Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:2040044 original size:18 final size:19
Alignment explanation
Indices: 2040010--2040064 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
2040000 AGTCTGACTT
*
2040010 ATAAACATTTTTATAAAAA
1 ATAAATATTTTTATAAAAA
2040029 ATAAATATTTTT-TAAAAA
1 ATAAATATTTTTATAAAAA
* *
2040047 ATATATATTTATATAAAA
1 ATAAATATTTTTATAAAA
2040065 TTCTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATATTTTTATAAAAA
Found at i:2040350 original size:12 final size:12
Alignment explanation
Indices: 2040324--2040371 Score: 66
Period size: 11 Copynumber: 4.2 Consensus size: 12
2040314 GATTATATAA
*
2040324 TAAAAATAA-AA
1 TAAAAATAATAT
2040335 TAAAAATAATAT
1 TAAAAATAATAT
2040347 TAAAAATAATA-
1 TAAAAATAATAT
2040358 TAAAAAT-ATAT
1 TAAAAATAATAT
2040369 TAA
1 TAA
2040372 TATATAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
10 3 0.09
11 19 0.56
12 12 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAAAATAATAT
Found at i:2040352 original size:23 final size:22
Alignment explanation
Indices: 2040318--2040371 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
2040308 CGATAAGATT
*
2040318 ATATAATAAAAATAAAATAAAA
1 ATATATTAAAAATAAAATAAAA
*
2040340 ATAATATTAAAAATAATATAAAA
1 AT-ATATTAAAAATAAAATAAAA
2040363 ATATATTAA
1 ATATATTAA
2040372 TATATAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
ATATATTAAAAATAAAATAAAA
Found at i:2040470 original size:26 final size:27
Alignment explanation
Indices: 2040428--2040491 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
2040418 AAAATTTAAG
*
2040428 TAAATATA-AAAATTATAAACATAAT-
1 TAAATAAATAAAATTATAAACATAATA
*
2040453 TATAATAAATAAAA-TATAAATATAATA
1 TA-AATAAATAAAATTATAAACATAATA
*
2040480 TAAATATATAAA
1 TAAATAAATAAA
2040492 TTTTTAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 25 0.76
27 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAATAAATAAAATTATAAACATAATA
Found at i:2040486 original size:11 final size:11
Alignment explanation
Indices: 2040457--2040487 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2040447 CATAATTATA
*
2040457 ATAAATAAAAT
1 ATAAATATAAT
2040468 ATAAATATAAT
1 ATAAATATAAT
2040479 ATAAATATA
1 ATAAATATA
2040488 TAAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2041356 original size:18 final size:18
Alignment explanation
Indices: 2041333--2041367 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2041323 TAATAGTATT
2041333 AGCATTAATTCCTTAGAA
1 AGCATTAATTCCTTAGAA
2041351 AGCATTAATTCCTTAGA
1 AGCATTAATTCCTTAGA
2041368 CAGGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
AGCATTAATTCCTTAGAA
Found at i:2042904 original size:38 final size:39
Alignment explanation
Indices: 2042851--2042924 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
2042841 TGTCACAATT
* *
2042851 ATGACACAATTAAAATTGATCCATTTACGTTTAATAAAC
1 ATGACACAATTAAAATTAATCCATTTAAGTTTAATAAAC
*
2042890 ATGACAC-ATTAAAATTAATCCGTTTAAGTTTAATA
1 ATGACACAATTAAAATTAATCCATTTAAGTTTAATA
2042925 TGACACAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (39 bp):
ATGACACAATTAAAATTAATCCATTTAAGTTTAATAAAC
Found at i:2042983 original size:8 final size:9
Alignment explanation
Indices: 2042943--2042983 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2042933 CATGATTATG
2042943 ACATGAATA
1 ACATGAATA
2042952 ACAT-AATTA
1 ACATGAA-TA
*
2042961 ACATGAATT
1 ACATGAATA
2042970 ACATGAA-A
1 ACATGAATA
2042978 ACATGA
1 ACATGA
2042984 TTAGGACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 8 0.29
9 18 0.64
10 2 0.07
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (9 bp):
ACATGAATA
Found at i:2044291 original size:2 final size:2
Alignment explanation
Indices: 2044284--2044319 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2044274 CATATTTTTC
2044284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2044320 CAACATCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2044855 original size:14 final size:13
Alignment explanation
Indices: 2044839--2044863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2044829 AAAATTAACA
2044839 AAAAAAGCATTAG
1 AAAAAAGCATTAG
2044852 AAAAAAGCATTA
1 AAAAAAGCATTA
2044864 TCTTATGTCA
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:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAAAAGCATTAG
Found at i:2047318 original size:15 final size:15
Alignment explanation
Indices: 2047298--2047327 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2047288 GGTACTTCTT
2047298 ATTTCCTAATTACTA
1 ATTTCCTAATTACTA
*
2047313 ATTTCCTACTTACTA
1 ATTTCCTAATTACTA
2047328 CTAATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTCCTAATTACTA
Found at i:2052681 original size:32 final size:33
Alignment explanation
Indices: 2052622--2052685 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2052612 CACATCTAGA
*
2052622 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCATTGTATCGATACAT
* *
2052655 TGTATCGATGCA-TATTCATTGTATCGATACA
1 TGTATCGATACATTATGCATTGTATCGATACA
2052686 CACTCAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATGCATTGTATCGATACAT
Found at i:2052697 original size:20 final size:19
Alignment explanation
Indices: 2052652--2052705 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
2052642 TGTATCGATA
* * *
2052652 CATTGTATCGATGCATATT
1 CATTGTATCGATACACACT
2052671 CATTGTATCGATACACACT
1 CATTGTATCGATACACACT
2052690 CAATTGTATCGATACA
1 C-ATTGTATCGATACA
2052706 TGAAACTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACACACT
Found at i:2058948 original size:13 final size:13
Alignment explanation
Indices: 2058930--2058954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2058920 CAAAGATCTT
2058930 TGTATCGATACAC
1 TGTATCGATACAC
2058943 TGTATCGATACA
1 TGTATCGATACA
2058955 AGGGTTACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2064085 original size:23 final size:23
Alignment explanation
Indices: 2064055--2064102 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2064045 CGAACGTTTT
2064055 ATCCTAGCCGAAACATGATTACC
1 ATCCTAGCCGAAACATGATTACC
2064078 ATCCTAGCCGAAACATGATTACC
1 ATCCTAGCCGAAACATGATTACC
2064101 AT
1 AT
2064103 ACAGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.23
Consensus pattern (23 bp):
ATCCTAGCCGAAACATGATTACC
Found at i:2067724 original size:19 final size:19
Alignment explanation
Indices: 2067697--2067733 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2067687 GTTTAAGAAC
*
2067697 TAATTTTGTGTAGTAAGTA
1 TAATATTGTGTAGTAAGTA
2067716 TAATATTGTGTAGTAAGT
1 TAATATTGTGTAGTAAGT
2067734 CTTAGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (19 bp):
TAATATTGTGTAGTAAGTA
Found at i:2068092 original size:29 final size:30
Alignment explanation
Indices: 2068036--2068095 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
2068026 TTATATGAAT
* *
2068036 ATAAAATATTTTACATATAATTATAATATG
1 ATAAAATATTATAAATATAATTATAATATG
2068066 ATAAAATA-TATAAATATAA-TATAAATATG
1 ATAAAATATTATAAATATAATTAT-AATATG
2068095 A
1 A
2068096 ATTGTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 16 0.59
30 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (30 bp):
ATAAAATATTATAAATATAATTATAATATG
Found at i:2068856 original size:13 final size:13
Alignment explanation
Indices: 2068838--2068886 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
2068828 GAGGCTCCGT
2068838 CATCCCTCTCAAG
1 CATCCCTCTCAAG
*
2068851 CATCCCTCTTAAG
1 CATCCCTCTCAAG
* *
2068864 CATCTCTTTCAAG
1 CATCCCTCTCAAG
2068877 CATCCCTCTC
1 CATCCCTCTC
2068887 TTGTATTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.20, C:0.43, G:0.06, T:0.31
Consensus pattern (13 bp):
CATCCCTCTCAAG
Found at i:2069173 original size:20 final size:20
Alignment explanation
Indices: 2069150--2069205 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2069140 TTTTTCAATA
*
2069150 TATCGATACATGTATG-AATT
1 TATCGATACAT-TATGTAATG
* *
2069170 TATCGATATATTCTGTAATG
1 TATCGATACATTATGTAATG
2069190 TATCGATACATTATGT
1 TATCGATACATTATGT
2069206 CTTTTTACCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (20 bp):
TATCGATACATTATGTAATG
Found at i:2076281 original size:17 final size:16
Alignment explanation
Indices: 2076238--2076286 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
2076228 AAGTCGAAAG
2076238 CAAAAGCACAAAAAAAT
1 CAAAAGCA-AAAAAAAT
*
2076255 GAAAAG-AAAAAAAAT
1 CAAAAGCAAAAAAAAT
2076270 ACAAAAGCAAAATAAAA
1 -CAAAAGCAAAA-AAAA
2076287 AGGGAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
17 9 0.33
18 4 0.15
ACGTcount: A:0.76, C:0.10, G:0.08, T:0.06
Consensus pattern (16 bp):
CAAAAGCAAAAAAAAT
Found at i:2077681 original size:28 final size:28
Alignment explanation
Indices: 2077538--2078740 Score: 1263
Period size: 28 Copynumber: 41.7 Consensus size: 28
2077528 TAGTACTGTG
*
2077538 ACCTTTTCAAAGCCCACAAGTCAATGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
2077566 ATTCTTTTCAAAGCCCACAAGTCAATGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGC
*
2077595 ATCCTTCTCAAAGCCCACAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGC
* *
2077624 ATCCTTCTCAAAGCCCACACAAATCAGTGGC
1 A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC
*
2077655 ACATTTTCAAAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
*
2077683 ATCCTTTTCAAAGCCCACACAAGTTAGTGGC
1 A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC
* * *
2077714 ATCATTTCAAAGCCCACATGAGTCGGTGGC
1 ACCTTTTCAAAGCCCACA--AGTCAGTGGC
**
2077744 AATTCTTTCTAAAGCCCACAAGTCAGTGGC
1 ACCT-TTTC-AAAGCCCACAAGTCAGTGGC
* *
2077774 ACCCTTTCGAAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* * *
2077802 ACCCTTTCGAAGCCCACAATTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
2077830 A-CTCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGC
* *
2077858 ATCC-TTTCAAAGCCCATACAACTCGGTGGC
1 A-CCTTTTCAAAGCCC--ACAAGTCAGTGGC
*
2077888 AACTCTTTTCAAAGCCCACAAGTCTGTGGC
1 -AC-CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
2077918 ACTCTTTTCAAAGCCCACGAGTTAGTGGT
1 AC-CTTTTCAAAGCCCACAAGTCAGTGGC
* *
2077947 ACCCTTTC-AAGCCCACAAGTTAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
2077974 ACATTTTCAAAGCCCACGAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
2078002 A-CTCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGC
* *
2078030 ATCC-TTTCAAAGCCCACGCAAGTCAATGGT
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
2078060 ACCCTTTT-AAAGCCCACGCAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
* *
2078090 ACCTTTTCAAAGCCCACGAGTCAATGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* * *
2078118 ACATTTTTTTAAAGCCCACGAGTCAGTGGC
1 AC--CTTTTCAAAGCCCACAAGTCAGTGGC
2078148 A-CTCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGC
2078176 ATCC-TTTCAAAGCCCACGCAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
2078206 ACCCTTTT-AAAGCCCACGCAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
* * * *
2078236 ACATTTTCAAAGCCCACGAGTCAGCGAC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
*
2078264 ACTTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
2078292 ATCC-TTTCAAAGCCCACGCAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
2078322 ACCCTTTT-AAAGCCCACGCAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
* *
2078352 ACATTTTC-AAGCCCACGAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
*
2078379 A-TTCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGC
*
2078407 ATCC-TTTCCAAGCCCACGCAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCA--CAAGTCAGTGGC
* *
2078437 ACCTTTTTAAAGCCCATGCAAGTCAGTAGC
1 ACCTTTTCAAAGCCCA--CAAGTCAGTGGC
*
2078467 ACTCTTTTCAAAGCCTACGCAAGTCAGTGGC
1 AC-CTTTTCAAAGCC--CACAAGTCAGTGGC
* * **
2078498 ACTCCTTTCAAAGCCAATGAGTCAGTGGC
1 AC-CTTTTCAAAGCCCACAAGTCAGTGGC
2078527 ACCTTTTCAAA-CCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
2078554 ACTTTTTC-AAGCCCATAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* * *
2078581 ACTTTTTCAAAGTCCATAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
2078609 ACTTTTTC-AAGCCCACAAGTCAGTGGA
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
*
2078636 ACTTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
2078664 ATCC-TTTCAAAGCCCACAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGC
*
2078692 ACCTTTTCAAAGCCCACAAGTCAGTGAC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGC
2078720 ACTCTTTTCAAAGCCCACAAG
1 AC-CTTTTCAAAGCCCACAAG
2078741 CCAATACTAA
Statistics
Matches: 1021, Mismatches: 98, Indels: 111
0.83 0.08 0.09
Matches are distributed among these distances:
26 3 0.00
27 111 0.11
28 385 0.38
29 167 0.16
30 254 0.25
31 79 0.08
32 21 0.02
33 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
ACCTTTTCAAAGCCCACAAGTCAGTGGC
Found at i:2077903 original size:116 final size:111
Alignment explanation
Indices: 2077538--2078740 Score: 1210
Period size: 116 Copynumber: 10.4 Consensus size: 111
2077528 TAGTACTGTG
* * *
2077538 ACCTTTTCAAAGCCCACAAGTCAATGGCATTCTTTTCAAAGCCCACAAGTCAATGGCATCCTTCT
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTT-T
*
2077603 CAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACACAAATCAGTGGC
63 CAAAGCCCACAAGTCAGTGGCA-CCTT-TCAAAGCCCA-ACAAGTCAGTGGC
* *
2077655 ACATTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACACAAGTTAGTGGCATCATT
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG-CC-CACAAGTCAGTGGCATC-TT
* *
2077720 TCAAAGCCCACATGAGTCGGTGGCAATTCTTTCTAAAGCCC-ACAAGTCAGTGGC
62 TCAAAGCCCACA--AGTCAGTGGC-A-CCTTTC-AAAGCCCAACAAGTCAGTGGC
* * * * *
2077774 ACCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAATTCAGTGGCACTCTTTCA
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTCA
* *
2077839 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATACAACTCGGTGGC
65 AAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCA-ACAAGTCAGTGGC
* * * * *
2077888 AACTCTTTTCAAAGCCCACAAGTCTGTGGCACTCTTTTCAAAGCCCACGAGTTAGTGGTACCCTT
1 -AC-CTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCA-TCTT
* * *
2077953 TC-AAGCCCACAAGTTAGTGGCACATTTTCAAAGCCC-ACGAGTCAGTGGC
62 TCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCAACAAGTCAGTGGC
* * *
2078002 A-CTCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACGCAAGTCAATGGTACCCT
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCA--CAAGTCAGTGGCA-TCT
* * *
2078065 TTTAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGCCC-ACGAGTCAATGGC
61 TTCAAAGCCCA--CAAGTCAGTGGCACC-TTTCAAAGCCCAACAAGTCAGTGGC
* * *
2078118 ACATTTTTTTAAAGCCCACGAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGCATCCTT
1 AC--CTTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCAT-CTT
* *
2078182 TCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACGCAAGTCAGTGGC
62 TCAAAGCCCA--CAAGTCAGTGGCA-CCTTTCAAAGCCCA-ACAAGTCAGTGGC
* * * * *
2078236 ACATTTTCAAAGCCCACGAGTCAGCGACACTTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCA
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTCA
* *
2078301 AAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACGCAAGTCAGTGGC
65 AAGCCCA--CAAGTCAGTGGCA-CCTTTCAAAGCCCA-ACAAGTCAGTGGC
* * *
2078352 ACATTTTC-AAGCCCACGAGTCAGTGGCA-TTCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCAT-CTTTC
* * * *
2078415 CAAGCCCACGCAAGTCAGTGGCACCTTTTTAAAGCCCATGCAAGTCAGTAGC
64 AAAGCCCA--CAAGTCAGTGGCACC-TTTCAAAGCCCA-ACAAGTCAGTGGC
* * * ** *
2078467 ACTCTTTTCAAAGCCTACGCAAGTCAGTGGCACTCCTTTCAAAGCCAATGAGTCAGTGGCACCTT
1 AC-CTTTTCAAAGCC--CACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCATC-T
* *
2078532 TTCAAA-CCCACAAGTCAGTGGCACTTTTTC-AAGCCC-ATAAGTCAGTGGC
61 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCAACAAGTCAGTGGC
* * * * * *
2078581 ACTTTTTCAAAGTCCATAAGTCAGTGGCACTTTTTC-AAGCCCACAAGTCAGTGGAACTTTTTCA
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTCA
2078645 AAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC-ACAAGTCAGTGGC
65 AAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCAACAAGTCAGTGGC
*
2078692 ACCTTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAGCCCACAAG
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAG
2078741 CCAATACTAA
Statistics
Matches: 941, Mismatches: 97, Indels: 100
0.83 0.09 0.09
Matches are distributed among these distances:
109 23 0.02
110 25 0.03
111 73 0.08
112 37 0.04
113 46 0.05
114 53 0.06
115 101 0.11
116 294 0.31
117 94 0.10
118 71 0.08
119 73 0.08
120 39 0.04
121 12 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (111 bp):
ACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTCAA
AGCCCACAAGTCAGTGGCACCTTTCAAAGCCCAACAAGTCAGTGGC
Found at i:2079638 original size:80 final size:79
Alignment explanation
Indices: 2079453--2079710 Score: 256
Period size: 79 Copynumber: 3.3 Consensus size: 79
2079443 AAATAAAGCT
* * * * * *
2079453 GGGGTTGGAGTATCCCCAATTATGAAAAATCGATGGTTTGGAAATAAAAC-CGGAGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTGAAAATAAAACACGG-GTTAGAGTAT
**
2079517 CCTTTCAGAAATAAC
65 CCCCTCAGAAATAAC
** * *
2079532 AAGGTTAGAGTATCCCCGA-TGATGAAAAATTTG-TGCTTTGAAAATAAAACACGGGTTTAGAGT
1 GGGGTTGGAGTATCCCCGATTG-TGAAAAA-TTGATGATTTGAAAATAAAACACGGG-TTAGAGT
*
2079595 ATCCCCTCAGAATTAAC
63 ATCCCCTCAGAAATAAC
* * * **
2079612 GGGGTTGGAGTATTCCTGATTGTGAAAAATTGAT-ATTTTAGAAATAAAGTTA-GGGTTAGAGTA
1 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTGA-AAATAAA-ACACGGGTTAGAGTA
2079675 TCCCCTCAGAAATAAC
64 TCCCCTCAGAAATAAC
*
2079691 GGGGTTGGAGTGTCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
2079711 GGTGGATACT
Statistics
Matches: 146, Mismatches: 25, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
78 1 0.01
79 85 0.58
80 57 0.39
81 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTGAAAATAAAACACGGGTTAGAGTATC
CCCTCAGAAATAAC
Found at i:2079862 original size:18 final size:18
Alignment explanation
Indices: 2079839--2079879 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2079829 GGTCCTAAAA
2079839 GGGTTCCAAGGCTGATTG
1 GGGTTCCAAGGCTGATTG
2079857 GGGTTCCAAGGCTGATTG
1 GGGTTCCAAGGCTGATTG
2079875 GGGTT
1 GGGTT
2079880 ACGAGGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (18 bp):
GGGTTCCAAGGCTGATTG
Found at i:2084053 original size:21 final size:22
Alignment explanation
Indices: 2084027--2084068 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2084017 AAGTTACAAT
2084027 ATAAAGATGCTTG-TAGATAGC
1 ATAAAGATGCTTGTTAGATAGC
*
2084048 ATAAAGGTGCTTGTTAGATAG
1 ATAAAGATGCTTGTTAGATAG
2084069 AAAAAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (22 bp):
ATAAAGATGCTTGTTAGATAGC
Found at i:2084074 original size:21 final size:21
Alignment explanation
Indices: 2084029--2084074 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2084019 GTTACAATAT
*
2084029 AAAGATGCTTGTAGATAGCAT
1 AAAGATGCTTGTAGATAGCAA
*
2084050 AAAGGTGCTTGTTAGATAG-AA
1 AAAGATGCTTG-TAGATAGCAA
2084071 AAAG
1 AAAG
2084075 TTTACTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (21 bp):
AAAGATGCTTGTAGATAGCAA
Found at i:2090185 original size:11 final size:12
Alignment explanation
Indices: 2090171--2090210 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
2090161 ACATAACATA
2090171 AAAATATAAT-T
1 AAAATATAATAT
2090182 AAAATATAATAT
1 AAAATATAATAT
*
2090194 AAAA-ATAAAAT
1 AAAATATAATAT
2090205 AAAATA
1 AAAATA
2090211 ATATTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:2090195 original size:24 final size:23
Alignment explanation
Indices: 2090163--2090210 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2090153 TATAATAAAC
*
2090163 ATAACATAAAAATATAATTAAAAT
1 ATAACATAAAAATA-AAATAAAAT
*
2090187 ATAATATAAAAATAAAATAAAAT
1 ATAACATAAAAATAAAATAAAAT
2090210 A
1 A
2090211 ATATTACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAACATAAAAATAAAATAAAAT
Found at i:2090614 original size:19 final size:18
Alignment explanation
Indices: 2090590--2090630 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2090580 CTTGTACAAA
*
2090590 TAATTAAATTAATTAATAT
1 TAATTAAATTAAATAAT-T
*
2090609 TAATTAATTTAAATAATT
1 TAATTAAATTAAATAATT
2090627 TAAT
1 TAAT
2090631 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAAATTAAATAATT
Found at i:2090647 original size:24 final size:23
Alignment explanation
Indices: 2090593--2090648 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
2090583 GTACAAATAA
2090593 TTAAATTAATTAATATTAATTAAT
1 TTAAA-TAATTAATATTAATTAAT
*
2090617 TTAAATAATTTAATATTTAATT-TT
1 TTAAATAA-TTAATA-TTAATTAAT
2090641 TTAAATAA
1 TTAAATAA
2090649 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 3 0.10
24 20 0.69
25 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAATAATTAATATTAATTAAT
Found at i:2090672 original size:27 final size:27
Alignment explanation
Indices: 2090618--2090677 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2090608 TTAATTAATT
* *
2090618 TAAATAATTTAATATTTAATTTTTTAAA
1 TAAA-AATTTAATATTTAAATTTATAAA
2090646 TAAAAATTTAA-ATTTAAAATTTATAAA
1 TAAAAATTTAATATTT-AAATTTATAAA
2090673 TAAAA
1 TAAAA
2090678 TAATAATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 21 0.72
28 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAAATTTAATATTTAAATTTATAAA
Found at i:2090734 original size:15 final size:15
Alignment explanation
Indices: 2090711--2090744 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2090701 TTTTATAATG
* *
2090711 AATTGAATTAATTTA
1 AATTAAATTAATTAA
2090726 AATTAAATTAATTAA
1 AATTAAATTAATTAA
2090741 AATT
1 AATT
2090745 TTATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTAAATTAATTAA
Found at i:2090892 original size:9 final size:10
Alignment explanation
Indices: 2090866--2090904 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
2090856 AACGTCTTAT
2090866 TTATTTTTAA
1 TTATTTTTAA
2090876 TTATTTTTAA
1 TTATTTTTAA
*
2090886 TTATTTTTTA
1 TTATTTTTAA
2090896 TATATTTTT
1 T-TATTTTT
2090905 TAAAAAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTTTTAA
Found at i:2090893 original size:11 final size:11
Alignment explanation
Indices: 2090869--2090907 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2090859 GTCTTATTTA
2090869 TTTTTAATTA-
1 TTTTTAATTAT
2090879 TTTTTAATTAT
1 TTTTTAATTAT
2090890 TTTTT-ATATAT
1 TTTTTAAT-TAT
2090901 TTTTTAA
1 TTTTTAA
2090908 AAAATGTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 12 0.46
11 13 0.50
12 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTAATTAT
Found at i:2091592 original size:2 final size:2
Alignment explanation
Indices: 2091587--2091625 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2091577 ATATATATAT
* *
2091587 TG TG TG TG TG TG TG TG TG TG CG TG TG TG CG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2091626 CGGTTAGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.05, G:0.49, T:0.46
Consensus pattern (2 bp):
TG
Found at i:2092273 original size:20 final size:19
Alignment explanation
Indices: 2092230--2092280 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
2092220 TATAATATTT
*
2092230 TAAAAATAATTATTATACA
1 TAAAAATAATTAATATACA
2092249 T-AAAATAATATCAATATA-A
1 TAAAAATAAT-T-AATATACA
*
2092268 TAAAAATACTTAA
1 TAAAAATAATTAA
2092281 ATATTTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 10 0.37
19 5 0.19
20 12 0.44
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATAATTAATATACA
Found at i:2092364 original size:2 final size:2
Alignment explanation
Indices: 2092352--2092386 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2092342 GGCATCAGCA
2092352 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2092387 GTATGGTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2092583 original size:14 final size:14
Alignment explanation
Indices: 2092564--2092590 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2092554 CCAACTTTAA
2092564 AAAAAAATATATAT
1 AAAAAAATATATAT
2092578 AAAAAAATATATA
1 AAAAAAATATATA
2092591 AAATAATTTT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAAATATATAT
Found at i:2092587 original size:12 final size:13
Alignment explanation
Indices: 2092565--2092593 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2092555 CAACTTTAAA
2092565 AAAAAATATATAT
1 AAAAAATATATAT
2092578 AAAAAA-ATATAT
1 AAAAAATATATAT
2092590 AAAA
1 AAAA
2092594 TAATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATATATAT
Found at i:2103202 original size:11 final size:11
Alignment explanation
Indices: 2103186--2103211 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2103176 TATTTAAATT
2103186 TAAAAATTTAA
1 TAAAAATTTAA
2103197 TAAAAATTTAA
1 TAAAAATTTAA
2103208 TAAA
1 TAAA
2103212 TTATTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATTTAA
Found at i:2103998 original size:23 final size:23
Alignment explanation
Indices: 2103927--2104000 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2103917 ATTAAAATAT
* * *
2103927 TAAAAAATTATTTTTATATTTACA
1 TAAAAATTTATTATTATA-TTAAA
* * * *
2103951 T-AAATTTTATAATTAATTTTTAA
1 TAAAAATTTATTATT-ATATTAAA
2103974 TAAAAATTTATTATTATATTAAA
1 TAAAAATTTATTATTATATTAAA
2103997 TAAA
1 TAAA
2104001 TAATAATTTG
Statistics
Matches: 37, Mismatches: 11, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAAATTTATTATTATATTAAA
Found at i:2104957 original size:15 final size:14
Alignment explanation
Indices: 2104936--2105026 Score: 76
Period size: 15 Copynumber: 6.3 Consensus size: 14
2104926 AACCGTCTAG
2104936 AGTACTTGTGCCAA
1 AGTACTTGTGCCAA
*
2104950 AGGTACTTGTGCTAA
1 A-GTACTTGTGCCAA
*
2104965 AGGTA-TCTATGCCAA
1 A-GTACT-TGTGCCAA
* *
2104980 AGTACCTGTGTCAA
1 AGTACTTGTGCCAA
*
2104994 AGTACCTGTGCCAA
1 AGTACTTGTGCCAA
* *
2105008 GAGTACCTATGCCAA
1 -AGTACTTGTGCCAA
2105023 AGTA
1 AGTA
2105027 TCTGTACTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
14 28 0.43
15 37 0.57
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (14 bp):
AGTACTTGTGCCAA
Found at i:2104989 original size:29 final size:28
Alignment explanation
Indices: 2104944--2105067 Score: 97
Period size: 29 Copynumber: 4.2 Consensus size: 28
2104934 AGAGTACTTG
* *
2104944 TGCCAAAGGTACTTGTGCTAAAGGTATCTA
1 TGCCAAA-GTACCTGTGCTAAA-GTACCTA
*
2104974 TGCCAAAGTACCTGTG-TCAAAGTACCTG
1 TGCCAAAGTACCTGTGCT-AAAGTACCTA
* * * *
2105002 TGCCAAGAGTACCTATGCCAAAGTATCTG
1 TGCCAA-AGTACCTGTGCTAAAGTACCTA
* *
2105031 TACTAAAAGTACCTGTGCTAAAAGTACCTA
1 TGC-CAAAGTACCTGTGCT-AAAGTACCTA
*
2105061 TGTCAAA
1 TGCCAAA
2105068 ATACTGCCAA
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
28 12 0.16
29 44 0.59
30 18 0.24
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (28 bp):
TGCCAAAGTACCTGTGCTAAAGTACCTA
Found at i:2104995 original size:44 final size:43
Alignment explanation
Indices: 2104936--2105067 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 43
2104926 AACCGTCTAG
* * * *
2104936 AGTACTTGTGCCAAAGGTACTTGTGCTAAAGGTATCTATGCCAA
1 AGTACCTGTGACAAA-GTACCTGTGCTAAAGGTACCTATGCCAA
* *
2104980 AGTACCTGTGTCAAAGTACCTGTGC-CAAGAGTACCTATGCCAA
1 AGTACCTGTGACAAAGTACCTGTGCTAAAG-GTACCTATGCCAA
* * *
2105023 AGTATCTGT-ACTAAAAGTACCTGTGCTAAAAGTACCTATGTCAA
1 AGTACCTGTGAC--AAAGTACCTGTGCTAAAGGTACCTATGCCAA
2105067 A
1 A
2105068 ATACTGCCAA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 4 0.05
43 29 0.39
44 39 0.53
45 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (43 bp):
AGTACCTGTGACAAAGTACCTGTGCTAAAGGTACCTATGCCAA
Found at i:2105068 original size:15 final size:15
Alignment explanation
Indices: 2104978--2105068 Score: 73
Period size: 15 Copynumber: 6.2 Consensus size: 15
2104968 TATCTATGCC
2104978 AAAGTACCTGTGTC-
1 AAAGTACCTGTGTCA
*
2104992 AAAGTACCTGTGCCA
1 AAAGTACCTGTGTCA
* * *
2105007 AGAGTACCTATG-CC
1 AAAGTACCTGTGTCA
* *
2105021 AAAGTATCTGT-ACTA
1 AAAGTACCTGTGTC-A
2105036 AAAGTACCTGTG-CTA
1 AAAGTACCTGTGTC-A
*
2105051 AAAGTACCTATGTCA
1 AAAGTACCTGTGTCA
2105066 AAA
1 AAA
2105069 TACTGCCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
14 23 0.37
15 38 0.61
16 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (15 bp):
AAAGTACCTGTGTCA
Found at i:2105954 original size:67 final size:67
Alignment explanation
Indices: 2105807--2106125 Score: 211
Period size: 67 Copynumber: 4.8 Consensus size: 67
2105797 TCACATAGTT
* * * * ** * * **
2105807 GACTTCTCTATTAAGAATACTTGTATTA-AAGTGAATGACGGAAGTGACGCATAAGACCACAATA
1 GACTTTTCCATTAAGAATACTTGTATTAGAA-AGAGTGATAGAAGTGGCGCACAAGACCACAACG
*
2105871 ATC
65 GTC
* * * * * *
2105874 GAATTCTCAATTAAGAACACTTGTATTAGAAAGAGTGAT-GAAAGTGGTGCACAAGACCACCACG
1 GACTTTTCCATTAAGAATACTTGTATTAGAAAGAGTGATAG-AAGTGGCGCACAAGACCACAACG
2105938 GTC
65 GTC
* * * * * * *
2105941 GACTTTTCCATTAA-AAGAACTTGCATATA-TAAGAGTGACAGAAGT-G-GCATATGGACCATAA
1 GACTTTTCCATTAAGAA-TACTTGTAT-TAGAAAGAGTGATAGAAGTGGCGCACA-AGACCACAA
* *
2106002 TGGTT
63 CGGTC
* ** *
2106007 GTCTTTTCCATTAAGAATACTTGTATTAGAGTGAATGATAGAAGTGGCGCACGAA-ACCACAACG
1 GACTTTTCCATTAAGAATACTTGTATTAGAAAGAGTGATAGAAGTGGCGCAC-AAGACCACAACG
2106071 GTC
65 GTC
* * * * **
2106074 GAATTCTCTATTAAGAATACTTGTACTAGGGAGAGTGATAGAAGTGGCGCAC
1 GACTTTTCCATTAAGAATACTTGTATTAGAAAGAGTGATAGAAGTGGCGCAC
2106126 GTGACCACCA
Statistics
Matches: 194, Mismatches: 47, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
65 6 0.03
66 44 0.23
67 135 0.70
68 8 0.04
69 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (67 bp):
GACTTTTCCATTAAGAATACTTGTATTAGAAAGAGTGATAGAAGTGGCGCACAAGACCACAACGG
TC
Found at i:2106068 original size:200 final size:199
Alignment explanation
Indices: 2105804--2106219 Score: 473
Period size: 200 Copynumber: 2.1 Consensus size: 199
2105794 ATATCACATA
* * * *
2105804 GTTGACTTCTCTATTAAGAATACTTGTATTAAAGTGAATGACGGAAGTGACGCATAAGACCACAA
1 GTTGACTTTTCCATTAAGAATACTTGTATTAAAGTGAATGACAGAAGTGACGCAGAAGACCACAA
* * *
2105869 TAATCGAATTCTCAATTAAGAACACTTGTATTAGAAAGAGTGAT-GAAAGTGGTGCACAAGACCA
66 CAATCGAATTCTCAATTAAGAACACTTGTACTAGAAAGAGTGATAG-AAGTGGCGCACAAGACCA
* * * *
2105933 CCACGG-TCGACTTTTCCATT-AAAAGAACTTGCATATA-TAAGAGTGACAGAAGTGGCATATGG
130 CCAAGGTTC-ACTTCTCCATTGAAAA-AACTT-CATATAGGAA-AGTGACAGAAGTGGCACATGG
2105995 ACCATAATG
191 ACCATAATG
* * * *
2106004 GTTGTCTTTTCCATTAAGAATACTTGTATTAGAGTGAATGATAGAAGTGGCGCACGAA-ACCACA
1 GTTGACTTTTCCATTAAGAATACTTGTATTAAAGTGAATGACAGAAGTGACGCA-GAAGACCACA
** * * ** **
2106068 ACGGTCGAATTCTCTATTAAGAATACTTGTACTAGGGAGAGTGATAGAAGTGGCGCACGTGACCA
65 ACAATCGAATTCTCAATTAAGAACACTTGTACTAGAAAGAGTGATAGAAGTGGCGCACAAGACCA
** * * * *
2106133 CCAAGGTTCACTTCTCTGTTGGAAAAACTTTATATAGGAAAGTGATAGAAGTGGTACATGGACCA
130 CCAAGGTTCACTTCTCCATTGAAAAAACTTCATATAGGAAAGTGACAGAAGTGGCACATGGACCA
2106198 TAATG
195 TAATG
*
2106203 GTTGACTTTTCTATTAA
1 GTTGACTTTTCCATTAA
2106220 AAGTACCTAT
Statistics
Matches: 180, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
199 47 0.26
200 125 0.69
201 8 0.04
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (199 bp):
GTTGACTTTTCCATTAAGAATACTTGTATTAAAGTGAATGACAGAAGTGACGCAGAAGACCACAA
CAATCGAATTCTCAATTAAGAACACTTGTACTAGAAAGAGTGATAGAAGTGGCGCACAAGACCAC
CAAGGTTCACTTCTCCATTGAAAAAACTTCATATAGGAAAGTGACAGAAGTGGCACATGGACCAT
AATG
Found at i:2107732 original size:491 final size:488
Alignment explanation
Indices: 2106922--2107878 Score: 1385
Period size: 491 Copynumber: 2.0 Consensus size: 488
2106912 TGCCTTCATC
* * * * *
2106922 TACCTATTTATTCAAAAGCTTAAGAACTTTTTGCATAGAGCATAGAAATGGCGCTAGGGAGACCT
1 TACCCATTTATTAAAAAGCTCAAGAACTTTTTCCATAGAGCATAGAAATGGCACTAGGGAGACCT
** *
2106987 TTTCATCATAGTTAAGTTTGGCACTCTTACGTGATTTCTCTTATTTGAGGCTAAGAAACACCTTT
66 TTTCATCATAGTTAAGTTTGAAACTCTTACGTGATTGCTCTTATTTGAGGCTAAGAAACACCTTT
* *
2107052 CTCTCTAGTAAAAGTGATAGGTATATTTCTTTTTCCCTATGATAGTACTGTTGGTTCTCCTCGTA
131 CTCTCTAGTAAAAGCGATAGATATATTTCTTTTTCCCTATGATAGTACTGTTGGTTCTCCTCGTA
* * * * *
2107117 GCCTTCACCAAACTAGAAAAAGAAGATAGTGATAAATTTTTTCAGTGAAATTGAAATTCATCAAA
196 ACCTTCACCAAACTAGAAAAAAAAGATACTGATAAATTTTGTAAGTGAAATTGAAATTCATCAAA
2107182 CATTTCTTGTATGCATATTTAAACCAATTCCTTCTCATTATGTGCTTATTGTATATCTAACACTT
261 CATTTCTTGTATGCATATTTAAACCAATTCCTTCTCATTATGTGCTTATTGTATATCTAACAC-T
* * *
2107247 TTTCTCTAAAGCGTTGCATGTAATCCATGACATCTTCCTTTGGTCTTTGATATTCCTTACCTAAG
325 TTTCTCTAAAGCGTTGAATGTAATCCATGACATCTTCCTTTAGTCTTTGATATTCCCTACCTAAG
* *
2107312 TCAATAAAACTAA-TTTTCTCTT-GGTGGAAAAGAACTTTTCACTAAACATTTTACACATTTGGC
390 TCAACAAAACTAACTTTT-TCTTAGGTGGAAAAGAACTTTTCACTAAACATTCTACACATTTGGC
2107375 TCCATGACTCCATGGAACCTAGAGCACGGTTGACA
454 TCCATGACTCCATGGAACCTAGAGCACGGTTGACA
*
2107410 TACCCATTTATTAAAAAGCTCAAGAACTTTTTCCATAGAGCATGGAAATGGCACT-GAGGAGACC
1 TACCCATTTATTAAAAAGCTCAAGAACTTTTTCCATAGAGCATAGAAATGGCACTAG-GGAGACC
* *
2107474 TTTTCATCATAGTTACGTTTGAAACTCTTACGTGATTGCTCCTTATTTTAGGCTAAGAAACACCC
65 TTTTCATCATAGTTAAGTTTGAAACTCTTACGTGATTGCT-CTTATTTGAGGCTAAGAAACA--C
* * * * * *
2107539 CTTT-T-TCTGGTGAAAGCGATAGAT-TCGTTT-TTTATTCTCTGTGATAGTATTGTTGGTTCTC
127 CTTTCTCTCTAGTAAAAGCGATAGATAT-ATTTCTTT-TTCCCTATGATAGTACTGTTGGTTCTC
* *
2107600 CTTGTAACC-TCTACCAAACTAGAAAAAAAAAGGTAACTGATAAATTTTGTAAGTGAAATTGAAA
190 CTCGTAACCTTC-ACCAAACTAG-AAAAAAAAGAT-ACTGATAAATTTTGTAAGTGAAATTGAAA
* * * *
2107664 TTCATCAAACATTTCTTGTATGTGCA-CTTT-AACTAATTCCTTCTTATTATGTGCTTCTTGTAT
252 TTCATCAAACATTTCTTGTA--TGCATATTTAAACCAATTCCTTCTCATTATGTGCTTATTGTAT
*
2107727 ATCTAACACTTTTCTCTAAAGCGTTGAATGTAATCTATGACATCTTCCTTTAGTCTTTGATATTC
315 ATCTAACACTTTTCTCTAAAGCGTTGAATGTAATCCATGACATCTTCCTTTAGTCTTTGATATTC
* *
2107792 CCTATCTAAGTTAACAAAACTAACTTTTTCTTAGGTGGAAAAGAACTTTTCACTAAACATTCTAC
380 CCTACCTAAGTCAACAAAACTAACTTTTTCTTAGGTGGAAAAGAACTTTTCACTAAACATTCTAC
2107857 ACATTTGGCTCCATGACTCCAT
445 ACATTTGGCTCCATGACTCCAT
2107879 AAAATCGAGA
Statistics
Matches: 418, Mismatches: 38, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
487 1 0.00
488 98 0.23
489 79 0.19
490 86 0.21
491 147 0.35
492 3 0.01
493 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (488 bp):
TACCCATTTATTAAAAAGCTCAAGAACTTTTTCCATAGAGCATAGAAATGGCACTAGGGAGACCT
TTTCATCATAGTTAAGTTTGAAACTCTTACGTGATTGCTCTTATTTGAGGCTAAGAAACACCTTT
CTCTCTAGTAAAAGCGATAGATATATTTCTTTTTCCCTATGATAGTACTGTTGGTTCTCCTCGTA
ACCTTCACCAAACTAGAAAAAAAAGATACTGATAAATTTTGTAAGTGAAATTGAAATTCATCAAA
CATTTCTTGTATGCATATTTAAACCAATTCCTTCTCATTATGTGCTTATTGTATATCTAACACTT
TTCTCTAAAGCGTTGAATGTAATCCATGACATCTTCCTTTAGTCTTTGATATTCCCTACCTAAGT
CAACAAAACTAACTTTTTCTTAGGTGGAAAAGAACTTTTCACTAAACATTCTACACATTTGGCTC
CATGACTCCATGGAACCTAGAGCACGGTTGACA
Found at i:2109364 original size:14 final size:15
Alignment explanation
Indices: 2109340--2109394 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2109330 GAAGTACTTG
2109340 TGCCAAAAGTATCTA
1 TGCCAAAAGTATCTA
2109355 TGCC-AAAGTATCTA
1 TGCCAAAAGTATCTA
* * *
2109369 TGCCGAAAGTATTTG
1 TGCCAAAAGTATCTA
2109384 TGCCAAAAGTA
1 TGCCAAAAGTA
2109395 CTTGTACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 14 0.39
15 22 0.61
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (15 bp):
TGCCAAAAGTATCTA
Found at i:2109364 original size:29 final size:29
Alignment explanation
Indices: 2109331--2109415 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
2109321 ACTTATACTG
2109331 AAGTACTTGTGCCAAAAGTATCTATGCC-A
1 AAGTACTTGTGCCAAAAGTAT-TATGCCAA
* * *
2109360 AAGTA-TCTATGCCGAAAGTATTTGTGCCAA
1 AAGTACT-TGTGCCAAAAGTA-TTATGCCAA
*
2109390 AAGTACTTGTACCAAAAAGTATTATG
1 AAGTACTTGTGCC-AAAAGTATTATG
2109416 GCAATGAGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.02
29 21 0.48
30 15 0.34
31 7 0.16
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (29 bp):
AAGTACTTGTGCCAAAAGTATTATGCCAA
Found at i:2109399 original size:15 final size:14
Alignment explanation
Indices: 2109331--2109412 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 14
2109321 ACTTATACTG
2109331 AAGTACTTGTGCCAA
1 AAGTA-TTGTGCCAA
*
2109346 AAGTATCTATGCC-A
1 AAGTAT-TGTGCCAA
* *
2109360 AAGTATCTATGCCGA
1 AAGTAT-TGTGCCAA
2109375 AAGTATTTGTGCCAA
1 AAGTA-TTGTGCCAA
*
2109390 AAGTACTTGTACCAAA
1 AAGTA-TTGTGCC-AA
2109406 AAGTATT
1 AAGTATT
2109413 ATGGCAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
14 15 0.26
15 35 0.60
16 8 0.14
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (14 bp):
AAGTATTGTGCCAA
Found at i:2109680 original size:39 final size:38
Alignment explanation
Indices: 2109637--2109719 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 38
2109627 CAATGATTGG
* *
2109637 TTAA-AGATTATTTAATTATTAATTTA-AAAAATTATTTCA
1 TTAATAGATTATTT--TTATTAAATTATAAAAATAATTT-A
2109676 TTAAATAGATTATTTTTATTAAATTATAAAAATAATTTA
1 TT-AATAGATTATTTTTATTAAATTATAAAAATAATTTA
2109715 TTAAT
1 TTAAT
2109720 TATATGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
38 3 0.08
39 15 0.38
40 12 0.31
41 9 0.23
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (38 bp):
TTAATAGATTATTTTTATTAAATTATAAAAATAATTTA
Found at i:2111293 original size:19 final size:23
Alignment explanation
Indices: 2111250--2111298 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 23
2111240 TTATTTTTTA
2111250 TATTTTTAATTTATTTATGTAAT
1 TATTTTTAATTTATTTATGTAAT
2111273 TATTTTTAA-TT-TTTAT-T-AT
1 TATTTTTAATTTATTTATGTAAT
2111292 TATTTTT
1 TATTTTT
2111299 TTAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.35
20 1 0.04
21 5 0.19
22 2 0.08
23 9 0.35
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTTTAATTTATTTATGTAAT
Found at i:2116028 original size:26 final size:26
Alignment explanation
Indices: 2115992--2116046 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
2115982 TAAACAATAT
* *
2115992 ATATATATATATATATCATGAGAAAA
1 ATATAAATATATATATAATGAGAAAA
2116018 ATATAAATATATATATAATGAGAAAA
1 ATATAAATATATATATAATGAGAAAA
2116044 ATA
1 ATA
2116047 CTTCTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (26 bp):
ATATAAATATATATATAATGAGAAAA
Found at i:2118815 original size:20 final size:21
Alignment explanation
Indices: 2118771--2118816 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
2118761 GATTTCATAG
*
2118771 CATTTTTATGTCATTTTAGGT
1 CATTTTTATATCATTTTAGGT
2118792 -ATTTTTATATCATTTTA-GT
1 CATTTTTATATCATTTTAGGT
2118811 CATTTT
1 CATTTT
2118817 CAAAGACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (21 bp):
CATTTTTATATCATTTTAGGT
Found at i:2124512 original size:21 final size:21
Alignment explanation
Indices: 2124488--2124539 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2124478 TTCTACAATT
2124488 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATTAGTGAA
* *
2124509 TGTATTGATACAATTGGTGAA
1 TGTATCGATACAATTAGTGAA
2124530 TGTATCGATA
1 TGTATCGATA
2124540 AATGTCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (21 bp):
TGTATCGATACAATTAGTGAA
Found at i:2124640 original size:20 final size:19
Alignment explanation
Indices: 2124617--2124665 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2124607 TAAATGTGTT
2124617 GATACATTTCCATATGTATC
1 GATACATTT-CATATGTATC
** *
2124637 GATACAATTTGTTTTGTATC
1 GATAC-ATTTCATATGTATC
2124657 GATACATTT
1 GATACATTT
2124666 TAGGTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (19 bp):
GATACATTTCATATGTATC
Found at i:2137378 original size:27 final size:27
Alignment explanation
Indices: 2137348--2137399 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2137338 TAATAAATGT
2137348 TAATAATAAAAAAATTATAATATAAAA
1 TAATAATAAAAAAATTATAATATAAAA
* * * *
2137375 TAATAATTATAATATTATATTATAA
1 TAATAATAAAAAAATTATAATATAA
2137400 TTATTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TAATAATAAAAAAATTATAATATAAAA
Found at i:2137399 original size:19 final size:19
Alignment explanation
Indices: 2137360--2137403 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2137350 ATAATAAAAA
2137360 AATTATAATATAAAATAAT
1 AATTATAATATAAAATAAT
* * *
2137379 AATTATAATATTATATTAT
1 AATTATAATATAAAATAAT
2137398 AATTAT
1 AATTAT
2137404 TATTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATAATATAAAATAAT
Found at i:2141216 original size:11 final size:11
Alignment explanation
Indices: 2141200--2141234 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
2141190 GAGAAAAGAA
2141200 AAAAAAGAGAG
1 AAAAAAGAGAG
2141211 AAAAAAGAGA-
1 AAAAAAGAGAG
2141221 AAAAAAGA-AG
1 AAAAAAGAGAG
2141231 AAAA
1 AAAA
2141235 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.04
10 12 0.52
11 10 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:2141218 original size:20 final size:20
Alignment explanation
Indices: 2141193--2141234 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2141183 AGTTTTCGAG
2141193 AAAAGA-AAAAAAAGAGAGAA
1 AAAAGAGAAAAAAAGA-AGAA
2141213 AAAAGAGAAAAAAAGAAGAA
1 AAAAGAGAAAAAAAGAAGAA
2141233 AA
1 AA
2141235 TTTAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAAAAAAGAAGAA
Found at i:2141231 original size:13 final size:11
Alignment explanation
Indices: 2141196--2141226 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2141186 TTTCGAGAAA
2141196 AGAAAAAAAAG
1 AGAAAAAAAAG
*
2141207 AGAGAAAAAAG
1 AGAAAAAAAAG
2141218 AGAAAAAAA
1 AGAAAAAAA
2141227 GAAGAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:2145714 original size:26 final size:26
Alignment explanation
Indices: 2145685--2145734 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2145675 CATCTAAAAC
2145685 GTTGGCCATTGTAATGATTCTTAAAT
1 GTTGGCCATTGTAATGATTCTTAAAT
2145711 GTTGGCCATTGTAATGATTCTTAA
1 GTTGGCCATTGTAATGATTCTTAA
2145735 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (26 bp):
GTTGGCCATTGTAATGATTCTTAAAT
Found at i:2150042 original size:30 final size:29
Alignment explanation
Indices: 2150006--2150100 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 29
2149996 TGAACAGTAC
2150006 ATGTATCGATACATTATGTTTTTTACCCAG
1 ATGTATCGATACATTATGTTTTTTA-CCAG
2150036 ATGTATCGATAC---A---TTTTT--CA-
1 ATGTATCGATACATTATGTTTTTTACCAG
*
2150056 ATGTATCGATACATTCTGTTTTTTATCCAG
1 ATGTATCGATACATTATGTTTTTTA-CCAG
*
2150086 ATGTATCAATACATT
1 ATGTATCGATACATT
2150101 TTTCAATGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
20 12 0.23
21 2 0.04
24 5 0.09
26 5 0.09
27 1 0.02
29 2 0.04
30 26 0.49
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (29 bp):
ATGTATCGATACATTATGTTTTTTACCAG
Found at i:2150078 original size:26 final size:26
Alignment explanation
Indices: 2150049--2150129 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 26
2150039 TATCGATACA
*
2150049 TTTTTCAATGTATCGATACATTCTGTT
1 TTTTTCAATGTATCAATACATTCTG-T
2150076 TTTTATCCAGATGTATCAATACA------
1 TTTT-T-CA-ATGTATCAATACATTCTGT
2150099 TTTTTCAATGTATCAATACATTCTGT
1 TTTTTCAATGTATCAATACATTCTGT
2150125 TTTTT
1 TTTTT
2150130 AACCCAGATG
Statistics
Matches: 44, Mismatches: 1, Indels: 19
0.69 0.02 0.30
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 1 0.02
23 4 0.09
26 5 0.11
27 4 0.09
28 1 0.02
29 2 0.05
30 12 0.27
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (26 bp):
TTTTTCAATGTATCAATACATTCTGT
Found at i:2150153 original size:51 final size:50
Alignment explanation
Indices: 2150006--2150169 Score: 267
Period size: 50 Copynumber: 3.3 Consensus size: 50
2149996 TGAACAGTAC
*
2150006 ATGTATCGATACATTATGTTTTTTACCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTGTTTTTTACCCAGATGTATCGATACATTTTTCA
* *
2150056 ATGTATCGATACATTCTGTTTTTTATCCAGATGTATCAATACATTTTTCA
1 ATGTATCGATACATTCTGTTTTTTACCCAGATGTATCGATACATTTTTCA
* *
2150106 ATGTATCAATACATTCTGTTTTTTAACCCAGATGTATCGATATATTTTTCA
1 ATGTATCGATACATTCTGTTTTTT-ACCCAGATGTATCGATACATTTTTCA
2150157 ATGTATC-ATACAT
1 ATGTATCGATACAT
2150170 CTAGTTAATT
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 76 0.72
51 30 0.28
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (50 bp):
ATGTATCGATACATTCTGTTTTTTACCCAGATGTATCGATACATTTTTCA
Found at i:2152334 original size:24 final size:24
Alignment explanation
Indices: 2152300--2152345 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2152290 CATTCACGTC
*
2152300 AATTTTTTTTATCAAAAATACTAA
1 AATTTTATTTATCAAAAATACTAA
* *
2152324 AATTTTATTTATCTAGAATACT
1 AATTTTATTTATCAAAAATACT
2152346 CTAACCCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (24 bp):
AATTTTATTTATCAAAAATACTAA
Found at i:2154135 original size:164 final size:164
Alignment explanation
Indices: 2153907--2154398 Score: 511
Period size: 163 Copynumber: 3.0 Consensus size: 164
2153897 AAAATTTTTT
* * * * *
2153907 AAATATTATTATTTAATT-ATCATTAAATCAGTTTTAAAAAATTTATTTATTCTT-ATGAGTTTT
1 AAATATCATCATTTAATTCAT-AGTAAATCAATTTTAAAAAATTCATTTATT-TTCA-GAGTTTT
* ** *
2153970 TCATTTTTTCTTGAAATTTTTCTATTTTCGAAAAACGGAGTTTTCTACTCTATAAATGTTTTTAA
63 TCATTTTTTCTTGAAATTTTCCTATTTTCGAAAAACAAAGTTTTCTACTCGATAAATG-TTTTAA
2154035 GAG-AATTTTTCTCAGTTTAAAATTTTTAAAATTCATC
127 GAGAAATTTTTCTCAGTTTAAAATTTTTAAAATTCATC
* * *
2154072 AAATATCATCGTTTAATTCATAGTATAAT-AGTTTT-AATAATT-ATTTTATTTTCACGAGTTTT
1 AAATATCATCATTTAATTCATAGTA-AATCAATTTTAAAAAATTCA-TTTATTTTCA-GAGTTTT
* * **
2154134 TCATTTTTTCTCGAAA-TTTCCTATTTTTGAAAAACAAAGTTTTCTACTCGATAAATGTTTTCGG
63 TCATTTTTTCTTGAAATTTTCCTATTTTCGAAAAACAAAGTTTTCTACTCGATAAATGTTTTAAG
* **
2154198 GGAAATTTTTCTTGGTTTAAAATTTTTAAAATTCATC
128 AGAAATTTTTCTCAGTTTAAAATTTTTAAAATTCATC
* *
2154235 AAATATCATCATTTATTTCATAGTAAATCAATTTTAAAAAATTCATTTATTTTCATAGGTTTTTC
1 AAATATCATCATTTAATTCATAGTAAATCAATTTTAAAAAATTCATTTATTTTCAGA-GTTTTTC
** * * * *
2154300 ATTTTTTCTTTGAAATTTTATTA-TTTCTAAAAAACCAAGTTTTCTAGTTC-ATAAAAGTTTT-A
65 ATTTTTTC-TTGAAATTTTCCTATTTTC-GAAAAACAAAGTTTTCTA-CTCGATAAATGTTTTAA
** * * *
2154362 GAGGGATGTTTCATGA-TTTATAATTTTTAAAATTCAT
127 GAGAAATTTTTC-TCAGTTTAAAATTTTTAAAATTCAT
2154399 TTCTCATTAG
Statistics
Matches: 275, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
162 9 0.03
163 100 0.36
164 66 0.24
165 61 0.22
166 37 0.13
167 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (164 bp):
AAATATCATCATTTAATTCATAGTAAATCAATTTTAAAAAATTCATTTATTTTCAGAGTTTTTCA
TTTTTTCTTGAAATTTTCCTATTTTCGAAAAACAAAGTTTTCTACTCGATAAATGTTTTAAGAGA
AATTTTTCTCAGTTTAAAATTTTTAAAATTCATC
Found at i:2154948 original size:21 final size:21
Alignment explanation
Indices: 2154924--2154963 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2154914 GGAGAGATAA
* *
2154924 AGAAATAAAAAAGACAAAATT
1 AGAAAGAAAAAAGAAAAAATT
*
2154945 AGAAAGAAAATAGAAAAAA
1 AGAAAGAAAAAAGAAAAAA
2154964 AAAATCTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (21 bp):
AGAAAGAAAAAAGAAAAAATT
Found at i:2156268 original size:21 final size:20
Alignment explanation
Indices: 2156218--2156276 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
2156208 GCCGTTGGGC
2156218 CAAATT-TATCGATACAATT
1 CAAATTGTATCGATACAATT
*
2156237 CATATTGTATCGATACAATT
1 CAAATTGTATCGATACAATT
*
2156257 TAAATATGTATCGATACAAT
1 CAAAT-TGTATCGATACAAT
2156277 CACAGGGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 5 0.14
20 16 0.46
21 14 0.40
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (20 bp):
CAAATTGTATCGATACAATT
Found at i:2156395 original size:33 final size:33
Alignment explanation
Indices: 2156347--2156409 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2156337 TTCCATAGTG
*
2156347 TATCGATACAAAGCAATTTGTATCGATACAATA
1 TATCGATACAAAGCAATTCGTATCGATACAATA
**
2156380 TATCGATACTTAGCAATTCGTATCGATACA
1 TATCGATACAAAGCAATTCGTATCGATACA
2156410 TCTAGGTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (33 bp):
TATCGATACAAAGCAATTCGTATCGATACAATA
Found at i:2157095 original size:25 final size:26
Alignment explanation
Indices: 2157067--2157117 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2157057 CCCCTTCCAA
2157067 TTTTATTCA-CTCTCCAAATTTATTC
1 TTTTATTCACCTCTCCAAATTTATTC
*
2157092 TTTTATTCACCTCTCTAAATTTATTC
1 TTTTATTCACCTCTCCAAATTTATTC
2157118 ACCACAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTATTCACCTCTCCAAATTTATTC
Found at i:2163828 original size:20 final size:20
Alignment explanation
Indices: 2163803--2163855 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
2163793 AAATTCCTGA
2163803 ATGTATCGATACAAAGATCC
1 ATGTATCGATACAAAGATCC
2163823 ATGTATCGATACAAAGATCC
1 ATGTATCGATACAAAGATCC
2163843 ATGTATCGATACA
1 ATGTATCGATACA
2163856 TTTCCTTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACAAAGATCC
Found at i:2171277 original size:16 final size:18
Alignment explanation
Indices: 2171256--2171288 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2171246 TTTTGAAATG
2171256 TTTCTT-GATTT-AAACA
1 TTTCTTAGATTTGAAACA
2171272 TTTCTTAGATTTGAAAC
1 TTTCTTAGATTTGAAAC
2171289 TGTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTCTTAGATTTGAAACA
Found at i:2173449 original size:71 final size:71
Alignment explanation
Indices: 2173319--2173450 Score: 167
Period size: 71 Copynumber: 1.9 Consensus size: 71
2173309 TTGATTTTGT
* * * * * *
2173319 TATACCAGATTTTTTATTTTACATCTCGATTTCAAATTATCTTTTTGATTAGCTCCAATTTTCGA
1 TATACCAAATTTTTTATATTACATATCGATTTCAAATTATCCTTTTGACTAGATCCAATTTTCGA
2173384 TTCTGC
66 TTCTGC
* * *
2173390 TATACCAAATTTTTTGTATTACATATTGATTTCAAA-TAGTCCTTTTGACTAGATGCAATTT
1 TATACCAAATTTTTTATATTACATATCGATTTCAAATTA-TCCTTTTGACTAGATCCAATTT
2173451 GTTAACAGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 2 0.04
71 49 0.96
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (71 bp):
TATACCAAATTTTTTATATTACATATCGATTTCAAATTATCCTTTTGACTAGATCCAATTTTCGA
TTCTGC
Found at i:2183037 original size:20 final size:20
Alignment explanation
Indices: 2182993--2183046 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2182983 ATTTCAACGA
2182993 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATAAAAT
* ***
2183013 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATAAAAT
2183033 TTTGTATCGATACA
1 TTTGTATCGATACA
2183047 ATGTAAGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTGTATCGATACATAAAAT
Found at i:2183110 original size:13 final size:13
Alignment explanation
Indices: 2183092--2183116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2183082 ATTACTCACA
2183092 TGTATCGATACAT
1 TGTATCGATACAT
2183105 TGTATCGATACA
1 TGTATCGATACA
2183117 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2183181 original size:52 final size:52
Alignment explanation
Indices: 2183125--2183249 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
2183115 CACTGATCTT
*
2183125 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2183177 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2183229 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2183250 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2187846 original size:10 final size:11
Alignment explanation
Indices: 2187799--2187836 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
2187789 TATTCTTTAC
2187799 TTTTTTTTCAAA
1 TTTTTTTTC-AA
2187811 TTTTTTTCTCAA
1 TTTTTTT-TCAA
2187823 TTTTTTTT-AA
1 TTTTTTTTCAA
2187833 TTTT
1 TTTT
2187837 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.24
11 1 0.04
12 16 0.64
13 2 0.08
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:2195918 original size:20 final size:20
Alignment explanation
Indices: 2195885--2195923 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2195875 ATTTTAATTT
* *
2195885 TATTTAGTTTTAATATTTGA
1 TATTTAATTATAATATTTGA
*
2195905 TATTTAATTATAATCTTTG
1 TATTTAATTATAATATTTG
2195924 TAGATAATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (20 bp):
TATTTAATTATAATATTTGA
Found at i:2196967 original size:155 final size:154
Alignment explanation
Indices: 2196607--2196988 Score: 385
Period size: 155 Copynumber: 2.5 Consensus size: 154
2196597 TAAATTTAAG
* * * * * *
2196607 AAAAATTACGAAAAT-GCCTCTATGAGATACCTTCGATGTAAAAGTACCCAATATCCGTAAAGGA
1 AAAAATTACGAAAATACCCT-TA-GGGATTCCTTCGACGTAAAAGTACCCGATATCCCTAAAGGA
* ** * * *
2196671 CTTAAAAAGGATTATAAATGAGACAAACCTATTTTAAATACCCACCTTCAACATAAAAGTAGACC
64 CTT-AAAAGGATTAAAAATGAGACAAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAAAC
* *
2196736 CGGTGACAACCTAAGACTTAGTTCTAA
128 CAGTGACAACCTAAGACTCAGTTCTAA
* * * * * *
2196763 AAAAATAACCAAAATACCCCTAGGGATAT-CTTCGACATAGAAGTGCCCGATATCCCTAAAGGAC
1 AAAAATTACGAAAATACCCTTAGGGAT-TCCTTCGACGTAAAAGTACCCGATATCCCTAAAGGAC
** * * *
2196827 TTAAAAGGATTACAAAATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGCAAAACC
65 TTAAAAGGATTA-AAAATGAGACAAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAAACC
* *
2196892 AGTGACAACCTAGGACTCGGTTCT-A
129 AGTGACAACCTAAGACTCAGTTCTAA
* ** *
2196917 AAAAATTACGAAAATATCCTTAGGGGATTCCTTCGACGTAAAAAAACCCGATA-CTCCTAAAGAA
1 AAAAATTACGAAAATACCCTTA-GGGATTCCTTCGACGTAAAAGTACCCGATATC-CCTAAAGGA
2196981 CTTTAAAA
64 C-TTAAAA
2196989 AAAAGATTTT
Statistics
Matches: 182, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
154 31 0.17
155 128 0.70
156 21 0.12
157 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (154 bp):
AAAAATTACGAAAATACCCTTAGGGATTCCTTCGACGTAAAAGTACCCGATATCCCTAAAGGACT
TAAAAGGATTAAAAATGAGACAAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAAACCAG
TGACAACCTAAGACTCAGTTCTAA
Found at i:2197096 original size:158 final size:153
Alignment explanation
Indices: 2196842--2197259 Score: 378
Period size: 158 Copynumber: 2.7 Consensus size: 153
2196832 AGGATTACAA
* * ** **
2196842 AATGAGATGAACCTATCCTAAATATCTACCTTCAGCATAAAAGCAAAACCAG-TGACAACCTAGG
1 AATG-GATGAACCTATCCTAAATATCCACTTTCAGCATAAAAGC-GGACCAGATGATGACCTAGG
* * ** * *
2196906 ACTCGGTTCTAAAAAATTACGAAAATATCCTTAGGGGATTCCTTCGACGTAAAAAAACCCGATAC
64 AGTCGGTTCTAAGAAATTAC-AAAATGCCCTTAGGGGATACCTTCAACGTAAAAAAACCCGATAC
* *
2196971 TCCTAAAGAACTTTAAAAAAAAGATTTTA-
128 TCCTAAAAAAC--T-AAAAAAA-ATTGTAG
* * *
2197000 ATTGGGATGAACCTA-CCTTAAATATCCACTTTCAGCATAAAAACGGACCGGATGATGACCTAGG
1 AAT-GGATGAACCTATCC-TAAATATCCACTTTCAGCATAAAAGCGGACCAGATGATGACCTAGG
* * * * ** **
2197064 AGTTGGTTCTAAGAAATTACAAAAATGCCCTTAAGGGATACATTTAACGTAAAAGTACCTTATAC
64 AGTCGGTTCTAAGAAATTAC-AAAATGCCCTTAGGGGATACCTTCAACGTAAAAAAACCCGATAC
* *
2197129 TCTTAAAAAACTAAAAATAATTGTAG
128 TCCTAAAAAACTAAAAAAAATTGTAG
* * * * *
2197155 AATGGATGAACCTATCCTAATTACCCACCTTT-GGCATAAAAGCGGACCCGATGATGACCTAAGA
1 AATGGATGAACCTATCCTAAATATCCA-CTTTCAGCATAAAAGCGGACCAGATGATGACCTAGGA
* ** *
2197219 GTGGGTT-TTGGAAATTACGAAATGCCCTTAGGGGATACCTT
65 GTCGGTTCTAAGAAATTACAAAATGCCCTTAGGGGATACCTT
2197260 TGATGCAAAA
Statistics
Matches: 213, Mismatches: 41, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
152 20 0.09
153 9 0.04
154 58 0.27
155 14 0.07
156 1 0.00
157 6 0.03
158 104 0.49
159 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (153 bp):
AATGGATGAACCTATCCTAAATATCCACTTTCAGCATAAAAGCGGACCAGATGATGACCTAGGAG
TCGGTTCTAAGAAATTACAAAATGCCCTTAGGGGATACCTTCAACGTAAAAAAACCCGATACTCC
TAAAAAACTAAAAAAAATTGTAG
Found at i:2198815 original size:9 final size:9
Alignment explanation
Indices: 2198797--2198840 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
2198787 TTTGCCTTAG
*
2198797 TTTTTATTT
1 TTTTTCTTT
2198806 TTTTTCTTT
1 TTTTTCTTT
*
2198815 TTTCTCTCTT
1 TTTTTCT-TT
2198825 TTTTTCTTT
1 TTTTTCTTT
2198834 ATTTTTC
1 -TTTTTC
2198841 CTTCACTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 16 0.53
10 14 0.47
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2198991 original size:23 final size:23
Alignment explanation
Indices: 2198947--2198991 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2198937 GCTACTACTT
* **
2198947 TTGCTTGTTGTTTGATGTTGCTC
1 TTGCTTGCTGTTTGATACTGCTC
*
2198970 TTGCTTGCTGTTTGTTACTGCT
1 TTGCTTGCTGTTTGATACTGCT
2198992 TTACTTGTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.04, C:0.16, G:0.24, T:0.56
Consensus pattern (23 bp):
TTGCTTGCTGTTTGATACTGCTC
Found at i:2199202 original size:43 final size:43
Alignment explanation
Indices: 2199094--2199211 Score: 101
Period size: 43 Copynumber: 2.7 Consensus size: 43
2199084 TTTTTTCTTA
* * * * * * *
2199094 CTTACCATTGCTTGCTATTACTACTGGTGCTGTTTACTTGCTTG
1 CTTACCGTTACTTGCTATTGCTACTAGTGTTG-ATGCTTGCTTG
* * * *
2199138 TTTACCGTTGCTTGTTGTTGCTACTAGTGTTGATGCTTGCTTG
1 CTTACCGTTACTTGCTATTGCTACTAGTGTTGATGCTTGCTTG
* * *
2199181 CTTGCCGTTACTTGCTATTGCTGCTGGTGTT
1 CTTACCGTTACTTGCTATTGCTACTAGTGTT
2199212 TGTTGTTTTG
Statistics
Matches: 58, Mismatches: 16, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
43 33 0.57
44 25 0.43
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (43 bp):
CTTACCGTTACTTGCTATTGCTACTAGTGTTGATGCTTGCTTG
Found at i:2199331 original size:25 final size:25
Alignment explanation
Indices: 2199282--2199331 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2199272 TTCCTTCTTT
* * *
2199282 TTTAGCTGCTGCCGTTGCTTGCTTC
1 TTTAGCTACTGCCGTTGCCTACTTC
*
2199307 TTTAGCTACTGTCGTTGCCTACTTC
1 TTTAGCTACTGCCGTTGCCTACTTC
2199332 AGCTGCTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.08, C:0.28, G:0.20, T:0.44
Consensus pattern (25 bp):
TTTAGCTACTGCCGTTGCCTACTTC
Found at i:2206622 original size:50 final size:49
Alignment explanation
Indices: 2206568--2206663 Score: 131
Period size: 48 Copynumber: 1.9 Consensus size: 49
2206558 TAGATATATC
* * *
2206568 ATTTAATAATAAAGTAAAAAACTAAAGGTCACTATGTC-AATTATTTAGGT
1 ATTTAAAAATAAAAT-AAAAA-TAAAGATCACTATGTCAAATTATTTAGGT
*
2206618 ATTTAAAAATAAAATAAAAATAAATATCACTATGTCAAATTATTTA
1 ATTTAAAAATAAAATAAAAATAAAGATCACTATGTCAAATTATTTA
2206664 AATATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 14 0.34
49 14 0.34
50 13 0.32
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (49 bp):
ATTTAAAAATAAAATAAAAATAAAGATCACTATGTCAAATTATTTAGGT
Found at i:2206670 original size:49 final size:50
Alignment explanation
Indices: 2206568--2206670 Score: 129
Period size: 49 Copynumber: 2.1 Consensus size: 50
2206558 TAGATATATC
* * * **
2206568 ATTTAATAATAAAGTAAAAAACTAAAGGTCACTATGTCAATTATTTAGGT
1 ATTTAAAAATAAAATAAAAAACTAAAGATCACTATGTCAATTATTTAAAT
*
2206618 ATTTAAAAATAAAAT-AAAAA-TAAATATCACTATGTCAAATTATTTAAAT
1 ATTTAAAAATAAAATAAAAAACTAAAGATCACTATGTC-AATTATTTAAAT
2206667 ATTT
1 ATTT
2206671 TATATTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 14 0.30
49 19 0.41
50 13 0.28
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (50 bp):
ATTTAAAAATAAAATAAAAAACTAAAGATCACTATGTCAATTATTTAAAT
Found at i:2207259 original size:15 final size:14
Alignment explanation
Indices: 2207239--2207268 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2207229 GAAACACAAA
2207239 TATTTTCTTTCTTTT
1 TATTTTCTTT-TTTT
2207254 TATTTTCTTTTTTT
1 TATTTTCTTTTTTT
2207268 T
1 T
2207269 CCCCACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (14 bp):
TATTTTCTTTTTTT
Found at i:2213244 original size:13 final size:13
Alignment explanation
Indices: 2213226--2213273 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2213216 TTACAATATG
2213226 AATATATGAAAGA
1 AATATATGAAAGA
*
2213239 AATATATTG---TA
1 AATATA-TGAAAGA
2213250 AATATATGAAAGA
1 AATATATGAAAGA
2213263 AATATATGAAA
1 AATATATGAAA
2213274 TAAAAACCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.07
11 7 0.24
13 18 0.62
14 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.29
Consensus pattern (13 bp):
AATATATGAAAGA
Found at i:2213698 original size:20 final size:20
Alignment explanation
Indices: 2213673--2213711 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2213663 ATATCTTTTT
2213673 AAAAATTATTTTTTAATACG
1 AAAAATTATTTTTTAATACG
2213693 AAAAATTATTTTTTAATAC
1 AAAAATTATTTTTTAATAC
2213712 AGCATAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAAATTATTTTTTAATACG
Found at i:2214343 original size:6 final size:6
Alignment explanation
Indices: 2214332--2214387 Score: 60
Period size: 6 Copynumber: 8.8 Consensus size: 6
2214322 TACTTTTTAC
*
2214332 CTTTTT CTTTTT CTTTTT -TTTCTT AACTTTTT CTTTTT CTTTTT GTCTTTT
1 CTTTTT CTTTTT CTTTTT CTTT-TT --CTTTTT CTTTTT CTTTTT CT-TTTT
2214383 CTTTT
1 CTTTT
2214388 GTTTCCTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
5 3 0.07
6 30 0.70
7 5 0.12
8 2 0.05
9 3 0.07
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:2214381 original size:20 final size:18
Alignment explanation
Indices: 2214333--2214387 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
2214323 ACTTTTTACC
2214333 TTTTTCTTTTTCTTTTTT
1 TTTTTCTTTTTCTTTTTT
*
2214351 TTCTTAACTTTTTCTTTTTCT
1 TT-TT-TCTTTTTCTTTTT-T
2214372 TTTTGTC-TTTTCTTTT
1 TTTT-TCTTTTTCTTTT
2214388 GTTTCCTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 15 0.48
21 3 0.10
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTTT
Found at i:2214798 original size:23 final size:23
Alignment explanation
Indices: 2214772--2214816 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2214762 GGATATAAAT
2214772 TGCCTGATGTTGAATTCATGAAC
1 TGCCTGATGTTGAATTCATGAAC
2214795 TGCCTGATGTTGAATTCATGAA
1 TGCCTGATGTTGAATTCATGAA
2214817 TTTTACTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (23 bp):
TGCCTGATGTTGAATTCATGAAC
Found at i:2216032 original size:15 final size:15
Alignment explanation
Indices: 2215995--2216026 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2215985 CCAAGAACGC
2215995 TTGAAGAACACAGCA
1 TTGAAGAACACAGCA
2216010 TTGAAGAACACAGCA
1 TTGAAGAACACAGCA
2216025 TT
1 TT
2216027 ACAGAATCTC
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:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (15 bp):
TTGAAGAACACAGCA
Found at i:2216497 original size:16 final size:15
Alignment explanation
Indices: 2216474--2216549 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 15
2216464 TTATAAAATT
2216474 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
2216489 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* * *
2216504 TTTATTTTAA-AATA
1 TTTAATTAAATAAAA
2216518 TTTAA-TAAATAAAA
1 TTTAATTAAATAAAA
*
2216532 -TTAA--AATTAAAA
1 TTTAATTAAATAAAA
2216544 TTTAAT
1 TTTAAT
2216550 CATATAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
12 7 0.14
13 11 0.22
14 14 0.28
15 13 0.26
16 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:2216541 original size:28 final size:26
Alignment explanation
Indices: 2216477--2216558 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 26
2216467 TAAAATTTTT
*
2216477 AATTAAA-TAAAATTATAATTAATAA
1 AATTAAATTAAAATTATAATAAATAA
** *
2216502 AATTTATTTTAAAATATTTAATAAATAA
1 AA-TTAAATTAAAAT-TATAATAAATAA
*
2216530 AATTAAAATTAAAATT-TAATCATATAA
1 AATT-AAATTAAAATTATAAT-AAATAA
2216557 AA
1 AA
2216559 AATTTATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
25 2 0.04
26 7 0.16
27 16 0.36
28 20 0.44
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (26 bp):
AATTAAATTAAAATTATAATAAATAA
Found at i:2216548 original size:13 final size:14
Alignment explanation
Indices: 2216474--2216549 Score: 59
Period size: 15 Copynumber: 5.4 Consensus size: 14
2216464 TTATAAAATT
2216474 TTTAATTAAATAAAA
1 TTTAA-TAAATAAAA
*
2216489 TTATAATTAATAAAA
1 TT-TAATAAATAAAA
* * *
2216504 TTTATTTTAA-AATA
1 TTTA-ATAAATAAAA
2216518 TTTAATAAATAAAA
1 TTTAATAAATAAAA
*
2216532 -TTAA-AATTAAAA
1 TTTAATAAATAAAA
2216544 TTTAAT
1 TTTAAT
2216550 CATATAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 7 0.14
13 11 0.22
14 12 0.24
15 16 0.33
16 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAATAAATAAAA
Found at i:2216558 original size:43 final size:42
Alignment explanation
Indices: 2216464--2216570 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
2216454 GTTTTAATAT
*
2216464 TTATAAAATTTTTAATTAAATAAAATTATAATTAATAAAATTTA
1 TTATAAAATATTTAA-TAAATAAAATTATAA-TAATAAAATTTA
* *
2216508 TTTTAAAATATTTAATAAATAAAATTA-AA-ATTAAAATTTAA
1 TTATAAAATATTTAATAAATAAAATTATAATAATAAAATTT-A
*
2216549 TCATATAAAAAATTTATATAAA
1 T--TATAAAATATTTA-ATAAA
2216571 ATATAGGATA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
40 9 0.17
41 2 0.04
42 2 0.04
43 23 0.43
44 18 0.33
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (42 bp):
TTATAAAATATTTAATAAATAAAATTATAATAATAAAATTTA
Found at i:2217620 original size:13 final size:13
Alignment explanation
Indices: 2217602--2217626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2217592 AATACAAACA
2217602 TATAAATTTTTTT
1 TATAAATTTTTTT
2217615 TATAAATTTTTT
1 TATAAATTTTTT
2217627 CTTTTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATAAATTTTTTT
Found at i:2217644 original size:4 final size:4
Alignment explanation
Indices: 2217624--2217669 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
2217614 TTATAAATTT
*
2217624 TTTC TTT- TTTT TCTTC TTTC TTT- TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
2217670 TTCACCATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
3 6 0.16
4 29 0.76
5 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:2217670 original size:23 final size:23
Alignment explanation
Indices: 2217621--2217671 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
2217611 TTTTTATAAA
*
2217621 TTTTTTCTTTTTTTTCTTCTTTC
1 TTTTTTCTTTTTTCTCTTCTTTC
2217644 TTTTTTCTTTCTTTCT-TTCTTTC
1 TTTTTTCTTT-TTTCTCTTCTTTC
2217667 TTTTT
1 TTTTT
2217672 CACCATGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTCTTTTTTCTCTTCTTTC
Found at i:2217935 original size:129 final size:128
Alignment explanation
Indices: 2217772--2218012 Score: 351
Period size: 129 Copynumber: 1.9 Consensus size: 128
2217762 ATTAAAAAAA
* * *
2217772 TAAAGAAAAAAACAATAACAAAGAAAGAATTAATAAATTAATGAAAAAGTAGGAAAAAAATAAGA
1 TAAAGAAAAAAACAATAACAAAGAAAGAAGTAATAAATTAATGAAAAAATAAGAAAAAAATAA-A
* *
2217837 ACAAGTGTTAAATT-TTTTACATACGTATGTAATTCAAAATATATATATATATATATGTTAGAAG
65 ACAAGTG-TAAATTCTTTTACACACGTATATAATTCAAAATATATATATATATATATGTTAGAAG
* *
2217901 TAAAGAAAAAGACAATAACAAGTGAAA-AAGTAATAAATTAATGAAAAAATAAGAAAAAAATAAA
1 TAAAGAAAAAAACAATAACAA-AGAAAGAAGTAATAAATTAATGAAAAAATAAGAAAAAAATAAA
* * *
2217965 ATAGGTGTCAATTCTTTTACACACGTATATAATTCAAAATATATATAT
65 ACAAGTGTAAATTCTTTTACACACGTATATAATTCAAAATATATATAT
2218013 GTTAGATACC
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
127 5 0.05
128 38 0.38
129 53 0.53
130 4 0.04
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.27
Consensus pattern (128 bp):
TAAAGAAAAAAACAATAACAAAGAAAGAAGTAATAAATTAATGAAAAAATAAGAAAAAAATAAAA
CAAGTGTAAATTCTTTTACACACGTATATAATTCAAAATATATATATATATATATGTTAGAAG
Found at i:2218477 original size:20 final size:20
Alignment explanation
Indices: 2218452--2218498 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2218442 ATTCTTTGAG
2218452 GATTCTAA-ATTACTGATTTA
1 GATTCTAAGA-TACTGATTTA
2218472 GATTCTAAGATACTGATTTA
1 GATTCTAAGATACTGATTTA
2218492 GATTCTA
1 GATTCTA
2218499 TCTTTCCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (20 bp):
GATTCTAAGATACTGATTTA
Found at i:2219690 original size:20 final size:20
Alignment explanation
Indices: 2219662--2219736 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2219652 TTTTACCCAG
2219662 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2219682 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
2219702 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
2219722 ATGTATCGATACATT
1 ATGTATCGATACATT
2219737 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2219729 original size:40 final size:39
Alignment explanation
Indices: 2219662--2219739 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2219652 TTTTACCCAG
* *
2219662 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
2219702 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
2219740 TCTTTTTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:2223303 original size:20 final size:20
Alignment explanation
Indices: 2223278--2223349 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
2223268 TACCTAGATG
2223278 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * * *
2223298 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATA
* * *
2223318 TATCGATATATTCTACAATA
1 TATCGATACATTTTTCAATA
2223338 TATCGATACATT
1 TATCGATACATT
2223350 ATGTCTTTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:2223337 original size:40 final size:39
Alignment explanation
Indices: 2223275--2223352 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
2223265 TTTTACCTAG
* *
2223275 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
*
2223315 ATGTATCGATATATTCTACAATATATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
2223353 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2227163 original size:19 final size:19
Alignment explanation
Indices: 2227139--2227189 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2227129 TATCATTAAC
2227139 AAAATTTATATTAATATAT
1 AAAATTTATATTAATATAT
* *
2227158 AAAATTT-TTTTATATATTT
1 AAAATTTATATTA-ATATAT
2227177 AAAA-TTATATTAA
1 AAAATTTATATTAA
2227190 ATTAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATTTATATTAATATAT
Found at i:2227322 original size:19 final size:19
Alignment explanation
Indices: 2227271--2227323 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
2227261 AAAATAAAGC
2227271 AAATAAATTAT--TTAAT-
1 AAATAAATTATCATTAATA
**
2227287 -AA-AAATTATCAAAAATA
1 AAATAAATTATCATTAATA
2227304 AAATAAATTATCATTAATA
1 AAATAAATTATCATTAATA
2227323 A
1 A
2227324 TTAACTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.25
15 2 0.07
16 3 0.11
18 2 0.07
19 14 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAAATTATCATTAATA
Found at i:2228731 original size:21 final size:19
Alignment explanation
Indices: 2228707--2228791 Score: 81
Period size: 21 Copynumber: 4.5 Consensus size: 19
2228697 AGGTTTTTTT
2228707 AATATAATTTTAATTATATTA
1 AATATAATTTTAA-TAT-TTA
2228728 AATATAATTATT--TATTTA
1 AATATAATT-TTAATATTTA
2228746 AATAT--TTTTAATATTTA
1 AATATAATTTTAATATTTA
*
2228763 AATATATATATTAATATGTTA
1 AATATA-ATTTTAATAT-TTA
2228784 AA-ATAATT
1 AATATAATT
2228792 ATCTTTTCCA
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.04
16 2 0.04
17 11 0.20
18 8 0.15
19 5 0.09
20 11 0.20
21 14 0.25
22 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
AATATAATTTTAATATTTA
Found at i:2228748 original size:18 final size:17
Alignment explanation
Indices: 2228719--2228768 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2228709 TATAATTTTA
2228719 ATTATATTAAATATAATT
1 ATTAT-TTAAATATAATT
**
2228737 ATTTATTTAAATATTTTT
1 A-TTATTTAAATATAATT
*
2228755 AATATTTAAATATA
1 ATTATTTAAATATA
2228769 TATATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 11 0.41
18 12 0.44
19 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATTTAAATATAATT
Found at i:2228788 original size:39 final size:38
Alignment explanation
Indices: 2228704--2228791 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 38
2228694 TGGAGGTTTT
*
2228704 TTTAATATAATTTTAATTATATTAAATATAATTATTTA
1 TTTAAAATAATTTTAATTATATTAAATATAATTATTTA
*
2228742 TTT-AAATATTTTTAA-TAT-TTAAATAT-ATATATTAATA
1 TTTAAAATAATTTTAATTATATTAAATATAAT-TATT--TA
2228779 TGTTAAAATAATT
1 T-TTAAAATAATT
2228792 ATCTTTTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
34 2 0.05
35 12 0.29
36 3 0.07
37 13 0.31
38 5 0.12
39 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTAAAATAATTTTAATTATATTAAATATAATTATTTA
Found at i:2230091 original size:13 final size:13
Alignment explanation
Indices: 2230073--2230099 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2230063 ACATTATGCT
2230073 TTGTATCGATACA
1 TTGTATCGATACA
2230086 TTGTATCGATACA
1 TTGTATCGATACA
2230099 T
1 T
2230100 GTACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2231011 original size:15 final size:16
Alignment explanation
Indices: 2230982--2231014 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2230972 TTTCATGAAT
*
2230982 TTTTTTCGAATTTAAA
1 TTTTTTCGAAATTAAA
2230998 TTTTTT-GAAATTAAA
1 TTTTTTCGAAATTAAA
2231013 TT
1 TT
2231015 GAGTTCGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTTTTCGAAATTAAA
Found at i:2231511 original size:2 final size:2
Alignment explanation
Indices: 2231504--2231531 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2231494 AAATTACTTG
2231504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2231532 TAATAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2235291 original size:2 final size:2
Alignment explanation
Indices: 2235284--2235319 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2235274 ATTCGATTAG
2235284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2235320 TTGTATGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2236254 original size:343 final size:339
Alignment explanation
Indices: 2235720--2236420 Score: 1084
Period size: 343 Copynumber: 2.1 Consensus size: 339
2235710 AAGTAAAAAT
* * * *
2235720 AATTAATAAAATAATTTTTTTATTTTTTCTTAAGTGGAATAAAAATCTTAAATTGATCTATGTGT
1 AATTAATAAAATAATTTTATTATTTTTTCTTAAGTGGAATAAAAATCTTAAATCGACCTATGAGT
* * *
2235785 TAATTTGCATATTAACTCCTTTAAGTAAGTTATTTAAAACTAAAATAATTAATAAAATAAAATAT
66 TAAGTTGCATATCAACTCCTTTAAGTAAATTATTTAAAACTAAAATAATTAATAAAATAAAATAT
2235850 TTCAGTGGATTAAGTACAGATTCTAAATTGATCTATAAGTTATCATATGAATTAACTTTTTTAAT
131 TTCAGTGGATTAAGTACAGATTCTAAATTGATCTATAAGTTATCATATGAATTAACTTTTTTAAT
* *
2235915 ACATTATTTAAAAACAAAATAAAAAAATTAATAAAATAAATTTCAATATTTTAACTTTTTTCCTG
196 ACATTATTTAAAAACAAAAT-AAAAAATTAAGAAAATAAATTTCAATATTTTAACTTTTTTCCTA
* * * * * *
2235980 AGTGAATTAAGTATAAATCATGAGTTAATTTACGAATCAATT-TTTAAATATATTATTTAAAATT
260 AATGAATCAAGTATAAATCACGAGTTAATTTACGAATCAATTCTTTAAATATATCATTAAAAAAT
* *
2236044 TTAATAAAAATTATC
325 TAAATAAAAATGATC
* *
2236059 AATTAATAAAATAATTTTATTATTTTTTTCTAAGTAAGTGGGATAGAAATCTTAAATCGACCTAT
1 AATTAATAAAATAATTTTATTA-TTTTTTCT---TAAGTGGAATAAAAATCTTAAATCGACCTAT
*
2236124 GAGTTAAGTTGTATATCAACTCCTTTAAGTAAATTATTT-AAACTCAAAATAATTAATAAAATAA
62 GAGTTAAGTTGCATATCAACTCCTTTAAGTAAATTATTTAAAACT-AAAATAATTAATAAAATAA
* * *
2236188 AATTATTTCAGTGGATTAAGTATAGATTCTAAATTGATCTATAAGTTATCATA-GGATTATCTTT
126 AA-TATTTCAGTGGATTAAGTACAGATTCTAAATTGATCTATAAGTTATCATATGAATTAACTTT
* *
2236252 TTTAATACATTATTTAAAAATAAAATAAAAAATTAAGGAAATAAATTTCAATATTTTAACTTTTT
190 TTTAATACATTATTTAAAAACAAAATAAAAAATTAAGAAAATAAATTTCAATATTTTAACTTTTT
2236317 TCCTAAATGAATCAAGTATAAATCACGAGTTAATTTACGAATCAATTCTTTAAATATATCATTAA
255 TCCTAAATGAATCAAGTATAAATCACGAGTTAATTTACGAATCAATTCTTTAAATATATCATTAA
2236382 AAAATTAAATAAAAATGATC
320 AAAATTAAATAAAAATGATC
2236402 AATTAATAAAATAAATTTT
1 AATTAATAAAAT-AATTTT
2236421 TAAATTTTTT
Statistics
Matches: 329, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
339 21 0.06
340 8 0.02
342 85 0.26
343 160 0.49
344 55 0.17
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (339 bp):
AATTAATAAAATAATTTTATTATTTTTTCTTAAGTGGAATAAAAATCTTAAATCGACCTATGAGT
TAAGTTGCATATCAACTCCTTTAAGTAAATTATTTAAAACTAAAATAATTAATAAAATAAAATAT
TTCAGTGGATTAAGTACAGATTCTAAATTGATCTATAAGTTATCATATGAATTAACTTTTTTAAT
ACATTATTTAAAAACAAAATAAAAAATTAAGAAAATAAATTTCAATATTTTAACTTTTTTCCTAA
ATGAATCAAGTATAAATCACGAGTTAATTTACGAATCAATTCTTTAAATATATCATTAAAAAATT
AAATAAAAATGATC
Found at i:2236812 original size:20 final size:21
Alignment explanation
Indices: 2236789--2236832 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2236779 TTAAATACAT
2236789 AATTTTAAAATAA-AATAAAA
1 AATTTTAAAATAATAATAAAA
*
2236809 AATTTTAAATTAATTAATAAAA
1 AATTTTAAAATAA-TAATAAAA
2236831 AA
1 AA
2236833 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTTTAAAATAATAATAAAA
Found at i:2237190 original size:21 final size:22
Alignment explanation
Indices: 2237151--2237194 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
2237141 TATTTTTATT
2237151 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
2237173 TAAATATTAA-TA-AAAAATATA
1 TAAAT-TTAATTATAAAAATATA
2237194 T
1 T
2237195 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Done.