AACACATGTG
Statistics
Matches: 264, Mismatches: 35, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
333 6 0.02
334 117 0.44
335 6 0.02
336 128 0.48
337 7 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (334 bp):
TTATGAAGTCCATGAAGCCCTCTACCAAAATTGTGAAATCCATGGACCCTGGGTCAGGGGTTCTG
GCTCTAGAGGCGGGCCAACATGGCCATATAGTAAAAATGTATCAAATCTTAGAAAATAGGCTCCT
CTACTACCATATATATTGTAAAAACTAAATGCATGATTATAAAGTCCATGAAGCCAGCAACCAAA
ATTGTGAAATTCATGACCCATTGCTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATAT
AGTAAAAATGTATTAAATCTTAAAAAATCTTCTCTTCTACTCCCATATATATTTATTAAAAACTA
AATGCATTA
Found at i:1192069 original size:16 final size:16
Alignment explanation
Indices: 1192031--1192080 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1192021 GCAGTTTGAC
*
1192031 TTCGAGAGATCAAGGG
1 TTCGAGAGATCAAGAG
1192047 TTTCGAGAGATCAAGAG
1 -TTCGAGAGATCAAGAG
*
1192064 TTCGAGAAATCAAGAG
1 TTCGAGAGATCAAGAG
1192080 T
1 T
1192081 AAATTTCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (16 bp):
TTCGAGAGATCAAGAG
Found at i:1195664 original size:11 final size:11
Alignment explanation
Indices: 1195648--1195687 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
1195638 AAATACAAGC
1195648 AGATAAATGTT
1 AGATAAATGTT
1195659 AGATAAATGTT
1 AGATAAATGTT
1195670 AGATGTTAAATGTT
1 AGA---TAAATGTT
1195684 AGAT
1 AGAT
1195688 GTAACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 15 0.58
14 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (11 bp):
AGATAAATGTT
Found at i:1195681 original size:14 final size:14
Alignment explanation
Indices: 1195651--1195689 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1195641 TACAAGCAGA
1195651 TAAATGTTAGA---
1 TAAATGTTAGATGT
1195662 TAAATGTTAGATGT
1 TAAATGTTAGATGT
1195676 TAAATGTTAGATGT
1 TAAATGTTAGATGT
1195690 AACAACAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.44
14 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
TAAATGTTAGATGT
Found at i:1201246 original size:10 final size:10
Alignment explanation
Indices: 1201231--1201268 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
1201221 AAAACTATAA
1201231 ATATAATACT
1 ATATAATACT
1201241 ATATAATACT
1 ATATAATACT
1201251 ATATAATACT
1 ATATAATACT
*
1201261 ATGTAATA
1 ATATAATA
1201269 TAAAAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (10 bp):
ATATAATACT
Found at i:1201866 original size:1 final size:1
Alignment explanation
Indices: 1201860--1201894 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
1201850 ATTTTGCACA
1201860 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1201895 NGCATCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1204228 original size:4 final size:4
Alignment explanation
Indices: 1204211--1204241 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1204201 GAATCACCTT
*
1204211 GTCC GTCT GTCC GTCC GTCC GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
1204242 TGACTGTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.45, G:0.26, T:0.29
Consensus pattern (4 bp):
GTCC
Found at i:1204517 original size:146 final size:146
Alignment explanation
Indices: 1204253--1204534 Score: 501
Period size: 146 Copynumber: 1.9 Consensus size: 146
1204243 GACTGTGCAA
* * *
1204253 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTTGAAGTTCTTACTTTACACAAATATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
1204318 TTATGACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCAAAGGGTGTGTCATGACATTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
1204383 AGAAAAAATACAAAAT
131 AGAAAAAATACAAAAT
1204399 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * *
1204464 TTATGACCTAAGGGTGTGTCATGACATTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCAAAGGGTGTGTCATGACATTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
1204529 AGAAAA
131 AGAAAA
1204535 GCATTGAATG
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
146 129 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCAAAGGGTGTGTCATGACATTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATACAAAAT
Found at i:1205801 original size:21 final size:21
Alignment explanation
Indices: 1205777--1205932 Score: 77
Period size: 21 Copynumber: 7.4 Consensus size: 21
1205767 TGCAACTTTA
** *
1205777 GTATCGTATAAGAGGCGTATC
1 GTATCGTATAAGAAACGTACC
**
1205798 GTATCGTGCAAGAAACGTACC
1 GTATCGTATAAGAAACGTACC
* **
1205819 GTATCGTATAA-AATCGTTTC
1 GTATCGTATAAGAAACGTACC
**
1205839 GT-TCCGTGCGCGAA-AAACGTACC
1 GTAT-CGT---ATAAGAAACGTACC
* * *
1205862 GTTTCGTATAAGACACGTATC
1 GTATCGTATAAGAAACGTACC
*
1205883 GTATCGTATGAA-AAATGTACC
1 GTATCGTAT-AAGAAACGTACC
* * * *
1205904 GTACCGTATGAGAAACCTATC
1 GTATCGTATAAGAAACGTACC
1205925 GTATCGTA
1 GTATCGTA
1205933 CAAAGTGTAT
Statistics
Matches: 98, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 14 0.14
21 67 0.68
22 2 0.02
23 13 0.13
24 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (21 bp):
GTATCGTATAAGAAACGTACC
Found at i:1205912 original size:42 final size:42
Alignment explanation
Indices: 1205850--1205932 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
1205840 TTCCGTGCGC
** * *
1205850 GAAAAACGTACCGTTTCGTATAAGACACGTATCGTATCGTAT
1 GAAAAACGTACCGTACCGTATAAGAAACCTATCGTATCGTAT
* *
1205892 GAAAAATGTACCGTACCGTATGAGAAACCTATCGTATCGTA
1 GAAAAACGTACCGTACCGTATAAGAAACCTATCGTATCGTA
1205933 CAAAGTGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (42 bp):
GAAAAACGTACCGTACCGTATAAGAAACCTATCGTATCGTAT
Found at i:1206832 original size:2 final size:2
Alignment explanation
Indices: 1206825--1206880 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1206815 AAGAGTTTCT
1206825 GA GA GA GA -A GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1206865 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1206881 ACGTGGTACA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1207092 original size:2 final size:2
Alignment explanation
Indices: 1207085--1207162 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
1207075 CTCTGAAAAA
1207085 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
1207127 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1207163 GTTAGTCCGT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1211485 original size:2 final size:2
Alignment explanation
Indices: 1211478--1211524 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1211468 ACTGAAAATA
* *
1211478 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1211520 TC TC T
1 TC TC T
1211525 ATGTCGTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1212909 original size:34 final size:34
Alignment explanation
Indices: 1212866--1213036 Score: 290
Period size: 34 Copynumber: 5.0 Consensus size: 34
1212856 GAACTGTCGA
1212866 AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
1 AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
*
1212900 AGCGCCGGTAAACG-TTAATCCAGGCGTCCAAGAT
1 AGCGCCGGTAAACGACT-ATCCAGGCGTCCAAGAT
1212934 AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
1 AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
*
1212968 AGCGCCGGTAAACGACGATCCAGGCGTCCAAGAT
1 AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
* *
1213002 AGCGCCGGTAAACGTCTATCCAGGCGTCTAAGAT
1 AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
1213036 A
1 A
1213037 TTTTTTACCA
Statistics
Matches: 129, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
33 1 0.01
34 127 0.98
35 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (34 bp):
AGCGCCGGTAAACGACTATCCAGGCGTCCAAGAT
Found at i:1217058 original size:14 final size:14
Alignment explanation
Indices: 1217039--1217065 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1217029 TCTACAAGAT
1217039 TATTCGAAAAATAG
1 TATTCGAAAAATAG
1217053 TATTCGAAAAATA
1 TATTCGAAAAATA
1217066 TTTCATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (14 bp):
TATTCGAAAAATAG
Found at i:1218213 original size:30 final size:30
Alignment explanation
Indices: 1218179--1218237 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
1218169 ATTAAATACG
1218179 AAATACAGTTTAAAAATACATGATCCACTA
1 AAATACAGTTTAAAAATACATGATCCACTA
1218209 AAATACAGTTTAAAAATACATGATCCACT
1 AAATACAGTTTAAAAATACATGATCCACT
1218238 TAATGGATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (30 bp):
AAATACAGTTTAAAAATACATGATCCACTA
Found at i:1221800 original size:17 final size:17
Alignment explanation
Indices: 1221778--1221812 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1221768 ACAGCGGAGT
*
1221778 TTTATTTCTTGCTTTTA
1 TTTATTTATTGCTTTTA
1221795 TTTATTTATTGCTTTTA
1 TTTATTTATTGCTTTTA
1221812 T
1 T
1221813 ATCTTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.09, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATTTATTGCTTTTA
Found at i:1239764 original size:16 final size:16
Alignment explanation
Indices: 1239743--1239776 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1239733 TAAAGGTAGT
*
1239743 CTCATACAGGTGATGC
1 CTCATAAAGGTGATGC
1239759 CTCATAAAGGTGATGC
1 CTCATAAAGGTGATGC
1239775 CT
1 CT
1239777 TGTCTCGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (16 bp):
CTCATAAAGGTGATGC
Found at i:1241764 original size:4 final size:4
Alignment explanation
Indices: 1241755--1241800 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
1241745 AAAGTTTACA
* *
1241755 GACG GACG GACA GACA GACG GACG GACG GACG GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
1241801 AACAGGTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.30, C:0.26, G:0.43, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1256981 original size:2 final size:2
Alignment explanation
Indices: 1256974--1257046 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1256964 NNNNNNNNNN
1256974 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1257016 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1257047 CAGACAGACA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1257051 original size:4 final size:4
Alignment explanation
Indices: 1257044--1257076 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1257034 AGAGAGAGAG
1257044 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC A
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC A
1257077 ATGGTATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:1259767 original size:170 final size:166
Alignment explanation
Indices: 1259384--1259852 Score: 631
Period size: 170 Copynumber: 2.8 Consensus size: 166
1259374 CCCGCTGTCC
** * *
1259384 TGAACCCCTGACCCAGGGG-CAATGAATTTCACAATTTTGGTTGAAAGCCTCATGAACATCATAA
1 TGAACCCCTGA-CCAGGGGTC-ATGAATTTCACAATTTTGGTTGAGGGCTTCATGGACATCAT-A
* * * ** *
1259448 CCAGGCATTTAGTTTTGAACAAATATATATGGGAGT--AG-AGAAGATTTTCTAGGATTCAATAC
63 TCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAAATTTAATAC
* *
1259510 ATTTTTACAATATGGCCATATTGGCCCCACCCTAGAGCC
128 ATTTTAACAATATGGCCATATTGGCCCCACCCTAGAGCA
*
1259549 TGAACCCCTGACACAGGTGTCATGAATTTCACAATTTTGGTTGAGGGCTTCATGGACATCATATT
1 TGAACCCCTGAC-CAGGGGTCATGAATTTCACAATTTTGGTTGAGGGCTTCATGGACATCATA-T
*
1259614 CATGCATTTATTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAAATTTAATACA
64 CATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAAATTTAATACA
* *
1259679 TTTTAACTATATGTCCATATTGGCCCCAACCCCTAGAGCA
129 TTTTAACAATATGGCCATATTGGCCCC-A-CCCTAGAGCA
* * *
1259719 TGAACCCCTGACCTTGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATGAT
1 TGAACCCCTGACC-AGGGGTCATGAATTTCACAATTTTGGTTGAGGGCTTCATGGACATCAT-AT
* * *
1259784 CATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAACAAGATTTTCTAAAATGTAATACA
64 CATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAAATTTAATACA
1259849 TTTT
129 TTTT
1259853 TACACCCTAG
Statistics
Matches: 270, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
164 2 0.01
165 85 0.31
166 1 0.00
167 2 0.01
168 46 0.17
169 2 0.01
170 131 0.49
171 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (166 bp):
TGAACCCCTGACCAGGGGTCATGAATTTCACAATTTTGGTTGAGGGCTTCATGGACATCATATCA
TGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAAATTTAATACATT
TTAACAATATGGCCATATTGGCCCCACCCTAGAGCA
Found at i:1260001 original size:148 final size:148
Alignment explanation
Indices: 1259709--1259981 Score: 350
Period size: 148 Copynumber: 1.8 Consensus size: 148
1259699 TGGCCCCAAC
** *
1259709 CCCTAGAGCATGAACCCCTGACCTTGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGG
1 CCCTAGAGCATGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGG
* *** * * *
1259774 ACATCATGATCATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAGAACAAGATTTTCTAAA
66 ACATCATAATCATGCAACCAGTTTTTAACAAACATATATGGGAATAGAGAACAAGATTTTCTAAA
1259839 ATGTAATACATTTTTACA
131 ATGTAATACATTTTTACA
* * *
1259857 CCCTAGAGCCTGAACCCCTGACCCAGGGGCCATGAATTTTACAATTTTGGTAGAGGGCTTCATGG
1 CCCTAGAGCATGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGG
** ** * * *
1259922 ACATCATAA-CTATGCAACCAGTTTTTTCCTCACATGTGTGGGAATAGAGAAGAAGATTTT
66 ACATCATAATC-ATGCAACCAGTTTTTAACAAACATATATGGGAATAGAGAACAAGATTTT
1259982 TTTTTAAATT
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
147 1 0.01
148 103 0.99
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (148 bp):
CCCTAGAGCATGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGG
ACATCATAATCATGCAACCAGTTTTTAACAAACATATATGGGAATAGAGAACAAGATTTTCTAAA
ATGTAATACATTTTTACA
Found at i:1267970 original size:166 final size:169
Alignment explanation
Indices: 1267667--1267999 Score: 512
Period size: 166 Copynumber: 2.0 Consensus size: 169
1267657 ATCATCTGGC
* * *
1267667 TGATTAGTTTCTGAGAAGAAGATTTTTAAAGATATATTCTATATATTCCTATGTAAAACTTTGAC
1 TGATTAATTTCTGAGAAGAAGATTTTTAAAGATATACTCTATATATTCCTATGTAAAACTTTCAC
* *
1267732 CCCCCCCTAATTGTTGCCCAACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACAC
66 ACCCCCC-AATTGTGGCCCAACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACAC
*
1267797 TACCTGAGGAGGCTTCCACACAAGTTTCAGCTTTCCTATA
130 CACCTGAGGAGGCTTCCACACAAGTTTCAGCTTTCCTATA
* *
1267837 TGATTAATTTCTGCA-AAGATGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-TTCA
1 TGATTAATTTCTG-AGAAGAAGATTTTTAAAGATATACTCTATATATTCCTATGTAAAACTTTCA
* * *
1267900 -ACCCCCC-ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAC
65 CACCCCCCAATTGTGGCCCAACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACAC
*
1267963 CACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCT
130 CACCTGAGGAGGCTTCCACACAAGTTTCAGCTTTCCT
1268000 GTCTGTTGAG
Statistics
Matches: 150, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
166 87 0.58
168 6 0.04
169 3 0.02
170 53 0.35
171 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (169 bp):
TGATTAATTTCTGAGAAGAAGATTTTTAAAGATATACTCTATATATTCCTATGTAAAACTTTCAC
ACCCCCCAATTGTGGCCCAACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACC
ACCTGAGGAGGCTTCCACACAAGTTTCAGCTTTCCTATA
Found at i:1270599 original size:49 final size:48
Alignment explanation
Indices: 1270494--1270625 Score: 133
Period size: 49 Copynumber: 2.7 Consensus size: 48
1270484 TTAAAAAATT
*
1270494 ACACACTTTG-AAATATTTTTCAAAGTGTGTTAATATTGAGACTAAATCA
1 ACACACTTTGAAAATA-TTTTCAAAGTGTGTT-ATATTGAGACCAAATCA
** * * *
1270543 ATGCACTTTGAAAATTATTTTCAAAGTGTGTT-TACTTGGGACCAAGTTA
1 ACACACTTTGAAAA-TATTTTCAAAGTGTGTTATA-TTGAGACCAAATCA
* *
1270592 ACACACTTTGAAAAAAATTTTCAAAGTGGGTTAT
1 ACACACTTTG-AAAATATTTTCAAAGTGTGTTAT
1270626 GAAGATATAT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
48 2 0.03
49 41 0.60
50 23 0.34
51 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (48 bp):
ACACACTTTGAAAATATTTTCAAAGTGTGTTATATTGAGACCAAATCA
Found at i:1275338 original size:25 final size:25
Alignment explanation
Indices: 1275299--1275349 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1275289 AATTTTTAAC
*
1275299 CAAAAGTGTTAATAAATACTGTAAA
1 CAAAAGTATTAATAAATACTGTAAA
*
1275324 CAAAAGTATTCATAAATACTGTAAA
1 CAAAAGTATTAATAAATACTGTAAA
1275349 C
1 C
1275350 GTACTACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (25 bp):
CAAAAGTATTAATAAATACTGTAAA
Found at i:1276536 original size:16 final size:16
Alignment explanation
Indices: 1276517--1276551 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1276507 TCACCGAGAC
1276517 GAGGCATCACCCTTAT
1 GAGGCATCACCCTTAT
*
1276533 GAGGCATCACCTTTAT
1 GAGGCATCACCCTTAT
1276549 GAG
1 GAG
1276552 ACCACCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (16 bp):
GAGGCATCACCCTTAT
Found at i:1278989 original size:18 final size:18
Alignment explanation
Indices: 1278966--1279040 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
1278956 AACTATTTGT
* *
1278966 AGTTCATGATAAACTACA
1 AGTTAATGATGAACTACA
*
1278984 AGTTCATGATG-ACGTACA
1 AGTTAATGATGAAC-TACA
* *
1279002 AGTTAATGACGAAGTACA
1 AGTTAATGATGAACTACA
1279020 AGTTAATGATGAACTACA
1 AGTTAATGATGAACTACA
1279038 AGT
1 AGT
1279041 CACACGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.04
18 46 0.94
19 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (18 bp):
AGTTAATGATGAACTACA
Found at i:1279724 original size:31 final size:31
Alignment explanation
Indices: 1279689--1279750 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1279679 AACTTAGTGT
*
1279689 AATGTATCATTTAATTGGTATATTCAGAGTC
1 AATGTATCATTTAATAGGTATATTCAGAGTC
*
1279720 AATGTATCATTTACTAGGTATATTCAGAGTC
1 AATGTATCATTTAATAGGTATATTCAGAGTC
1279751 TAAAGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (31 bp):
AATGTATCATTTAATAGGTATATTCAGAGTC
Found at i:1280289 original size:2 final size:2
Alignment explanation
Indices: 1280282--1280309 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1280272 TTTATCAAAA
1280282 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1280310 ACCCACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1287104 original size:2 final size:2
Alignment explanation
Indices: 1287097--1287131 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1287087 CTGAGTGCAA
1287097 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1287132 TACAATGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1287570 original size:4 final size:4
Alignment explanation
Indices: 1287561--1287589 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1287551 TGTAATGCAG
1287561 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1287590 TATGAGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1299111 original size:30 final size:30
Alignment explanation
Indices: 1299075--1299135 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1299065 TTTTTGAACT
1299075 GCCGGTCAATAGACTGCGATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTAGACC
* *
1299105 GCCGGTCAATAGACTTCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTAGACC
1299135 G
1 G
1299136 GCAACGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTAGACC
Found at i:1306891 original size:2 final size:2
Alignment explanation
Indices: 1306884--1306925 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1306874 CAAGCATTTT
1306884 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1306926 AATTCTAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1308934 original size:32 final size:32
Alignment explanation
Indices: 1308893--1309005 Score: 208
Period size: 32 Copynumber: 3.5 Consensus size: 32
1308883 TTTTTCCTAA
1308893 ATCTTTATATTGAACTTTTCTTAAGGTACTTT
1 ATCTTTATATTGAACTTTTCTTAAGGTACTTT
*
1308925 ATCTTTATATTGAACTTTTCTTAAGGTACTAT
1 ATCTTTATATTGAACTTTTCTTAAGGTACTTT
*
1308957 ATCTTTACATTGAACTTTTCTTAAGGTACTTT
1 ATCTTTATATTGAACTTTTCTTAAGGTACTTT
1308989 ATCTTTATATTGAACTT
1 ATCTTTATATTGAACTT
1309006 CCTTCAGGTA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (32 bp):
ATCTTTATATTGAACTTTTCTTAAGGTACTTT
Found at i:1308973 original size:64 final size:63
Alignment explanation
Indices: 1308893--1309024 Score: 219
Period size: 64 Copynumber: 2.1 Consensus size: 63
1308883 TTTTTCCTAA
* * *
1308893 ATCTTTATATTGAACTTTTCTTAAGGTACTTTATCTTTATATTGAACTTTTCTTAAGGTACTAT
1 ATCTTTACATTGAACTTTTCTTAAGGTACTTTATCTTTATATTGAAC-TTCCTTAAGGTACTAC
*
1308957 ATCTTTACATTGAACTTTTCTTAAGGTACTTTATCTTTATATTGAACTTCCTTCAGGTACTAC
1 ATCTTTACATTGAACTTTTCTTAAGGTACTTTATCTTTATATTGAACTTCCTTAAGGTACTAC
1309020 ATCTT
1 ATCTT
1309025 ACAATGGCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 18 0.28
64 46 0.72
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (63 bp):
ATCTTTACATTGAACTTTTCTTAAGGTACTTTATCTTTATATTGAACTTCCTTAAGGTACTAC
Found at i:1314454 original size:4 final size:4
Alignment explanation
Indices: 1314445--1314477 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1314435 TATTGTTAAC
*
1314445 CTGT CTGT CTGT C-CT CTGT CTGT CTGT CTGT CT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CT
1314478 CTCTCTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.00, C:0.30, G:0.21, T:0.48
Consensus pattern (4 bp):
CTGT
Found at i:1314469 original size:19 final size:18
Alignment explanation
Indices: 1314445--1314487 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1314435 TATTGTTAAC
*
1314445 CTGTCTGTCTGTCCTCTGT
1 CTGTCTGTCTGT-CTCTCT
1314464 CTGTCTGTCTGTCTCTCT
1 CTGTCTGTCTGTCTCTCT
1314482 CTGTCT
1 CTGTCT
1314488 CACTCTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.00, C:0.33, G:0.19, T:0.49
Consensus pattern (18 bp):
CTGTCTGTCTGTCTCTCT
Found at i:1315747 original size:1 final size:1
Alignment explanation
Indices: 1315741--1315768 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1315731 GAGAGGGGTT
1315741 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1315769 TTCTTCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1327992 original size:23 final size:23
Alignment explanation
Indices: 1327962--1328012 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1327952 TCAATATGTG
1327962 TATTTCTTGAATGGAAGCTCGTC
1 TATTTCTTGAATGGAAGCTCGTC
1327985 TATTTCTTGAATGGAAGCTCGTC
1 TATTTCTTGAATGGAAGCTCGTC
1328008 TATTT
1 TATTT
1328013 TGACTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (23 bp):
TATTTCTTGAATGGAAGCTCGTC
Found at i:1331496 original size:18 final size:18
Alignment explanation
Indices: 1331470--1331505 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1331460 AACACAAAGT
1331470 TTCTCTATAGCTTGGTGA
1 TTCTCTATAGCTTGGTGA
*
1331488 TTCTTTATAGCTTGGTGA
1 TTCTCTATAGCTTGGTGA
1331506 GAACAGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (18 bp):
TTCTCTATAGCTTGGTGA
Found at i:1331506 original size:47 final size:44
Alignment explanation
Indices: 1331439--1331528 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 44
1331429 GTCACTTTCA
1331439 ATTCTCTATAAGCTTAGTGAGAACACAAAGTTTCTCTATAGCTTGGTG
1 ATTCTCTATAAGCTTAGTGAG-A-AC--AGTTTCTCTATAGCTTGGTG
* *
1331487 ATTCTTTAT-AGCTTGGTGAGAACAGTTTCTCTATAGCTTGGT
1 ATTCTCTATAAGCTTAGTGAGAACAGTTTCTCTATAGCTTGGT
1331529 AAGACCACCT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 19 0.47
45 2 0.05
46 1 0.03
47 10 0.25
48 8 0.20
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (44 bp):
ATTCTCTATAAGCTTAGTGAGAACAGTTTCTCTATAGCTTGGTG
Found at i:1331554 original size:31 final size:31
Alignment explanation
Indices: 1331512--1331616 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
1331502 GTGAGAACAG
1331512 TTTCTCTATAGCTTGGTAAGACCACCTAAAA
1 TTTCTCTATAGCTTGGTAAGACCACCTAAAA
* * * * *
1331543 TTTATCTATAGCTTGG--AGA-AAAC-ACAG
1 TTTCTCTATAGCTTGGTAAGACCACCTAAAA
1331570 TTTCTCTATAGCTTGGTAAGACCACCTAAAA
1 TTTCTCTATAGCTTGGTAAGACCACCTAAAA
1331601 TTTCTCTATAGCTTGG
1 TTTCTCTATAGCTTGG
1331617 AGAAAACACA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
27 17 0.28
28 2 0.03
29 6 0.10
30 2 0.03
31 33 0.55
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (31 bp):
TTTCTCTATAGCTTGGTAAGACCACCTAAAA
Done.