Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold27
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: 2789374
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 115785 characters in sequence are not A, C, G, or T
File 12 of 16
Found at i:1975798 original size:21 final size:21
Alignment explanation
Indices: 1975757--1975800 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1975747 CTCTCCTTTA
* *
1975757 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1975778 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1975799 TC
1 TC
1975801 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1977623 original size:13 final size:13
Alignment explanation
Indices: 1977601--1977639 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1977591 ATAATCACCC
*
1977601 TGTATTGATACAA
1 TGTATCGATACAA
1977614 TGTATCGATACAA
1 TGTATCGATACAA
*
1977627 TATATCGATACAA
1 TGTATCGATACAA
1977640 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1977696 original size:20 final size:20
Alignment explanation
Indices: 1977629--1977704 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
1977619 CGATACAATA
*
1977629 TATCGATACAAAGAAAAATG
1 TATCGATACATAGAAAAATG
* *
1977649 TATCGATACATTGAATTTCCAGATG
1 TATCGATACATAGAA-----AAATG
*
1977674 TATCGATACATAGAAACATG
1 TATCGATACATAGAAAAATG
1977694 TATCGATACAT
1 TATCGATACAT
1977705 TTTGGACATT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 28 0.61
25 18 0.39
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
TATCGATACATAGAAAAATG
Found at i:1979737 original size:15 final size:15
Alignment explanation
Indices: 1979717--1979747 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1979707 ATTTCGTTTG
*
1979717 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1979732 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1979747 G
1 G
1979748 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1981580 original size:21 final size:21
Alignment explanation
Indices: 1981551--1981595 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1981541 AAGTTTTCAT
*
1981551 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1981571 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1981593 TTT
1 TTT
1981596 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1983832 original size:13 final size:13
Alignment explanation
Indices: 1983814--1983839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1983804 CAATTTTTTG
1983814 TGTATCGATACAT
1 TGTATCGATACAT
1983827 TGTATCGATACAT
1 TGTATCGATACAT
1983840 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1985117 original size:21 final size:21
Alignment explanation
Indices: 1985093--1985134 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1985083 AAAATACTTT
*
1985093 GATTTTCAAAATTAACTTAAA
1 GATTTTCAAAATCAACTTAAA
*
1985114 GATTTTCAATATCAACTTAAA
1 GATTTTCAAAATCAACTTAAA
1985135 CCTGATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
GATTTTCAAAATCAACTTAAA
Found at i:1989812 original size:161 final size:161
Alignment explanation
Indices: 1989574--1989997 Score: 486
Period size: 160 Copynumber: 2.6 Consensus size: 161
1989564 TATTTCAATA
* *
1989574 TTAATTATTTTTCAATCTTTTATATTCCTAT-GAGGGTCCAT-AGGAGTATAAAAGA-TTTAAAA
1 TTAATT-TTTTT-AATCTTTTATATTTCTATGGA-GATCCATGAGGAGTATAAAAGATTTTAAAA
* * *
1989636 ACTTTTCGTATCTTTTCGGGTTTTCATTAAGATACGAAATGGTATTTTTCAAAAATAAAAAAATT
63 ACTTTTCGTATCTTTTCGGGTTTTCATTAAGGTACGAAATGGTA-TTTTCAAAAACAAAAAAATA
* * ** *
1989701 AAATTAAATTAACACTTTCATAATTGA-AATAAAT
127 AAATTAAACTAACACATTCATAAACGAGAAGAAAT
* *
1989735 GTTAATTTTTTTAATCTTTTATTTTTCTATGGAAATCCATGAGG-GTATAAAAGATTTTAAAAAC
1 -TTAATTTTTTTAATCTTTTATATTTCTATGGAGATCCATGAGGAGTATAAAAGATTTTAAAAAC
* * * * *
1989799 TTTTCGTATCTTTTCGAGTTTACATTAAGGTACGAAAAGGTATTTTCAAAAACAAATACATAAAA
65 TTTTCGTATCTTTTCGGGTTTTCATTAAGGTACGAAATGGTATTTTCAAAAACAAAAAAATAAAA
* * * * *
1989864 TTAAGCTAATACATTCATAAACGAGAGGGACT
130 TTAAACTAACACATTCATAAACGAGAAGAAAT
* * * *
1989896 TTAATTTTTTTTATCTTTTATATTTCTATGGGGA-CC-TGTAGGAGTATAAAAGATTTCAAAAAA
1 TTAATTTTTTTAATCTTTTATATTTCTATGGAGATCCATG-AGGAGTATAAAAGATTTTAAAAAC
*
1989959 TTTTTGTATCTTTTCGGGCTTTT-ATTAAGGTACGAAATG
65 TTTTCGTATCTTTTCGGG-TTTTCATTAAGGTACGAAATG
1989998 AAATTGGTGG
Statistics
Matches: 223, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
158 2 0.01
159 5 0.02
160 147 0.66
161 63 0.28
162 6 0.03
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (161 bp):
TTAATTTTTTTAATCTTTTATATTTCTATGGAGATCCATGAGGAGTATAAAAGATTTTAAAAACT
TTTCGTATCTTTTCGGGTTTTCATTAAGGTACGAAATGGTATTTTCAAAAACAAAAAAATAAAAT
TAAACTAACACATTCATAAACGAGAAGAAAT
Found at i:1990155 original size:52 final size:52
Alignment explanation
Indices: 1990099--1990197 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
1990089 ATTGTCGCTA
* * * * * *
1990099 ACCTTGAATCAGCATATTAGCACTCTTATCATCTTTAAGTTTAATGTCAATG
1 ACCTTGAATCAACACATTAGCACCCTCATCATCTTTAAATCTAATGTCAATG
* *
1990151 ACCTTTAATCAACACATTGGCACCCTCATCATCTTTAAATCTAATGT
1 ACCTTGAATCAACACATTAGCACCCTCATCATCTTTAAATCTAATGT
1990198 TTCTACCCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.36
Consensus pattern (52 bp):
ACCTTGAATCAACACATTAGCACCCTCATCATCTTTAAATCTAATGTCAATG
Found at i:1994441 original size:11 final size:11
Alignment explanation
Indices: 1994425--1994462 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1994415 CATCATCATC
1994425 ATTTTTTTATT
1 ATTTTTTTATT
* *
1994436 ATTTTTTGATG
1 ATTTTTTTATT
1994447 ATTTTTTTATT
1 ATTTTTTTATT
1994458 -TTTTT
1 ATTTTT
1994463 ATTTTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:1994458 original size:8 final size:8
Alignment explanation
Indices: 1994428--1994532 Score: 70
Period size: 8 Copynumber: 12.5 Consensus size: 8
1994418 CATCATCATT
1994428 TTTTTATTA
1 TTTTT-TTA
1994437 TTTTTTGATGA
1 TTTTTT--T-A
1994448 TTTTTTTA
1 TTTTTTTA
1994456 TTTTTTTA
1 TTTTTTTA
*
1994464 TTTTTTGA
1 TTTTTTTA
*
1994472 TTTCTTTGA
1 TTT-TTTTA
*
1994481 -TTTTTAA
1 TTTTTTTA
*
1994488 TTGTTTTGA
1 TT-TTTTTA
*
1994497 TTTCTTTGA
1 TTT-TTTTA
*
1994506 TTTCTTTA
1 TTTTTTTA
1994514 -TTTTTTA
1 TTTTTTTA
*
1994521 TTTTTTAA
1 TTTTTTTA
1994529 TTTT
1 TTTT
1994533 ATATCAAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
7 10 0.12
8 37 0.46
9 26 0.32
10 1 0.01
11 7 0.09
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1994479 original size:9 final size:8
Alignment explanation
Indices: 1994445--1994532 Score: 83
Period size: 8 Copynumber: 10.9 Consensus size: 8
1994435 TATTTTTTGA
1994445 TGATTTTT
1 TGATTTTT
*
1994453 TTATTTTT
1 TGATTTTT
*
1994461 TTATTTTT
1 TGATTTTT
1994469 TGATTTCTT
1 TGATTT-TT
1994478 TGA-TTTT
1 TGATTTTT
*
1994485 TAATTGTTT
1 TGATT-TTT
1994494 TGATTTCTT
1 TGATTT-TT
1994503 TGATTTCTT
1 TGATTT-TT
1994512 T-ATTTTT
1 TGATTTTT
1994519 T-ATTTTT
1 TGATTTTT
*
1994526 TAATTTT
1 TGATTTT
1994533 ATATCAAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
7 14 0.20
8 33 0.46
9 24 0.34
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (8 bp):
TGATTTTT
Found at i:1994494 original size:25 final size:24
Alignment explanation
Indices: 1994429--1994532 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 24
1994419 ATCATCATTT
* *
1994429 TTTTATTATTTTTTGATGATTTTTTTA
1 TTTT-TTATTTTTTGAT--TTCTTTGA
1994456 TTTTTTTATTTTTTGATTTCTTTGA
1 -TTTTTTATTTTTTGATTTCTTTGA
*
1994481 TTTTTAATTGTTTTGATTTCTTTGA
1 TTTTTTATT-TTTTGATTTCTTTGA
*
1994506 TTTCTTTATTTTTT-ATTT-TTTAA
1 TTT-TTTATTTTTTGATTTCTTTGA
1994529 TTTT
1 TTTT
1994533 ATATCAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.01
23 7 0.10
24 12 0.17
25 28 0.41
26 5 0.07
27 12 0.17
28 4 0.06
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (24 bp):
TTTTTTATTTTTTGATTTCTTTGA
Found at i:1995963 original size:20 final size:20
Alignment explanation
Indices: 1995932--1995988 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1995922 GTCAAAACCC
*
1995932 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
1995952 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
1995972 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
1995989 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:1995992 original size:13 final size:13
Alignment explanation
Indices: 1995974--1996002 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1995964 ATACAGATTG
1995974 CATTGTATCGATA
1 CATTGTATCGATA
1995987 CATTGTATCGATA
1 CATTGTATCGATA
1996000 CAT
1 CAT
1996003 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1996015 original size:20 final size:21
Alignment explanation
Indices: 1995990--1996042 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1995980 ATCGATACAT
**
1995990 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1996010 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1996031 TGTATCGATACA
1 TGTATCGATACA
1996043 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1996132 original size:20 final size:20
Alignment explanation
Indices: 1996107--1996172 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1996097 ATCAATATAT
1996107 TGTATCGATACATCATAAAA
1 TGTATCGATACATCATAAAA
1996127 TGTATCGAT--A-CAT----
1 TGTATCGATACATCATAAAA
*
1996140 TGTTTCGATACATCATAAAA
1 TGTATCGATACATCATAAAA
1996160 TGTATCGATACAT
1 TGTATCGATACAT
1996173 TGGCTTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 8 0.22
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
20 21 0.57
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATCATAAAA
Found at i:1996142 original size:33 final size:33
Alignment explanation
Indices: 1996093--1996174 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
1996083 TACACACAGT
* *
1996093 ATGTATCAATATATTGTATCGATACATCATAAA
1 ATGTATCGATACATTGTATCGATACATCATAAA
*
1996126 ATGTATCGATACATTGTTTCGATACATCATAAA
1 ATGTATCGATACATTGTATCGATACATCATAAA
1996159 ATGTATCGATACATTG
1 ATGTATCGATACATTG
1996175 GCTTGTAACG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTATCGATACATCATAAA
Found at i:2004761 original size:20 final size:20
Alignment explanation
Indices: 2004730--2004786 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
2004720 GTCAAAACCC
*
2004730 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
2004750 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
2004770 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
2004787 ATGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:2004793 original size:13 final size:13
Alignment explanation
Indices: 2004775--2004799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2004765 CAGATTGCAT
2004775 TGTATCGATACAA
1 TGTATCGATACAA
2004788 TGTATCGATACA
1 TGTATCGATACA
2004800 TGACCAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2004811 original size:20 final size:20
Alignment explanation
Indices: 2004786--2004840 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2004776 GTATCGATAC
*
2004786 AATGTATCGATACATGACCA-
1 AATGTATCGATACATGA-AAG
*
2004806 AATGTATCGATACTTGAAAGG
1 AATGTATCGATACATGAAA-G
2004827 AATGTATCGATACA
1 AATGTATCGATACA
2004841 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACATGAAAG
Found at i:2004940 original size:33 final size:33
Alignment explanation
Indices: 2004872--2004972 Score: 141
Period size: 33 Copynumber: 3.1 Consensus size: 33
2004862 GTAGCCAAAC
* ** *
2004872 TTGTATCGATACA-CACAGTATGTATGGATACA
1 TTGTATCGATACATCATAAAATGTATCGATACA
* *
2004904 TTGTATCGATACATCATACAATGAATCGATACA
1 TTGTATCGATACATCATAAAATGTATCGATACA
2004937 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACATCATAAAATGTATCGATACA
2004970 TTG
1 TTG
2004973 GCTTGTAACG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
32 13 0.21
33 48 0.79
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATCATAAAATGTATCGATACA
Found at i:2005885 original size:13 final size:13
Alignment explanation
Indices: 2005867--2005891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2005857 ATTCTTCATA
2005867 TATCGATACATTG
1 TATCGATACATTG
2005880 TATCGATACATT
1 TATCGATACATT
2005892 ATGCTATGTA
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:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:2013052 original size:58 final size:58
Alignment explanation
Indices: 2012988--2013103 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
2012978 TTCATCTGAG
* *
2012988 TCAACATCATCATCATCACCATCATCTTCATCGTTTTTGATGGTTGACTTGAAGGCGA
1 TCAACATCATCACCATCACCATCATCTTCATCGTTTTTGATGGCTGACTTGAAGGCGA
2013046 TCAACATCATCACCATCACCATCATCTTCATCGTTTTTGATGGCTGACTTGAAGGCGA
1 TCAACATCATCACCATCACCATCATCTTCATCGTTTTTGATGGCTGACTTGAAGGCGA
2013104 CACTTGCCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (58 bp):
TCAACATCATCACCATCACCATCATCTTCATCGTTTTTGATGGCTGACTTGAAGGCGA
Found at i:2014701 original size:13 final size:13
Alignment explanation
Indices: 2014683--2014707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2014673 ATTCTTCATG
2014683 TATCGATACATTA
1 TATCGATACATTA
2014696 TATCGATACATT
1 TATCGATACATT
2014708 GTGCCATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:2014705 original size:33 final size:33
Alignment explanation
Indices: 2014663--2014725 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2014653 TGAGTTAATG
*
2014663 TATCGATACAATTCT-TCATGTATCGATACATTA
1 TATCGATAC-ATTCTGCCATGTATCGATACATTA
*
2014696 TATCGATACATTGTGCCATGTATCGATACA
1 TATCGATACATTCTGCCATGTATCGATACA
2014726 AATAGTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (33 bp):
TATCGATACATTCTGCCATGTATCGATACATTA
Found at i:2014778 original size:20 final size:20
Alignment explanation
Indices: 2014753--2014809 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
2014743 TACTGCCAGT
2014753 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
*
2014773 TTCATGTATCGATACA-ATG
1 TTCATGTATCGATACATTTG
**
2014792 AACATGTATCGATACATT
1 TTCATGTATCGATACATT
2014810 ATATCGATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACATTTG
Found at i:2014840 original size:33 final size:32
Alignment explanation
Indices: 2014779--2014841 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
2014769 TTTGTTCATG
* *
2014779 TATCGATACAATGAACATGTATCGATACATTA
1 TATCGATACAAAGAACATGTATCAATACATTA
2014811 TATCGATACAAAGCATA-ATGTATCAATACAT
1 TATCGATACAAAG-A-ACATGTATCAATACAT
2014842 CTGAAAGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCAATACATTA
Found at i:2017915 original size:20 final size:19
Alignment explanation
Indices: 2017878--2017919 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2017868 TAAACCTTGA
*
2017878 TCATGCATTTTTACCATGCT
1 TCATGCATTTATACCATG-T
*
2017898 TCATGCATTTATAGCATGT
1 TCATGCATTTATACCATGT
2017917 TCA
1 TCA
2017920 GCACCTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (19 bp):
TCATGCATTTATACCATGT
Found at i:2023173 original size:22 final size:23
Alignment explanation
Indices: 2023129--2023171 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2023119 TACATAATTA
2023129 AAATATAAAATTAAACACAAAAT
1 AAATATAAAATTAAACACAAAAT
*
2023152 AAAT-TAAAA-TAATCACAAAA
1 AAATATAAAATTAAACACAAAA
2023172 ATCACATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATATAAAATTAAACACAAAAT
Found at i:2023904 original size:19 final size:19
Alignment explanation
Indices: 2023880--2023933 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2023870 ATTCAACGAT
*
2023880 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
2023899 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
2023918 TTGTATCGATACATAA
1 TTGTATCGATACATAA
2023934 TTAGCTACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:2027851 original size:23 final size:22
Alignment explanation
Indices: 2027783--2027857 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 22
2027773 TTGAAACTCG
2027783 TAAA-AAAAAGTTATAAA-TAAAA
1 TAAATAAAAA-TTA-AAACTAAAA
*
2027805 TAAA-ATAAAATTAAAACAACAAA
1 TAAATA-AAAATTAAAACTA-AAA
*
2027828 TAAATAAACAATTAAAATTAAAA
1 TAAATAAA-AATTAAAACTAAAA
*
2027851 TTAATAA
1 TAAATAA
2027858 TCATAAACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.07
22 9 0.20
23 22 0.50
24 10 0.23
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (22 bp):
TAAATAAAAATTAAAACTAAAA
Found at i:2027852 original size:12 final size:11
Alignment explanation
Indices: 2027783--2027854 Score: 51
Period size: 12 Copynumber: 6.3 Consensus size: 11
2027773 TTGAAACTCG
2027783 TAAAA-AAAAGT
1 TAAAATAAAA-T
2027794 TATAAATAAAA-
1 TA-AAATAAAAT
2027805 TAAAATAAAAT
1 TAAAATAAAAT
* *
2027816 TAAAACAACAAA
1 TAAAATAA-AAT
2027828 T-AAATAAACAAT
1 TAAAAT-AA-AAT
2027840 TAAAATTAAAAT
1 TAAAA-TAAAAT
2027852 TAA
1 TAA
2027855 TAATCATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.16
11 14 0.28
12 18 0.36
13 9 0.18
14 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (11 bp):
TAAAATAAAAT
Found at i:2029246 original size:64 final size:64
Alignment explanation
Indices: 2029175--2029545 Score: 284
Period size: 64 Copynumber: 5.8 Consensus size: 64
2029165 CAGTTAGGCA
* * * *
2029175 AAGATGACCAGGATGTAACCTTGGTCTAGAAGGTTGATTAGGGTAAAACTAATACAGTCAAATG
1 AAGATGACCAAGATATAACCTAGGTCTAGAAGGTTGATTAGGGCAAAACTAATACAGTCAAATG
* * * * * * *
2029239 AAAATGACTAAGATATAATCCTAGGTCTAAAAAGGTTGACTAGGGCGAAACCAATACAGTCAAGT
1 AAGATGACCAAGATATAA-CCTAGGTCT-AGAAGGTTGATTAGGGCAAAACTAATACAGTCAAAT
2029304 G
64 G
* * * ** *** *
2029305 AAGGTGACTAAGATATAATCCTAGGTCTAAAAGAGTT-AACAGGGCAAAACCGTTATAGTCAAAT
1 AAGATGACCAAGATATAA-CCTAGGTCTAGAAG-GTTGATTAGGGCAAAACTAATACAGTCAAAT
2029369 G
64 G
* * ** * * *
2029370 AAGTTGACCAAGATATAACCTAGGTCTAGAGGGTTGACCAAGGCAAAACTAATATAGTCAAA-C
1 AAGATGACCAAGATATAACCTAGGTCTAGAAGGTTGATTAGGGCAAAACTAATACAGTCAAATG
* * * * * *
2029433 AAGGATGAGCAAGACATAACCTAGGCCTAGAGGGTTGACTT-GGGTAAAACTAATACAATCAAA-
1 AA-GATGACCAAGATATAACCTAGGTCTAGAAGGTTGA-TTAGGGCAAAACTAATACAGTCAAAT
*
2029496 C
64 G
* * * * *
2029497 AAGAATGA-CTAGAATGTAACCTAGATGTAGAGGGTTGATTAGGGCAAAA
1 AAG-ATGACCAAG-ATATAACCTAGGTCTAGAAGGTTGATTAGGGCAAAA
2029546 TCGATATAGT
Statistics
Matches: 251, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
63 11 0.04
64 130 0.52
65 50 0.20
66 60 0.24
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (64 bp):
AAGATGACCAAGATATAACCTAGGTCTAGAAGGTTGATTAGGGCAAAACTAATACAGTCAAATG
Found at i:2029372 original size:65 final size:66
Alignment explanation
Indices: 2029204--2029397 Score: 232
Period size: 66 Copynumber: 3.0 Consensus size: 66
2029194 CTTGGTCTAG
* * * * *
2029204 AAGGTTGATTAGGGTAAAACTAATACAGTCAAATGAAAATGACTAAGATATAATCCTAGGTCTAA
1 AAGGTTAACTAGGGCAAAACCAATACAGTCAAATGAAGATGACTAAGATATAATCCTAGGTCTAA
2029269 A
66 A
* * * *
2029270 AAGGTTGACTAGGGCGAAACCAATACAGTCAAGTGAAGGTGACTAAGATATAATCCTAGGTCT-A
1 AAGGTTAACTAGGGCAAAACCAATACAGTCAAATGAAGATGACTAAGATATAATCCTAGGTCTAA
2029334 A
66 A
** * * *
2029335 AAGAGTTAAC-AGGGCAAAACCGTTATAGTCAAATGAAGTTGACCAAGATATAA-CCTAGGTCTA
1 AAG-GTTAACTAGGGCAAAACCAATACAGTCAAATGAAGATGACTAAGATATAATCCTAGGTCTA
2029398 GAGGGTTGAC
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
64 9 0.08
65 41 0.37
66 61 0.55
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (66 bp):
AAGGTTAACTAGGGCAAAACCAATACAGTCAAATGAAGATGACTAAGATATAATCCTAGGTCTAA
A
Found at i:2030374 original size:59 final size:59
Alignment explanation
Indices: 2030296--2030613 Score: 155
Period size: 60 Copynumber: 5.2 Consensus size: 59
2030286 ACTTAGACAT
* * *
2030296 AACCAAGACTTAAAAAAATGATCTAGAT-AGAACAAGAAATCTAAA-AATGAT-TTGGGCAA
1 AACCAAGACTCAAATAAATGAT-TAGATGA-AACAAGAAACCTAAACAATG-TCTTGGGCAA
* * * *
2030355 AACCAAGACTCAACTAAATGGATTGGATGAAACTAGAAACCTAAACATTGTCTTGGGCAA
1 AACCAAGACTCAAATAAAT-GATTAGATGAAACAAGAAACCTAAACAATGTCTTGGGCAA
* * * * * * * *
2030415 AACTAAGACTCAATTAAATGGCTTCGA-CAAACCAA-AAACCTAAACAATGACCTAGGTAAACCA
1 AACCAAGACTCAAATAAAT-GATTAGATGAAA-CAAGAAACCTAAACAATG-TCTTGG----GC-
2030478 TAA
58 -AA
* * * * * * *
2030481 AACCAAGGCTC-AATGAAATGACCTAGATAAAACTAGGAACCTAAACAATGACTTAGGCAA
1 AACCAAGACTCAAAT-AAATGA-TTAGATGAAACAAGAAACCTAAACAATGTCTTGGGCAA
* ** * ** *
2030541 AACCAAAACTC-AATGAAATGGCCTAGATAAAATTAGAAACCTAAACAATGACTTGGGCAA
1 AACCAAGACTCAAAT-AAAT-GATTAGATGAAACAAGAAACCTAAACAATGTCTTGGGCAA
* *
2030601 AACTAAAACTCAA
1 AACCAAGACTCAA
2030614 TGAAATGGCC
Statistics
Matches: 204, Mismatches: 37, Indels: 34
0.74 0.13 0.12
Matches are distributed among these distances:
59 50 0.25
60 108 0.53
61 2 0.01
62 1 0.00
64 1 0.00
65 3 0.01
66 23 0.11
67 16 0.08
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (59 bp):
AACCAAGACTCAAATAAATGATTAGATGAAACAAGAAACCTAAACAATGTCTTGGGCAA
Found at i:2030531 original size:30 final size:29
Alignment explanation
Indices: 2030497--2030592 Score: 70
Period size: 30 Copynumber: 3.2 Consensus size: 29
2030487 GGCTCAATGA
2030497 AATGACCTAGATAAAACTAGGAACCTAAAC
1 AATGACCTAGATAAAACTA-GAACCTAAAC
* ** * *
2030527 AATGACTTAGGCAAAACCA-AAACTCAATGA-
1 AATGACCTAGATAAAACTAGAACCT-AA--AC
* *
2030557 AATGGCCTAGATAAAATTAGAAACCTAAAC
1 AATGACCTAGATAAAACTAG-AACCTAAAC
2030587 AATGAC
1 AATGAC
2030593 TTGGGCAAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
28 4 0.09
29 3 0.06
30 33 0.70
31 3 0.06
32 4 0.09
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.18
Consensus pattern (29 bp):
AATGACCTAGATAAAACTAGAACCTAAAC
Found at i:2030553 original size:60 final size:60
Alignment explanation
Indices: 2030479--2030654 Score: 262
Period size: 60 Copynumber: 2.9 Consensus size: 60
2030469 GGTAAACCAT
** * *
2030479 AAAACCAAGGCTCAATGAAATGACCTAGATAAAACTAGGAACCTAAACAATGACTTAGGC
1 AAAACCAAAACTCAATGAAATGGCCTAGATAAAACTAGAAACCTAAACAATGACTTAGGC
* *
2030539 AAAACCAAAACTCAATGAAATGGCCTAGATAAAATTAGAAACCTAAACAATGACTTGGGC
1 AAAACCAAAACTCAATGAAATGGCCTAGATAAAACTAGAAACCTAAACAATGACTTAGGC
* * * *
2030599 AAAACTAAAACTCAATGAAATGGCCTAGATAAAACCAAAAACCTAAATAATGACTT
1 AAAACCAAAACTCAATGAAATGGCCTAGATAAAACTAGAAACCTAAACAATGACTT
2030655 TAAATGAGCA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 105 1.00
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (60 bp):
AAAACCAAAACTCAATGAAATGGCCTAGATAAAACTAGAAACCTAAACAATGACTTAGGC
Found at i:2030608 original size:126 final size:120
Alignment explanation
Indices: 2030384--2030654 Score: 283
Period size: 126 Copynumber: 2.2 Consensus size: 120
2030374 GGATTGGATG
* * * * * * * * *
2030384 AAACTAGAAACCTAAACATTGTCTTGGGCAAAACTAAGACTCAATTAAATGGCTTCGACAAACCA
1 AAACTAGAAACCTAAACAATGACTTAGGCAAAACCAAAACTCAATGAAATGGCCTAGAAAAACCA
* *
2030449 AAAACCTAAACAATGACCTAGGTAAACCATAAAACCAAGGCTCAATGAAATGACCTAGATA
66 AAAACCTAAACAATGACCTAGGCAAAACAT--AA--AA--CTCAATGAAATGACCTAGATA
* **
2030510 AAACTAGGAACCTAAACAATGACTTAGGCAAAACCAAAACTCAATGAAATGGCCTAGATAAAATT
1 AAACTAGAAACCTAAACAATGACTTAGGCAAAACCAAAACTCAATGAAATGGCCTAGA-AAAACC
* * * *
2030575 AGAAACCTAAACAATGACTTGGGCAAAAC-TAAAACTCAATGAAATGGCCTAGATA
65 AAAAACCTAAACAATGACCTAGGCAAAACATAAAACTCAATGAAATGACCTAGATA
* * *
2030630 AAACCAAAAACCTAAATAATGACTT
1 AAACTAGAAACCTAAACAATGACTT
2030655 TAAATGAGCA
Statistics
Matches: 122, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
120 41 0.34
122 2 0.02
124 2 0.02
126 50 0.41
127 27 0.22
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.19
Consensus pattern (120 bp):
AAACTAGAAACCTAAACAATGACTTAGGCAAAACCAAAACTCAATGAAATGGCCTAGAAAAACCA
AAAACCTAAACAATGACCTAGGCAAAACATAAAACTCAATGAAATGACCTAGATA
Found at i:2030633 original size:30 final size:30
Alignment explanation
Indices: 2030539--2030638 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
2030529 TGACTTAGGC
2030539 AAAACCAAAACTCAATGAAATGGCCTAGAT
1 AAAACCAAAACTCAATGAAATGGCCTAGAT
** * * * **
2030569 AAAATTAGAAAC-CTAA--ACAATGACTTGGGC
1 AAAACCA-AAACTC-AATGA-AATGGCCTAGAT
*
2030599 AAAACTAAAACTCAATGAAATGGCCTAGAT
1 AAAACCAAAACTCAATGAAATGGCCTAGAT
2030629 AAAACCAAAA
1 AAAACCAAAA
2030639 ACCTAAATAA
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
29 7 0.14
30 36 0.72
31 7 0.14
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.17
Consensus pattern (30 bp):
AAAACCAAAACTCAATGAAATGGCCTAGAT
Found at i:2031101 original size:20 final size:20
Alignment explanation
Indices: 2031073--2031139 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
2031063 AACGTCATTT
*
2031073 AATGGTGTAGATGCACATGA
1 AATGATGTAGATGCACATGA
* *
2031093 AATGATGTAAATGCAAGCATCAA
1 AATGATGTAGATGC-A-CAT-GA
* *
2031116 TAAAGAGGTAGATGCACATGA
1 -AATGATGTAGATGCACATGA
2031137 AAT
1 AAT
2031140 AATGCAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 14 0.40
21 2 0.06
22 6 0.17
23 2 0.06
24 11 0.31
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
AATGATGTAGATGCACATGA
Found at i:2032022 original size:112 final size:114
Alignment explanation
Indices: 2031737--2032024 Score: 388
Period size: 112 Copynumber: 2.6 Consensus size: 114
2031727 AAATTTTGGT
* * *
2031737 TGGCTTAAAAATTTCAAAACTGATATGATATATGCCC-ACTTTCCTAGGCACGAATGGATC-GAA
1 TGGCTAAAAAATTTCAAAACTGATAGGATATATGCCCTACTTTCCTAGGCACAAATGGATCAGAA
* * *
2031800 TTGTATAAAACATGAATTTCATTAAAAATCACACAAATTTGATATTGTG
66 TTGTATAAAACATGAATTGCATTAAAAATCAAACAAATTTGATATTATG
* *
2031849 TGGCTAAAAAATTTCAAAACTAATAGGATATATGCCCTACTTTCCTAGGCACAAATGGATCAG-G
1 TGGCTAAAAAATTTCAAAACTGATAGGATATATGCCCTACTTTCCTAGGCACAAATGGATCAGAA
* * * *
2031913 TTGTATACAACATGAATTGCTTTGAAAATCAAACAAATTTGTTATTAT-
66 TTGTATAAAACATGAATTGCATTAAAAATCAAACAAATTTGATATTATG
* * * *
2031961 TGGC-ACAAAATTTTTAAAATTGATAGGATACATGCCCTACTTTCCTAGGCACAAATGGATCAGA
1 TGGCTA-AAAAATTTCAAAACTGATAGGATATATGCCCTACTTTCCTAGGCACAAATGGATCAGA
2032025 CAAATTTGAC
Statistics
Matches: 155, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
111 1 0.01
112 90 0.58
113 63 0.41
114 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (114 bp):
TGGCTAAAAAATTTCAAAACTGATAGGATATATGCCCTACTTTCCTAGGCACAAATGGATCAGAA
TTGTATAAAACATGAATTGCATTAAAAATCAAACAAATTTGATATTATG
Found at i:2032285 original size:17 final size:17
Alignment explanation
Indices: 2032265--2032302 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2032255 TTTATACTGC
*
2032265 TTTTT-TTTTATTCCTT
1 TTTTTCTTTTTTTCCTT
*
2032281 TTTTTCTTTTTTTTCTT
1 TTTTTCTTTTTTTCCTT
2032298 TTTTT
1 TTTTT
2032303 GATTGCTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTCTTTTTTTCCTT
Found at i:2032291 original size:9 final size:9
Alignment explanation
Indices: 2032268--2032302 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2032258 ATACTGCTTT
2032268 TTTTTTATTC
1 TTTTTT-TTC
*
2032278 CTTTTTTTC
1 TTTTTTTTC
2032287 TTTTTTTTC
1 TTTTTTTTC
2032296 TTTTTTT
1 TTTTTTT
2032303 GATTGCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2035820 original size:16 final size:17
Alignment explanation
Indices: 2035799--2035830 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2035789 AAGATATTGC
2035799 TTTAATTTT-TTAAAAT
1 TTTAATTTTATTAAAAT
2035815 TTTAATTTTATTAAAA
1 TTTAATTTTATTAAAA
2035831 ATATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAATTTTATTAAAAT
Found at i:2035837 original size:18 final size:16
Alignment explanation
Indices: 2035800--2035838 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
2035790 AGATATTGCT
*
2035800 TTAATTTTTTAAAATT
1 TTAATTTTTTAAAATA
2035816 TTAATTTTATTAAAAATA
1 TTAATTTT-TT-AAAATA
2035834 TTAAT
1 TTAAT
2035839 AAGGTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTTTTTAAAATA
Found at i:2036371 original size:155 final size:154
Alignment explanation
Indices: 2036166--2036445 Score: 355
Period size: 155 Copynumber: 1.8 Consensus size: 154
2036156 TATGAAAAGA
* * * * * * *
2036166 TCATAAAAGGATAAATATATCCTAAATGCACATCTTTAGTATAAAAGCATCTCGATGATTATCTA
1 TCATAAAAGGATAAACATATCCTAAAGGCACACCTTTAGCATAAAAGCATCCCGATAACTATCTA
* * * * * ** *
2036231 GGACTTTG-TTCTAGGGAAATTACTAAAATGCCTTTGGGTTATACCTTTGATATGAAAGTATTTT
66 GGAC-TCGATTCTAAGGAAATTACCAAAATACCTTAGGG-TATACCTTCAACATGAAAGTATTTT
2036295 AGTAATCTAAATGACACGAAGAAAAT
129 AGTAATCTAAATGACACGAAGAAAAT
* * * *
2036321 TCATAAAAGGATGAACCTATTCTAAAGGCACACCTTTGGCATAAAAGCATCCCGATAACTATCTA
1 TCATAAAAGGATAAACATATCCTAAAGGCACACCTTTAGCATAAAAGCATCCCGATAACTATCTA
*
2036386 GGACTCGATTCTAAGGAAATTACCCAAATACCTTAGGGTATACCTTCAACATGAAAGTAT
66 GGACTCGATTCTAAGGAAATTACCAAAATACCTTAGGGTATACCTTCAACATGAAAGTAT
2036446 CTCAGTAACC
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
154 21 0.20
155 83 0.80
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (154 bp):
TCATAAAAGGATAAACATATCCTAAAGGCACACCTTTAGCATAAAAGCATCCCGATAACTATCTA
GGACTCGATTCTAAGGAAATTACCAAAATACCTTAGGGTATACCTTCAACATGAAAGTATTTTAG
TAATCTAAATGACACGAAGAAAAT
Found at i:2037969 original size:13 final size:13
Alignment explanation
Indices: 2037953--2037997 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2037943 TCACAATTAA
*
2037953 AATAAATTAAAAT
1 AATAAATAAAAAT
2037966 AATAAATAAATAAT
1 AATAAATAAA-AAT
2037980 AA-AAATAAAAATT
1 AATAAATAAAAA-T
2037993 AATAA
1 AATAA
2037998 TCATAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 19 0.68
14 7 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:2037991 original size:19 final size:20
Alignment explanation
Indices: 2037961--2037998 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2037951 AAAATAAATT
2037961 AAAATAATAAATAAATAATA
1 AAAATAATAAATAAATAATA
*
2037981 AAAATAA-AAATTAATAAT
1 AAAATAATAAATAAATAAT
2037999 CATAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATAAATAAATAATA
Found at i:2038003 original size:16 final size:16
Alignment explanation
Indices: 2037956--2038004 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2037946 CAATTAAAAT
2037956 AAATTAA-AATAATAA
1 AAATTAATAATAATAA
* *
2037971 ATAAATAATAAAAATAA
1 A-AATTAATAATAATAA
*
2037988 AAATTAATAATCATAA
1 AAATTAATAATAATAA
2038004 A
1 A
2038005 CAAAATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 1 0.04
16 18 0.67
17 8 0.30
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTAATAATAATAA
Found at i:2047673 original size:20 final size:21
Alignment explanation
Indices: 2047648--2047700 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
2047638 ATCAATACAT
*
2047648 TGTATCGATACATGAACA-AA
1 TGTATCGATACATGAAAAGAA
*
2047668 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
2047689 TGTATCGATACA
1 TGTATCGATACA
2047701 AGTCATTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:2052017 original size:13 final size:13
Alignment explanation
Indices: 2052001--2052030 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2051991 ATACATTGTT
2052001 CATTGTATCGATA
1 CATTGTATCGATA
2052014 CATTGTATCGATA
1 CATTGTATCGATA
2052027 CATT
1 CATT
2052031 CTGAGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2054464 original size:79 final size:79
Alignment explanation
Indices: 2054374--2054793 Score: 304
Period size: 79 Copynumber: 5.3 Consensus size: 79
2054364 GATTCTTCAT
* *
2054374 ATCGGGGATACTCTAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
*
2054439 ATCAATTTTTCACA
66 ATCGATTTTTCACA
* **** * ** ** *** *
2054453 ATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACATCAATTTTTTATA-ATCGAGGATA-C
1 ATCGGGGATACTCCAACCCCG---TTATTTCCGAGGGGAT--A--CTCCA-ACCCCGATTTTATT
**
2054515 TCT--AACCCCG-TTATTT--C-
58 TCTAAAACATCGATT-TTTCACA
* * * *
2054532 ATCGGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
* *
2054597 ATTGATTTCTCACA
66 ATCGATTTTTCACA
** * * * * *
2054611 ATCGGGGATACTCCAACCCTATTATTTTCGCGGGAATACTCCAATCTCGATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCT-AAAA
*
2054675 CATCGA-TTTTCTATA
65 CATCGATTTTTC-ACA
* * * *
2054690 ATCGGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCCGATTTTTATTTCTAGAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGA-TTTTATTTCTAAAA
* *
2054755 CACCGATTTTTCATA
65 CATCGATTTTTCACA
2054770 ATCGGGGATACTCCAACCCCGTTA
1 ATCGGGGATACTCCAACCCCGTTA
2054794 GTATCTCCAA
Statistics
Matches: 258, Mismatches: 60, Indels: 45
0.71 0.17 0.12
Matches are distributed among these distances:
72 1 0.00
73 7 0.03
74 3 0.01
75 1 0.00
76 12 0.05
77 5 0.02
78 6 0.02
79 142 0.55
80 43 0.17
81 11 0.04
82 15 0.06
83 1 0.00
84 3 0.01
85 7 0.03
86 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
ATCGATTTTTCACA
Found at i:2054465 original size:51 final size:51
Alignment explanation
Indices: 2054405--2054524 Score: 186
Period size: 51 Copynumber: 2.4 Consensus size: 51
2054395 TTATTTCCAA
*
2054405 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
* * *
2054456 GGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
* *
2054507 GAGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
2054525 TTATTTCATC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
Found at i:2054540 original size:28 final size:28
Alignment explanation
Indices: 2054504--2054580 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
2054494 ATTTTTTATA
* *
2054504 ATCGAGGATACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2054532 ATCGGGGATACTCCAACCCCATTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2054560 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
2054581 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2054614 original size:107 final size:107
Alignment explanation
Indices: 2054456--2054654 Score: 249
Period size: 107 Copynumber: 1.9 Consensus size: 107
2054446 TTTCACAATC
* * * * * *
2054456 GGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTTATAATCGAGGATACTCTAAC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
*
2054521 CCCGTTATTTCATCG-GGG-ATACTCCAACCCCATTATTTCTGA
66 CCCATTATTT--TCGCGGGAATACTCCAACCCCATTATTTCTGA
* * ** *
2054563 GGGGATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
*
2054628 CCTATTATTTTCGCGGGAATACTCCAA
66 CCCATTATTTTCGCGGGAATACTCCAA
2054655 TCTCGATTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
105 3 0.04
106 3 0.04
107 71 0.92
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
CCCATTATTTTCGCGGGAATACTCCAACCCCATTATTTCTGA
Found at i:2054788 original size:80 final size:78
Alignment explanation
Indices: 2054532--2054789 Score: 315
Period size: 79 Copynumber: 3.3 Consensus size: 78
2054522 CCGTTATTTC
*
2054532 ATCGGGGATACTCCAACCCCATTA-TTTCTGAGGGGATACTCCAACCCCGACTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTC-GA-GGGATACTCCAACCCCGATTTTATTTCTAAAA
* * * *
2054596 TATTGATTTCTCACA
64 CATCGATTTTTCATA
* * * *
2054611 ATCGGGGATACTCCAACCCTATTATTTTCGCGGGAATACTCCAATCTCGATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGG-ATACTCCAACCCCGATTTTATTTCT-AAAA
2054675 CATCGA-TTTTCTATA
64 CATCGATTTTTC-ATA
** *
2054690 ATCGGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCCGATTTTTATTTCTAGAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAG-GGATACTCCAACCCCGA-TTTTATTTCTAAAA
*
2054755 CACCGATTTTTCATA
64 CATCGATTTTTCATA
2054770 ATCGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
2054790 GTTAGTATCT
Statistics
Matches: 155, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
78 8 0.05
79 97 0.63
80 44 0.28
81 6 0.04
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGATACTCCAACCCCGATTTTATTTCTAAAACA
TCGATTTTTCATA
Found at i:2059627 original size:28 final size:28
Alignment explanation
Indices: 2059587--2060576 Score: 916
Period size: 28 Copynumber: 34.5 Consensus size: 28
2059577 CACTAACTTG
2059587 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2059615 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
2059644 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2059672 TGTGGACTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2059700 TATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
2059729 TATGGGCTTTAAAAGG-GGGC-C--ACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2059753 TGTGGGCTTTGAAAAGAGTGCCATTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
2059782 TGTGGGCTTTGAAAAGG-TGCCACTCACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
2059810 TGTGGGCTTCTAAAAAAAAGG-TGCCACTAACTT
1 TGTGGGCTT-T----GAAAGGATGCCACTGAC-T
2059843 GTGTGGGCTTT-AAAGAGATGCCACTGACT
1 -TGTGGGCTTTGAAAG-GATGCCACTGACT
2059872 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2059900 TGTGGGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
2059928 CGTGGGTTTTGAAAAGTTGCCACTAACG
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * * *
2059956 CATGGGCTTTGAAAAGTTGCCACTAACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
2059985 GTGTGGGCTTT-AAAGAGATGCCACTGACT
1 -TGTGGGCTTTGAAAG-GATGCCACTGACT
2060014 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
2060042 CGTGGGCTTTGAAAAGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2060070 TGTGGGCTTGGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2060098 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2060126 TGTGGGCTTTAAAAAGATGCCACCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2060154 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* *
2060185 GTGTGGGCTTTGAAATAGGTTGCCACCGACTT
1 -TGTGGGCTTTG-AA-AGGATGCCACTGAC-T
* *
2060217 GTGTGGGCTTTGAAGTAGGTTGCCACCGACTT
1 -TGTGGGCTTTGAA--AGGATGCCACTGAC-T
* **
2060249 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * *
2060281 GTGTGGGCTTTGAAATGAGTTGCCACCGACG
1 -TGTGGGCTTTGAAA-G-GATGCCACTGACT
* * * *
2060312 CGTGGGCTTTGAAAAGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2060340 TGTGGGCTTGGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2060368 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2060396 TGTGGACTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2060424 CGTGGGCTTTAAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * ** *
2060452 TGTGGGCTTTAAAAAGTTACCACCAACA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
2060480 CGTGGGCTTTAAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2060508 TGTGGGCTTTGAAAGGTTGTCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
2060536 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
**
2060564 CATGGGCTTTGAA
1 TGTGGGCTTTGAA
2060577 GAGGTCACAG
Statistics
Matches: 815, Mismatches: 115, Indels: 64
0.82 0.12 0.06
Matches are distributed among these distances:
24 16 0.02
26 3 0.00
27 2 0.00
28 518 0.64
29 79 0.10
30 56 0.07
31 4 0.00
32 123 0.15
33 4 0.00
34 10 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:2061925 original size:16 final size:17
Alignment explanation
Indices: 2061884--2061928 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2061874 CCCTTTTTTA
2061884 TTTTGCTTTTGCACTTT
1 TTTTGCTTTTGCACTTT
*
2061901 TTTTTCTTTT-CA-TTT
1 TTTTGCTTTTGCACTTT
2061916 TTTATGCTTTTGC
1 TTT-TGCTTTTGC
2061929 TTTTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
17 10 0.42
ACGTcount: A:0.07, C:0.16, G:0.09, T:0.69
Consensus pattern (17 bp):
TTTTGCTTTTGCACTTT
Found at i:2069173 original size:14 final size:14
Alignment explanation
Indices: 2069154--2069180 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2069144 ATTCACTCTT
2069154 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
2069168 TTTTTATTTTTTT
1 TTTTTATTTTTTT
2069181 TAAAAAAAAT
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:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:2070126 original size:24 final size:26
Alignment explanation
Indices: 2070078--2070129 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
2070068 CTAATGTATA
*
2070078 TATAAAATAAATATCACTAATTCAGAT
1 TATAAAATAAATA-CACTAAATCAGAT
2070105 TATAAAA-AAATA-ACTAAATCAGAT
1 TATAAAATAAATACACTAAATCAGAT
2070129 T
1 T
2070130 TCCAATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 12 0.50
26 5 0.21
27 7 0.29
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.31
Consensus pattern (26 bp):
TATAAAATAAATACACTAAATCAGAT
Found at i:2070197 original size:2 final size:2
Alignment explanation
Indices: 2070188--2070223 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2070178 AAATAGATTA
2070188 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2070224 AACAGAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2070286 original size:2 final size:2
Alignment explanation
Indices: 2070279--2070314 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2070269 AACAAAGAAA
2070279 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
2070315 GTAAAAGCAG
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:2074379 original size:2 final size:2
Alignment explanation
Indices: 2074374--2074427 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2074364 AAGCACACAC
2074374 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
2074416 AG AG AG AG AG AG
1 AG AG AG AG AG AG
2074428 GGGCAGGGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2074682 original size:2 final size:2
Alignment explanation
Indices: 2074675--2074710 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2074665 TAGCTTTTTG
2074675 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
2074711 TTCTAATCTC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2078080 original size:17 final size:19
Alignment explanation
Indices: 2078058--2078094 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2078048 TCCTCTATTC
2078058 TTTTCT-TGT-TGGTTTTT
1 TTTTCTGTGTGTGGTTTTT
2078075 TTTTCTGTGTGGTGGTTTTT
1 TTTTCTGTGT-GTGGTTTTT
2078095 ACTTTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
20 8 0.47
ACGTcount: A:0.00, C:0.05, G:0.24, T:0.70
Consensus pattern (19 bp):
TTTTCTGTGTGTGGTTTTT
Found at i:2084618 original size:13 final size:13
Alignment explanation
Indices: 2084600--2084624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2084590 CAAAGATCAG
2084600 TGTATCGATACAA
1 TGTATCGATACAA
2084613 TGTATCGATACA
1 TGTATCGATACA
2084625 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2084706 original size:33 final size:33
Alignment explanation
Indices: 2084664--2084733 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2084654 GGCAGTAGCT
2084664 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
2084697 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
2084730 TACA
1 TACA
2084734 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:2084707 original size:13 final size:13
Alignment explanation
Indices: 2084689--2084713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2084679 CAAAAAAATA
2084689 TGTATCGATACAT
1 TGTATCGATACAT
2084702 TGTATCGATACA
1 TGTATCGATACA
2084714 ACATTTTATG
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:2088029 original size:38 final size:39
Alignment explanation
Indices: 2087987--2088061 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
2087977 TAAATTTTGA
* *
2087987 AAAATTCCT-TTTATTTTTTAAGTTATTGA-TTTTCTTTT
1 AAAATTCCTCTTT-TTTTTTAAATTAATGAGTTTTCTTTT
2088025 AAAATTCCTCTTTTTTTTTAAATTAATGAGTTTTCTT
1 AAAATTCCTCTTTTTTTTTAAATTAATGAGTTTTCTT
2088062 CTTCGTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 23 0.70
39 10 0.30
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.60
Consensus pattern (39 bp):
AAAATTCCTCTTTTTTTTTAAATTAATGAGTTTTCTTTT
Found at i:2088539 original size:16 final size:15
Alignment explanation
Indices: 2088509--2088562 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 15
2088499 TCAATAATTT
2088509 AAATTTTTTTATATA
1 AAATTTTTTTATATA
2088524 TATTAATTTTTTTATATA
1 -A--AATTTTTTTATATA
*
2088542 AAATTTTTTT-CATA
1 AAATTTTTTTATATA
2088556 AAATTTT
1 AAATTTT
2088563 ACGAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 1 0.03
17 1 0.03
18 14 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
AAATTTTTTTATATA
Found at i:2088834 original size:10 final size:10
Alignment explanation
Indices: 2088811--2088843 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2088801 GCTGAAAAAA
2088811 AAAAAGAAAG
1 AAAAAGAAAG
*
2088821 -AAAAGAGAG
1 AAAAAGAAAG
2088830 AAAAAGAAAG
1 AAAAAGAAAG
2088840 AAAA
1 AAAA
2088844 TAGGTAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:2089823 original size:162 final size:161
Alignment explanation
Indices: 2089642--2089937 Score: 427
Period size: 162 Copynumber: 1.8 Consensus size: 161
2089632 TTTATTATTA
* * * * * * *
2089642 TTTTTAATCTTTTATATTCCTATGGGTATTCGTAGGGGTATAAAAGATTTCAAAAATATTTTGTA
1 TTTTTAATATTTTATATTCCTATAGGCATCCGTAGGGGTAAAAAAGATTTCAAAAACATTTCGTA
*
2089707 TCATTTC-AGGCTTCCATTAGGGTACG-AAATGTTATTTTC-AAAAGTAAATAAAATCAAAGTGA
66 TCATTTCGA-GCTTCCATTAGGGTA-GAAAATGATATTTTCGAAAA-TAAATAAAATCAAAGTGA
2089769 ATTAATATATTCAGGATAAATTTTAATATCTTTT
128 ATTAATATATTCAGGATAAATTTTAATATCTTTT
*
2089803 TTTTCTAATATTTTATATTCCTATAGGCATCCGTAGGGGTAAAAAAGATTTCAAAAACCTTTCGT
1 TTTT-TAATATTTTATATTCCTATAGGCATCCGTAGGGGTAAAAAAGATTTCAAAAACATTTCGT
* * *
2089868 ATCTTTTCGAGCTTCCATTAGGGTAGAAAATGATATTTTCGAAAATAAATAAAATTAAATTGAAT
65 ATCATTTCGAGCTTCCATTAGGGTAGAAAATGATATTTTCGAAAATAAATAAAATCAAAGTGAAT
2089933 TAATA
130 TAATA
2089938 CTTTTGAGAA
Statistics
Matches: 119, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
161 5 0.04
162 109 0.92
163 5 0.04
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (161 bp):
TTTTTAATATTTTATATTCCTATAGGCATCCGTAGGGGTAAAAAAGATTTCAAAAACATTTCGTA
TCATTTCGAGCTTCCATTAGGGTAGAAAATGATATTTTCGAAAATAAATAAAATCAAAGTGAATT
AATATATTCAGGATAAATTTTAATATCTTTT
Found at i:2093540 original size:79 final size:78
Alignment explanation
Indices: 2093407--2093892 Score: 511
Period size: 79 Copynumber: 6.2 Consensus size: 78
2093397 ATAATAACAC
* * *
2093407 GGTTGGAGTATCTCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATAGATGATTT
1 GGTTGGAGTATCCCCTCG-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATAGATGATTT
*
2093472 AGAAATAAAATCGG
65 AGAAATAAAACCGG
* * * * *
2093486 GATTGGAATATCTCCTCAGAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAA-AGGATGTTT
1 GGTTGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATA-GATGATT
*
2093550 TAGAAATAAAACCAG
64 TAGAAATAAAACCGG
* * *
2093565 GGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCTGATTATGAGAAATTA-AT-ATT
1 GGTTGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATTATGA-AAAATAGATGA-T
*
2093628 TTAGAAATAAAATCGG
63 TTAGAAATAAAACCGG
* ** *
2093644 GGTTAGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTA-AT-ATT
1 GGTTGGAGTATCCCCT-CGAAATAACGGGGTTGGAGTATCCCCGATTATGA-AAAATAGATGA-T
*
2093707 TTAGAAATAAAGCCGG
63 TTAGAAATAAAACCGG
* * * *
2093723 GGTTGGGGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTTTT
1 GGTTGGAGTATCCCCTCG-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATAGATGATTT
2093785 AGAAATAAAACCGG
65 AGAAATAAAACCGG
* ** * * * * *
2093799 GGTTGGAGTGTCCCCTCGGAAATAACGGGGTTGGAGTATCCTTGATTGTGAAAAGTCGACGTTTT
1 GGTTGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATAGATGATTT
* *
2093864 GGAAATAAAATCGG
65 AGAAATAAAACCGG
*
2093878 AGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2093893 GATTATGGAA
Statistics
Matches: 348, Mismatches: 46, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
75 4 0.01
76 59 0.17
77 1 0.00
78 1 0.00
79 278 0.80
80 4 0.01
81 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (78 bp):
GGTTGGAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATAGATGATTTA
GAAATAAAACCGG
Found at i:2093709 original size:158 final size:157
Alignment explanation
Indices: 2093376--2093839 Score: 567
Period size: 158 Copynumber: 2.9 Consensus size: 157
2093366 ATCTTCCGAC
* * * * *
2093376 GAGAAATTTAATATTTTGGAGATAATAA-CACGGTTGGAGTATCTCCTCGAAAATAATGGGGTTG
1 GAGAAA-TTAATATTTTAGAAATAA-AACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
* * * * *
2093440 GAGTATCCCCGATTGTGAAAAATAGATGA-TTTAGAAATAAAATCGGGATTGGAATATCTCCTCA
64 GAGTATCCCCGATTATGAAAATTA-AT-ATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCA
2093504 GAAATAACGGGGTTGGAGTATCCCCGACTAT
127 GAAATAACGGGGTTGGAGTATCCCCGACTAT
* *** * * *
2093535 GAAAAAAGGATGTTTTAGAAATAAAACCAGGGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGA
1 GAGAAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGA
* * * *
2093600 GTATCCCTGATTATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTAAAAA
66 GTATCCCCGATTATGA-AAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAA
*
2093665 ATAACGGGGTTGGAGTATCCCCGATTAT
130 ATAACGGGGTTGGAGTATCCCCGACTAT
* * * *
2093693 GAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGGGTATCCCTTCGAAAATAACGGGGTTGGA
1 GAGAAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGA
* * * * * *
2093758 GTATCCCCGATGA--AAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCCCTCGGAAA
66 GTATCCCCGATTATGAAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAA
2093821 TAACGGGGTTGGAGTATCC
131 TAACGGGGTTGGAGTATCC
2093840 TTGATTGTGA
Statistics
Matches: 259, Mismatches: 43, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
155 60 0.23
156 1 0.00
157 3 0.01
158 185 0.71
159 10 0.04
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (157 bp):
GAGAAATTAATATTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGA
GTATCCCCGATTATGAAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAA
TAACGGGGTTGGAGTATCCCCGACTAT
Found at i:2093889 original size:51 final size:50
Alignment explanation
Indices: 2093828--2094004 Score: 187
Period size: 51 Copynumber: 3.5 Consensus size: 50
2093818 AAATAACGGG
** * *
2093828 GTTGGAGTATCCTTGATTGTGAAAAGTCGACGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-TCGATGTTTTGGAAATAAAATCGGA
* * *
2093879 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTGGAAATAAAATCGGA
* * * * *
2093930 GTTAGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATCGATGTTTTGGAAATAAAATCGGA
*
2093980 GATTGGAGTATCCCCGA-GATGAAAA
1 G-TTGGAGTATCCCCGATTATGAAAA
2094005 ATCTAGAAAT
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 4 0.04
50 4 0.04
51 93 0.88
52 5 0.05
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATCGATGTTTTGGAAATAAAATCGGA
Found at i:2093889 original size:234 final size:235
Alignment explanation
Indices: 2093408--2093892 Score: 640
Period size: 234 Copynumber: 2.1 Consensus size: 235
2093398 TAATAACACG
* ** * *
2093408 GTTGGAGTATCTCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATAGATGATTTA
1 GTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATAGATGATTTA
*
2093473 GAAATAAAATCGGGATTGGAATATCTCCTCAGAAATAACGGGGTTGGAGTATCCCCGACTATGAA
66 GAAATAAAACCGGGATTGGAATATCTCCTCAGAAATAACGGGGTTGGAGTATCCCCGA--ATGAA
2093538 AAAAGGATGTTTTAGAAATAAAACCAGGGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGTA
129 AAAAGGATGTTTTAGAAATAAAACCAGGGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGTA
* * *
2093603 TCCCTGATTATGAGAAATTAATATTTTAGAAATAAAATCGGG
194 TCCCTGATTATGAGAAATCAACATTTTAGAAATAAAATCGGA
* *
2093645 GTTAGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTA-AT-ATTT
1 GTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGA-AAAATAGATGA-TT
* * **
2093708 TAGAAATAAAGCCGGGGTTGGGGTATC-CCTTC-GAAAATAACGGGGTTGGAGTATCCCCG-ATG
64 TAGAAATAAAACCGGGATTGGAATATCTCC-TCAG-AAATAACGGGGTTGGAGTATCCCCGAATG
** * * *
2093770 AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCCCTCGGAAATAACGGGGTTGGAG
127 AAAAAAGGATGTTTTAGAAATAAAACCAGGGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGAG
* * * * *
2093835 TATCCTTGATTGTGA-AAAGTCGACGTTTTGGAAATAAAATCGGA
192 TATCCCTGATTATGAGAAA-TCAACATTTTAGAAATAAAATCGGA
2093879 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2093893 GATTATGGAA
Statistics
Matches: 217, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
233 3 0.01
234 108 0.50
236 4 0.02
237 97 0.45
238 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (235 bp):
GTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATAGATGATTTA
GAAATAAAACCGGGATTGGAATATCTCCTCAGAAATAACGGGGTTGGAGTATCCCCGAATGAAAA
AAGGATGTTTTAGAAATAAAACCAGGGTTAGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATC
CCTGATTATGAGAAATCAACATTTTAGAAATAAAATCGGA
Found at i:2096316 original size:20 final size:20
Alignment explanation
Indices: 2096291--2096345 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
2096281 GAAATGCCTG
*
2096291 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAC
2096311 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
2096331 AATGTATCGATACAA
1 AATGTATCGATACAA
2096346 ATTGTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:2097185 original size:41 final size:41
Alignment explanation
Indices: 2097057--2097222 Score: 144
Period size: 41 Copynumber: 4.0 Consensus size: 41
2097047 TAGATAAAGG
*
2097057 AAAAAAGAAAAACGAAATGCGTCCTGCTCTTTGAGGACAAA
1 AAAAAAGGAAAACGAAATGCGTCCTGCTCTTTGAGGACAAA
* * * *
2097098 AGAAAAA-GAAAAGGAAAAT--TTCCT-AT-TTCTCGAGGATAAA
1 A-AAAAAGGAAAACG-AAATGCGTCCTGCTCTT-T-GAGGACAAA
* *
2097138 GGAAAAAAGGAAAACGAAATGCGTCTTGCTCTTTAAGGACAAA
1 --AAAAAAGGAAAACGAAATGCGTCCTGCTCTTTGAGGACAAA
* * * *
2097181 AAAAAAAGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAA
1 AAAAAAGGAAAACGAAATGCGTCCTGCTCTTTGAGGACAAA
2097222 A
1 A
2097223 GGGAAAAGAA
Statistics
Matches: 97, Mismatches: 17, Indels: 22
0.71 0.12 0.16
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 12 0.12
41 51 0.53
42 16 0.16
43 10 0.10
44 2 0.02
45 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAAAAGGAAAACGAAATGCGTCCTGCTCTTTGAGGACAAA
Found at i:2097353 original size:61 final size:61
Alignment explanation
Indices: 2097270--2097421 Score: 165
Period size: 61 Copynumber: 2.6 Consensus size: 61
2097260 GGACAAAGGA
*
2097270 GAAAAGGAAAAGGCATCTTGCTCTTTGAAGACTAAAA-AGTGCCACCAACTCATGTGGGCTTT
1 GAAAA-GAAAAGGCATCCTGCTCTTTGAAGACTAAAAGA-TGCCACCAACTCATGTGGGCTTT
* * ** **
2097332 GAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGATGCCACCAACTTGTGTGGGCTTT
1 GAAAAGAAAAGGCATCCTGCTCTTTGAAGACTAAAAGATGCCACCAACTCATGTGGGCTTT
*
2097393 -AAAAG---A--CATCCTGCTCTTTGAGGACTAAA
1 GAAAAGAAAAGGCATCCTGCTCTTTGAAGACTAAA
2097422 GGGCGAAAGG
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
55 20 0.25
57 1 0.01
60 5 0.06
61 47 0.59
62 6 0.08
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (61 bp):
GAAAAGAAAAGGCATCCTGCTCTTTGAAGACTAAAAGATGCCACCAACTCATGTGGGCTTT
Found at i:2097455 original size:94 final size:94
Alignment explanation
Indices: 2097343--2097515 Score: 285
Period size: 94 Copynumber: 1.8 Consensus size: 94
2097333 AAAAGAAAAG
*
2097343 GCGTCCTGCTCTTTGAGGACT-GGAAGATGCCACCAACTTGTGTGGGCTTTAAAAGACATCCTGC
1 GCGTCCTGCTCTTTGAGGACTGGGAA-ATGCCACCAACTTGTGTGGGCTTCAAAAGACATCCTGC
2097407 TCTTTGAGGACTAAAGGGCGAAAGGAGAGA
65 TCTTTGAGGACTAAAGGGCGAAAGGAGAGA
* * * *
2097437 GCGTCCTGCTCTTTGAGGACTGGGAATTGCCACCAACTTGTGTGGGCTTCGAAAGGCATCTTGCT
1 GCGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTCAAAAGACATCCTGCT
2097502 CTTTGAGGACTAAA
66 CTTTGAGGACTAAA
2097516 AAAAAATGCT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
94 69 0.95
95 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (94 bp):
GCGTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTCAAAAGACATCCTGCT
CTTTGAGGACTAAAGGGCGAAAGGAGAGA
Found at i:2097665 original size:111 final size:109
Alignment explanation
Indices: 2097440--2098074 Score: 561
Period size: 111 Copynumber: 5.7 Consensus size: 109
2097430 GGAGAGAGCG
* * * * *
2097440 TCCTGCTCTTTGAGGACTGGGAA-TTGCCACCAACTTGTGTGGGCTTCGAAAGGCATCTTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT-TAAAGGCGTCCTGCTCT
*
2097504 TTGAGGACTAAAAAAAAATGCTACCAACTTGTGTGGGCTTTGAAAGGCA
64 TTGAGGACT---AAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * *
2097553 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTAAAGGCGTCCTGCTCCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGCGTCCTGCTCTTT
2097618 GAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
66 GAGGACT--AAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* *
2097664 TCCTGCTTTTTGAGGA-TTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAGGCGTCCTGCTCTT
* * *
2097728 TGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCA
65 TGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCA
* * * ** *
2097779 TCTTACTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGTTTTGAAAGGCGTCCTGCTC
1 TCCTGCTCTTTGAGGACT--GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGCGTCCTGCTC
* ** *
2097844 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGCG
63 TTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * *
2097890 TCCTGCTCTTTGAGGACT-AAAGG-GCGA--AA------TGAG----AGA-GCGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGCGTCCTGCTCTTT
** *
2097940 GAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCA
66 GAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCA
* *
2097990 TCCTGCTCTTTGAGGACTGGAAA-ATACCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCC
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-------AAAGGCGTCC
*
2098054 TGCTTTTTGAGGACTAAAAAA
58 TGCTCTTTGAGGACTAAAAAA
2098075 GTGAAAGGAG
Statistics
Matches: 429, Mismatches: 51, Indels: 75
0.77 0.09 0.14
Matches are distributed among these distances:
93 45 0.10
94 2 0.00
99 4 0.01
100 22 0.05
102 5 0.01
104 2 0.00
105 2 0.00
107 3 0.01
108 3 0.01
109 27 0.06
110 7 0.02
111 120 0.28
112 26 0.06
113 38 0.09
114 2 0.00
115 18 0.04
116 1 0.00
117 22 0.05
118 54 0.13
121 2 0.00
122 24 0.06
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (109 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGCGTCCTGCTCTTT
GAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
Found at i:2097831 original size:172 final size:166
Alignment explanation
Indices: 2097464--2097908 Score: 615
Period size: 172 Copynumber: 2.6 Consensus size: 166
2097454 GACTGGGAAT
* * ** *
2097464 TGCCACCAACTTGTGTGGGCTTCGAAAGGCATCTTGCTCTTTGAGGACTAAAAAAAAATGCTACC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACT---AAAAGGTGCCACC
* *
2097529 AACTTGTGTGGGCTTTGAAAGGCATCTTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGT
63 AACTTGTGTGGGCTTT-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGT
* *
2097593 GAGCTTTAAAGGCGTCCTGCTCCTTGAGGACTAAAAAAAA
127 GAGCTTTAAAGGCATCCTACTCCTTGAGGACTAAAAAAAA
* * *
2097633 TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTTTTTGAGGATTAAAGGGTGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAC
*
2097698 TTGTGTGGGCTTTAAAGGCGTCCTGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGC
66 TTGTGTGGGCTTTAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGAGC
* *
2097762 TTTAAAAGGAGAAAGCATCTTACTCTTTGAGGACTAAAAAAAA
131 TTT--AA--AG---GCATCCTACTCCTTGAGGACTAAAAAAAA
* * *
2097805 TGCCACCAACTTGTGTGGGTTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAAC
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAC
2097870 TTGTGTGGGCTTTAAAGGCGTCCTGCTCTTTGAGGACTA
66 TTGTGTGGGCTTTAAAGGCGTCCTGCTCTTTGAGGACTA
2097909 AAGGGCGAAA
Statistics
Matches: 247, Mismatches: 21, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
165 46 0.19
166 29 0.12
167 2 0.01
169 47 0.19
172 123 0.50
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (166 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAC
TTGTGTGGGCTTTAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGAGC
TTTAAAGGCATCCTACTCCTTGAGGACTAAAAAAAA
Found at i:2098024 original size:61 final size:61
Alignment explanation
Indices: 2097920--2098069 Score: 223
Period size: 61 Copynumber: 2.5 Consensus size: 61
2097910 AGGGCGAAAT
* *
2097920 GAGAGAGCGTCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 GAGAAAGCGTCCTGCTCTTTGAGGACTAGGAAATACCACCAACTTGTGTGGGCTTTAAAAG
* *
2097981 GAGAAAGCATCCTGCTCTTTGAGGACT-GGAAAATACCACCAACTTGTGTGGGCTTTGAAAG
1 GAGAAAGCGTCCTGCTCTTTGAGGACTAGG-AAATACCACCAACTTGTGTGGGCTTTAAAAG
*
2098042 GA-AAAGGCGTCCTGCTTTTTGAGGACTA
1 GAGAAA-GCGTCCTGCTCTTTGAGGACTA
2098070 AAAAAGTGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
60 5 0.06
61 75 0.94
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (61 bp):
GAGAAAGCGTCCTGCTCTTTGAGGACTAGGAAATACCACCAACTTGTGTGGGCTTTAAAAG
Found at i:2098623 original size:12 final size:12
Alignment explanation
Indices: 2098606--2098634 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2098596 GATAAACATG
2098606 ATGCACTATGAT
1 ATGCACTATGAT
2098618 ATGCACTATGAT
1 ATGCACTATGAT
2098630 ATGCA
1 ATGCA
2098635 AGGTCCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (12 bp):
ATGCACTATGAT
Found at i:2098734 original size:40 final size:39
Alignment explanation
Indices: 2098637--2098750 Score: 104
Period size: 40 Copynumber: 2.7 Consensus size: 39
2098627 GATATGCAAG
* *
2098637 GTCCTGCTTTTCGAGGATAAAGGAAAAAAGGAAAACGAAATA
1 GTCCTGCTTTT-GAGGACAAAAG-AAAAA-GAAAACGAAATA
*
2098679 CGTCCTGCTATTTGAGGACAAAAGAAAAAGAAAAGGAAAGT-
1 -GTCCTGCT-TTTGAGGACAAAAGAAAAAGAAAACGAAA-TA
* *
2098720 GTCCTGCTTCTTGAGGGCAAAGTGAAAAAGA
1 GTCCTGCTT-TTGAGGACAAA-AGAAAAAGA
2098751 GTACGTCCTG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
39 1 0.02
40 18 0.29
41 17 0.27
42 6 0.10
43 17 0.27
44 3 0.05
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.19
Consensus pattern (39 bp):
GTCCTGCTTTTGAGGACAAAAGAAAAAGAAAACGAAATA
Found at i:2103624 original size:46 final size:46
Alignment explanation
Indices: 2103572--2104256 Score: 603
Period size: 46 Copynumber: 14.8 Consensus size: 46
2103562 ATTTCATCTC
* *
2103572 GTTTGACTGTATTGGCATTAAGACCTGGTCAAATTCTTCTCACCTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
** * * * * *
2103618 GTTTGACTGTATTGGTGTTAGGACCTAGTCAAACACTTTTTACCCCT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCA-CCTT
* * * * * * *
2103665 GTTTAACTGTATTGGCATTTGGACCTAGACAAATTGTTCTTACCATT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACC-TT
* * * *
2103712 GTTTGACTGTATTGGCATGAGGACCTAGTCAAAATCTTCTCATCTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
** * *
2103758 GTTTGACTGTATTGGTGTTAGTACCTGGTCAAACTTTTCTCACC--
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
* * * *
2103802 CTTTGACTGTATTGACATTAGGATCTGGTCAAACTCTT-TCACCCTC
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCA-CCTT
* * * * *
2103848 ATTTAACTATATTGGCATTAGGACTTAGTCAAACTCTT-TC-CACTAT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCAC-CT-T
* * * *
2103894 CTTTGATTGTATTGGCATTAGGACCTGGTTAAACTCTTTTCACCATT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACC-TT
* * * *
2103941 GTTTGATTGTATTGACGTTAGGACCTGGTCAAACTTTTCTCACCTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
* * * * *
2103987 GTTTGA-TCATATTGGCGTTAGGACCTAGTCAAACACTT-TGTACCCTT
1 GTTTGACT-GTATTGGCATTAGGACCTGGTCAAACTCTTCT-CA-CCTT
* * * * * * *
2104034 GCTTGATTGTGTTGGCGTTAAGAACTAGTCAAACTCTTCTCACCTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
* * * *
2104080 GTTTGATTGTATTAGCATTAGGACTTGGTCAAACTCTTCTCACTTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
* * ** * *
2104126 GTTTGACTATGTTGGTGTTAGGACCTGCTCAAACTTTTCTCACCCTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCA-CCTT
* * * *
2104173 GTTTGACTGTATTGGCATTAGGATCTGGTCAAACTCTTTTTACTTT
1 GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
*
2104219 GTTTGACTGTATCT-GCATTAGGACCTAGTCAAACTCTT
1 GTTTGACTGTAT-TGGCATTAGGACCTGGTCAAACTCTT
2104257 TCCACTATCA
Statistics
Matches: 515, Mismatches: 107, Indels: 34
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.01
44 34 0.07
45 4 0.01
46 283 0.55
47 187 0.36
48 4 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (46 bp):
GTTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTCTCACCTT
Found at i:2104001 original size:139 final size:139
Alignment explanation
Indices: 2103572--2104258 Score: 614
Period size: 139 Copynumber: 4.9 Consensus size: 139
2103562 ATTTCATCTC
* * * * * *
2103572 GTTTGACTGTATTGGCATTAAGACCTGGTCAAATTC-TTCTCACCTTGTTTGACTGTATTGGTGT
1 GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTTCTCACCTTCTTTGACTGTATTGGCGT
* * * * * * * * *
2103636 TAGGACCTAGTCAAACACTTTTTACCCCTGTTTAACTGTATTGGCATTTGGACCTAGACAAA-TT
66 TAGGACCTGGTCAAACTCTTTTCA-CCTTGTTTGACTGTATTGACATTAGGACCTGGTCAAACTT
*
2103700 GTTCTTACCATT
130 -TTCTCACC-TT
* * * * * *
2103712 GTTTGACTGTATTGGCATGAGGACCTAGTCAAAATC-TTCTCATCTTGTTTGACTGTATTGGTGT
1 GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTTCTCACCTTCTTTGACTGTATTGGCGT
* * * *
2103776 TAGTACCTGGTCAAACT-TTTCTCACC--CTTTGACTGTATTGACATTAGGATCTGGTCAAACTC
66 TAGGACCTGGTCAAACTCTTT-TCACCTTGTTTGACTGTATTGACATTAGGACCTGGTCAAACTT
*
2103838 TT-TCACCCTC
130 TTCTCA-CCTT
* * * * *
2103848 ATTTAACTATATTGGCATTAGGACTTAGTCAAACTCTTTC-CA-CTATCTTTGATTGTATTGGCA
1 GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTTCTCACCT-TCTTTGACTGTATTGGCG
* * *
2103911 TTAGGACCTGGTTAAACTCTTTTCACCATTGTTTGATTGTATTGACGTTAGGACCTGGTCAAACT
65 TTAGGACCTGGTCAAACTCTTTTCACC-TTGTTTGACTGTATTGACATTAGGACCTGGTCAAACT
2103976 TTTCTCACCTT
129 TTTCTCACCTT
* * * * *
2103987 GTTTGA-TCATATTGGCGTTAGGACCTAGTCAAACACTTTGT-ACCCTTGC-TTGATTGTGTTGG
1 GTTTGACT-ATATTGGCATTAGGACCTAGTCAAACTCTTTCTCA-CCTT-CTTTGACTGTATTGG
* * * * * *
2104049 CGTTAAGAACTAGTCAAACTCTTCTCACCTTGTTTGATTGTATT-AGCATTAGGACTTGGTCAAA
63 CGTTAGGACCTGGTCAAACTCTTTTCACCTTGTTTGACTGTATTGA-CATTAGGACCTGGTCAAA
* *
2104113 CTCTTCTCACTTT
127 CTTTTCTCACCTT
* ** *
2104126 GTTTGACTATGTTGGTGTTAGGACCT-GCTCAAACT-TTTCTCACCCTTGTTTGACTGTATTGGC
1 GTTTGACTATATTGGCATTAGGACCTAG-TCAAACTCTTTCTCA-CCTTCTTTGACTGTATTGGC
* * * * *
2104189 ATTAGGATCTGGTCAAACTCTTTTTACTTTGTTTGACTGTATCTG-CATTAGGACCTAGTCAAAC
64 GTTAGGACCTGGTCAAACTCTTTTCACCTTGTTTGACTGTAT-TGACATTAGGACCTGGTCAAAC
2104253 TCTTTC
128 T-TTTC
2104259 CACTATCATT
Statistics
Matches: 452, Mismatches: 72, Indels: 46
0.79 0.13 0.08
Matches are distributed among these distances:
135 2 0.00
136 70 0.15
137 36 0.08
138 8 0.02
139 214 0.47
140 119 0.26
141 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (139 bp):
GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTTCTCACCTTCTTTGACTGTATTGGCGT
TAGGACCTGGTCAAACTCTTTTCACCTTGTTTGACTGTATTGACATTAGGACCTGGTCAAACTTT
TCTCACCTT
Found at i:2104252 original size:93 final size:93
Alignment explanation
Indices: 2103572--2104306 Score: 640
Period size: 93 Copynumber: 7.9 Consensus size: 93
2103562 ATTTCATCTC
* * **
2103572 GTTTGACTGTATTGGCATTAAGACCTGGTCAAA-TTCTTCTCACCTTGTTTGACTGTATTGGTGT
1 GTTTGACTGTATTGGCATTAGGACCTAGTCAAACTT-TTCTCACCTTGTTTGACTGTATTGGCAT
* * * *
2103636 TAGGACCTAGTCAAACACTTTTTACCCCT
65 TAGGACCTGGTCAAACTCTTTTCACCCTT
* * * *
2103665 GTTTAACTGTATTGGCATTTGGACCTAGACAAA-TTGTTCTTACCATTGTTTGACTGTATTGGCA
1 GTTTGACTGTATTGGCATTAGGACCTAGTCAAACTT-TTCTCACC-TTGTTTGACTGTATTGGCA
* * * * *
2103729 TGAGGACCTAGTCAAAATCTTCTCA-TCTT
64 TTAGGACCTGGTCAAACTCTTTTCACCCTT
** * * * *
2103758 GTTTGACTGTATTGGTGTTAGTACCTGGTCAAACTTTTCTCACC--CTTTGACTGTATTGACATT
1 GTTTGACTGTATTGGCATTAGGACCTAGTCAAACTTTTCTCACCTTGTTTGACTGTATTGGCATT
* *
2103821 AGGATCTGGTCAAACTC-TTTCACCCTC
66 AGGACCTGGTCAAACTCTTTTCACCCTT
* * * * * *
2103848 ATTTAACTATATTGGCATTAGGACTTAGTCAAACTCTTTC-CA-CTATCTTTGATTGTATTGGCA
1 GTTTGACTGTATTGGCATTAGGACCTAGTCAAACT-TTTCTCACCT-TGTTTGACTGTATTGGCA
* *
2103911 TTAGGACCTGGTTAAACTCTTTTCACCATT
64 TTAGGACCTGGTCAAACTCTTTTCACCCTT
* * * * * *
2103941 GTTTGATTGTATTGACGTTAGGACCTGGTCAAACTTTTCTCACCTTGTTTGA-TCATATTGGCGT
1 GTTTGACTGTATTGGCATTAGGACCTAGTCAAACTTTTCTCACCTTGTTTGACT-GTATTGGCAT
* *
2104005 TAGGACCTAGTCAAACACTTTGT-ACCCTT
65 TAGGACCTGGTCAAACTCTTT-TCACCCTT
* * * * * * * * *
2104034 GCTTGATTGTGTTGGCGTTAAGAACTAGTCAAACTCTTCTCACCTTGTTTGATTGTATTAGCATT
1 GTTTGACTGTATTGGCATTAGGACCTAGTCAAACTTTTCTCACCTTGTTTGACTGTATTGGCATT
* * *
2104099 AGGACTTGGTCAAACTCTTCTCA-CTTT
66 AGGACCTGGTCAAACTCTTTTCACCCTT
* * **
2104126 GTTTGACTATGTTGGTGTTAGGACCT-GCTCAAACTTTTCTCACCCTTGTTTGACTGTATTGGCA
1 GTTTGACTGTATTGGCATTAGGACCTAG-TCAAACTTTTCTCA-CCTTGTTTGACTGTATTGGCA
* * *
2104190 TTAGGATCTGGTCAAACTCTTTTTA-CTTT
64 TTAGGACCTGGTCAAACTCTTTTCACCCTT
* * *
2104219 GTTTGACTGTATCT-GCATTAGGACCTAGTCAAACTCTTTC-CA-CTATCATTTGACCGTATTAG
1 GTTTGACTGTAT-TGGCATTAGGACCTAGTCAAACT-TTTCTCACCT-T-GTTTGACTGTATTGG
* * *
2104281 CATTAGTA-TTGGTCAAACTTTTTTCA
62 CATTAGGACCTGGTCAAACTCTTTTCA
2104307 TCTTCACCCG
Statistics
Matches: 520, Mismatches: 101, Indels: 43
0.78 0.15 0.06
Matches are distributed among these distances:
89 5 0.01
90 61 0.12
91 7 0.01
92 90 0.17
93 308 0.59
94 49 0.09
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (93 bp):
GTTTGACTGTATTGGCATTAGGACCTAGTCAAACTTTTCTCACCTTGTTTGACTGTATTGGCATT
AGGACCTGGTCAAACTCTTTTCACCCTT
Found at i:2105931 original size:22 final size:23
Alignment explanation
Indices: 2105903--2105946 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2105893 CAACATAGTT
2105903 ACTTTGTCGA-TTT-ATTTTCTAG
1 ACTTTGTC-ACTTTCATTTTCTAG
2105925 ACTTTGTCACTTTCATTTTCTA
1 ACTTTGTCACTTTCATTTTCTA
2105947 TTTTTGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.55
23 8 0.40
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (23 bp):
ACTTTGTCACTTTCATTTTCTAG
Found at i:2109857 original size:18 final size:18
Alignment explanation
Indices: 2109805--2109849 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2109795 AAGTTTTGAA
2109805 TTTTTTCTTTGAAAATCC
1 TTTTTTCTTTGAAAATCC
2109823 TTTTTTCTTTGAAAATCC
1 TTTTTTCTTTGAAAATCC
2109841 TTTTTTCTT
1 TTTTTTCTT
2109850 GAGAAATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTTCTTTGAAAATCC
Found at i:2111429 original size:162 final size:160
Alignment explanation
Indices: 2111132--2111450 Score: 426
Period size: 162 Copynumber: 2.0 Consensus size: 160
2111122 CCATGTTTAT
* * * * * *
2111132 TATTTTTTATATCTTTTATATTCTTAGGGAATCCGTAGGGATATAAAAGATTTTAAAAATATTTC
1 TATTTTTTATATCTTCTATATTCCTAAGGAATCCGTAGGGATATAAAAAATTTCAAAAACATTTC
* * *
2111197 GTATCCTTTCGGGCTTCCATTAGGGTACGAAATGTTATTTTCGAAAGTAAATAAAATCAAAGTGA
66 GTATCCTTTCGGGCTTCCATAAGGGTACGAAATGTTATTTTCAAAAATAAATAAAATCAAAGTGA
*
2111262 ATTAATA-TTTTCAGGATAAATTTTAATATC
131 ATTAATACTTTTCA-GAAAAATTTTAATATC
* * * *
2111292 TATTTTTTCTAGTCTTCTATATTCCTACAGGCATCCGTAGGGGTATAAAAAATTTCAAAAACCTT
1 TATTTTTTATA-TCTTCTATATTCCTA-AGGAATCCGTAGGGATATAAAAAATTTCAAAAACATT
* * *
2111357 TCGTATCCTTTCGGGCTTCCATAAGGGTATGAAATAG-TATTTTCAAAAATAAATAAAATTAAAT
64 TCGTATCCTTTCGGGCTTCCATAAGGGTACGAAAT-GTTATTTTCAAAAATAAATAAAATCAAAG
*
2111421 TGAATTAATACTTTTGAGAAAAATTTTAAT
128 TGAATTAATACTTTTCAGAAAAATTTTAAT
2111451 CTTTTATATT
Statistics
Matches: 137, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
160 10 0.07
161 13 0.09
162 108 0.79
163 6 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (160 bp):
TATTTTTTATATCTTCTATATTCCTAAGGAATCCGTAGGGATATAAAAAATTTCAAAAACATTTC
GTATCCTTTCGGGCTTCCATAAGGGTACGAAATGTTATTTTCAAAAATAAATAAAATCAAAGTGA
ATTAATACTTTTCAGAAAAATTTTAATATC
Found at i:2111884 original size:48 final size:48
Alignment explanation
Indices: 2111808--2111910 Score: 197
Period size: 48 Copynumber: 2.1 Consensus size: 48
2111798 TGCCGAGTCC
2111808 GCTTCAATGTCGAAGGTAAGGGTTAGGGTAGGTTTATTTTTACCTGTTA
1 GCTT-AATGTCGAAGGTAAGGGTTAGGGTAGGTTTATTTTTACCTGTTA
2111857 GCTTAATGTCGAAGGTAAGGGTTAGGGTAGGTTTATTTTTACCTGTTA
1 GCTTAATGTCGAAGGTAAGGGTTAGGGTAGGTTTATTTTTACCTGTTA
2111905 GCTTAA
1 GCTTAA
2111911 AATAGGGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 50 0.93
49 4 0.07
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (48 bp):
GCTTAATGTCGAAGGTAAGGGTTAGGGTAGGTTTATTTTTACCTGTTA
Found at i:2112220 original size:35 final size:36
Alignment explanation
Indices: 2112175--2112280 Score: 160
Period size: 36 Copynumber: 3.0 Consensus size: 36
2112165 GATAAAAACC
** *
2112175 TCCCTATC-TTTTCACGGGCTAAGATAGAACCTCTT
1 TCCCTATCTTTTTCAAAGGCTGAGATAGAACCTCTT
*
2112210 TCCCCATCTTTTTCAAAGGCTGAGATAGAACCTCTT
1 TCCCTATCTTTTTCAAAGGCTGAGATAGAACCTCTT
*
2112246 TCCCTATCTTTTTCAAAGGTTGAGATAGAACCTCT
1 TCCCTATCTTTTTCAAAGGCTGAGATAGAACCTCT
2112281 CAATTACTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
35 7 0.11
36 57 0.89
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (36 bp):
TCCCTATCTTTTTCAAAGGCTGAGATAGAACCTCTT
Found at i:2112858 original size:20 final size:19
Alignment explanation
Indices: 2112833--2112903 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
2112823 GCTAGTTTTG
2112833 TGTATCGATACAATAAATGA
1 TGTATCGATACAATAAA-GA
* *
2112853 TGTATCGATACAATGAACA
1 TGTATCGATACAATAAAGA
* *
2112872 TGTATCGATACTATACAAAA
1 TGTATCGATACAATA-AAGA
2112892 TGTATCGATACA
1 TGTATCGATACA
2112904 TATGGGTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAATAAAGA
Found at i:2116992 original size:36 final size:35
Alignment explanation
Indices: 2116914--2117006 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 35
2116904 CAATACTATC
*
2116914 TTTC-AAGGCTAAGATAGAA--AC-CTCCCGATCT
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCGATCT
** *
2116945 TTTCATGGGCTAAGATAGAACCTCTCTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCGATC-T
*
2116981 TTTCAAAGGCTAAGAAAGAACCTCTC
1 TTTCAAAGGCTAAGATAGAACCTCTC
2117007 AATCACTTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 4 0.08
32 13 0.26
34 1 0.02
35 8 0.16
36 24 0.48
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (35 bp):
TTTCAAAGGCTAAGATAGAACCTCTCTCCCGATCT
Found at i:2122542 original size:13 final size:13
Alignment explanation
Indices: 2122524--2122551 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2122514 ATACAAAGAT
2122524 CAATGTATCGATA
1 CAATGTATCGATA
2122537 CAATGTATCGATA
1 CAATGTATCGATA
2122550 CA
1 CA
2122552 TTTCCTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2122607 original size:19 final size:21
Alignment explanation
Indices: 2122578--2122635 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
2122568 TTCGTAGCGA
2122578 TATATTGTATCGATACAA-TAC
1 TATA-TGTATCGATACAATTAC
* *
2122599 T-TATGTATCAATACAATTGC
1 TATATGTATCGATACAATTAC
*
2122619 TATTTGTATCGATACAA
1 TATATGTATCGATACAA
2122636 ATTGTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.39
20 5 0.16
21 14 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATGTATCGATACAATTAC
Found at i:2126999 original size:33 final size:33
Alignment explanation
Indices: 2126956--2127021 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2126946 GCTTAGGAAA
2126956 TGTATCGATACATTAATAAATGTATCGATACAT
1 TGTATCGATACATTAATAAATGTATCGATACAT
* * * * *
2126989 TGTATTGATACTTTTATCATTGTATCGATACAT
1 TGTATCGATACATTAATAAATGTATCGATACAT
2127022 GCAGGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTAATAAATGTATCGATACAT
Found at i:2129650 original size:13 final size:13
Alignment explanation
Indices: 2129632--2129656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2129622 CATAAAGTGT
2129632 TGTATCGATACAA
1 TGTATCGATACAA
2129645 TGTATCGATACA
1 TGTATCGATACA
2129657 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2129654 original size:33 final size:33
Alignment explanation
Indices: 2129612--2129678 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2129602 TTCAACGATT
2129612 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2129645 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2129678 T
1 T
2129679 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2129737 original size:13 final size:13
Alignment explanation
Indices: 2129719--2129746 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2129709 ATTACTCAAA
2129719 TGTATCGATACAT
1 TGTATCGATACAT
2129732 TGTATCGATACAT
1 TGTATCGATACAT
2129745 TG
1 TG
2129747 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2129796 original size:52 final size:52
Alignment explanation
Indices: 2129752--2129876 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
2129742 CATTGATCTT
2129752 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
2129804 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
2129856 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2129877 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):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:2134673 original size:28 final size:28
Alignment explanation
Indices: 2134580--2135226 Score: 682
Period size: 28 Copynumber: 22.5 Consensus size: 28
2134570 CATTAACTTG
** *
2134580 TGTGGGCTTTGAAAAGAATTGCCACGGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
2134610 CGTGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 --TGTGGGCTTTG-AAAG-GGTGCCACTGACT
*
2134642 TGTGGGCTTTGAAAGGGTGCCACTGACC
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
2134670 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*** *
2134698 TGTGGGCTTTGAAAAAATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
2134726 TGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
2134755 TGTGGGTTTTGAAAGGGTGCCACTAACTTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC--T
2134785 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
2134813 TGTGGGCTTTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2134841 TGTGGGCTTTGAAAAGGTGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2134869 GGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2134897 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2134925 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * * *
2134955 CGTGAGCTTTGAAAGGATGCCACTTACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2134983 TGTCGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
2135013 CGTGTGGGTTTTGAAAGGGTGCCACTAACT
1 --TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2135043 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
2135071 TGTGGGCTTTAAAAGAGTGCCATTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2135099 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
2135128 TGTGGGCTTTAAAAAGAGTGCCACTAACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* * * *
2135157 TGTGGGCTTTAAAAGAGTGCCATTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2135185 TGTGGGCTTTAAAAAGAGTGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
2135214 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2135227 GAGATGAACG
Statistics
Matches: 531, Mismatches: 72, Indels: 28
0.84 0.11 0.04
Matches are distributed among these distances:
28 297 0.56
29 118 0.22
30 77 0.15
31 4 0.01
32 35 0.07
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2134683 original size:58 final size:56
Alignment explanation
Indices: 2134580--2135226 Score: 688
Period size: 58 Copynumber: 11.2 Consensus size: 56
2134570 CATTAACTTG
** * * *
2134580 TGTGGGCTTTGAAAAGAATTGCCACGGACTCGTGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAG-G-TGCCACTGACT
* *
2134642 TGTGGGCTTTGAAAGGGTGCCACTGACCTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
*** * *
2134698 TGTGGGCTTTGAAAAAATGCCACTAACTTGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAAGGTGCCACTGACT
* * *
2134755 TGTGGGTTTTGAAAGGGTGCCACTAACTTTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC--TTGTGGGCTTTGAAAAGGTGCCACTGACT
** *
2134813 TGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
2134869 GGTGGGCTTTAAAAGGGTGCCACTGACTCGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * * *
2134925 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGAGCTTTG-AAAGGATGCCACTTACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * * * *
2134983 TGTCGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGTTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGGTGCCACTGACT
* * * *
2135043 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT-AAAAGAGTGCCATTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * *
2135099 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * * * *
2135157 TGTGGGCTTTAAAAGAGTGCCATTGATTTGTGGGCTTTAAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
2135214 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2135227 GAGATGAACG
Statistics
Matches: 509, Mismatches: 64, Indels: 29
0.85 0.11 0.05
Matches are distributed among these distances:
55 9 0.02
56 152 0.30
57 122 0.24
58 155 0.30
59 15 0.03
60 37 0.07
61 8 0.02
62 11 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:2135167 original size:86 final size:86
Alignment explanation
Indices: 2134580--2135226 Score: 758
Period size: 86 Copynumber: 7.5 Consensus size: 86
2134570 CATTAACTTG
* * * *
2134580 TGTGGGCTTTGAAAAGAATTGCCACGGACTCGTGTGGGCTTTGAAAAGAGTTACCACTGGCTTGT
1 TGTGGGCTTTGAAAAG-AGTGCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGT
* * *
2134645 GGGCTTTGAAAGGGTGCCACTGACC
62 GGGCTTTAAAAGAGTGCCACTGACT
* * *
2134670 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-AATGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2134733 TTTGAAAAAAGTGCCACTGACT
66 TTT-AAAAGAGTGCCACTGACT
* * * *
2134755 TGTGGGTTTTG-AAAGGGTGCCACTAACTTTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGAC--TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
2134818 GCTTTGAAAA-AGTGCCACTGACT
64 GCTTT-AAAAGAGTGCCACTGACT
* * * *
2134841 TGTGGGCTTTGAAAAG-GTGTCACTGACTGGTGGGCTTT-AAAAGGGTGCCACTGACTCGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2134904 TTTGAAAG-GATGCCACTGACT
66 TTTAAAAGAG-TGCCACTGACT
* * * * * *
2134925 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGAGCTTTGAAAGGA-TGCCACTTACTTGTCGG
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
*
2134989 CTTTGAAAAGAGTTGCCACCGACT
65 CTTT-AAAAGAG-TGCCACTGACT
* * *
2135013 CGTGTGGGTTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGG
1 --TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
2135076 GCTTTAAAAGAGTGCCATTGATT
64 GCTTTAAAAGAGTGCCACTGACT
* *
2135099 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2135164 TTTAAAAGAGTGCCATTGATT
66 TTTAAAAGAGTGCCACTGACT
*
2135185 TGTGGGCTTTAAAAAGAGTGCCACTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAA
2135227 GAGATGAACG
Statistics
Matches: 487, Mismatches: 53, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
83 4 0.01
84 91 0.19
85 72 0.15
86 171 0.35
87 56 0.11
88 63 0.13
89 9 0.02
90 21 0.04
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
TTTAAAAGAGTGCCACTGACT
Found at i:2136468 original size:24 final size:22
Alignment explanation
Indices: 2136441--2136516 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 22
2136431 CCTCTTTCTG
2136441 TTTTTTTGCTATTTGTTTCTTGGT
1 TTTTTTTGCTATTTGTTT-TT-GT
* * *
2136465 TTTTTTTGTTTTTTGTTTTTTT
1 TTTTTTTGCTATTTGTTTTTGT
*
2136487 TGTTTTTTTCTATTT-TTTTTGT
1 T-TTTTTTGCTATTTGTTTTTGT
2136509 TTTTTTTG
1 TTTTTTTG
2136517 TTTTTTAGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.14
22 9 0.21
23 12 0.28
24 16 0.37
ACGTcount: A:0.03, C:0.04, G:0.12, T:0.82
Consensus pattern (22 bp):
TTTTTTTGCTATTTGTTTTTGT
Found at i:2136470 original size:1 final size:1
Alignment explanation
Indices: 2136464--2136522 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
2136454 TGTTTCTTGG
* * * * * * *
2136464 TTTTTTTTGTTTTTTGTTTTTTTTGTTTTTTTCTATTTTTTTTGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2136523 AGGTATAAAG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:2136474 original size:17 final size:16
Alignment explanation
Indices: 2136452--2136521 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 16
2136442 TTTTTTGCTA
2136452 TTTGTTTCTTGGTTTTT
1 TTTGTTT-TTGGTTTTT
*
2136469 TTTGTTTTTTGTTTTT
1 TTTGTTTTTGGTTTTT
* *
2136485 TTTGTTTTT--TTCTA
1 TTTGTTTTTGGTTTTT
2136499 TTT-TTTTT-GTTTTT
1 TTTGTTTTTGGTTTTT
2136513 TTTGTTTTT
1 TTTGTTTTT
2136522 TAGGTATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
13 5 0.11
14 12 0.26
15 5 0.11
16 17 0.37
17 7 0.15
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.84
Consensus pattern (16 bp):
TTTGTTTTTGGTTTTT
Found at i:2136477 original size:9 final size:9
Alignment explanation
Indices: 2136463--2136522 Score: 88
Period size: 9 Copynumber: 6.8 Consensus size: 9
2136453 TTGTTTCTTG
2136463 GTTTTTTTT
1 GTTTTTTTT
2136472 G--TTTTTT
1 GTTTTTTTT
2136479 GTTTTTTTT
1 GTTTTTTTT
2136488 GTTTTTTTCT
1 GTTTTTTT-T
*
2136498 ATTTTTTTT
1 GTTTTTTTT
2136507 GTTTTTTTT
1 GTTTTTTTT
2136516 GTTTTTT
1 GTTTTTT
2136523 AGGTATAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 7 0.15
9 31 0.67
10 8 0.17
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (9 bp):
GTTTTTTTT
Found at i:2140294 original size:22 final size:22
Alignment explanation
Indices: 2140268--2140317 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
2140258 ATCAACTTGA
2140268 GTCGTTCAATCCTTGCTTGATT
1 GTCGTTCAATCCTTGCTTGATT
**
2140290 GTCGTTTTATCCTTGCTTGATT
1 GTCGTTCAATCCTTGCTTGATT
2140312 GTCGTT
1 GTCGTT
2140318 TTCTATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (22 bp):
GTCGTTCAATCCTTGCTTGATT
Found at i:2140318 original size:22 final size:22
Alignment explanation
Indices: 2140276--2140319 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2140266 GAGTCGTTCA
2140276 ATCCTTGCTTGATTGTCGTTTT
1 ATCCTTGCTTGATTGTCGTTTT
2140298 ATCCTTGCTTGATTGTCGTTTT
1 ATCCTTGCTTGATTGTCGTTTT
2140320 CTATGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.55
Consensus pattern (22 bp):
ATCCTTGCTTGATTGTCGTTTT
Found at i:2148711 original size:23 final size:23
Alignment explanation
Indices: 2148676--2148720 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2148666 ACCTCACAAT
*
2148676 TTCTTCAAGAATTATACCCCAAA
1 TTCTTCAAGAATTATAACCCAAA
*
2148699 TTCTT-AAGAAATTGTAACCCAA
1 TTCTTCAAG-AATTATAACCCAA
2148721 GGTTGAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (23 bp):
TTCTTCAAGAATTATAACCCAAA
Found at i:2149228 original size:20 final size:20
Alignment explanation
Indices: 2149202--2149254 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2149192 GCGAGTTTCA
*
2149202 TGTATCGATACAATTGAGTAC
1 TGTATCGATACAA-TGAGCAC
2149223 -GTATCGATACAATGAGCAC
1 TGTATCGATACAATGAGCAC
2149242 TGTATCGATACAA
1 TGTATCGATACAA
2149255 AGTATAATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAATGAGCAC
Found at i:2150819 original size:13 final size:13
Alignment explanation
Indices: 2150801--2150827 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2150791 ACAAATAGTA
2150801 AATGTATCGATAC
1 AATGTATCGATAC
2150814 AATGTATCGATAC
1 AATGTATCGATAC
2150827 A
1 A
2150828 TAACTGTTGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2150901 original size:20 final size:20
Alignment explanation
Indices: 2150876--2150930 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2150866 CTGCTAAGGA
2150876 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
2150896 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
2150916 TTTGTATCGATACAT
1 AATGTATCGATACAT
2150931 CTGGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:2155482 original size:79 final size:79
Alignment explanation
Indices: 2155351--2155571 Score: 227
Period size: 79 Copynumber: 2.8 Consensus size: 79
2155341 ACAACGGGGC
* * * *
2155351 TGGAGTTTCCCCGATTATGGAAAATCTGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATTATAGAAAATCTGTATTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTC
2155416 GAAAATAAAAGGGA
66 GAAAATAAAAGGGA
* *
2155430 TGGAGTATCCCTGATTATAGAAAAT-TGATATTTT-GAAAATAAAATCGGGGTTGAAGTATCCCC
1 TGGAGTATCCCCGATTATAGAAAATCTG-TATTTTAG-AAATAAAACCGGGGTTGAAGTATCCCC
** *
2155493 TCGAAAATAACGGGGT
64 TCGAAAATAAAAGGGA
** * ** *
2155509 TGGAGTATTTCCGATTGT-GAAAAATC-G-ATGATTTAGAAATAAGGCCGGGGTTGAACTATCCC
1 TGGAGTATCCCCGATTATAG-AAAATCTGTAT--TTTAGAAATAAAACCGGGGTTGAAGTATCCC
2155571 C
63 C
2155572 GATTATGAGA
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 111 0.94
80 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATAGAAAATCTGTATTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTC
GAAAATAAAAGGGA
Found at i:2155669 original size:51 final size:51
Alignment explanation
Indices: 2155503--2155673 Score: 130
Period size: 51 Copynumber: 3.4 Consensus size: 51
2155493 TCGAAAATAA
* ** * * * ***
2155503 CGGGGTTGGAGTATTTCCGATTGTGAAAAATCGATGA-TTTAGAAATAAGGC
1 CGGGGTTGAAGTATCCCCGATTATGAGAAATCAAT-ATTTTAGAAATAAAAT
* *
2155554 CGGGGTTGAACTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAAT
1 CGGGGTTGAAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAAT
*** * * *** *
2155605 CAAAGTTGGAGTATCCCCGATTGTG-GAAAATTGGTATTTTATAAATAAAAT
1 CGGGGTTGAAGTATCCCCGATTATGAG-AAATCAATATTTTAGAAATAAAAT
2155656 CGGGGTTGAAGTATCCCC
1 CGGGGTTGAAGTATCCCC
2155674 TCGGAAATAA
Statistics
Matches: 92, Mismatches: 26, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
50 2 0.02
51 90 0.98
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
CGGGGTTGAAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAAT
Found at i:2158276 original size:20 final size:19
Alignment explanation
Indices: 2158251--2158324 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
2158241 AAAATGCCTG
*
2158251 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
2158271 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
*
2158291 AATGTATTGATACAATGCAA
1 AATGTATCGATACAATG-AA
2158311 AATGTATCGATACA
1 AATGTATCGATACA
2158325 TCTGGGTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:2158358 original size:13 final size:13
Alignment explanation
Indices: 2158340--2158369 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2158330 GTAAACCCAG
2158340 AATGTATCGATAC
1 AATGTATCGATAC
2158353 AATGTATCGATAC
1 AATGTATCGATAC
2158366 AATG
1 AATG
2158370 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Done.