Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1401256 original size:13 final size:13
Alignment explanation
Indices: 1401235--1401269 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1401225 TCGATACTTT
* *
1401235 ATACCATGTATCG
1 ATACAATGTATCA
1401248 ATACAATGTATCA
1 ATACAATGTATCA
1401261 ATACAATGT
1 ATACAATGT
1401270 CCCATGTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (13 bp):
ATACAATGTATCA
Found at i:1401257 original size:33 final size:33
Alignment explanation
Indices: 1401219--1401285 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1401209 CGTTGGACAT
* **
1401219 AATGTATCGATACTTTATACCATGTATCGATAC
1 AATGTATCAATACAATATACCATGTATCGATAC
* *
1401252 AATGTATCAATACAATGTCCCATGTATCGATAC
1 AATGTATCAATACAATATACCATGTATCGATAC
1401285 A
1 A
1401286 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (33 bp):
AATGTATCAATACAATATACCATGTATCGATAC
Found at i:1401357 original size:19 final size:19
Alignment explanation
Indices: 1401314--1401369 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
1401304 TTGCCAGTTT
1401314 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
1401334 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
1401353 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1401370 TATCCATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:1403816 original size:19 final size:19
Alignment explanation
Indices: 1403773--1403846 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
1403763 TACACCCAAA
* *
1403773 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
1403793 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
1403812 TGTATCGATACATGGA-CAAT
1 TGTATCGATACAT-GATC-AT
1403832 TGTATCGATACATGA
1 TGTATCGATACATGA
1403847 AACTGGCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.36
20 32 0.64
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:1410635 original size:15 final size:16
Alignment explanation
Indices: 1410604--1410636 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1410594 AAAAATCTTG
1410604 AAAAATTATTTTCTAA
1 AAAAATTATTTTCTAA
1410620 AAAAATTATTTT-TAA
1 AAAAATTATTTTCTAA
1410635 AA
1 AA
1410637 TTAGATTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAATTATTTTCTAA
Found at i:1411571 original size:20 final size:20
Alignment explanation
Indices: 1411546--1411642 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
1411536 TTTTACCTAG
* *
1411546 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
1411566 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1411586 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
1411606 ATGTATCAATACATTCTTTA
1 ATGTATCGATACATTCTTCA
1411626 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1411643 ATCTTTTTAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1420135 original size:20 final size:20
Alignment explanation
Indices: 1420112--1420185 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1420102 ACAATTCAAA
1420112 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
* ****
1420132 GTATCGATATATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1420153 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1420173 GTATCGATACATG
1 GTATCGATACATG
1420186 AAAAAGATGT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1420156 original size:21 final size:21
Alignment explanation
Indices: 1420130--1420205 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1420120 ACATGTTGCA
*
1420130 ATGTATCGATATATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1420151 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1420171 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1420192 ATGTATCGATACAT
1 ATGTATCGATACAT
1420206 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1420161 original size:41 final size:41
Alignment explanation
Indices: 1420112--1420205 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1420102 ACAATTCAAA
*
1420112 GTATCGATACATGTTGCAATGTATCGATATATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1420153 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1420194 GTATCGATACAT
1 GTATCGATACAT
1420206 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1420262 original size:13 final size:13
Alignment explanation
Indices: 1420244--1420269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1420234 TACAGCAAGT
1420244 ATGTATCGATACA
1 ATGTATCGATACA
1420257 ATGTATCGATACA
1 ATGTATCGATACA
1420270 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1420790 original size:34 final size:35
Alignment explanation
Indices: 1420727--1420793 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1420717 CTAAGTGATT
1420727 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1420763 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1420794 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1430314 original size:20 final size:20
Alignment explanation
Indices: 1430266--1430317 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1430256 TGGGTGAATA
* *
1430266 TATCAATACATTCACTTGTG
1 TATCAATATATTCACTTATG
1430286 TATCAATATATTCACTTATG
1 TATCAATATATTCACTTATG
1430306 TATCAATATATT
1 TATCAATATATT
1430318 TTAGTCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (20 bp):
TATCAATATATTCACTTATG
Found at i:1431664 original size:112 final size:112
Alignment explanation
Indices: 1431467--1431686 Score: 431
Period size: 112 Copynumber: 2.0 Consensus size: 112
1431457 TTTATTAAAC
1431467 TAAGCCCATGGTAATACTTTGAAACACAATTAGACCTTGCTATCATTAATAACTCATTTAAGAAG
1 TAAGCCCATGGTAATACTTTGAAACACAATTAGACCTTGCTATCATTAATAACTCATTTAAGAAG
1431532 AGCTAGGCATAGAAAATTCCAATCAACTTGTAAAAACAAAAAACAAA
66 AGCTAGGCATAGAAAATTCCAATCAACTTGTAAAAACAAAAAACAAA
1431579 TAAGCCCATGGTAATACTTTGAAACACAATTAGACCTTGCTATCATTAATAACTCATTTAAGAAG
1 TAAGCCCATGGTAATACTTTGAAACACAATTAGACCTTGCTATCATTAATAACTCATTTAAGAAG
*
1431644 AGCTAGGCATAGAAAATTCCAATCAACTTGTACAAACAAAAAA
66 AGCTAGGCATAGAAAATTCCAATCAACTTGTAAAAACAAAAAA
1431687 AAAAATAATT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (112 bp):
TAAGCCCATGGTAATACTTTGAAACACAATTAGACCTTGCTATCATTAATAACTCATTTAAGAAG
AGCTAGGCATAGAAAATTCCAATCAACTTGTAAAAACAAAAAACAAA
Found at i:1432107 original size:21 final size:21
Alignment explanation
Indices: 1432074--1432113 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1432064 TGACTTTAAT
1432074 TTTCTTATATTT-AATTATAA
1 TTTCTTATATTTAAATTATAA
*
1432094 TTTCTATATTTTTAAATTAT
1 TTTCT-TATATTTAAATTAT
1432114 TTAAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTCTTATATTTAAATTATAA
Found at i:1432875 original size:59 final size:58
Alignment explanation
Indices: 1432757--1432881 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 58
1432747 AAAGTGACCT
* * * *
1432757 TAGATTATGCAAATACCCTAAATGGCCTTAACAAGCATGAAAATTACTAAATTTACCC
1 TAGATTATGCAAATACCCTAAATGGCCTTAACAAGCATAAAAAATACAAAATGTACCC
* *
1432815 TAGATTATGTTAAATTA-CCTAAATGGTCTTAA-AATGCATAAAAAATACAAAATGGT-CCC
1 TAGATTATG-CAAA-TACCCTAAATGGCCTTAACAA-GCATAAAAAATACAAAAT-GTACCC
*
1432874 TAAATTAT
1 TAGATTAT
1432882 ATGAACTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
58 11 0.20
59 42 0.75
60 3 0.05
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.30
Consensus pattern (58 bp):
TAGATTATGCAAATACCCTAAATGGCCTTAACAAGCATAAAAAATACAAAATGTACCC
Found at i:1436724 original size:31 final size:31
Alignment explanation
Indices: 1436681--1436746 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
1436671 ATTGAAAAAT
1436681 GATACATCTGGGTAAAAAGACAGAATGTATC
1 GATACATCTGGGTAAAAAGACAGAATGTATC
*
1436712 GATACATTTGGGTAAAAAGACAGAATGTATC
1 GATACATCTGGGTAAAAAGACAGAATGTATC
1436743 GATA
1 GATA
1436747 TATTAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (31 bp):
GATACATCTGGGTAAAAAGACAGAATGTATC
Found at i:1436758 original size:20 final size:20
Alignment explanation
Indices: 1436735--1436809 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1436725 AAAAAGACAG
*
1436735 AATGTATCGATATATT-AAA
1 AATGTATCGATACATTCAAA
*
1436754 GAATGTATCGATACATTCATA
1 -AATGTATCGATACATTCAAA
* *
1436775 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
1436795 AATGTATCGATACAT
1 AATGTATCGATACAT
1436810 CTGGGTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 46 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1436759 original size:51 final size:51
Alignment explanation
Indices: 1436702--1436871 Score: 184
Period size: 51 Copynumber: 3.5 Consensus size: 51
1436692 GTAAAAAGAC
* *
1436702 AGAATGTATCGATACATTTGGGTAAAAAGACAGAATGTATCGATATATTAA
1 AGAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTAA
* *
1436753 AGAATGTATCGATACA--T---T---CATAC---ATGTATCGATACATTGAA
1 AGAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATT-AA
* *
1436794 A-AATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACATTGA
1 AGAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTAA
*
1436844 AGAATGTATCGATACATCAGGGTAAAAA
1 AGAATGTATCGATACATCTGGGTAAAAA
1436872 TGTGACTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
40 28 0.29
41 3 0.03
42 1 0.01
43 3 0.03
45 1 0.01
46 1 0.01
48 2 0.02
49 1 0.01
50 2 0.02
51 56 0.57
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (51 bp):
AGAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTAA
Found at i:1437918 original size:30 final size:29
Alignment explanation
Indices: 1437777--1438591 Score: 475
Period size: 28 Copynumber: 28.4 Consensus size: 29
1437767 CCAACTTGTA
1437777 TGGGCTTTGGAAG-GGTTGCCACTGACTTG
1 TGGGCTTT-GAAGAGGTTGCCACTGACTTG
** * * * *
1437806 TGAACTTT-AAAAGGATACCACTGATTTG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1437834 TGGGCTTCGAA-AGAG-TGCCACTAACTTC
1 TGGGCTTTGAAGAG-GTTGCCACTGACTTG
* * *
1437862 TGAGCTTTGAA-AGGGTGCCACTAACTTG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* **
1437890 TGGGCTTCGAGAGAGGTTGCCACCAACTTGCG
1 TGGGCTTTGA-AGAGGTTGCCACTGACTT--G
* * *
1437922 TGGGTTTTAAAG-GGTTGCCACCGACTTG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1437950 TTTAGGCTTT-AAGGGGTTGCCATTGACTTG
1 --TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1437980 TGAGCTTTGAA-AGGGTGCCACTAACTTG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1438008 TGAGCTTTGAA-AGGGTGCCACTAACTTG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1438036 TAGGCTTCGAGAGAGGTTGCCACCGACTTGTG
1 TGGGCTTTGA-AGAGGTTGCCACTGAC-T-TG
* *
1438068 TGGGCTTT-AAGGGGTTGCCACCGACTTG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
*
1438096 TGAGCTTTGAGAGAGGTTGCCACTGACTTG
1 TGGGCTTTGA-AGAGGTTGCCACTGACTTG
*
1438126 TGTGGCCTTT-AAG-GGTTACCACTGACTTG
1 TG-GG-CTTTGAAGAGGTTGCCACTGACTTG
*
1438155 TGGGCTTTGAGAGAGGTTGCCTCTGACTTG
1 TGGGCTTTGA-AGAGGTTGCCACTGACTTG
* **
1438185 TGGGCTTTTGAA-AGGATGCCACTGACGCG
1 TGGGC-TTTGAAGAGGTTGCCACTGACTTG
* * * *
1438214 TAGGCTTTTGAA-AGGGTGCCATTAACTTG
1 TGGGC-TTTGAAGAGGTTGCCACTGACTTG
* *
1438243 TGGGCTTCGAGAGAGGTTGCCACCGACTTG
1 TGGGCTTTGA-AGAGGTTGCCACTGACTTG
* * * *
1438273 TGGGCTTTGAAAAAG-TACCACTGACTGG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* *
1438301 TGGGCCTTGAA-A-ATATGCCACTGACTTG
1 TGGGCTTTGAAGAGGT-TGCCACTGACTTG
*
1438329 TGGGCTTTGGAAG-GATT-CCACTGACTTG
1 TGGGCTTT-GAAGAGGTTGCCACTGACTTG
* * * * *
1438357 TGGGCCTAGAA-AGGGTGCCGCTGACTGG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1438385 TGGGCTTTGAAAAAG-TGCCACTGA-TCGG
1 TGGGCTTTGAAGAGGTTGCCACTGACT-TG
* * * *
1438413 TGGGCTTTGAA-AAGATGCCATTGACTTA
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * *
1438441 TGGGCTTTGAA-AGGATGCCATTGACTCG
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * * * * **
1438469 TGGGCTTTGGA-AGGATGCTAGTAACTCA
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
* * * *
1438497 TGGGATTTGGAA-A-GATGCCATTGACTTA
1 TGGGCTTT-GAAGAGGTTGCCACTGACTTG
* *
1438525 TGGGCTAT--AGAAGGATGCCACTGACTTG
1 TGGGCTTTGAAG-AGGTTGCCACTGACTTG
* * **
1438553 TGGGCTTAGAA-AGGATGCCACTGACTCA
1 TGGGCTTTGAAGAGGTTGCCACTGACTTG
1438581 TGGGCTTTGAA
1 TGGGCTTTGAA
1438592 AAGAGATCAT
Statistics
Matches: 630, Mismatches: 113, Indels: 87
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.00
27 18 0.03
28 349 0.55
29 91 0.14
30 140 0.22
31 11 0.02
32 20 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (29 bp):
TGGGCTTTGAAGAGGTTGCCACTGACTTG
Found at i:1437964 original size:88 final size:88
Alignment explanation
Indices: 1437787--1438284 Score: 350
Period size: 88 Copynumber: 5.7 Consensus size: 88
1437777 TGGGCTTTGG
** * * * * * * * * *
1437787 AAGGGTTGCCACTGACTTGTGAACTT-TA-AAAGGATACCACTGATTTGTGGGCTTCGAAAGAG-
1 AAGGGTTGCCACTGACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGAGCTTTGAAAGGGT
* *
1437849 TGCCACTAACTTCTG-A-GCTTT
66 TGCCACTGACTTGTGTAGGCTTT
* * * *
1437870 GAAAGGG-TGCCACTAACTTGTGGGCTTCGAGAGAGGTTGCCACCAACTTGCGTG-GGTTTTAAA
1 --AAGGGTTGCCACTGACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTT--GTGAGCTTTGAAA
* *
1437933 GGGTTGCCACCGACTTGTTTAGGCTTT
62 GGGTTGCCACTGACTTGTGTAGGCTTT
* * * * **
1437960 AAGGGGTTGCCATTGACTTGTGAGCTTTGA-A-AGGGTGCCACTAACTTGTGAGCTTTGAAAGGG
1 AA-GGGTTGCCACTGACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGAGCTTTGAAAGGG
* *
1438023 -TGCCACTAAC-T-TGTAGGCTTCG
65 TTGCCACTGACTTGTGTAGGCTT-T
* * * *
1438045 AGAGAGGTTGCCACCGACTTGTGTGGGCTT-TA-AGGGGTTGCCACCGACTTGTGAGCTTTGAGA
1 A-AG-GGTTGCCACTGAC-T-TGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGAGCTTTGAAA
1438108 GAGGTTGCCACTGACTTGTGT-GGCCTTT
62 G-GGTTGCCACTGACTTGTGTAGG-CTTT
* * * * *
1438136 AAGGGTTACCACTGACTTGTGGGCTTTGAGAGAGGTTGCCTCTGACTTGTGGGCTTTTGAAA-GG
1 AAGGGTTGCCACTGACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGAGC-TTTGAAAGGG
* *
1438200 ATGCCACTGAC--GCGTAGGCTTTT
65 TTGCCACTGACTTGTGTAGGC-TTT
* * *
1438223 GAAAGGG-TGCCATTAACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGGGCTTTGAAA
1 --AAGGGTTGCCACTGACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGAGCTTTGAAA
1438285 AAGTACCACT
Statistics
Matches: 328, Mismatches: 57, Indels: 54
0.75 0.13 0.12
Matches are distributed among these distances:
84 25 0.08
85 9 0.03
86 39 0.12
87 42 0.13
88 119 0.36
89 43 0.13
90 41 0.12
91 4 0.01
92 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (88 bp):
AAGGGTTGCCACTGACTTGTGGGCTTCGAGAGAGGTTGCCACCGACTTGTGAGCTTTGAAAGGGT
TGCCACTGACTTGTGTAGGCTTT
Found at i:1438012 original size:146 final size:146
Alignment explanation
Indices: 1437753--1438335 Score: 531
Period size: 146 Copynumber: 4.0 Consensus size: 146
1437743 TGTAGGCTTT
* ** * * *
1437753 AGAGAAGGTTGCTACCAACTTGTATGGGCTTTGGAAGGGTTGCCACTGACTTGTGAACTTT-A-A
1 AGAG-AGGTTGCCACCAACTTGCGTGGGCTTT-AAAGGGTTGCCACCGACTTGTGAGCTTTGAGA
* * * * * * *
1437816 AAGGATACCACTGATTTGTGGGCTTCGAAAGAGTGCCACTAACTTCTGAGCTTTGAAAGGGTGCC
64 GAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGAGCTTTGAAAGGGTGCC
1437881 ACTAACTTGTGGGCTTCG
129 ACTAACTTGTGGGCTTCG
* *
1437899 AGAGAGGTTGCCACCAACTTGCGTGGGTTTTAAAGGGTTGCCACCGACTTGTTTAGGCTTT-A-A
1 AGAGAGGTTGCCACCAACTTGCGTGGGCTTTAAAGGGTTGCCACCGACTTG-TGA-GCTTTGAGA
* * *
1437962 GGGGTTGCCATTGACTTGTGAGCTTTGAAAGGGTGCCACTAACTTGTGAGCTTTGAAAGGGTGCC
64 GAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGAGCTTTGAAAGGGTGCC
*
1438027 ACTAACTTGTAGGCTTCG
129 ACTAACTTGTGGGCTTCG
* * *
1438045 AGAGAGGTTGCCACCGACTTGTGTGGGCTTTAAGGGGTTGCCACCGACTTGTGAGCTTTGAGAGA
1 AGAGAGGTTGCCACCAACTTGCGTGGGCTTTAAAGGGTTGCCACCGACTTGTGAGCTTTGAGAGA
* * * *
1438110 GGTTGCCACTGACTTGTGTGGCCTTT--AAGGGTTACCACTGACTTGTGGGCTTTGAGAGAGGTT
66 GGTTGCCACTGACTTGTG-GG-CTTTGAAAGGG-TGCCACTAACTTGTGAGCTTTGA-A-AGGGT
* * *
1438173 GCCTCTGACTTGTGGGCTTTTG
126 GCCACTAACTTGTGGGC-TTCG
* ** * *** * *
1438195 A-A-AGGATGCCACTGAC--GCGTAGGCTTTTGAAAGGG-TGCCATTAACTTGTGGGCTTCGAGA
1 AGAGAGGTTGCCACCAACTTGCGTGGGC-TTT-AAAGGGTTGCCACCGACTTGTGAGCTTTGAGA
* ** * * * * * ***
1438255 GAGGTTGCCACCGACTTGTGGGCTTTGAAAAAGTACCACTGACTGGTGGGCCTTGAAAATATGCC
64 GAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGAGCTTTGAAAGGGTGCC
*
1438320 ACTGACTTGTGGGCTT
129 ACTAACTTGTGGGCTT
1438336 TGGAAGGATT
Statistics
Matches: 369, Mismatches: 54, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
143 2 0.01
144 41 0.11
145 33 0.09
146 182 0.49
147 66 0.18
148 22 0.06
149 19 0.05
150 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (146 bp):
AGAGAGGTTGCCACCAACTTGCGTGGGCTTTAAAGGGTTGCCACCGACTTGTGAGCTTTGAGAGA
GGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGAGCTTTGAAAGGGTGCCAC
TAACTTGTGGGCTTCG
Found at i:1441842 original size:21 final size:21
Alignment explanation
Indices: 1441826--1441870 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1441816 ATTAATTCCA
1441826 CTTAGATTAAGTCTAATTAAG
1 CTTAGATTAAGTCTAATTAAG
1441847 CTTAGATTAAGTCTAATTAAG
1 CTTAGATTAAGTCTAATTAAG
1441868 CTT
1 CTT
1441871 CAATGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (21 bp):
CTTAGATTAAGTCTAATTAAG
Found at i:1443879 original size:21 final size:20
Alignment explanation
Indices: 1443847--1443890 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
1443837 TACAAAGGTC
1443847 ACAACCCTAGAAAGTATCGAT
1 ACAACCCTAG-AAGTATCGAT
1443868 ACAAGCCC-AGAAGTATCGAT
1 ACAA-CCCTAGAAGTATCGAT
1443888 ACA
1 ACA
1443891 TATTGCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.59
21 6 0.27
22 3 0.14
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (20 bp):
ACAACCCTAGAAGTATCGAT
Found at i:1443903 original size:20 final size:19
Alignment explanation
Indices: 1443880--1443930 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1443870 AAGCCCAGAA
*
1443880 GTATCGATACATATTGCTTT
1 GTATCGATACATATT-CATT
*
1443900 GTATCGATACATGTTCATT
1 GTATCGATACATATTCATT
*
1443919 GTATCAATACAT
1 GTATCGATACAT
1443931 GAAGAATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
GTATCGATACATATTCATT
Found at i:1443922 original size:19 final size:20
Alignment explanation
Indices: 1443880--1443948 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1443870 AAGCCCAGAA
* *
1443880 GTATCGATACATATTGCTTT
1 GTATCGATACATGTTGCATT
1443900 GTATCGATACATGTT-CATT
1 GTATCGATACATGTTGCATT
* ** *
1443919 GTATCAATACATGAAGAATT
1 GTATCGATACATGTTGCATT
1443939 GTATCGATAC
1 GTATCGATAC
1443949 GTGAAATTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACATGTTGCATT
Found at i:1443941 original size:20 final size:20
Alignment explanation
Indices: 1443916--1443953 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1443906 ATACATGTTC
1443916 ATTGTATCAATACATGAAGA
1 ATTGTATCAATACATGAAGA
* *
1443936 ATTGTATCGATACGTGAA
1 ATTGTATCAATACATGAA
1443954 ATTGGCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
ATTGTATCAATACATGAAGA
Found at i:1443999 original size:13 final size:13
Alignment explanation
Indices: 1443981--1444005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1443971 TATCACTATT
1443981 TGTATCGATACAA
1 TGTATCGATACAA
1443994 TGTATCGATACA
1 TGTATCGATACA
1444006 TAGTAAAAAG
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:1445703 original size:10 final size:10
Alignment explanation
Indices: 1445688--1445715 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1445678 TTTATCTCAC
1445688 AATTATCCTT
1 AATTATCCTT
1445698 AATTATCCTT
1 AATTATCCTT
1445708 AATTATCC
1 AATTATCC
1445716 GAAAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.46
Consensus pattern (10 bp):
AATTATCCTT
Found at i:1448336 original size:20 final size:19
Alignment explanation
Indices: 1448288--1448346 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1448278 AAAAACCCAG
1448288 AATGTATCGATACAATTTAA
1 AATGTATCGATAC-ATTTAA
*
1448308 AGCATGTATCGATACATTTATT
1 A--ATGTATCGATACATTTA-A
*
1448330 AATGTATCAATACATTT
1 AATGTATCGATACATTT
1448347 CCTTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 16 0.47
21 5 0.15
22 13 0.38
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (19 bp):
AATGTATCGATACATTTAA
Found at i:1448416 original size:21 final size:19
Alignment explanation
Indices: 1448368--1448419 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1448358 TGCAGGGTGT
1448368 TTTTGTATCGATACAAAAC
1 TTTTGTATCGATACAAAAC
* *
1448387 TTATGTATCGATACAATTAC
1 TTTTGTATCGATACAA-AAC
1448407 TGTTTGTATCGAT
1 T-TTTGTATCGAT
1448420 GCCAATTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 15 0.54
20 3 0.11
21 10 0.36
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (19 bp):
TTTTGTATCGATACAAAAC
Found at i:1451997 original size:85 final size:88
Alignment explanation
Indices: 1451851--1452028 Score: 195
Period size: 85 Copynumber: 2.1 Consensus size: 88
1451841 GGTGTAAATA
** * *
1451851 AAAATACTAAAATGGCCTTAATGGACATGTTTTTACATAAAAAATGCTAACATAACCCTTAAAGA
1 AAAATACTAAAATACCCTTAATGGACATGTTTTAACATAAAAAATGCTAACACAACCCTTAAAGA
1451916 CTCAAAAATGACATAAAA-TACC
66 CTCAAAAATGACATAAAAGTACC
* * *
1451938 AAAATACTAAAATACCCTTAA-GG-CTTGATTTTAACAT-AAAAGTGCTAAACACAA-TCTTAAA
1 AAAATACTAAAATACCCTTAATGGACATG-TTTTAACATAAAAAATGCT-AACACAACCCTTAAA
** * * *
1451999 GGTTTAAGAATGACATAAAAGTACT
64 GACTCAAAAATGACATAAAAGTACC
1452024 AAAAT
1 AAAAT
1452029 GGCTTTAAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
85 33 0.43
86 24 0.32
87 19 0.25
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (88 bp):
AAAATACTAAAATACCCTTAATGGACATGTTTTAACATAAAAAATGCTAACACAACCCTTAAAGA
CTCAAAAATGACATAAAAGTACC
Found at i:1453064 original size:29 final size:29
Alignment explanation
Indices: 1453008--1453064 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1452998 CACCTAATCC
*
1453008 AAATAATAAAAAAAATGTAACAACAAATT
1 AAATAATAAAAAAAATGTAAAAACAAATT
* *
1453037 AAATAAATAAAAAACATG-AAAAAGAAAT
1 AAAT-AATAAAAAAAATGTAAAAACAAAT
1453065 AGCTTGGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (29 bp):
AAATAATAAAAAAAATGTAAAAACAAATT
Found at i:1453278 original size:10 final size:10
Alignment explanation
Indices: 1453263--1453298 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1453253 ATCAACTATA
1453263 TTTTTTTGCT
1 TTTTTTTGCT
1453273 TTTTTTTGCT
1 TTTTTTTGCT
*
1453283 TTTTTCT-CT
1 TTTTTTTGCT
1453292 TTTTTTT
1 TTTTTTT
1453299 CTCCCAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTTTTTGCT
Found at i:1463360 original size:20 final size:20
Alignment explanation
Indices: 1463332--1463379 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1463322 AAATAGAGTT
* *
1463332 GTTGAAAGGATATATCGAAC
1 GTTGGAAGGATAAATCGAAC
1463352 GTTGGAAGGATAAATCGAAC
1 GTTGGAAGGATAAATCGAAC
1463372 GTTGGAAG
1 GTTGGAAG
1463380 AAATGGCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (20 bp):
GTTGGAAGGATAAATCGAAC
Found at i:1465617 original size:19 final size:19
Alignment explanation
Indices: 1465593--1465631 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1465583 TGTTGAATGA
*
1465593 CCAAATATGCTTTTAACGC
1 CCAAATACGCTTTTAACGC
1465612 CCAAATACGCTTTTAACGC
1 CCAAATACGCTTTTAACGC
1465631 C
1 C
1465632 ATATATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (19 bp):
CCAAATACGCTTTTAACGC
Found at i:1468606 original size:32 final size:33
Alignment explanation
Indices: 1468548--1468610 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1468538 CACACTCAGA
* *
1468548 TGTATCGATACATATTGCTTTGTATCGATACGT
1 TGTATCGACACATATTGCATTGTATCGATACGT
*
1468581 TGTATCGACACATGTT-CATTGTATCGATAC
1 TGTATCGACACATATTGCATTGTATCGATAC
1468611 ACACTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (33 bp):
TGTATCGACACATATTGCATTGTATCGATACGT
Found at i:1468789 original size:20 final size:20
Alignment explanation
Indices: 1468761--1468807 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1468751 TACATATATT
*
1468761 GATATATTATGAATTGTATC
1 GATACATTATGAATTGTATC
1468781 GATACATTATGAATTGTATC
1 GATACATTATGAATTGTATC
1468801 GATACAT
1 GATACAT
1468808 AGGAGCATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (20 bp):
GATACATTATGAATTGTATC
Found at i:1470441 original size:19 final size:20
Alignment explanation
Indices: 1470419--1470460 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1470409 AAAGGTCCTT
*
1470419 AAAATG-TTAAAAATGCCTA
1 AAAATGTTTAAAAATGCATA
*
1470438 AAAATGTTTAAACATGCATA
1 AAAATGTTTAAAAATGCATA
1470458 AAA
1 AAA
1470461 CACATCTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAATGTTTAAAAATGCATA
Found at i:1478041 original size:13 final size:13
Alignment explanation
Indices: 1478023--1478047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1478013 CACCAAGGGA
1478023 TACAAAATTTTTT
1 TACAAAATTTTTT
1478036 TACAAAATTTTT
1 TACAAAATTTTT
1478048 CATTTTTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TACAAAATTTTTT
Found at i:1479243 original size:20 final size:20
Alignment explanation
Indices: 1479218--1479271 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1479208 CTACCATTGT
** *
1479218 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGAAAAA
1479238 TTGTATCGATACATGAAAAA
1 TTGTATCGATACATGAAAAA
1479258 TTGTATCGATACAT
1 TTGTATCGATACAT
1479272 TGCTTCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGAAAAA
Found at i:1485438 original size:13 final size:13
Alignment explanation
Indices: 1485420--1485455 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1485410 TGTTCTTTGT
*
1485420 ATCGATATATTGC
1 ATCGATACATTGC
1485433 ATCGATACATTGC
1 ATCGATACATTGC
1485446 ATCGATACAT
1 ATCGATACAT
1485456 GGTTACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
ATCGATACATTGC
Found at i:1487906 original size:13 final size:13
Alignment explanation
Indices: 1487888--1487914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1487878 ACATTATGCT
1487888 TTGTATCGATATA
1 TTGTATCGATATA
1487901 TTGTATCGATATA
1 TTGTATCGATATA
1487914 T
1 T
1487915 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATCGATATA
Found at i:1487924 original size:19 final size:20
Alignment explanation
Indices: 1487900--1487953 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1487890 GTATCGATAT
* **
1487900 ATTGTATCGATATATGTTC-
1 ATTGTATCGATACATGCACA
1487919 ATTGTATCGATACATGCACA
1 ATTGTATCGATACATGCACA
1487939 ATTGTATCGATACAT
1 ATTGTATCGATACAT
1487954 AAAAGTGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
ATTGTATCGATACATGCACA
Found at i:1488019 original size:33 final size:33
Alignment explanation
Indices: 1487977--1488041 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1487967 TACCACTATT
* *
1487977 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGACAAATTGTATCGATACAA
* *
1488010 TGTATCGATAGATGATAAATTGTATCGATACA
1 TGTATCGATACATGACAAATTGTATCGATACA
1488042 TTACTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTGTATCGATACAA
Found at i:1489137 original size:60 final size:60
Alignment explanation
Indices: 1489073--1489198 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
1489063 GTTTTCTTTG
* * * * *
1489073 TTTTCTTCTTGTTTTGGTTCTAATTTTTCTTAATTTCTCTCTTTTTTACTGTTTCATCTT
1 TTTTCTGCTTGTTTCGATTCTAATTTCTCTTAATTTCTCTCTCTTTTACTGTTTCATCTT
* ** ** **
1489133 TTTTCTGCTTGTTTCGATTTTGGTTTCTCTTGCTTTCTCTCTCTTTTGTTGTTTCATCTT
1 TTTTCTGCTTGTTTCGATTCTAATTTCTCTTAATTTCTCTCTCTTTTACTGTTTCATCTT
1489193 TTTTCT
1 TTTTCT
1489199 ATTTCAATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.06, C:0.18, G:0.10, T:0.66
Consensus pattern (60 bp):
TTTTCTGCTTGTTTCGATTCTAATTTCTCTTAATTTCTCTCTCTTTTACTGTTTCATCTT
Found at i:1489650 original size:14 final size:14
Alignment explanation
Indices: 1489614--1489654 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1489604 CTTTAGCTTT
1489614 AATGCATGAAA-GC
1 AATGCATGAAATGC
*
1489627 AATACAATGAAATGC
1 AATGC-ATGAAATGC
1489642 AATGCATGAAATG
1 AATGCATGAAATG
1489655 TTTTTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (14 bp):
AATGCATGAAATGC
Found at i:1489762 original size:25 final size:24
Alignment explanation
Indices: 1489734--1489827 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 24
1489724 ACATGAAACA
1489734 AAATGCATGACATGAACATTACGTG
1 AAATGCATGACATGAA-ATTACGTG
* * *
1489759 AAATACATG-CGTGAAATGTAATGTATG
1 AAATGCATGACATGAAAT-T-ACG--TG
*
1489786 AAATGCATGAAATGAAAATTACGTG
1 AAATGCATGACATG-AAATTACGTG
*
1489811 AAATGCATG-TATGAAAT
1 AAATGCATGACATGAAAT
1489828 GCATGAAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
23 6 0.11
24 9 0.16
25 21 0.38
27 12 0.22
28 3 0.05
29 4 0.07
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (24 bp):
AAATGCATGACATGAAATTACGTG
Found at i:1489787 original size:57 final size:52
Alignment explanation
Indices: 1489702--1489828 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 52
1489692 AAATATGAAA
* *
1489702 GAAA-ACATGCATGAAATGTAATACATGAAACAAAATGCATGACATGAACATTACGT
1 GAAATACATGCATGAAATGTAATACATG-----AAATGCATGAAATGAAAATTACGT
* **
1489758 GAAATACATGCGTGAAATGTAATGTATGAAATGCATGAAATGAAAATTACGT
1 GAAATACATGCATGAAATGTAATACATGAAATGCATGAAATGAAAATTACGT
* *
1489810 GAAATGCATGTATGAAATG
1 GAAATACATGCATGAAATG
1489829 CATGAAATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
52 38 0.61
56 4 0.06
57 20 0.32
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (52 bp):
GAAATACATGCATGAAATGTAATACATGAAATGCATGAAATGAAAATTACGT
Found at i:1489821 original size:38 final size:38
Alignment explanation
Indices: 1489768--1489909 Score: 176
Period size: 38 Copynumber: 3.6 Consensus size: 38
1489758 GAAATACATG
*
1489768 CGTGAAATGTAATGTATGAAATGCATGAAATGAAAATTA
1 CGTGAAATG-CATGTATGAAATGCATGAAATGAAAATTA
*
1489807 CGTGAAATGCATGTATGAAATGCATGAAATGAACATTA
1 CGTGAAATGCATGTATGAAATGCATGAAATGAAAATTA
* * *
1489845 CGTAAAATGCATGCATGAAATGTAATGCATGAAATGCAAATTA
1 CGTGAAATGCATG--T---ATGAAATGCATGAAATGAAAATTA
*
1489888 CGTGAAATGCATGCATGAAATG
1 CGTGAAATGCATGTATGAAATG
1489910 AAAATTACGT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
38 46 0.52
39 9 0.10
40 1 0.01
43 33 0.37
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (38 bp):
CGTGAAATGCATGTATGAAATGCATGAAATGAAAATTA
Found at i:1489873 original size:43 final size:42
Alignment explanation
Indices: 1489783--1489912 Score: 180
Period size: 43 Copynumber: 3.1 Consensus size: 42
1489773 AATGTAATGT
1489783 ATGAAATGCATGAAATGAAAATTACGTGAAATGCATG--T---
1 ATGAAATGCATGAAATG-AAATTACGTGAAATGCATGCATGAA
*
1489821 ATGAAATGCATGAAATGAACATTACGTAAAATGCATGCATGAA
1 ATGAAATGCATGAAATGAA-ATTACGTGAAATGCATGCATGAA
*
1489864 ATGTAATGCATGAAATGCAAATTACGTGAAATGCATGCATGAA
1 ATGAAATGCATGAAATG-AAATTACGTGAAATGCATGCATGAA
1489907 ATGAAA
1 ATGAAA
1489913 ATTACGTGAA
Statistics
Matches: 81, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
37 2 0.02
38 33 0.41
40 1 0.01
43 43 0.53
44 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGAAATGCATGAAATGAAATTACGTGAAATGCATGCATGAA
Found at i:1489895 original size:16 final size:16
Alignment explanation
Indices: 1489874--1489926 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1489864 ATGTAATGCA
1489874 TGAAATGCAAATTACG
1 TGAAATGCAAATTACG
* *
1489890 TGAAATGC--A-TGCA
1 TGAAATGCAAATTACG
*
1489903 TGAAATGAAAATTACG
1 TGAAATGCAAATTACG
1489919 TGAAATGC
1 TGAAATGC
1489927 TTGCATGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
13 9 0.32
14 1 0.04
15 1 0.04
16 17 0.61
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (16 bp):
TGAAATGCAAATTACG
Found at i:1489944 original size:81 final size:81
Alignment explanation
Indices: 1489736--1489945 Score: 203
Period size: 81 Copynumber: 2.6 Consensus size: 81
1489726 ATGAAACAAA
* * * *
1489736 ATGCATGACATGAACATTACGTGAAATACATGCGTGAAATGTAATG-TATGAAATGCATGAAATG
1 ATGCATGAAATGAACATTACGTGAAATACTTGCATGAAATGT-ATGAAATGAAATGCATGAAATG
1489800 AAAATTACGTGAAATGC
65 AAAATTACGTGAAATGC
* * ** *** * * *
1489817 ATGTATGAAATG--CATGAAATGAACATTACGTAAAATG-CATGCATGAAATGTAATGCATGAAA
1 ATGCATGAAATGAACATTACGTGAA-A-TAC-TTGCATGAAATGTATGAAATGAAATGCATGAAA
*
1489879 TGCAAATTACGTGAAATGC
63 TGAAAATTACGTGAAATGC
* *
1489898 ATGCATGAAATGAAAATTACGTGAAATGCTTGCATGAAATGTATGAAA
1 ATGCATGAAATGAACATTACGTGAAATACTTGCATGAAATGTATGAAA
1489946 ATATGCATGC
Statistics
Matches: 96, Mismatches: 26, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
79 8 0.08
80 8 0.08
81 70 0.73
82 3 0.03
83 7 0.07
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.26
Consensus pattern (81 bp):
ATGCATGAAATGAACATTACGTGAAATACTTGCATGAAATGTATGAAATGAAATGCATGAAATGA
AAATTACGTGAAATGC
Found at i:1489947 original size:33 final size:29
Alignment explanation
Indices: 1489860--1489938 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
1489850 AATGCATGCA
* *
1489860 TGAAATGTAATGCATGAAATGCAAATTACG
1 TGAAATG-CATGCATGAAATGAAAATTACG
1489890 TGAAATGCATGCATGAAATGAAAATTACG
1 TGAAATGCATGCATGAAATGAAAATTACG
*
1489919 TGAAATGCTTGCATGAAATG
1 TGAAATGCATGCATGAAATG
1489939 TATGAAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 39 0.85
30 7 0.15
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (29 bp):
TGAAATGCATGCATGAAATGAAAATTACG
Found at i:1490713 original size:42 final size:42
Alignment explanation
Indices: 1490659--1492039 Score: 714
Period size: 42 Copynumber: 32.7 Consensus size: 42
1490649 GGGTAAAAAG
* * * *
1490659 GTCTCCAAGGTCAAAGTCGACAGGTAGACTTTAGGTAAGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * * *
1490701 GTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGGTAAGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * * * * *
1490743 GTCTC-CAGTGTCAAAGCCAACAGACA-AATTGAGGGTAAGAAA
1 GTCTCTAAG-GTCAAAGCCGACAGGCAGACTTTA-GGTAAGGAA
* * *
1490785 GTCTCCATAA--TCAAAGCCGACAGGCAGACTTGAGGTAAAGCA
1 GTCT-C-TAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * * *
1490827 GTCTCTAAAGTCAAAGCCGATAGGCAGAC-TGAGGGT-GGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTA-GGTAAGG-AA
* * * * * *
1490869 GTCTCTAGGGTCAACGTCGATAGGCAGACTTTAGGTAAAGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * ** **
1490911 GTCTCCAAGGTCAAAGCCAACAGGCAGACTGAAGGGTAAAAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTA-GGTAAGGAA
* * *
1490954 ATCTCTAAGGTCAAAGCCGACACGCAGACTTGT-GGTGAGGCAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTT-TAGGTAAGG-AA
* * * ** *
1490997 -TCTCTAAGGTCAAAGTCGACAGGTAAACTGAAGGATAAGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGG-TAAGGAA
* * * * * *
1491039 ATCTCCAAGGTCAAAACCGACAGGCAGA-TTTGAAGTGAGGTA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTT-AGGTAAGGAA
** **
1491081 GTCTCTAAGGTCAAAATCGACAGGCAGACTGAAGGT-AGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGG-AA
* * * * * * * *
1491123 GTCTTTAGGGTTAAAGTCGATACGTAGACTTTAGGTGAA-GCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGT-AAGGAA
* **
1491165 GTCTCTAAGGTCAAAGCTGACAGGCAGACTGAAGGT-AGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGG-AA
* * * **
1491207 GTCTCTAAGGTCAAAGCTGACAGGTAGACTTTAGATAAGGCT
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* ** ** *
1491249 GTCTCT-AGAGTCAAAGCTGACAAACAGACTGAAGAGGTAAGAAA
1 GTCTCTAAG-GTCAAAGCCGACAGGCAGACT--TTAGGTAAGGAA
* * * * * * ** *
1491293 GTCTCCAGGGTCAAAGTCGATAGACAGACTTTAGATGGGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* ** * * *
1491335 GTCTCCAAGGTCAAAGATGATAGGCAGAC-TGAGG-ATAGAAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTA-AG-GAA
* * * * * ** *
1491377 GTCTCCAAGGTCAAAACCGATAAGCAGACTTTAGATGGGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* *
1491419 GTCTCTAGGGTCAAAGCCGACAGGCAGAC-TGAGGGT-AGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTA-GGTAAGG-AA
* * * * * * * *
1491461 GTTTCCAGGGTCAACGCCGACAGACAGACTTTAGATGAGGTA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * * * * *
1491503 GTCTCTAGGGTTAAAGCCGACAGGTAGACTTTAGATGAGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * **
1491545 GTCTCCAAGGTCAAAGCCGACAGGTAGACTGAAGGGTAAGGAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTA-GGTAAGGAA
* * * *
1491588 GTCTCCAAGGTCAAAGCCGACAGGTAGA-TTAAGGGTAAGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTA-GGTAAGGAA
* * **
1491630 GTCTCCAAGGTCAAAGCCGACAGGTAGACTGAAGG-ATAGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTA-AGG-AA
* * * * * * * *
1491673 GTCTCCAAAGTCAAAGCTGATAGGCAAACTTTAGATGAGGTA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* * * * **
1491715 GTCTCCAAGGTCAAAGCCAATAAGCAGACTGAAGGT-AGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGG-AA
* * *
1491757 GTCTCTAAGGTCAAAGCCAACAGACAGACTTTAGATGAA--ATA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGT-AAGGA-A
* * * * *
1491799 GTCTCCAAGGTCAAAGCTGACAAGCAGA-TTGAAGGGT-CGGAAA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTT-TA-GGTAAGG-AA
* ** * *
1491842 GTCT-TCAAGTTCAAAGCCAGA-AGGCAGACTGAAGAT-AGAAAA
1 GTCTCT-AAGGTCAAAGCC-GACAGGCAGACTTTAGGTAAG-GAA
* * * * * *
1491884 GTCTCCAAGGTCAATGTCGAGAGGCAGACTTTAGATAAGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
** * * *
1491926 GTCTCT-AGAGTCAAAGCCGACAGATAGACTCTGGGT-AGAAAA
1 GTCTCTAAG-GTCAAAGCCGACAGGCAGACTTTAGGTAAG-GAA
* * * *
1491968 GTCTCTAGGGTCAAAGCCGATAGGCAGACTTTAGATAAGGCA
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
* *
1492010 GTCTCTAGGGTCAAAGTCGACAGGCAGACT
1 GTCTCTAAGGTCAAAGCCGACAGGCAGACT
1492040 GAGAGTAAAA
Statistics
Matches: 1022, Mismatches: 254, Indels: 126
0.73 0.18 0.09
Matches are distributed among these distances:
40 4 0.00
41 37 0.04
42 761 0.74
43 184 0.18
44 34 0.03
45 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (42 bp):
GTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGGTAAGGAA
Found at i:1490788 original size:84 final size:83
Alignment explanation
Indices: 1490659--1492047 Score: 841
Period size: 84 Copynumber: 16.4 Consensus size: 83
1490649 GGGTAAAAAG
* * * ** * * *
1490659 GTCTCCAAGGTCAAAGTCGACAGGTAGACTTTA-GGTAAGGCAGTCTCTAGGGTCAAAGCCGATA
1 GTCTCC-AGGTCAAAGCCGACAGGCAGAC-TGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACA
*
1490723 GGTAGACTTTAGGTAAGGCA
64 GGCAGACTTTAGGTAAGGCA
* * * * *
1490743 GTCTCCAGTGTCAAAGCCAACAGACAAATTGAGGGTAAGAAAGTCTCCATA-ATCAAAGCCGACA
1 GTCTCCAG-GTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCA-AGGTCAAAGCCGACA
* *
1490807 GGCAGACTTGAGGTAAAGCA
64 GGCAGACTTTAGGTAAGGCA
* * * ** * * * * *
1490827 GTCTCTAAAGTCAAAGCCGATAGGCAGACTGAGGGTGGGAAAGTCTCTAGGGTCAACGTCGATAG
1 GTCTC-CAGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
*
1490892 GCAGACTTTAGGTAAAGCA
65 GCAGACTTTAGGTAAGGCA
* * * *
1490911 GTCTCCAAGGTCAAAGCCAACAGGCAGACTGAAGGGTAAAAAAATCTCTAAGGTCAAAGCCGACA
1 GTCTCC-AGGTCAAAGCCGACAGGCAGACTG-AGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACA
* *
1490976 CGCAGACTTGT-GGTGAGGCA
64 GGCAGACTT-TAGGTAAGGCA
* * * * * * * *
1490996 ATCTCTAAGGTCAAAGTCGACAGGTAAACTGAAGGATAAGAAAATCTCCAAGGTCAAAACCGACA
1 GTCTC-CAGGTCAAAGCCGACAGGCAGACTG-AGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACA
* * *
1491061 GGCAGA-TTTGAAGTGAGGTA
64 GGCAGACTTT-AGGTAAGGCA
* ** * * ** * * * * *
1491081 GTCTCTAAGGTCAAAATCGACAGGCAGACTGAAGGTAGGAAAGTCTTTAGGGTTAAAGTCGATAC
1 GTCTC-CAGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
*
1491146 GTAGACTTTAGGTGAA-GCA
65 GCAGACTTTAGGT-AAGGCA
* * * * * *
1491165 GTCTCTAAGGTCAAAGCTGACAGGCAGACTGAAGGTAGGAAAGTCTCTAAGGTCAAAGCTGACAG
1 GTCTC-CAGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
* * *
1491230 GTAGACTTTAGATAAGGCT
65 GCAGACTTTAGGTAAGGCA
* * ** * * *
1491249 GTCTCTAGAGTCAAAGCTGACAAACAGACTGAAGAGGTAAGAAAGTCTCCAGGGTCAAAGTCGAT
1 GTCTCCAG-GTCAAAGCCGACAGGCAGACTG-AG-GGTAAGAAAGTCTCCAAGGTCAAAGCCGAC
* * **
1491314 AGACAGACTTTAGATGGGGCA
63 AGGCAGACTTTAGGTAAGGCA
** * * * *
1491335 GTCTCCAAGGTCAAAGATGATAGGCAGACTGAGGAT-AGAAAAGTCTCCAAGGTCAAAACCGATA
1 GTCTCC-AGGTCAAAGCCGACAGGCAGACTGAGGGTAAG-AAAGTCTCCAAGGTCAAAGCCGACA
* * **
1491399 AGCAGACTTTAGATGGGGCA
64 GGCAGACTTTAGGTAAGGCA
* * * * *
1491419 GTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAGTTTCCAGGGTCAACGCCGACAG
1 GTCTCCA-GGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
* * * *
1491484 ACAGACTTTAGATGAGGTA
65 GCAGACTTTAGGTAAGGCA
* * * * * * **
1491503 GTCTCTAGGGTTAAAGCCGACAGGTAGACTTTA-GATGAGGCAGTCTCCAAGGTCAAAGCCGACA
1 GTCTCCA-GGTCAAAGCCGACAGGCAGAC-TGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACA
* ** *
1491567 GGTAGACTGAAGGGTAAGGAA
64 GGCAGACTTTA-GGTAAGGCA
* * *
1491588 GTCTCCAAGGTCAAAGCCGACAGGTAGATTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
1 GTCTCC-AGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
* ** *
1491653 GTAGACTGAAGG-ATAGGAAA
65 GCAGACTTTAGGTA-AGG-CA
* * * * * * * ** * *
1491673 GTCTCCAAAGTCAAAGCTGATAGGCAAACTTTA-GATGAGGTAGTCTCCAAGGTCAAAGCCAATA
1 GTCTCC-AGGTCAAAGCCGACAGGCAGAC-TGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACA
* ** *
1491737 AGCAGACTGAAGGT-AGGAAA
64 GGCAGACTTTAGGTAAGG-CA
* * * * * * *
1491757 GTCTCTAAGGTCAAAGCCAACAGACAGACTTTA-GATGAA-ATAGTCTCCAAGGTCAAAGCTGAC
1 GTCTC-CAGGTCAAAGCCGACAGGCAGAC-TGAGGGT-AAGAAAGTCTCCAAGGTCAAAGCCGAC
* * * *
1491820 AAGCAGA-TTGAAGGGT-CGGAAA
63 AGGCAGACTT-TA-GGTAAGG-CA
* * * * * * *
1491842 GTCTTCAAGTTCAAAGCCAGA-AGGCAGACTGAAGAT-AGAAAAGTCTCCAAGGTCAATGTCGAG
1 GTC-TCCAGGTCAAAGCC-GACAGGCAGACTGAGGGTAAG-AAAGTCTCCAAGGTCAAAGCCGAC
*
1491905 AGGCAGACTTTAGATAAGGCA
63 AGGCAGACTTTAGGTAAGGCA
* ** ** * * *
1491926 GTCTCTAGAGTCAAAGCCGACAGATAGACTCTGGGT-AGAAAAGTCTCTAGGGTCAAAGCCGATA
1 GTCTCCAG-GTCAAAGCCGACAGGCAGACTGAGGGTAAG-AAAGTCTCCAAGGTCAAAGCCGACA
*
1491990 GGCAGACTTTAGATAAGGCA
64 GGCAGACTTTAGGTAAGGCA
* * *
1492010 GTCTCTAGGGTCAAAGTCGACAGGCAGACTGAGAGTAA
1 GTCTCCA-GGTCAAAGCCGACAGGCAGACTGAGGGTAA
1492048 AAAATTTCAT
Statistics
Matches: 1040, Mismatches: 221, Indels: 87
0.77 0.16 0.06
Matches are distributed among these distances:
83 21 0.02
84 609 0.59
85 336 0.32
86 72 0.07
87 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (83 bp):
GTCTCCAGGTCAAAGCCGACAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGG
CAGACTTTAGGTAAGGCA
Found at i:1490828 original size:126 final size:127
Alignment explanation
Indices: 1490573--1490856 Score: 333
Period size: 126 Copynumber: 2.2 Consensus size: 127
1490563 AAAGTGAACA
* * *
1490573 AGTCTCCAGGGTCAAAGCC-ATCAGGCAAACTTAAGATGAGGCAGTCTCCAAAGTCAAAGCAAAC
1 AGTCTCTAGGGTCAAAGCCGAT-AGGCAGACTTAAGATAAGGCAGTCTCCAAAGTCAAAGCAAAC
** * * * * * *
1490637 AGGTAGACTGAAGGGTAAAAAGGTCTCCAAGGTCAAAGTCGACAGGTAGACTTTAGGTAAGGC
65 AGACAAACTGAAGGGTAAAAAGGTCTCCAAGATCAAAGCCGACAGGCAGACTTGAGGTAAAGC
* * * ** *
1490700 AGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGGTAAGGCAGTCTCCAGTGTCAAAGCCAACA
1 AGTCTCTAGGGTCAAAGCCGATAGGCAGACTTAAGATAAGGCAGTCTCCAAAGTCAAAGCAAACA
*
1490765 GACAAATTG-AGGGTAAGAAA-GTCTCCATA-ATCAAAGCCGACAGGCAGACTTGAGGTAAAGC
66 GACAAACTGAAGGGTAA-AAAGGTCTCCA-AGATCAAAGCCGACAGGCAGACTTGAGGTAAAGC
**
1490826 AGTCTCTAAAGTCAAAGCCGATAGGCAGACT
1 AGTCTCTAGGGTCAAAGCCGATAGGCAGACT
1490857 GAGGGTGGGA
Statistics
Matches: 133, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
126 69 0.52
127 62 0.47
128 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (127 bp):
AGTCTCTAGGGTCAAAGCCGATAGGCAGACTTAAGATAAGGCAGTCTCCAAAGTCAAAGCAAACA
GACAAACTGAAGGGTAAAAAGGTCTCCAAGATCAAAGCCGACAGGCAGACTTGAGGTAAAGC
Found at i:1491088 original size:254 final size:255
Alignment explanation
Indices: 1490702--1492025 Score: 764
Period size: 254 Copynumber: 5.2 Consensus size: 255
1490692 GGTAAGGCAG
* * * * * * * * ** *
1490702 TCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGGTAAGGCAGTCTCCAGTGTCAAAGCCAACAGA
1 TCTCTAAGGTCAAAGCCGACACGCAGACTTTAGATAAGGCAATCTCTAGAGTCAAAGCTGACAAA
* * * * * * *
1490767 CAAATTG-AG-GGTAAGAAAGTCTCCATA-ATCAAAGCCGACAGGCAGACTTGAGGTAAAGCAGT
66 CAAACTGAAGAGATAAGAAAGTCTCCA-AGGTCAAAGCCGACAGGCAGATTTGAAGTGAGGCAGT
* * * * *
1490829 CTCTAAAGTCAAAGCCGATAGGCAGACTGAGGGTGGGAAAGTCTCTAGGGTCAACGTCGATAGGC
130 CTCTAAGGTCAAAGACGATAGGCAGACTGAGGGTAGGAAAGTCTCTAGGGTCAAAGTCGATAAGC
* * *
1490894 AGACTTTAGGTAAAGCAGTCTCCAAGGTCAAAGCCAACAGGCAGACTGAAGGGTAAAAAAA
195 AGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAAAAAA
* *
1490955 TCTCTAAGGTCAAAGCCGACACGCAGACTTGT-GGTGAGGCAATCTCTA-AGGTCAAAG-TCGAC
1 TCTCTAAGGTCAAAGCCGACACGCAGACTT-TAGATAAGGCAATCTCTAGA-GTCAAAGCT-GAC
*** * * *
1491017 AGGTAAACTGAAG-GATAAGAAAATCTCCAAGGTCAAAACCGACAGGCAGATTTGAAGTGAGGTA
63 AAACAAACTGAAGAGATAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGATTTGAAGTGAGGCA
* * * *
1491081 GTCTCTAAGGTCAAA-ATCGACAGGCAGACTGAAGGTAGGAAAGTCTTTAGGGTTAAAGTCGATA
128 GTCTCTAAGGTCAAAGA-CGATAGGCAGACTGAGGGTAGGAAAGTCTCTAGGGTCAAAGTCGATA
* * * ** *
1491145 CGTAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCTGACAGGCAGACTGAA-GGTAGGAAAG
192 AGCAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAAAAAA
* * * **
1491208 TCTCTAAGGTCAAAGCTGACAGGTAGACTTTAGATAAGGCTGTCTCTAGAGTCAAAGCTGACAAA
1 TCTCTAAGGTCAAAGCCGACACGCAGACTTTAGATAAGGCAATCTCTAGAGTCAAAGCTGACAAA
* * * * * * *
1491273 CAGACTGAAGAGGTAAGAAAGTCTCCAGGGTCAAAGTCGATAGACAGACTTT--AGATGGGGCAG
66 CAAACTGAAGAGATAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGA-TTTGAAG-TGAGGCAG
* * * * * * **
1491336 TCTCCAAGGTCAAAGATGATAGGCAGACTGAGGATAGAAAAGTCTCCAAGGTCAAAACCGATAAG
129 TCTCTAAGGTCAAAGACGATAGGCAGACTGAGGGTAGGAAAGTCTCTAGGGTCAAAGTCGATAAG
* ** * ** *
1491401 CAGACTTTAGATGGGGCAGTCTCTAGGGTCAAAGCCGACAGGCAGACTG-AGGGTAGGAAAG
194 CAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAAAAAA
* * * * * * * * * * *
1491462 TTTCCAGGGTCAACGCCGACA-GACAGACTTTAGATGAGGTAGTCTCTAGGGTTAAAGCCGACAG
1 TCTCTAAGGTCAAAGCCGACACG-CAGACTTTAGATAAGGCAATCTCTAGAGTCAAAGCTGACAA
** * ** * ** * * * *
1491526 GTAGACT--TTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGTAGA-CTGAAGGGTAAGGAA
65 ACAAACTGAAGAGATAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGATTTGAA--GTGAGGCA
* * * * * * * * * * * *
1491588 GTCTCCAAGGTCAAAGCCGACAGGTAGATTAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAG
128 GTCTCTAAGGTCAAAGACGATAGGCAGACTGAGGGTAGGAAAGTCTCTAGGGTCAAAGTCGATAA
* ** * * * * * ** * * ***
1491653 GTAGACTGAAGGATAGGAA--AGTCTCCAAAGTCAAAGCTGATAGGCAAACTTTA-GATGAGGTA
193 GCAGACTTTAGG-T--GAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAAAAA
*
1491715 G
255 A
* * * * ** * * **
1491716 TCTCCAAGGTCAAAGCCAATAAGCAGACTGAAGGT-AGGAAAGTCTCTA-AGGTCAAAGCCAACA
1 TCTCTAAGGTCAAAGCCGACACGCAGACTTTAGATAAGGCAA-TCTCTAGA-GTCAAAGCTGACA
* * ** * * * * *
1491779 GACAGACT--TTAGATGAA-ATAGTCTCCAAGGTCAAAGCTGACAAGCAGA-TTGAAGGGTCGGA
64 AACAAACTGAAGAGAT-AAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGATTTGAAGTG-AGG-
* * * * * * * * *
1491840 AAGTCT-TCAAGTTCAAAGCCAGA-AGGCAGACTGAAGATAGAAAAGTCTCCAAGGTCAATGTCG
126 CAGTCTCT-AAGGTCAAAGAC-GATAGGCAGACTGAGGGTAGGAAAGTCTCTAGGGTCAAAGTCG
* * * ** ** *
1491903 AGAGGCAGACTTTAGAT-AAGGCAGTCTCT-AGAGTCAAAGCCGACAGATAGACT-CTGGGTAGA
189 ATAAGCAGACTTTAGGTGAA-GCAGTCTCTAAG-GTCAAAGCCGACAGGCAGACTGAAGGGTAAA
*
1491965 AAAG
252 AAAA
* * * * *
1491969 TCTCTAGGGTCAAAGCCGATAGGCAGACTTTAGATAAGGCAGTCTCTAGGGTCAAAG
1 TCTCTAAGGTCAAAGCCGACACGCAGACTTTAGATAAGGCAATCTCTAGAGTCAAAG
1492026 TCGACAGGCA
Statistics
Matches: 829, Mismatches: 204, Indels: 76
0.75 0.18 0.07
Matches are distributed among these distances:
250 3 0.00
252 33 0.04
253 264 0.32
254 519 0.63
255 9 0.01
256 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (255 bp):
TCTCTAAGGTCAAAGCCGACACGCAGACTTTAGATAAGGCAATCTCTAGAGTCAAAGCTGACAAA
CAAACTGAAGAGATAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGATTTGAAGTGAGGCAGTC
TCTAAGGTCAAAGACGATAGGCAGACTGAGGGTAGGAAAGTCTCTAGGGTCAAAGTCGATAAGCA
GACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGAAGGGTAAAAAAA
Found at i:1491678 original size:338 final size:340
Alignment explanation
Indices: 1490615--1492035 Score: 1019
Period size: 338 Copynumber: 4.2 Consensus size: 340
1490605 AAGATGAGGC
* ** * * *
1490615 AGTCTCCAAAGTCAAAGCAAACAGGTAGACTGAAGGGTA-AAAAGGTCTCCAAGGTCAAAGTCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAA-GTCTCCAAGGTCAAAGTCGA
* * * ** * * * * * *
1490679 CAGGTAGACTTTAGG-TA-AGGCAGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGGTAAGGC
65 CAGGCAAACTTGAGGATAGAGAAAGTCTCCAAGGTCAAAACCGATAAGCAGACTTTAGATAAGGC
* * * * * ***
1490742 AGTCTC-CAGTGTCAAAGCCAACAGACAAATTGAGGGTAAGAAAGTCTCCATAATCAAAGCCGAC
130 AGTCTCTAAG-GTCAAAGCCAACAGACAGACTGAGGGTAGGAAAGTTTCCAGGGTCAAAGCCGAC
* * * * * *
1490806 AGGCAGACTTGAGGTAAAGCAGTCTCTAAAGTCAAAGCCGATAGGCAGACTGAGGGTG-GGAAAG
194 A-GCAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTAAGGTGAGGAAAG
* * * * * * *
1490870 TCTCTAGGGTCAACGTCGATAGGCAGACTTTAGGTAAAGCAGTCTCCAAGGTCAAAGCCAACAGG
258 TCTCTAAGGTCAAAGCCGACAGGTAGACTTTAGGTAAGGCAGTCTCCAAGGTCAAAGCCGACAGG
*
1490935 CAGACTGAAGGGTAAAAA
323 CAGACTGAAGGGTAAGAA
* * * * * *
1490953 AATCTCTAAGGTCAAAGCCGACACGCAGACTTG-TGG-TGAGGCAA-TCTCTAAGGTCAAAGTCG
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGAT-AGGAAAGTCTCCAAGGTCAAAGTCG
* * * * *
1491015 ACAGGTAAAC-TGAAGGATA-AGAAAATCTCCAAGGTCAAAACCGACAGGCAGA-TTT-GAAGTG
64 ACAGGCAAACTTG-AGGATAGAGAAAGTCTCCAAGGTCAAAACCGATAAGCAGACTTTAG-A-TA
* ** * * * * * *
1491076 AGGTAGTCTCTAAGGTCAAAATCGACAGGCAGACTGAAGGTAGGAAAGTCTT-TAGGGTTAAAGT
126 AGGCAGTCTCTAAGGTCAAAGCCAACAGACAGACTGAGGGTAGGAAAGT-TTCCAGGGTCAAAGC
* * * *
1491140 CGATACGTAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCTGACAGGCAGACTGAAGGT-AGG
190 CGACA-GCAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTAAGGTGAGG
* * * * *
1491204 AAAGTCTCTAAGGTCAAAGCTGACAGGTAGACTTTAGATAAGGCTGTCT-CTAGAGTCAAAGCTG
254 AAAGTCTCTAAGGTCAAAGCCGACAGGTAGACTTTAGGTAAGGCAGTCTCCAAG-GTCAAAGCCG
**
1491268 ACAAACAGACTGAAGAGGTAAGAA
318 ACAGGCAGACTGAAG-GGTAAGAA
* * * * ** * **
1491292 AGTCTCCAGGGTCAAAGTCGATAGACAGACTTTA-GATGGGGCAGTCTCCAAGGTCAAAGAT-GA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAAGGTCAAAG-TCGA
* * **
1491355 TAGGCAGAC-TGAGGATAGA-AAAGTCTCCAAGGTCAAAACCGATAAGCAGACTTTAGATGGGGC
65 CAGGCAAACTTGAGGATAGAGAAAGTCTCCAAGGTCAAAACCGATAAGCAGACTTTAGATAAGGC
* * * *
1491418 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAAGTTTCCAGGGTCAACGCCGACA
130 AGTCTCTAAGGTCAAAGCCAACAGACAGACTGAGGGTAGGAAAGTTTCCAGGGTCAAAGCCGACA
* * * * * * * * *
1491483 GACAGACTTTAGATGAGGTAGTCTCTAGGGTTAAAGCCGACAGGTAGACTTTAGATGAGG-CAGT
195 G-CAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTAAGGTGAGGAAAGT
* ** *
1491547 CTCCAAGGTCAAAGCCGACAGGTAGACTGAAGGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGG
259 CTCTAAGGTCAAAGCCGACAGGTAGACTTTA-GGTAAGGCAGTCTCCAAGGTCAAAGCCGACAGG
* *
1491612 TAGA-TTAAGGGTAAGAA
323 CAGACTGAAGGGTAAGAA
* *
1491629 AGTCTCCAAGGTCAAAGCCGACAGGTAGACTGAAGGATAGGAAAGTCTCCAAAGTCAAAG-CTGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAAGGTCAAAGTC-GA
* * ** * * ** *
1491693 TAGGCAAACTTTA-GAT-GAGGTAGTCTCCAAGGTCAAAGCCAATAAGCAGACTGAAGGT-AGGA
65 CAGGCAAACTTGAGGATAGAGAAAGTCTCCAAGGTCAAAACCGATAAGCAGACTTTAGATAAGG-
* * * * * * *
1491755 AAGTCTCTAAGGTCAAAGCCAACAGACAGACTTTA-GAT-GAAATAGTCTCCAAGGTCAAAGCTG
129 CAGTCTCTAAGGTCAAAGCCAACAGACAGAC-TGAGGGTAGGAA-AGTTTCCAGGGTCAAAGCCG
* * * *
1491818 ACAAGCAGA-TTGAAGGGTCGGAA--AGTCT-TCAAGTTCAAAGCCAGA-AGGCAGACTGAAGAT
192 AC-AGCAGACTT-TA-GGT--GAAGCAGTCTCT-AAGGTCAAAGCC-GACAGGCAGACTTAAGGT
* * * * * * * *
1491878 -AGAAAAGTCTCCAAGGTCAATGTCGAGAGGCAGACTTTAGATAAGGCAGTCT-CTAGAGTCAAA
250 GAGGAAAGTCTCTAAGGTCAAAGCCGACAGGTAGACTTTAGGTAAGGCAGTCTCCAAG-GTCAAA
** **
1491941 GCCGACAGATAGACT-CTGGGT-AGAAA
314 GCCGACAGGCAGACTGAAGGGTAAG-AA
* * * ** * * *
1491967 AGTCTCTAGGGTCAAAGCCGATAGGCAGACTTTA-GATAAGG-CAGTCTCTAGGGTCAAAGTCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGGAAAGTCTCCAAGGTCAAAGTCGA
1492030 CAGGCA
65 CAGGCA
1492036 GACTGAGAGT
Statistics
Matches: 853, Mismatches: 185, Indels: 91
0.76 0.16 0.08
Matches are distributed among these distances:
336 2 0.00
337 112 0.13
338 572 0.67
339 158 0.19
340 7 0.01
341 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (340 bp):
AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCAAGGTCAAAGTCGAC
AGGCAAACTTGAGGATAGAGAAAGTCTCCAAGGTCAAAACCGATAAGCAGACTTTAGATAAGGCA
GTCTCTAAGGTCAAAGCCAACAGACAGACTGAGGGTAGGAAAGTTTCCAGGGTCAAAGCCGACAG
CAGACTTTAGGTGAAGCAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTAAGGTGAGGAAAGTCT
CTAAGGTCAAAGCCGACAGGTAGACTTTAGGTAAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAG
ACTGAAGGGTAAGAA
Found at i:1494475 original size:20 final size:19
Alignment explanation
Indices: 1494429--1494479 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1494419 GTTTGGGATA
1494429 ATGTATCGATATAATTCTTC
1 ATGTATCGATATAATTC-TC
*
1494449 ATCTATCGATATAATGTGC-C
1 ATGTATCGATATAAT-T-CTC
1494469 ATGTATCGATA
1 ATGTATCGATA
1494480 CAAACAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 25 0.93
21 1 0.04
22 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
ATGTATCGATATAATTCTC
Found at i:1494593 original size:33 final size:32
Alignment explanation
Indices: 1494532--1494596 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1494522 ACAATTGTGT
*
1494532 ATGTATCGATACAATAATCATGTATCGATACA
1 ATGTATCGATACAATAATAATGTATCGATACA
* *
1494564 ATGTATGGATACAAATCATAATGTATCGATACA
1 ATGTATCGATAC-AATAATAATGTATCGATACA
1494597 TCTGGTTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAATAATAATGTATCGATACA
Found at i:1494755 original size:21 final size:21
Alignment explanation
Indices: 1494707--1494761 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1494697 TTTTTACTTA
*
1494707 AAAACATTTGATTTAAAGCTCG
1 AAAACATTT-ATTCAAAGCTCG
*
1494729 AAAACATTTATTCATAA-CTCT
1 AAAACATTTATTCA-AAGCTCG
1494750 AAAACATTTATT
1 AAAACATTTATT
1494762 GTCATCGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAACATTTATTCAAAGCTCG
Found at i:1497113 original size:13 final size:13
Alignment explanation
Indices: 1497095--1497119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1497085 TAGTAACTCA
1497095 TGTATCGATACAT
1 TGTATCGATACAT
1497108 TGTATCGATACA
1 TGTATCGATACA
1497120 AAAAACATTG
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:1503267 original size:13 final size:13
Alignment explanation
Indices: 1503249--1503273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1503239 TAATTCTTCA
1503249 TGTATCGATACAT
1 TGTATCGATACAT
1503262 TGTATCGATACA
1 TGTATCGATACA
1503274 ATATTCTATG
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:1503293 original size:33 final size:33
Alignment explanation
Indices: 1503229--1503293 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
1503219 TTTGGGACAA
* * *
1503229 TGTATCGATATAATTCTTCATGTATCGATACAT
1 TGTATCGATACAATTATTCATGTATCAATACAT
*
1503262 TGTATCGATACAA-TATTCTATGTATTAATACA
1 TGTATCGATACAATTATTC-ATGTATCAATACA
1503294 AACAGTGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATTATTCATGTATCAATACAT
Found at i:1508387 original size:13 final size:13
Alignment explanation
Indices: 1508369--1508394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1508359 AATCTTTCTA
1508369 AATTTTTAATTTT
1 AATTTTTAATTTT
1508382 AATTTTTAATTTT
1 AATTTTTAATTTT
1508395 GAAAATTCTG
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTTAATTTT
Found at i:1509391 original size:19 final size:20
Alignment explanation
Indices: 1509369--1509407 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1509359 TCTTGCTTTC
1509369 TCTTTCTTT-TGC-TGTTTTG
1 TCTTT-TTTCTGCTTGTTTTG
1509388 TCTTTTTTCTGCTTGTTTTG
1 TCTTTTTTCTGCTTGTTTTG
1509408 GTTATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 8 0.44
20 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (20 bp):
TCTTTTTTCTGCTTGTTTTG
Found at i:1509886 original size:10 final size:10
Alignment explanation
Indices: 1509871--1509903 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1509861 GCATGAAAGC
1509871 AATGCAATGA
1 AATGCAATGA
*
1509881 AATGCAATGC
1 AATGCAATGA
1509891 AATGC-ATGA
1 AATGCAATGA
1509900 AATG
1 AATG
1509904 AATTCATGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (10 bp):
AATGCAATGA
Found at i:1509889 original size:15 final size:14
Alignment explanation
Indices: 1509858--1509894 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1509848 CCGCAGCTTT
1509858 AATGC-ATGAAAGC
1 AATGCAATGAAAGC
1509871 AATGCAATGAAATGC
1 AATGCAATGAAA-GC
1509886 AATGCAATG
1 AATGCAATG
1509895 CATGAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (14 bp):
AATGCAATGAAAGC
Found at i:1509992 original size:25 final size:24
Alignment explanation
Indices: 1509958--1510044 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 24
1509948 TGCATGAAAC
1509958 GAAATGCATGAAATGAACATTACGT
1 GAAATGCATGAAATGAA-ATTACGT
* *
1509983 GAAATGCATG-CATGAAATGTAAGGTAT
1 GAAATGCATGAAATGAAAT-T-ACG--T
*
1510010 GAAATGCATGAAATGAAAATTATGT
1 GAAATGCATGAAATG-AAATTACGT
*
1510035 GAAACGCATG
1 GAAATGCATG
1510045 CATGTAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
23 2 0.04
24 6 0.12
25 22 0.43
27 13 0.25
28 4 0.08
29 4 0.08
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (24 bp):
GAAATGCATGAAATGAAATTACGT
Found at i:1509995 original size:43 final size:43
Alignment explanation
Indices: 1509938--1510191 Score: 223
Period size: 43 Copynumber: 5.8 Consensus size: 43
1509928 AAAACATGCA
* * *
1509938 TGAAATGTAATGCATGAAACGAAATGCATGAAATGAACATTACG
1 TGAAATG-CATGCATGAAATGAAATGCATGAAATGAAAATTACG
*
1509982 TGAAATGCATGCATGAAATGTAAGGTATGAAATGCATGAAATGAAAATTATG
1 TGAAATGCATGC-----ATG-AA---ATGAAATGCATGAAATGAAAATTACG
* * * * * *
1510034 TGAAACGCATGCATGTAATGTAATGCATAAAATGAAACTTATG
1 TGAAATGCATGCATGAAATGAAATGCATGAAATGAAAATTACG
* * * *
1510077 T-AAA---ATGCATG-CATGAAATGCATGAAATTAACATTACA
1 TGAAATGCATGCATGAAATGAAATGCATGAAATGAAAATTACG
*
1510115 TAAAATGCATGCATGAAAT-ATAATGCATGAAATGAAAATTACG
1 TGAAATGCATGCATGAAATGA-AATGCATGAAATGAAAATTACG
*
1510158 TGAAATGCATGCATGAAATGTAATGCATGAAATG
1 TGAAATGCATGCATGAAATGAAATGCATGAAATG
1510192 TATGAAAATA
Statistics
Matches: 171, Mismatches: 23, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
38 20 0.12
39 10 0.06
42 11 0.06
43 80 0.47
44 7 0.04
46 1 0.01
47 3 0.02
48 3 0.02
49 2 0.01
52 34 0.20
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (43 bp):
TGAAATGCATGCATGAAATGAAATGCATGAAATGAAAATTACG
Found at i:1510046 original size:29 final size:28
Alignment explanation
Indices: 1509952--1510053 Score: 79
Period size: 29 Copynumber: 3.7 Consensus size: 28
1509942 ATGTAATGCA
* *
1509952 TGAAACGAAATGCATGAAATGAACATTACG
1 TGAAACG-CATGCATGAAATGAAAATTA-G
* * **
1509982 TGAAATGCATGCATGAAATGTAAGGTA-
1 TGAAACGCATGCATGAAATGAAAATTAG
1510009 TG-AA---ATGCATGAAATGAAAATTATG
1 TGAAACGCATGCATGAAATGAAAATTA-G
*
1510034 TGAAACGCATGCATGTAATG
1 TGAAACGCATGCATGAAATG
1510054 TAATGCATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
23 16 0.29
25 2 0.04
26 4 0.07
27 2 0.04
29 26 0.46
30 6 0.11
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (28 bp):
TGAAACGCATGCATGAAATGAAAATTAG
Found at i:1510067 original size:52 final size:52
Alignment explanation
Indices: 1509932--1510067 Score: 164
Period size: 52 Copynumber: 2.5 Consensus size: 52
1509922 TGAAAGAAAA
* *
1509932 CATGCATGAAATGTAATGCATGAAACGAAATGCATGAAATGAACATTACGTGAAATG
1 CATGCATGAAATGTAATGCAT---A--AAATGCATGAAATGAAAATTACGTGAAACG
* * * *
1509989 CATGCATGAAATGTAAGGTATGAAATGCATGAAATGAAAATTATGTGAAACG
1 CATGCATGAAATGTAATGCATAAAATGCATGAAATGAAAATTACGTGAAACG
*
1510041 CATGCATGTAATGTAATGCATAAAATG
1 CATGCATGAAATGTAATGCATAAAATG
1510068 AAACTTATGT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
52 50 0.72
57 19 0.28
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.25
Consensus pattern (52 bp):
CATGCATGAAATGTAATGCATAAAATGCATGAAATGAAAATTACGTGAAACG
Found at i:1510093 original size:81 final size:81
Alignment explanation
Indices: 1510008--1510177 Score: 232
Period size: 81 Copynumber: 2.1 Consensus size: 81
1509998 AATGTAAGGT
** * * * *
1510008 ATGAAATGCATGAAATGAAAATTATGTGAAACGCATGCATGTAATGTAATGCATAAAATGAAACT
1 ATGAAATGCATGAAATGAAAATTACATAAAACGCATGCATGAAATATAATGCATAAAATGAAAAT
*
1510073 TATGTAAAATGCATGC
66 TACGTAAAATGCATGC
* * * *
1510089 ATGAAATGCATGAAATTAACATTACATAAAATGCATGCATGAAATATAATGCATGAAATGAAAAT
1 ATGAAATGCATGAAATGAAAATTACATAAAACGCATGCATGAAATATAATGCATAAAATGAAAAT
*
1510154 TACGTGAAATGCATGC
66 TACGTAAAATGCATGC
1510170 ATGAAATG
1 ATGAAATG
1510178 TAATGCATGA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (81 bp):
ATGAAATGCATGAAATGAAAATTACATAAAACGCATGCATGAAATATAATGCATAAAATGAAAAT
TACGTAAAATGCATGC
Found at i:1510141 original size:18 final size:18
Alignment explanation
Indices: 1510118--1510186 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 18
1510108 CATTACATAA
1510118 AATGCATGCATGAAATAT
1 AATGCATGCATGAAATAT
*
1510136 AATGCATGAAATGAAAATTACGT
1 AATGCATG-CATG-AAA-TA--T
*
1510159 GAAATGCATGCATGAAATGT
1 --AATGCATGCATGAAATAT
1510179 AATGCATG
1 AATGCATG
1510187 AAATGTATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
18 16 0.39
19 3 0.07
20 4 0.10
21 2 0.05
22 1 0.02
23 4 0.10
24 3 0.07
25 8 0.20
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.26
Consensus pattern (18 bp):
AATGCATGCATGAAATAT
Found at i:1511807 original size:134 final size:133
Alignment explanation
Indices: 1511585--1511849 Score: 458
Period size: 134 Copynumber: 2.0 Consensus size: 133
1511575 TCATACTAAA
* *
1511585 TATGAGAGGCATTAAGGCCAAGGAAATATGTTAGACCTTTTAAAAAGTTAAATAATCTTGGCACT
1 TATGAGAAGCATTAAGGCCAAGGAAATATATTAGACCTTTTAAAAAGTTAAATAATCTTGGCACT
* *
1511650 TGAACTGATGGTTGGCAAAAAACTATTTTGCTTAACCTCAAACTTTGTAAGAGGTATATTTTTGT
66 TGAACTGATGGTTAGCAAAAAACTATTTTGCTTAACCTCAAACTTTGTAAGAGGCATATTTTTGT
1511715 TGC
131 TGC
* *
1511718 TATGAGAAGCATTGAGGCCAAGGAAATACTATTAGACCTTTTAAAAAGTTAAATACTCTTGGCAC
1 TATGAGAAGCATTAAGGCCAAGGAAATA-TATTAGACCTTTTAAAAAGTTAAATAATCTTGGCAC
*
1511783 TTGAACTGATGGTTAGCAAAAAACTGTTTTGCTTAACCTCAAACTTTGTAAGAGGCATATTTTTG
65 TTGAACTGATGGTTAGCAAAAAACTATTTTGCTTAACCTCAAACTTTGTAAGAGGCATATTTTTG
1511848 TT
130 TT
1511850 ACTCATTAGC
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
133 26 0.21
134 98 0.79
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (133 bp):
TATGAGAAGCATTAAGGCCAAGGAAATATATTAGACCTTTTAAAAAGTTAAATAATCTTGGCACT
TGAACTGATGGTTAGCAAAAAACTATTTTGCTTAACCTCAAACTTTGTAAGAGGCATATTTTTGT
TGC
Found at i:1512796 original size:22 final size:20
Alignment explanation
Indices: 1512754--1512824 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1512744 GAAATATATT
* *
1512754 GATACATTACTAAATGTATC
1 GATACATTTCTAATTGTATC
1512774 GATACATGCTTAC-AATTGTATC
1 GATACAT--TT-CTAATTGTATC
*
1512796 GATACATTTCTCATTGTATC
1 GATACATTTCTAATTGTATC
1512816 GATACATTT
1 GATACATTT
1512825 TGGGTTTCTG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.02
20 26 0.59
22 16 0.36
23 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
GATACATTTCTAATTGTATC
Found at i:1520924 original size:27 final size:27
Alignment explanation
Indices: 1520882--1520954 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 27
1520872 TTATCTTTAG
** *
1520882 ATTTTTAATTAAACTTTTAAAAATGAA
1 ATTTTTAATTGGACTTTTAAAAATAAA
** *
1520909 ATTTTTAATTGGACTTTTTGCATATAAA
1 ATTTTTAATTGGAC-TTTTAAAAATAAA
*
1520937 ATTTTCAATTGGACTTTT
1 ATTTTTAATTGGACTTTT
1520955 TGTACATACG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (27 bp):
ATTTTTAATTGGACTTTTAAAAATAAA
Found at i:1520968 original size:28 final size:28
Alignment explanation
Indices: 1520907--1520962 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1520897 TTTAAAAATG
* *
1520907 AAATTTTTAATTGGACTTTTTGCATATA
1 AAATTTTCAATTGGACTTTTTGCACATA
*
1520935 AAATTTTCAATTGGACTTTTTGTACATA
1 AAATTTTCAATTGGACTTTTTGCACATA
1520963 CGATTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (28 bp):
AAATTTTCAATTGGACTTTTTGCACATA
Found at i:1522847 original size:29 final size:27
Alignment explanation
Indices: 1522815--1522873 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
1522805 TCCTTGGTTT
1522815 TTTAATTCATGC-ATATTATTTTCACTTTA
1 TTTAATTCATGCTAT-TTATTTT-A-TTTA
* *
1522844 TTTATTTCTTGCTATTTATTTTATTTA
1 TTTAATTCATGCTATTTATTTTATTTA
1522871 TTT
1 TTT
1522874 TGTTTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
28 1 0.04
29 17 0.63
30 2 0.07
ACGTcount: A:0.22, C:0.10, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTAATTCATGCTATTTATTTTATTTA
Found at i:1524302 original size:26 final size:27
Alignment explanation
Indices: 1524238--1524302 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
1524228 TAAGATTTTG
* * *
1524238 AAATTTGTAATCTAATGGGAGATTATT
1 AAATTTGTAACCAAATGGGAGATTATC
*
1524265 ATAATTT-T-ACCAAATGGTAGATTA-C
1 A-AATTTGTAACCAAATGGGAGATTATC
1524290 AAATTTGTAACCA
1 AAATTTGTAACCA
1524303 TCTAATAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 17 0.55
27 2 0.06
28 5 0.16
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (27 bp):
AAATTTGTAACCAAATGGGAGATTATC
Found at i:1524420 original size:21 final size:20
Alignment explanation
Indices: 1524368--1524420 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1524358 GTATTTAGAT
*
1524368 TAAATGATGTATTGGTTGGA
1 TAAAAGATGTATTGGTTGGA
**
1524388 TAAAAGATTGTATTTTTTGGA
1 TAAAAGA-TGTATTGGTTGGA
1524409 TGAAAAGATGTA
1 T-AAAAGATGTA
1524421 ACTTTTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
22 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TAAAAGATGTATTGGTTGGA
Found at i:1524426 original size:21 final size:21
Alignment explanation
Indices: 1524383--1524426 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1524373 GATGTATTGG
**
1524383 TTGGATAAAAGATTGTATTTT
1 TTGGATAAAAGATTGTAACTT
1524404 TTGGATGAAAAGA-TGTAACTT
1 TTGGAT-AAAAGATTGTAACTT
1524425 TT
1 TT
1524427 ATAGCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (21 bp):
TTGGATAAAAGATTGTAACTT
Found at i:1524426 original size:22 final size:21
Alignment explanation
Indices: 1524383--1524426 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1524373 GATGTATTGG
*
1524383 TTGGATAAAAGATTGTATTTT
1 TTGGATAAAAGATTGTACTTT
1524404 TTGGATGAAAAGA-TGTAACTTT
1 TTGGAT-AAAAGATTGT-ACTTT
1524426 T
1 T
1524427 ATAGCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (21 bp):
TTGGATAAAAGATTGTACTTT
Found at i:1526092 original size:2 final size:2
Alignment explanation
Indices: 1526079--1526126 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1526069 TAAGCATGGC
*
1526079 AT AT AT AC 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 AT AT AT
1526121 AT AT AT
1 AT AT AT
1526127 GCTGGCTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1526668 original size:16 final size:16
Alignment explanation
Indices: 1526649--1526679 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1526639 TTTAAAATTT
1526649 TAAAAATCTTTAAAAG
1 TAAAAATCTTTAAAAG
*
1526665 TAAATATCTTTAAAA
1 TAAAAATCTTTAAAA
1526680 TTTAGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAAAATCTTTAAAAG
Found at i:1527002 original size:2 final size:2
Alignment explanation
Indices: 1526995--1527029 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1526985 TGGGAAATTA
1526995 AT AT 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 A
1527030 AAAGCCTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1528519 original size:19 final size:20
Alignment explanation
Indices: 1528482--1528531 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1528472 TAAAAATAAA
*
1528482 AATATATTAAA-ATTTATAT
1 AATATATTAAATATTAATAT
1528501 AATATATTAAATA-TAATAT
1 AATATATTAAATATTAATAT
1528520 AA-ATATATAAAT
1 AATATAT-TAAAT
1528532 TATCAAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 23 0.82
20 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATATTAAATATTAATAT
Found at i:1530704 original size:46 final size:47
Alignment explanation
Indices: 1530648--1530738 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
1530638 TATTGTGAAA
* *
1530648 TCTAAGTTGGTTGCTACTGA-ATAATCGTTTAATTAAAAAAAAAAAC
1 TCTAAATTGGTTCCTACTGATATAATCGTTTAATTAAAAAAAAAAAC
*
1530694 TCTAAATTGGTTCCTACTGATATAATTGTTTAATTAAAAAAAAAA
1 TCTAAATTGGTTCCTACTGATATAATCGTTTAATTAAAAAAAAAA
1530739 TTTTAATCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 18 0.44
47 23 0.56
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (47 bp):
TCTAAATTGGTTCCTACTGATATAATCGTTTAATTAAAAAAAAAAAC
Found at i:1530755 original size:45 final size:46
Alignment explanation
Indices: 1530661--1530755 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
1530651 AAGTTGGTTG
* *
1530661 CTACTGAATAATCGTTTAATTAAAAAAAAAAACTCTAAATTGGTTC
1 CTACTGAATAATCGTTTAATTAAAAAAAAAAACTCTAAATCGGTAC
* * *
1530707 CTACTGATATAATTGTTTAATT-AAAAAAAAAA-TTTTAATCGGTAC
1 CTACTGA-ATAATCGTTTAATTAAAAAAAAAAACTCTAAATCGGTAC
1530752 CTAC
1 CTAC
1530756 GACCTGTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 13 0.30
46 17 0.40
47 13 0.30
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (46 bp):
CTACTGAATAATCGTTTAATTAAAAAAAAAAACTCTAAATCGGTAC
Found at i:1531019 original size:9 final size:9
Alignment explanation
Indices: 1530975--1531029 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
1530965 ATATTTTTTA
1530975 TTATAATAAT
1 TTATAAT-AT
1530985 TTAT-A-AT
1 TTATAATAT
1530992 TTATAATTAAT
1 TTATAA-T-AT
1531003 TATAATAATAT
1 T-T-ATAATAT
1531014 TTATAATAT
1 TTATAATAT
1531023 TTATAAT
1 TTATAAT
1531030 CATAATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
7 6 0.15
8 1 0.03
9 15 0.38
10 5 0.13
11 6 0.15
12 2 0.05
13 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTATAATAT
Found at i:1531036 original size:27 final size:30
Alignment explanation
Indices: 1530977--1531037 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 30
1530967 ATTTTTTATT
*
1530977 ATAATAATTTATAATTTATAATTAATTATA
1 ATAATAATTTATAATTTATAATTAATCATA
1531007 ATAAT-ATTTATAATATT-T-A-TAATCATA
1 ATAATAATTTATAAT-TTATAATTAATCATA
1531034 ATAA
1 ATAA
1531038 ATACAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.38
28 1 0.03
29 10 0.34
30 7 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAATAATTTATAATTTATAATTAATCATA
Found at i:1531391 original size:2 final size:2
Alignment explanation
Indices: 1531386--1531422 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
1531376 CTGTGTGTGC
1531386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1531423 TTCATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1534269 original size:14 final size:14
Alignment explanation
Indices: 1534252--1534292 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1534242 ACAGAGTCCC
1534252 TAATATAAAATCAA
1 TAATATAAAATCAA
**
1534266 TAATATAGCATCAA
1 TAATATAAAATCAA
1534280 TAATATAAAATCA
1 TAATATAAAATCA
1534293 GTATTATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (14 bp):
TAATATAAAATCAA
Found at i:1536161 original size:36 final size:33
Alignment explanation
Indices: 1536114--1536197 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 33
1536104 GCTGTACAAC
* *
1536114 ACATAAAGATAACACATTCAGTTTAAAAAATGAGTA
1 ACATAATGATAACACATT-A--TAAAAAAATGAGTA
1536150 ACATAATGAT-A-ACA-TATAAAAAAATGAGTA
1 ACATAATGATAACACATTATAAAAAAATGAGTA
*
1536180 ACATAATGATATCACATT
1 ACATAATGATAACACATT
1536198 TTCTGTACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
30 23 0.55
32 4 0.10
33 2 0.05
34 3 0.07
35 1 0.02
36 9 0.21
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.26
Consensus pattern (33 bp):
ACATAATGATAACACATTATAAAAAAATGAGTA
Found at i:1540348 original size:17 final size:17
Alignment explanation
Indices: 1540326--1540365 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1540316 CTTGGAGAGT
1540326 GATGATGAAGAGAAGGC
1 GATGATGAAGAGAAGGC
1540343 GATGATGAAGAGAAGGC
1 GATGATGAAGAGAAGGC
*
1540360 AATGAT
1 GATGAT
1540366 AAAAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.38, T:0.15
Consensus pattern (17 bp):
GATGATGAAGAGAAGGC
Found at i:1543804 original size:19 final size:18
Alignment explanation
Indices: 1543776--1543839 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
1543766 AGCGATACAT
*
1543776 TGTATAGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1543795 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
1543808 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1543827 TGTATCGATACAA
1 TGTATCGATACAA
1543840 TGTATCAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1543809 original size:32 final size:32
Alignment explanation
Indices: 1543768--1543853 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
1543758 AGCTTCGTAG
1543768 CGATACATTGTATAGATACAAAACTTATGTAT
1 CGATACATTGTATAGATACAAAACTTATGTAT
* *
1543800 CGATACATTGTATTGATACAACACTTATGTAT
1 CGATACATTGTATAGATACAAAACTTATGTAT
*
1543832 CGATACAATGTATCA-ATACAAA
1 CGATACATTGTAT-AGATACAAA
1543854 TCGTTGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATAGATACAAAACTTATGTAT
Found at i:1544712 original size:49 final size:49
Alignment explanation
Indices: 1544605--1545148 Score: 583
Period size: 49 Copynumber: 11.1 Consensus size: 49
1544595 AATGCTAATG
* * ** *
1544605 TGCTGATTCAAGGCCAACGACATTGGGTTTTAAATGATGACGAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGATATT-GGACTTAAA-GAT---GAAGGTGCCAATA
* *
1544659 TGCTGATTCAAGGCCAGCGATACTGGACTTAAAGATGAAGGTGCCAAAA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
*
1544708 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
1544757 TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATA
*
1544809 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATA
* * *
1544861 TGCTAATTCAAGGCCAGCGATATTGGACCTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
* * * * *
1544910 TGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGATAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
* * * * *
1544959 TGCTAATTCAAGGCTAACGACATTGGACTTAAAGATGACAAAGGCGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATA
*
1545011 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
*
1545054 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
* ** * *
1545097 TGCTAATTCAAGGCCAGCGACGTTGGTCTTAAAGA-CAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
1545145 TGCT
1 TGCT
1545149 TGTAGACACC
Statistics
Matches: 432, Mismatches: 47, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
43 79 0.18
47 1 0.00
48 16 0.04
49 174 0.40
52 134 0.31
53 7 0.02
54 21 0.05
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:1544829 original size:150 final size:151
Alignment explanation
Indices: 1544601--1545087 Score: 679
Period size: 150 Copynumber: 3.3 Consensus size: 151
1544591 GAAGAATGCT
** *
1544601 AATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAATGATGACGAAGGCGCCAATATGCTGAT
1 AATGTGCTGATTCAAGGCCAACGACATT-GGACTTAAA-GATGACAAAGGCGCCAATATGCTGAT
* * *
1544666 TCAAGGCCAGCGATACTGGACTTAAAGATG-AAGGTGCCAAAATGCTGATTCAAGGCCAGCGATA
64 TCAAGGCCAGCGATATTGGACTTAAAGATGAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
1544730 TTGGACTTAAAGATGAAGGTGCC
129 TTGGACTTAAAGATGAAGGTGCC
1544753 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
*
1544818 AAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGGCCAGCGATA
66 AAGGCCAGCGATATTGGACTTAAAGATG--AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
*
1544883 TTGGACCTAAAGATGAAGGTGCC
129 TTGGACTTAAAGATGAAGGTGCC
* * * * * *
1544906 AATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGAT---AAATGTGCCAATATGCTAATTC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
* * *
1544968 AAGGCTAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
66 AAGGCCAGCGATATTGGACTTAAAGATG--AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
1545033 TTGGACTT----A--AAGGTGCC
129 TTGGACTTAAAGATGAAGGTGCC
* *
1545050 AATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAG
1545088 GTGCCAATGT
Statistics
Matches: 310, Mismatches: 22, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
144 43 0.14
146 1 0.00
150 141 0.45
151 7 0.02
152 28 0.09
153 90 0.29
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (151 bp):
AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAAGATGAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATT
GGACTTAAAGATGAAGGTGCC
Found at i:1544873 original size:202 final size:202
Alignment explanation
Indices: 1544605--1545044 Score: 700
Period size: 202 Copynumber: 2.2 Consensus size: 202
1544595 AATGCTAATG
* * ** * *
1544605 TGCTGATTCAAGGCCAACGACATTGGGTTTTAAATGATGACGAAGGCGCCAATATGCTGATTCAA
1 TGCTGATTCAAGGCCAGCGATATT-GGACTTAAA-GATGACAAAGGCGCCAATATGCTAATTCAA
* * *
1544670 GGCCAGCGATACTGGACTTAAAGATGAAGGTGCCAAAATGCTGATTCAAGGCCAGCGATATTGGA
64 GGCCAGCGATACTGGACCTAAAGATGAAGGTGCCAAAATGCTGATTCAAAGCCAGCGACATTGGA
* * *
1544735 CTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAG
129 CTTAAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAG
1544800 GCGCCAATA
194 GCGCCAATA
1544809 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGG
* ** *
1544874 CCAGCGATATTGGACCTAAAGATGAAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCT
66 CCAGCGATACTGGACCTAAAGATGAAGGTGCCAAAATGCTGATTCAAAGCCAGCGACATTGGACT
* *
1544939 TAAAGATAAATGTGCCAATATGCTAATTCAAGGCTAACGACATTGGACTTAAAGATGACAAAGGC
131 TAAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGC
1545004 GCCAATA
196 GCCAATA
1545011 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1545045 GTGCCAATGT
Statistics
Matches: 218, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
202 189 0.87
203 7 0.03
204 22 0.10
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (202 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGG
CCAGCGATACTGGACCTAAAGATGAAGGTGCCAAAATGCTGATTCAAAGCCAGCGACATTGGACT
TAAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGC
GCCAATA
Found at i:1545045 original size:22 final size:22
Alignment explanation
Indices: 1545020--1545088 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1545010 ATGCTGATTC
1545020 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
* * *
1545042 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCGATAT-TG--GACTTA
1545063 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
1545085 AAGG
1 AAGG
1545089 TGCCAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (22 bp):
AAGGCCAGCGATATTGGACTTA
Found at i:1545059 original size:43 final size:43
Alignment explanation
Indices: 1544998--1545130 Score: 212
Period size: 43 Copynumber: 3.1 Consensus size: 43
1544988 TAAAGATGAC
* *
1544998 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1545041 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
* ** *
1545084 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACGTTGGTCTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1545127 AAAG
1 AAAG
1545131 ACAAGGTGCC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (43 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1545093 original size:24 final size:24
Alignment explanation
Indices: 1545023--1545093 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
1545013 CTGATTCAAG
1545023 GCCAGCGATATTGGACTTAAAGGT
1 GCCAGCGATATTGGACTTAAAGGT
** ** *
1545047 GCCAATG-TGCT-GA-TTCAA-G-
1 GCCAGCGATATTGGACTTAAAGGT
1545066 GCCAGCGATATTGGACTTAAAGGT
1 GCCAGCGATATTGGACTTAAAGGT
1545090 GCCA
1 GCCA
1545094 ATGTGCTAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 5 0.16
20 3 0.09
21 6 0.19
22 6 0.19
23 3 0.09
24 9 0.28
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (24 bp):
GCCAGCGATATTGGACTTAAAGGT
Found at i:1545478 original size:13 final size:13
Alignment explanation
Indices: 1545460--1545484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1545450 CATAAAATGT
1545460 TGTATCGATACAA
1 TGTATCGATACAA
1545473 TGTATCGATACA
1 TGTATCGATACA
1545485 TATTTTTTTT
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:1545620 original size:52 final size:50
Alignment explanation
Indices: 1545561--1545709 Score: 190
Period size: 52 Copynumber: 2.9 Consensus size: 50
1545551 ATTGATACAT
* *
1545561 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCTAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1545613 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1545665 TGTATCGATACACTATTAAATGTATCGATACATGCAAGTAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
1545710 TCATATTTTG
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1548913 original size:28 final size:29
Alignment explanation
Indices: 1548849--1548920 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
1548839 AGACGCCACC
*
1548849 AACTTGTGTGGACTTTTGAAAGGGTTGTACT
1 AACTTGTGT-G-CTTTTGAAAGGGTTGCACT
1548880 AACTTGTGTGCTTTTG-AA-GGTTGCCACT
1 AACTTGTGTGCTTTTGAAAGGGTTG-CACT
* *
1548908 GACTTGTGGGCTT
1 AACTTGTGTGCTT
1548921 AAAAGGAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 16 0.43
29 6 0.16
30 1 0.03
31 9 0.24
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (29 bp):
AACTTGTGTGCTTTTGAAAGGGTTGCACT
Found at i:1548948 original size:33 final size:34
Alignment explanation
Indices: 1548901--1549090 Score: 156
Period size: 33 Copynumber: 5.6 Consensus size: 34
1548891 TTTTGAAGGT
* * *
1548901 TGCCACTGACTTGTGGGCTT-AAAAGGAGAAAGA
1 TGCCACGGAGTTGTGGGCTTAAAAAGGAAAAAGA
* *
1548934 TGCCACGGAGTTGTGGACTTAAAAAGGAAAAAAAA
1 TGCCACGGAGTTGTGGGCTTAAAAAGG-AAAAAGA
* * * *
1548969 TGCTACGAAGTTGT-GGATTTAAAAGGAAAAAG-
1 TGCCACGGAGTTGTGGGCTTAAAAAGGAAAAAGA
* * * *
1549001 TACCACGGAGTGGTGGGCTTTGAAAA--AAAAAGG
1 TGCCACGGAGTTGTGGGC-TTAAAAAGGAAAAAGA
* *
1549034 TGCCACGGAGTTGTGGGCTTTGAAGAAAAGAAAAAGG
1 TGCCACGGAGTTGTGGGC-TT-AA-AAAGGAAAAAGA
*
1549071 TGCAACGGAGTTGTGGGCTT
1 TGCCACGGAGTTGTGGGCTT
1549091 TGAAGAAAAG
Statistics
Matches: 127, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
32 16 0.13
33 43 0.34
34 22 0.17
35 20 0.16
36 2 0.02
37 24 0.19
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.21
Consensus pattern (34 bp):
TGCCACGGAGTTGTGGGCTTAAAAAGGAAAAAGA
Found at i:1548983 original size:35 final size:34
Alignment explanation
Indices: 1548911--1548999 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 34
1548901 TGCCACTGAC
* * * *
1548911 TTGTGGGCTTAAAAGG-AGAAAGATGCCACGGAG
1 TTGTGGACTTAAAAGGAAAAAAAATGCCACGAAG
*
1548944 TTGTGGACTTAAAAAGGAAAAAAAATGCTACGAAG
1 TTGTGGACTT-AAAAGGAAAAAAAATGCCACGAAG
*
1548979 TTGTGGATTTAAAAGGAAAAA
1 TTGTGGACTTAAAAGGAAAAA
1549000 GTACCACGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 9 0.19
34 17 0.35
35 22 0.46
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.21
Consensus pattern (34 bp):
TTGTGGACTTAAAAGGAAAAAAAATGCCACGAAG
Found at i:1548993 original size:34 final size:35
Alignment explanation
Indices: 1548911--1548999 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 35
1548901 TGCCACTGAC
* * * *
1548911 TTGTGGGC-TTAAAAGG-AGAAAGATGCCACGGAG
1 TTGTGGACTTTAAAAGGAAAAAAAATGCCACGAAG
* *
1548944 TTGTGGACTTAAAAAGGAAAAAAAATGCTACGAAG
1 TTGTGGACTTTAAAAGGAAAAAAAATGCCACGAAG
1548979 TTGTGGA-TTTAAAAGGAAAAA
1 TTGTGGACTTTAAAAGGAAAAA
1549000 GTACCACGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 7 0.15
34 20 0.43
35 20 0.43
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.21
Consensus pattern (35 bp):
TTGTGGACTTTAAAAGGAAAAAAAATGCCACGAAG
Found at i:1549072 original size:37 final size:37
Alignment explanation
Indices: 1548989--1549101 Score: 155
Period size: 37 Copynumber: 3.2 Consensus size: 37
1548979 TTGTGGATTT
* *
1548989 AAAAGGAAAAA-GTACCACGGAGTGGTGGGCTTT---G
1 AAAA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1549023 AAAA-AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
*
1549059 AAAAGAAAAAGGTGCAACGGAGTTGTGGGCTTTGAAG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1549096 AAAAGA
1 AAAAGA
1549102 TGCCACTGAG
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
32 5 0.07
33 20 0.28
34 4 0.06
36 5 0.07
37 37 0.52
ACGTcount: A:0.39, C:0.10, G:0.34, T:0.18
Consensus pattern (37 bp):
AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
Found at i:1549220 original size:31 final size:30
Alignment explanation
Indices: 1549078--1549219 Score: 169
Period size: 31 Copynumber: 4.6 Consensus size: 30
1549068 AGGTGCAACG
* *
1549078 GAGTTGTGGGCTTTGAAGAAAAGATGCCACT
1 GAGTCGTGGACTTTG-AGAAAAGATGCCACT
1549109 GAGTCGTGGACTTTGGAGAAAAGATGCCACT
1 GAGTCGTGGACTTT-GAGAAAAGATGCCACT
*
1549140 GAGTCGTGGACTTTGGGACAAA-ATGCCACT
1 GAGTCGTGGACTTTGAGA-AAAGATGCCACT
* * *
1549170 GAGTCATGGGCTTTGAGAAGAGATTGCCACT
1 GAGTCGTGGACTTTGAGAAAAGA-TGCCACT
* *
1549201 AAGTCGTGGACTTTAAGAA
1 GAGTCGTGGACTTTGAGAA
1549220 GGTATTTGAA
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.02
30 27 0.28
31 66 0.69
32 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (30 bp):
GAGTCGTGGACTTTGAGAAAAGATGCCACT
Found at i:1556820 original size:13 final size:13
Alignment explanation
Indices: 1556802--1556862 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
1556792 ATAGAAAGAT
1556802 CAATGTATCGATA
1 CAATGTATCGATA
*
1556815 CAATGTATTGATA
1 CAATGTATCGATA
1556828 CAA---A--GAT-
1 CAATGTATCGATA
1556835 CAATGTATCGATA
1 CAATGTATCGATA
1556848 CAATGTATCGATA
1 CAATGTATCGATA
1556861 CA
1 CA
1556863 TTTGAGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
7 3 0.07
8 3 0.07
10 2 0.05
12 3 0.07
13 30 0.73
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1556951 original size:32 final size:32
Alignment explanation
Indices: 1556804--1556992 Score: 145
Period size: 32 Copynumber: 5.9 Consensus size: 32
1556794 AGAAAGATCA
* *
1556804 ATGTATCGATACAATGTATTGATACAAAGA-TCA
1 ATGTATCGATACAATGTATCGATACAAA-ACT-T
** * *
1556837 ATGTATCGATACAATGTATCGATACATTTGAGTA
1 ATGTATCGATACAATGTATCGATACA--AAACTT
** * * *
1556871 ATGTATCGATAC-AT-T-TCCTTGGCAGTAGCTT
1 ATGTATCGATACAATGTATCGAT-ACA-AAACTT
* *
1556902 -TGTAGCGATACAATGTATCGCTACAAAACTT
1 ATGTATCGATACAATGTATCGATACAAAACTT
* *
1556933 ATGTATCGATACATTGTATCGATACAACACTT
1 ATGTATCGATACAATGTATCGATACAAAACTT
*
1556965 ATGTATCGATACAATGTATCAATACAAA
1 ATGTATCGATACAATGTATCGATACAAA
1556993 TCATTGAAAT
Statistics
Matches: 124, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
30 10 0.08
31 11 0.09
32 58 0.47
33 30 0.24
34 14 0.11
35 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (32 bp):
ATGTATCGATACAATGTATCGATACAAAACTT
Found at i:1556952 original size:13 final size:13
Alignment explanation
Indices: 1556934--1556958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1556924 ACAAAACTTA
1556934 TGTATCGATACAT
1 TGTATCGATACAT
1556947 TGTATCGATACA
1 TGTATCGATACA
1556959 ACACTTATGT
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:1556971 original size:19 final size:19
Alignment explanation
Indices: 1556914--1556978 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1556904 TAGCGATACA
* *
1556914 ATGTATCGCTACAAAACTT
1 ATGTATCGATACAACACTT
1556933 ATGTATCGAT---ACA--T
1 ATGTATCGATACAACACTT
1556947 -TGTATCGATACAACACTT
1 ATGTATCGATACAACACTT
1556965 ATGTATCGATACAA
1 ATGTATCGATACAA
1556979 TGTATCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.13
18 1 0.03
19 22 0.58
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAACACTT
Found at i:1557449 original size:20 final size:21
Alignment explanation
Indices: 1557424--1557474 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1557414 ACAGGGTCCA
*
1557424 GTATCGATACATTCACTT-AT
1 GTATCGATACATTAACTTGAT
* *
1557444 GTATCGATAAATTAACTTGTT
1 GTATCGATACATTAACTTGAT
1557465 GTATCGATAC
1 GTATCGATAC
1557475 TTTTTACCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
GTATCGATACATTAACTTGAT
Found at i:1560280 original size:20 final size:21
Alignment explanation
Indices: 1560255--1560303 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1560245 AAACAAATTA
*
1560255 TATCGATA-ATTCACATAATG
1 TATCGATACATTCACAAAATG
*
1560275 TATCGATACATTTACAAAATG
1 TATCGATACATTCACAAAATG
*
1560296 TATTGATA
1 TATCGATA
1560304 TATTTTCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (21 bp):
TATCGATACATTCACAAAATG
Found at i:1560388 original size:21 final size:21
Alignment explanation
Indices: 1560359--1560401 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1560349 GTGATTGCCA
1560359 ACAAAATGTATCGATACATTC
1 ACAAAATGTATCGATACATTC
*
1560380 ACAAGATGTATCGATACATTC
1 ACAAAATGTATCGATACATTC
1560401 A
1 A
1560402 GTCTTTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (21 bp):
ACAAAATGTATCGATACATTC
Found at i:1563004 original size:28 final size:29
Alignment explanation
Indices: 1562972--1563039 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
1562962 CATTATTCAT
* *
1562972 TGTATCGATACATTCT-GAAAAACCTAGA
1 TGTATCAATACATTCTGGAAAAACCAAGA
** *
1563000 TGTATTTATACATTCTGGAACAACCAAGA
1 TGTATCAATACATTCTGGAAAAACCAAGA
1563029 TGTATCAATAC
1 TGTATCAATAC
1563040 TTTGTTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 14 0.42
29 19 0.58
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (29 bp):
TGTATCAATACATTCTGGAAAAACCAAGA
Found at i:1564934 original size:151 final size:152
Alignment explanation
Indices: 1564651--1564934 Score: 360
Period size: 151 Copynumber: 1.9 Consensus size: 152
1564641 AAAAATTACT
* * *
1564651 AAAATACCCTTAAGGGATATCTTAGACATAGAAGTGCTCGATACCCTAAAGGACTTAAAAAAGAT
1 AAAATACCCTTAAGGGATACCTTAGACATAAAAGTACTCGATACCCTAAAGGACTTAAAAAAGAT
* * * * ***
1564716 TATAAAATGGGATGAACCTATCCTAAATATCTACCTTTGGCATTAAAGCGGACTCGATGATGGCC
66 TATAAAATGGGATAAACCTATCCTAAATATCTACCTTTAGCATAAAAGCGAACTCGATGACAACC
1564781 TAGAAATCGGTTCTAGAAAACC
131 TAGAAATCGGTTCTAGAAAACC
* * * * * *
1564803 AAAATGCCCTTAGGGGATACCTTCGACATAAAAGTACTTGATACCTTTAAAGGACTTAAAAAGGA
1 AAAATACCCTTAAGGGATACCTTAGACATAAAAGTACTCGATACC-CTAAAGGACTTAAAAAAGA
*
1564868 -TAT-AAATGGGATAAACCTATCCTAAATA-CTCACCTTTAGCATAAAAGCGAAC-CTACTGACA
65 TTATAAAATGGGATAAACCTATCCTAAATATCT-ACCTTTAGCATAAAAGCGAACTCGA-TGACA
1564929 ACCTAG
128 ACCTAG
1564935 GACTTAGTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
150 4 0.04
151 50 0.45
152 41 0.37
153 17 0.15
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (152 bp):
AAAATACCCTTAAGGGATACCTTAGACATAAAAGTACTCGATACCCTAAAGGACTTAAAAAAGAT
TATAAAATGGGATAAACCTATCCTAAATATCTACCTTTAGCATAAAAGCGAACTCGATGACAACC
TAGAAATCGGTTCTAGAAAACC
Done.