Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 9 of 52
Found at i:1468040 original size:16 final size:16
Alignment explanation
Indices: 1468021--1468070 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1468011 ATCCGGACCC
1468021 TTTTTGTTTTTGTTTT
1 TTTTTGTTTTTGTTTT
*
1468037 TTTTTGTTTTAGTTTT
1 TTTTTGTTTTTGTTTT
1468053 TTTTTG--TTTGTTTT
1 TTTTTGTTTTTGTTTT
1468067 TTTT
1 TTTT
1468071 GTGGAGGGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 11 0.34
16 21 0.66
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (16 bp):
TTTTTGTTTTTGTTTT
Found at i:1468042 original size:10 final size:10
Alignment explanation
Indices: 1468022--1468070 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
1468012 TCCGGACCCT
1468022 TTTTGTTTTTG
1 TTTT-TTTTTG
1468033 TTTTTTTTTG
1 TTTTTTTTTG
*
1468043 TTTTAGTTTT-
1 TTTT-TTTTTG
*
1468053 TTTTTGTTTG
1 TTTTTTTTTG
1468063 TTTTTTTT
1 TTTTTTTT
1468071 GTGGAGGGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 3 0.09
10 21 0.66
11 8 0.25
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1473878 original size:20 final size:20
Alignment explanation
Indices: 1473853--1473904 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1473843 CATTTTAGAC
1473853 ATGTATCGATAC-TTTCACTT
1 ATGTATCGATACATTT-ACTT
*
1473873 ATGTATCAATACATTTACTT
1 ATGTATCGATACATTTACTT
*
1473893 ATTATATCGATA
1 A-TGTATCGATA
1473905 AAAATTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Found at i:1475339 original size:21 final size:22
Alignment explanation
Indices: 1475315--1475365 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1475305 TAAGCCTAAT
*
1475315 ACCAATCAATC-AATCCAAAGA
1 ACCAATCAAGCTAATCCAAAGA
*
1475336 ACCAAT-AAGCTAATCCAAAGG
1 ACCAATCAAGCTAATCCAAAGA
1475357 ACCAATCAA
1 ACCAATCAA
1475366 CCTAGACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.51, C:0.27, G:0.08, T:0.14
Consensus pattern (22 bp):
ACCAATCAAGCTAATCCAAAGA
Found at i:1482648 original size:20 final size:20
Alignment explanation
Indices: 1482623--1482746 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
1482613 TTTTACCTAG
*
1482623 ATGTATCTATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* *
1482643 ATGTATCGATACA--TGTAA
1 ATGTATCGATACATTTTTCA
*
1482661 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTTTTCA
*
1482682 ATGTATCAATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
1482712 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1482733 ATGTATCGATACAT
1 ATGTATCGATACAT
1482747 CTAGTTAATA
Statistics
Matches: 81, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
18 3 0.04
19 13 0.16
20 38 0.47
21 4 0.05
24 5 0.06
27 4 0.05
30 2 0.02
31 12 0.15
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1482675 original size:39 final size:39
Alignment explanation
Indices: 1482621--1482695 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1482611 ATTTTTACCT
* * *
1482621 AGATGTATCTATACATTTTTCAATGTATCGATACATGTA
1 AGATGTATCGATACATTCTTCAATGTATCAATACATGTA
1482660 AGATGTATCGATACATTCTTCAATGTATCAATACAT
1 AGATGTATCGATACATTCTTCAATGTATCAATACAT
1482696 TCTGTCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (39 bp):
AGATGTATCGATACATTCTTCAATGTATCAATACATGTA
Found at i:1484936 original size:30 final size:30
Alignment explanation
Indices: 1484900--1484957 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1484890 ATTTTATTTA
1484900 TCGGGGATACTCCAACCTCATTCCTCCGCG
1 TCGGGGATACTCCAACCTCATTCCTCCGCG
1484930 TCGGGGATACTCCAACCTCATTCCTCCG
1 TCGGGGATACTCCAACCTCATTCCTCCG
1484958 AGAGGATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.17, C:0.40, G:0.19, T:0.24
Consensus pattern (30 bp):
TCGGGGATACTCCAACCTCATTCCTCCGCG
Found at i:1484972 original size:27 final size:30
Alignment explanation
Indices: 1484904--1484973 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
1484894 TATTTATCGG
* *
1484904 GGATACTCCAACCTCATTCCTCCGCGTCGG
1 GGATACTCCAACCTCATTCCTCCGCGTAGA
1484934 GGATACTCCAACCTCATTCCT-C-CG-AGA
1 GGATACTCCAACCTCATTCCTCCGCGTAGA
1484961 GGATACTCCAACC
1 GGATACTCCAACC
1484974 CCGTTTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 14 0.37
28 2 0.05
29 1 0.03
30 21 0.55
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (30 bp):
GGATACTCCAACCTCATTCCTCCGCGTAGA
Found at i:1498102 original size:28 final size:28
Alignment explanation
Indices: 1498070--1498469 Score: 315
Period size: 28 Copynumber: 13.6 Consensus size: 28
1498060 CAACATAACT
1498070 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1498098 CCTTTTCAAAGCCCAGAAGTTAGTGCCAAC
1 CC-TTTCAAAGCCCACAAGTCAGTGGC-AC
* *
1498128 TCTTTTTAAAGTCCACACAAGTCAGTGGCAAC
1 -CCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
* * *
1498160 TCTTTTCAAAGCCCACACAAATCGGTGGCA-
1 -CCTTTCAAAG-CC-CACAAGTCAGTGGCAC
1498190 CCTTTCCAAAGCCCACAAGTCTA-TGGCAC
1 CCTTT-CAAAGCCCACAAGTC-AGTGGCAC
* * *
1498219 CCTTCCAAAGCCCACAAGTTAATGGCA-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
1498246 CCTTTTAAAGCCCACAAGTCAGTGGCATAC
1 CCTTTCAAAGCCCACAAGTCAGTGGC--AC
1498276 CCTTTCAAAGCCCACAAGTCAGTGGCA-
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1498303 CTTTTACAAAGCCAACAAGAT-AGTGGCAT
1 CCTTT-CAAAGCCCACAAG-TCAGTGGCAC
** * * *
1498332 ATTTTCAAAGCGCATAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
1498360 CCTTTCAAAGCCCACACAAGTCAGTAGCAAC
1 CCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
* *
1498391 TCTTTTTTCAAAGCCTACAAGTCAGTGGCAC
1 -C--CTTTCAAAGCCCACAAGTCAGTGGCAC
*
1498422 CCTTTCAAAGCCCACGCAAGTTAGTGGCAAC
1 CCTTTCAAAGCCCA--CAAGTCAGTGGC-AC
*
1498453 TCTTTTCAAAGCCCACA
1 -CCTTTCAAAGCCCACA
1498470 TAACTTAGTG
Statistics
Matches: 305, Mismatches: 41, Indels: 50
0.77 0.10 0.13
Matches are distributed among these distances:
27 28 0.09
28 90 0.30
29 38 0.12
30 65 0.21
31 9 0.03
32 65 0.21
33 2 0.01
34 8 0.03
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:1498206 original size:62 final size:58
Alignment explanation
Indices: 1498070--1498487 Score: 374
Period size: 62 Copynumber: 7.1 Consensus size: 58
1498060 CAACATAACT
* * * *
1498070 CCTTTCAAAGCC-CACAAGTCAGTGGC-ACCCTTTTCAAAGCCCAGAAGTTAGTGCCAA
1 CCTTTCAAAGCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGC-A
* * *
1498127 CTCTTTTTAAAGTCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAATCGGTGGCA
1 C-C-TTTCAAAG-CCACACAAGTCAGTGGCAACTCTTTTCAAAG-CC-CACAAGTCAGTGGCA
* * * *
1498190 CCTTTCCAAAGCC-CACAAGTCTA-TGGC-AC-CCTTCCAAAGCCCACAAGTTAATGGCA
1 CCTTT-CAAAGCCACACAAGTC-AGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1498246 CCTTTTAAAGCC-CACAAGTCAGTGGCATAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCTTTCAAAGCCACACAAGTCAGTGGCA-ACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
1498303 CTTTTACAAAGCCA-ACAAGAT-AGTGGC-A-TATTTTCAAAGCGCATAAGTCAGTGGCA
1 CCTTT-CAAAGCCACACAAG-TCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1498359 TCCTTTCAAAGCCCACACAAGTCAGTAGCAACTCTTTTTTCAAAGCCTACAAGTCAGTGGCA
1 -CCTTTCAAAG-CCACACAAGTCAGTGGCAACTC--TTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
1498421 CCCTTTCAAAGCCCACGCAAGTTAGTGGCAACTCTTTTCAAAGCCCACATAACTTAGTGGCA
1 -CCTTTCAAAG-CCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCAC--AAGTCAGTGGCA
1498483 CCTTT
1 CCTTT
1498488 TTTTAAAAGC
Statistics
Matches: 298, Mismatches: 37, Indels: 48
0.78 0.10 0.13
Matches are distributed among these distances:
54 1 0.00
55 18 0.06
56 45 0.15
57 41 0.14
58 36 0.12
59 11 0.04
60 28 0.09
61 25 0.08
62 80 0.27
63 4 0.01
64 9 0.03
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (58 bp):
CCTTTCAAAGCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:1498289 original size:85 final size:84
Alignment explanation
Indices: 1498072--1498487 Score: 322
Period size: 85 Copynumber: 4.7 Consensus size: 84
1498062 ACATAACTCC
* * **
1498072 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCAGAAGT-TAGTGCCAACTCTTTTTA
1 TTTCAAAGCCCACAAGTCAGTGGCA-CC-TTTCAAAGCCCACAAGTCTAGTGGC-AC-CTTTACA
*
1498136 AAGTCCACACAAGTCAGTGGCAACTCT
62 AAG-CC-CACAAGTTAGTGGC-AC-CT
* * * *
1498163 TTTCAAAGCCCACACAAATCGGTGGCACCTTTCCAAAGCCCACAAGTCTA-TGGCACCCTTCCAA
1 TTTCAAAG-CC-CACAAGTCAGTGGCACCTTT-CAAAGCCCACAAGTCTAGTGGCACCTTTACAA
*
1498227 AGCCCACAAGTTAATGGCACCT
63 AGCCCACAAGTTAGTGGCACCT
*
1498249 TTT-AAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTC-AGTGGCACTTTTACAA
1 TTTCAAAGCCCACAAGTCAGTGGC--A-CCTTTCAAAGCCCACAAGTCTAGTGGCACCTTTACAA
* * **
1498312 AGCCAACAAGATAGTGGCATAT
63 AGCCCACAAGTTAGTGGCACCT
* * *
1498334 TTTCAAAGCGCATAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTC-AGTAGCAACTCTTTTT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAG-CC-CACAAGTCTAGTGGC-AC-C--TTT
* * * *
1498398 TCAAAGCCTACAAGTCAGTGGCACCC
59 ACAAAGCCCACAAGTTAGTGGCACCT
* *
1498424 TTTCAAAGCCCACGCAAGTTAGTGGCAACTCTTTTCAAAGCCCACATA-ACTTAGTGGCACCTTT
1 TTTCAAAGCCCA--CAAGTCAGTGGC-AC-C-TTTCAAAGCCCACA-AGTC-TAGTGGCACCTTT
1498488 TTTTAAAAGC
Statistics
Matches: 266, Mismatches: 36, Indels: 47
0.76 0.10 0.13
Matches are distributed among these distances:
83 12 0.05
84 14 0.05
85 53 0.20
86 41 0.15
87 4 0.02
88 12 0.05
89 2 0.01
90 43 0.16
91 13 0.05
92 37 0.14
93 22 0.08
94 13 0.05
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (84 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCTAGTGGCACCTTTACAAAGC
CCACAAGTTAGTGGCACCT
Found at i:1498497 original size:33 final size:32
Alignment explanation
Indices: 1498428--1498505 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
1498418 GCACCCTTTC
* * *
1498428 AAAGCCCACGCAAGTTAGTGGCAACTCTTTTC
1 AAAGCCCACACAACTTAGTGGCAACTCTTTTA
* * *
1498460 AAAGCCCACATAACTTAGTGGCACCTTTTTTTA
1 AAAGCCCACACAACTTAGTGGCAAC-TCTTTTA
1498493 AAAGCCCACACAA
1 AAAGCCCACACAA
1498506 GTCGGTGGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 21 0.55
33 17 0.45
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.24
Consensus pattern (32 bp):
AAAGCCCACACAACTTAGTGGCAACTCTTTTA
Found at i:1499453 original size:20 final size:19
Alignment explanation
Indices: 1499428--1499502 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1499418 CTTTTATCCA
1499428 AATGTATCGATACATTTTT
1 AATGTATCGATACATTTTT
* *
1499447 CAATGTATCGATACATGTAT
1 -AATGTATCGATACATTTTT
*
1499467 GATGTATCGATACATTCTTT
1 AATGTATCGATACATT-TTT
* *
1499487 AATATATTGATACATT
1 AATGTATCGATACATT
1499503 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 14 0.30
20 32 0.70
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (19 bp):
AATGTATCGATACATTTTT
Found at i:1499540 original size:90 final size:89
Alignment explanation
Indices: 1499378--1499552 Score: 246
Period size: 90 Copynumber: 2.0 Consensus size: 89
1499368 TTTTTACCCA
* * *
1499378 GATGTATCAATACATTTTTCAAAGTATCGATATATTCTATCTTTTATCCAAATGTATCGATACAT
1 GATGTATCAATACATTTTTCAAAGTATCGATACATTCTATCTTTTAACCAAATGTATCGATACAG
1499443 TTTTCAATGTATCGATACATGTAT
66 TTTTCAATGTATCGATACATGTAT
* * * *
1499467 GATGTATCGATACATTCTTT-AATA-TATTGATACATTCTGTCTTTTTAACCAGATGTATCGATA
1 GATGTATCAATACATT-TTTCAA-AGTATCGATACATTCTATC-TTTTAACCAAATGTATCGATA
1499530 CAGTTTTCAATGTATCGATACAT
63 CAGTTTTCAATGTATCGATACAT
1499553 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
89 31 0.41
90 45 0.59
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.42
Consensus pattern (89 bp):
GATGTATCAATACATTTTTCAAAGTATCGATACATTCTATCTTTTAACCAAATGTATCGATACAG
TTTTCAATGTATCGATACATGTAT
Found at i:1505795 original size:13 final size:13
Alignment explanation
Indices: 1505777--1505801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1505767 CAATTTTTTG
1505777 TGTATCGATACAT
1 TGTATCGATACAT
1505790 TGTATCGATACA
1 TGTATCGATACA
1505802 AGTTTGGCTA
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:1506522 original size:21 final size:21
Alignment explanation
Indices: 1506481--1506524 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1506471 CCCTCCTTTA
* *
1506481 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1506502 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1506523 TC
1 TC
1506525 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1508352 original size:13 final size:13
Alignment explanation
Indices: 1508334--1508383 Score: 100
Period size: 13 Copynumber: 3.8 Consensus size: 13
1508324 AATCACCCTA
1508334 TATCGATACAATG
1 TATCGATACAATG
1508347 TATCGATACAATG
1 TATCGATACAATG
1508360 TATCGATACAATG
1 TATCGATACAATG
1508373 TATCGATACAA
1 TATCGATACAA
1508384 GGAAAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1510482 original size:15 final size:15
Alignment explanation
Indices: 1510462--1510492 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1510452 ATTTCGTTTG
*
1510462 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1510477 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1510492 G
1 G
1510493 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1512324 original size:21 final size:21
Alignment explanation
Indices: 1512295--1512339 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1512285 AAGTTTTCAT
*
1512295 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1512315 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1512337 TTT
1 TTT
1512340 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1514573 original size:13 final size:13
Alignment explanation
Indices: 1514555--1514580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1514545 CAATTTTTTG
1514555 TGTATCGATACAT
1 TGTATCGATACAT
1514568 TGTATCGATACAT
1 TGTATCGATACAT
1514581 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1518397 original size:13 final size:13
Alignment explanation
Indices: 1518379--1518404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1518369 CAATTTTTTG
1518379 TGTATCGATACAT
1 TGTATCGATACAT
1518392 TGTATCGATACAT
1 TGTATCGATACAT
1518405 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1519152 original size:21 final size:21
Alignment explanation
Indices: 1519111--1519154 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1519101 CTCCCCTTTA
* *
1519111 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1519132 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1519153 TC
1 TC
1519155 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1520978 original size:13 final size:13
Alignment explanation
Indices: 1520960--1520985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1520950 ATAATCACCC
1520960 TGTATCGATACAA
1 TGTATCGATACAA
1520973 TGTATCGATACAA
1 TGTATCGATACAA
1520986 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:1523082 original size:15 final size:15
Alignment explanation
Indices: 1523062--1523092 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1523052 ATTTTGTTTG
*
1523062 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1523077 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1523092 G
1 G
1523093 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1524920 original size:21 final size:21
Alignment explanation
Indices: 1524891--1524935 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1524881 AAGTTTTCAT
*
1524891 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1524911 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1524933 TTT
1 TTT
1524936 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1526121 original size:13 final size:13
Alignment explanation
Indices: 1526103--1526128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1526093 CAATTTTTTG
1526103 TGTATCGATACAT
1 TGTATCGATACAT
1526116 TGTATCGATACAT
1 TGTATCGATACAT
1526129 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1527108 original size:20 final size:20
Alignment explanation
Indices: 1527083--1527199 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
1527073 TTTTACCTAG
*
1527083 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
1527103 ATGTATCAATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
1527123 ATGTACCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * * *
1527143 ATGTATCTATGCATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
* * *
1527163 ATGTATCAATACATTTTTAA
1 ATGTATCGATACATTCTTCA
*
1527183 ATGTATCGATATATTCT
1 ATGTATCGATACATTCT
1527200 GTCTTTTTAC
Statistics
Matches: 73, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.03
20 69 0.95
21 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1527138 original size:40 final size:40
Alignment explanation
Indices: 1527090--1527189 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 40
1527080 TAGATGTATT
1527090 GATACATTCTTCAATGTATCAATACATGTATGAATGTACC
1 GATACATTCTTCAATGTATCAATACATGTATGAATGTACC
* * *
1527130 GATACATTCTTCAATGTATCTATGCATGTATGAATGTATC
1 GATACATTCTTCAATGTATCAATACATGTATGAATGTACC
* * *
1527170 AATACATTTTTAAATGTATC
1 GATACATTCTTCAATGTATC
1527190 GATATATTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (40 bp):
GATACATTCTTCAATGTATCAATACATGTATGAATGTACC
Found at i:1532707 original size:21 final size:21
Alignment explanation
Indices: 1532681--1532746 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
1532671 AATTTCAAGC
*
1532681 CAGAAAGCGTATCATACAGTG
1 CAGAAAGCGTATCATACATTG
** *
1532702 CAGAAATTGTA-GA-A-ATTG
1 CAGAAAGCGTATCATACATTG
1532720 CAGAAAGCGTATCATACATTG
1 CAGAAAGCGTATCATACATTG
1532741 CAGAAA
1 CAGAAA
1532747 TTGCCTGACT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 12 0.34
19 2 0.06
20 2 0.06
21 19 0.54
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (21 bp):
CAGAAAGCGTATCATACATTG
Found at i:1541001 original size:13 final size:13
Alignment explanation
Indices: 1540983--1541014 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1540973 CTTTCGTACC
1540983 AAAAAAACAAACA
1 AAAAAAACAAACA
*
1540996 AAAAAAATAAACA
1 AAAAAAACAAACA
1541009 AAAAAA
1 AAAAAA
1541015 GAGGTCCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAACA
Found at i:1541892 original size:26 final size:27
Alignment explanation
Indices: 1541854--1541904 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1541844 CAGAAAAGTC
*
1541854 TGAATAGCCTACAA-CCCTAGTGGAGT
1 TGAATAGCCTACAATCCCTAATGGAGT
**
1541880 TGAATAGTTTACAATCCCTAATGGA
1 TGAATAGCCTACAATCCCTAATGGA
1541905 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (27 bp):
TGAATAGCCTACAATCCCTAATGGAGT
Found at i:1542628 original size:179 final size:178
Alignment explanation
Indices: 1542307--1542806 Score: 594
Period size: 179 Copynumber: 2.8 Consensus size: 178
1542297 TTTCAAAGCT
* * * * * * *
1542307 CACAAGTCAGTGGCATCCTTCTCAAAGCCAACAAGTCAAT-AGCATCTTTTCAAAGCCCACAAGT
1 CACAAATCAATGGCA-CCTTTTCAAAGCCCACAAGTCAATGA-CACCCTTTCAAAGCCTACAAGT
* * * * *
1542371 CAATGGCAT--CCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTTTAAAGCCCACAAGTCAGTGG
64 TAGTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAGCCTACAAGTCAGTGG
***
1542434 TAACTCTTTTCAAAGTCCACACAAGTTGGTGGCAACTCTATTCAAAGCCCA
128 TAACTCTTTTCAAAGTCCACACAAGTCAATGGCAACTCTATTCAAAGCCCA
* *
1542485 CACAAATCAATGGTACCTTTTCAAAGCCCACAAGTTAATGACACCCTTTCAAAGCCTACAAGTTA
1 CACAAATCAATGGCACCTTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAGCCTACAAGTTA
1542550 GTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACCGTTTTCAAAGCCTACAAGTCAGTGGTA
66 GTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACC-TTTTCAAAGCCTACAAGTCAGTGGTA
* * *
1542615 ACTCTTATCAAAGTCCACACAAGTCAATGGCAACTGTGTTCAAAGCCCA
130 ACTCTTTTCAAAGTCCACACAAGTCAATGGCAACTCTATTCAAAGCCCA
* * * * * ** *
1542664 CATAAATCGATGGCACCCTTCCAAAGCCCACAAGTCAGTGGTACCCTCTCAAAG-CTCACAAGTT
1 CACAAATCAATGGCACCTTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAGCCT-ACAAGTT
* * * ** * *
1542728 AGCGACACACCCTTTCAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCTACACAAGTCGGTGG
65 AGTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCT--ACAAGTCAGTGG
1542793 TAACTCTTTTCAAA
128 TAACTCTTTTCAAA
1542807 TCACCACTTT
Statistics
Matches: 277, Mismatches: 38, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
177 47 0.17
178 28 0.10
179 178 0.64
180 24 0.09
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (178 bp):
CACAAATCAATGGCACCTTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAGCCTACAAGTTA
GTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCTACAAGTCAGTGGTAA
CTCTTTTCAAAGTCCACACAAGTCAATGGCAACTCTATTCAAAGCCCA
Found at i:1542657 original size:149 final size:144
Alignment explanation
Indices: 1542296--1542787 Score: 519
Period size: 149 Copynumber: 3.3 Consensus size: 144
1542286 AATACTACCT
* * * * *
1542296 TTTTCAAAGCTCACAAGTCAGTGGCATC-CTTCTCAAAGCCA-ACAAGTCAATAGCATCTTTTCA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAGCCACACAAGTCAATGGCAACTTTTCA
* *
1542359 AAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTTTAAAGCCCAC
66 AAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGTACCC-TTTCAAAGCCCAC
* * *
1542424 AAGTCAGTGGTAACTC
130 AAGTTAGTGG-CACAC
** * * *
1542440 TTTTCAAAGTCCACACAAGTTGGTGGCAACTC-TATTCAAAGCCCACACAAATCAATGGTACCTT
1 TTTTCAAAG-CC-CACAAGTCAGTGGCAACTCTTA-TCAAAG-CCACACAAGTCAATGGCAACTT
* * *
1542504 TTCAAAGCCCACAAGTTAATGACACCCTTTCAAAGCCTACAAGTTAGTGGCATACCCTTTCAAAG
62 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGG--TACCCTTTCAAAG
1542569 CCCACAAGTTAGTGGCAC-C
125 CCCACAAGTTAGTGGCACAC
* *
1542588 GTTTTCAAAGCCTACAAGTCAGTGGTAACTCTTATCAAAGTCCACACAAGTCAATGGCAACTGTG
1 -TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAG-CCACACAAGTCAATGGCAACT-T-
* * * * *
1542653 TTCAAAGCCCACATAAATCGATGGCACCCTTCCAAAGCCCACAAGTCAGTGGTACCCTCTCAAAG
62 TTCAAAGCCCAC--AAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTCAAAG
* * *
1542718 CTCACAAGTTAGCGACACACC
125 CCCACAAGTTAGTGGCACA-C
* * *
1542739 CTTTCAAAGCCCACAAGTCGGTGGC-ACCCTT-TCAAAGCCTACACAAGTC
1 TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAGCC-ACACAAGTC
1542788 GGTGGTAACT
Statistics
Matches: 291, Mismatches: 40, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
144 9 0.03
145 1 0.00
146 15 0.05
147 48 0.16
148 24 0.08
149 115 0.40
150 42 0.14
151 37 0.13
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (144 bp):
TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAGCCACACAAGTCAATGGCAACTTTTCA
AAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTCAAAGCCCACA
AGTTAGTGGCACAC
Found at i:1542784 original size:30 final size:28
Alignment explanation
Indices: 1542297--1542792 Score: 355
Period size: 28 Copynumber: 16.8 Consensus size: 28
1542287 ATACTACCTT
* *
1542297 TTTCAAAGCTCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
1542325 TTCTCAAAGCCAACAAGTCAATAGCATCT
1 TT-TCAAAGCCCACAAGTCAGTGGCACCC
* *
1542354 TTTCAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
1542382 TTTCAAAGCCCACAAGTTAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
1542410 TTTTTAAAGCCCACAAGTCAGTGGTAACTCT
1 -TTTCAAAGCCCACAAGTCAGTGG-CAC-CC
** *
1542441 TTTCAAAGTCCACACAAGTTGGTGGCAACTC
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC
* * * *
1542472 TATTCAAAGCCCACACAAATCAATGGTACCT
1 T-TTCAAAG-CC-CACAAGTCAGTGGCACCC
* * *
1542503 TTTCAAAGCCCACAAGTTAATGACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
1542531 TTTCAAAGCCTACAAGTTAGTGGCATACCC
1 TTTCAAAGCCCACAAGTCAGTGGC--ACCC
* *
1542561 TTTCAAAGCCCACAAGTTAGTGGCACCGT
1 TTTCAAAGCCCACAAGTCAGTGGCACC-C
* * *
1542590 TTTCAAAGCCTACAAGTCAGTGGTAACTC
1 TTTCAAAGCCCACAAGTCAGTGG-CACCC
* **
1542619 TTATCAAAGTCCACACAAGTCAATGGCAACTG
1 TT-TCAAAG-CC-CACAAGTCAGTGGC-ACCC
*
1542651 TGTTCAAAGCCCACATAAATC-GATGGCACCC
1 T-TTCAAAGCCCAC--AAGTCAG-TGGCACCC
* *
1542682 TTCCAAAGCCCACAAGTCAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
1542710 TCTCAAAGCTCACAAGTTAGCGACACACCC
1 TTTCAAAGCCCACAAGTCAGTG--GCACCC
*
1542740 TTTCAAAGCCCACAAGTCGGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
1542768 TTTCAAAGCCTACACAAGTCGGTGG
1 TTTCAAAGCC--CACAAGTCAGTGG
1542793 TAACTCTTTT
Statistics
Matches: 374, Mismatches: 69, Indels: 48
0.76 0.14 0.10
Matches are distributed among these distances:
28 129 0.34
29 70 0.19
30 99 0.26
31 14 0.04
32 61 0.16
33 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:1542940 original size:49 final size:49
Alignment explanation
Indices: 1542880--1543005 Score: 164
Period size: 49 Copynumber: 2.6 Consensus size: 49
1542870 TTAACCTAAT
*
1542880 GTCGCTGGCCTTGAATTAGAACATTGGTCCACTTTTCCCT-TAGCCCAAC
1 GTCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTATA-CCCAAC
* * * * * *
1542929 GTCTCTGGCCTTGAATGAGCACGTTAGTCTACTTTTCCCTATACCCAAT
1 GTCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTATACCCAAC
*
1542978 GTCGCTGGCCCTGAATTAGCACATTGGT
1 GTCGCTGGCCTTGAATTAGCACATTGGT
1543006 TATCTTCTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 62 0.97
50 2 0.03
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (49 bp):
GTCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTATACCCAAC
Found at i:1543671 original size:20 final size:20
Alignment explanation
Indices: 1543639--1543804 Score: 127
Period size: 20 Copynumber: 7.8 Consensus size: 20
1543629 TTTTACCCAG
*
1543639 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
1543659 ATTTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
1543679 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTCTTCA
1543699 ATGTATCGATACATTCTGTCTTTTTACCTA
1 ATGTATCGATACA---T-TC---TT--C-A
*
1543729 GATGTATCGATACATTCTACA
1 -ATGTATCGATACATTCTTCA
* * * *
1543750 ATGCATCGATACATGCATAA
1 ATGTATCGATACATTCTTCA
1543770 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1543790 ATGTATCGATACATT
1 ATGTATCGATACATT
1543805 TTGTCTTTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 26
0.72 0.11 0.16
Matches are distributed among these distances:
19 1 0.01
20 88 0.77
21 2 0.02
22 1 0.01
23 1 0.01
24 2 0.02
27 4 0.03
28 1 0.01
29 1 0.01
30 1 0.01
31 13 0.11
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1543758 original size:51 final size:50
Alignment explanation
Indices: 1543679--1543854 Score: 192
Period size: 51 Copynumber: 3.7 Consensus size: 50
1543669 ACATGTATGA
*
1543679 ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCTAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATT-TGTCTTTTTACCTAG
* * *
1543730 ATGTATCGATACATTCTACAATGCATCGATACA--TG-C-----A--TAA
1 ATGTATCGATACATTCTTCAATGTATCGATACATTTGTCTTTTTACCTAG
1543770 ATGTATCGATACATTCTTCAATGTATCGATACATTTTGTCTTTTTACCTAG
1 ATGTATCGATACATTCTTCAATGTATCGATACA-TTTGTCTTTTTACCTAG
* * * *
1543821 ATGTATCAATACATTATTCAATATATGGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACAT
1543855 CTAGTTAAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 23
0.75 0.08 0.17
Matches are distributed among these distances:
40 33 0.32
42 1 0.01
43 2 0.02
44 1 0.01
47 1 0.01
48 2 0.02
49 1 0.01
50 1 0.01
51 61 0.59
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (50 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTTGTCTTTTTACCTAG
Found at i:1543852 original size:91 final size:91
Alignment explanation
Indices: 1543628--1543854 Score: 337
Period size: 91 Copynumber: 2.5 Consensus size: 91
1543618 AAAAATCACA
* * * * *
1543628 TTTTTACCCAGATGTATTGATACATTCTTCAATTTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACATGCATAAATGTATCGATACAT
1543693 TATTCAATGTATCGATACATTCTGTC
66 TATTCAATGTATCGATACATTCTGTC
* **
1543719 TTTTTACCTAGATGTATCGATACATTCTACAATGCATCGATACATGCATAAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACATGCATAAATGTATCGATACAT
* *
1543784 TCTTCAATGTATCGATACATTTTGTC
66 TATTCAATGTATCGATACATTCTGTC
* * *
1543810 TTTTTACCTAGATGTATCAATACATTATTCAATATATGGATACAT
1 TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACAT
1543855 CTAGTTAAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 121 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (91 bp):
TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACATGCATAAATGTATCGATACAT
TATTCAATGTATCGATACATTCTGTC
Found at i:1548600 original size:13 final size:13
Alignment explanation
Indices: 1548582--1548607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1548572 CAATTTTTTG
1548582 TGTATCGATACAT
1 TGTATCGATACAT
1548595 TGTATCGATACAT
1 TGTATCGATACAT
1548608 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1548619 original size:32 final size:33
Alignment explanation
Indices: 1548562--1548625 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1548552 TACAAGCCAA
**
1548562 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1548595 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1548626 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1551197 original size:13 final size:13
Alignment explanation
Indices: 1551179--1551203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1551169 TAATCCCCCC
1551179 TGTATCGATACAT
1 TGTATCGATACAT
1551192 TGTATCGATACA
1 TGTATCGATACA
1551204 AAGAAAAATG
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:1553295 original size:15 final size:15
Alignment explanation
Indices: 1553275--1553305 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1553265 ATTTCGTTTG
*
1553275 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1553290 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1553305 G
1 G
1553306 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1557371 original size:10 final size:10
Alignment explanation
Indices: 1557337--1557364 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1557327 TTTGAAAATA
1557337 TAGCCGTTTC
1 TAGCCGTTTC
1557347 TAGCCGTTTC
1 TAGCCGTTTC
1557357 TAGCCGTT
1 TAGCCGTT
1557365 ACAAGCCAAT
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:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (10 bp):
TAGCCGTTTC
Found at i:1557412 original size:13 final size:13
Alignment explanation
Indices: 1557394--1557419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1557384 CAATTTTTTG
1557394 TGTATCGATACAT
1 TGTATCGATACAT
1557407 TGTATCGATACAT
1 TGTATCGATACAT
1557420 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1557431 original size:32 final size:33
Alignment explanation
Indices: 1557374--1557437 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1557364 TACAAGCCAA
**
1557374 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1557407 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1557438 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1557542 original size:20 final size:20
Alignment explanation
Indices: 1557489--1557544 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1557479 ACATCTTTTT
* *
1557489 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGAAA
1557509 CATGTATCGATACTTTGAAA
1 CATGTATCGATACTTTGAAA
**
1557529 TGTGTATCGATACTTT
1 CATGTATCGATACTTT
1557545 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGAAA
Found at i:1558007 original size:52 final size:52
Alignment explanation
Indices: 1557950--1558074 Score: 187
Period size: 52 Copynumber: 2.3 Consensus size: 52
1557940 CTATGTGGGG
* * *
1557950 ACCTTTTCCATTTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCATATTGGC
1 ACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGAC
*
1558002 ACCTTTTCCATCTTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGAC
1 ACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGAC
1558054 ATCCTTTTTCTCATCTTTAAG
1 A-CC-TTTTC-CATCTTTAAG
1558075 CCCCATATCG
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
52 49 0.74
53 2 0.03
54 5 0.08
55 10 0.15
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (52 bp):
ACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGAC
Found at i:1558089 original size:55 final size:52
Alignment explanation
Indices: 1557950--1558098 Score: 154
Period size: 52 Copynumber: 2.8 Consensus size: 52
1557940 CTATGTGGGG
* ** * * * *
1557950 ACCTTTTCCATTTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCATATTGGC
1 ACCTTTTCCATCTTTAAGCCCAATATAGTTGGCCTTGAATCAGCACATTGAC
** *
1558002 ACCTTTTCCATCTTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGAC
1 ACCTTTTCCATCTTTAAGCCCAATATAGTTGGCCTTGAATCAGCACATTGAC
* * *
1558054 ATCCTTTTTCTCATCTTTAAGCCCCATATCGTTGGCCGTGAATCA
1 A-CC-TTTTC-CATCTTTAAGCCCAATATAGTTGGCCTTGAATCA
1558099 ACATATTGGC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 49 0.58
53 2 0.02
54 5 0.06
55 28 0.33
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (52 bp):
ACCTTTTCCATCTTTAAGCCCAATATAGTTGGCCTTGAATCAGCACATTGAC
Found at i:1558923 original size:13 final size:13
Alignment explanation
Indices: 1558905--1558929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1558895 CATAAAGTGT
1558905 TGTATCGATACAA
1 TGTATCGATACAA
1558918 TGTATCGATACA
1 TGTATCGATACA
1558930 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1558927 original size:33 final size:33
Alignment explanation
Indices: 1558885--1558951 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1558875 TTCAACGATT
1558885 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1558918 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1558951 T
1 T
1558952 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1559010 original size:13 final size:13
Alignment explanation
Indices: 1558992--1559019 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1558982 ATTACTCAAA
1558992 TGTATCGATACAT
1 TGTATCGATACAT
1559005 TGTATCGATACAT
1 TGTATCGATACAT
1559018 TG
1 TG
1559020 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1559069 original size:52 final size:52
Alignment explanation
Indices: 1559025--1559149 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1559015 CATTGATCTT
1559025 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
1559077 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
1559129 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1559150 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:1567404 original size:52 final size:52
Alignment explanation
Indices: 1567326--1567453 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
1567316 CGAAATATGA
*
1567326 AAATTTGCCTGCATGTATCGATACA-TTTAATAGGGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AAGGTATCGATACATCTGGGC
*
1567378 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAAGGTATCGATACATCTGGGC
1567430 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1567454 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAAGGTATCGATACATCTGGGC
Found at i:1567466 original size:51 final size:50
Alignment explanation
Indices: 1567326--1567473 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 50
1567316 CGAAATATGA
* *
1567326 AAATTTGCCTGCATGTATCGATACATTTAATAGGGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
1567378 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
1567430 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1567474 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:1567480 original size:13 final size:13
Alignment explanation
Indices: 1567462--1567486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1567452 CAAAGATCAG
1567462 TGTATCGATACAA
1 TGTATCGATACAA
1567475 TGTATCGATACA
1 TGTATCGATACA
1567487 TTTGAGTAAT
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:1567568 original size:13 final size:13
Alignment explanation
Indices: 1567550--1567574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1567540 AAAAAAAATA
1567550 TGTATCGATACAT
1 TGTATCGATACAT
1567563 TGTATCGATACA
1 TGTATCGATACA
1567575 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1568458 original size:67 final size:68
Alignment explanation
Indices: 1568336--1568462 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
1568326 ATTGGGTTTT
* * *
1568336 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGACG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGACG
1568401 AGA
66 AGA
* * * * *
1568404 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATTTTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
1568463 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGACG
AGA
Found at i:1568596 original size:49 final size:49
Alignment explanation
Indices: 1568475--1569653 Score: 1440
Period size: 49 Copynumber: 24.7 Consensus size: 49
1568465 AAAAGGATGT
* *
1568475 CAATCTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
1568527 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGATGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1568576 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1568619 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1568668 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAAGGGGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1568717 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1568766 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G-A--TGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1568809 CAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1568858 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1568907 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1568956 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1568999 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1569048 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1569097 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1569146 CAATATGCTGATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1569189 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1569238 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAAGGGGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1569287 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATGATGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1569336 CAATATGCTGATTCAAGGCCAACGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1569379 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1569428 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAAGGGGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1569477 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATGATGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1569526 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1569569 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1569618 CAATATGCTGATTCAATGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
1569654 GAAGGGTTGC
Statistics
Matches: 965, Mismatches: 126, Indels: 75
0.83 0.11 0.06
Matches are distributed among these distances:
43 217 0.22
44 2 0.00
45 6 0.01
46 1 0.00
47 7 0.01
48 2 0.00
49 692 0.72
51 1 0.00
52 37 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1568769 original size:190 final size:190
Alignment explanation
Indices: 1568475--1569658 Score: 1990
Period size: 190 Copynumber: 6.2 Consensus size: 190
1568465 AAAAGGATGT
* * ** * * * *
1568475 CAATCTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGT-G--AAGGGGCCAATGTGCTGAGT
* *
1568540 CAAGGCCAGCTATATTGGACTTAAAGGTGATGATGCCAATATGCTGATTCAAGGCCAGCGATATT
63 CAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATT
1568605 GGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
128 GGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1568668 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
* * * * *
1568733 GGCCAGCTACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
66 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
* * *
1568798 CTTAAAGATGCCAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * * *
1568858 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
1568923 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
66 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1568988 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1569048 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
*
1569113 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCTAGCGATATTGGA
66 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1569178 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1569238 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
* *
1569303 GGCCAGCTACATTGGTCTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAACGATATTGGA
66 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1569368 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1569428 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
*
1569493 GGCCAGCTACATTGGTCTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
66 GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
*
1569558 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
131 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1569618 CAATATGCTGATTCAATGCCAGCTATATTGGGCTTAGAAGG
1 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA-AAGG
1569659 GTTGCGACCG
Statistics
Matches: 941, Mismatches: 49, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
190 901 0.96
191 4 0.00
192 1 0.00
193 35 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (190 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGGGCCAATGTGCTGAGTCAA
GGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1569909 original size:35 final size:34
Alignment explanation
Indices: 1569694--1570391 Score: 803
Period size: 34 Copynumber: 20.8 Consensus size: 34
1569684 AGAAAGGGTG
* * *
1569694 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1569727 CAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAA-G--AA
* *
1569764 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1569798 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1569832 AAAGAGTGCCACGGAGTTGTGGGC-TT-AGAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1569865 AAAGAGTGCCACGTAGTTGTGGGCTTTAAGAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1569900 AAATTGTGCCACAGAGTTGTGGGCTTT-AAAAGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1569934 AAAGGTGCCACGGAGTTGTGGGC-TTAGAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG-AA
1569968 AGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 A-AAGGTGCCACGGAGTTGTGGGCTTTAAAAA--GAA
*
1570005 AAAGAGTGCCACGGAGTTGTGGGTTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1570040 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
1570074 AAAGGTGCCACGGAGTTGTGGGTTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1570108 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
1570142 AAAGGTGCCATGGAGTTGTGGGC-TT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * **
1570172 ---GGTGCCACGGAGTCGTGGACTTTAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1570203 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
1570238 AAATTGTGCCACAGAGTTGTGGGCTTTGAAAAG--
1 AAA-GGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
1570271 -AAGGTGCCACGGAGTTGTGGGCTTTGAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
1570302 -AAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1570335 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
1570367 -AAGGTGCCACGGAGTCGTGGACTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
1570392 GAGACAAAAT
Statistics
Matches: 592, Mismatches: 46, Indels: 56
0.85 0.07 0.08
Matches are distributed among these distances:
27 17 0.03
28 2 0.00
29 3 0.01
31 81 0.14
32 9 0.02
33 67 0.11
34 232 0.39
35 114 0.19
36 9 0.02
37 39 0.07
38 19 0.03
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
Found at i:1570178 original size:27 final size:27
Alignment explanation
Indices: 1570140--1570200 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1570130 CTTTAAAAAG
* * * *
1570140 AAAAAGGTGCCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
1570167 AAAAGGGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
1570194 TAAAGGG
1 AAAAGGG
1570201 AAAAAGAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.38, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:1570412 original size:30 final size:29
Alignment explanation
Indices: 1570340--1570484 Score: 157
Period size: 31 Copynumber: 4.7 Consensus size: 29
1570330 AAGAAGAAGG
* * *
1570340 TGCCACGGAGTTGTGGGCTTTGA-AAAGAA
1 TGCCACTGAGTCGTGGACTTTGAGAAA-AA
*
1570369 GGTGCCACGGAGTCGTGGACTTTGAGACAAAA
1 --TGCCACTGAGTCGTGGACTTTGAGA-AAAA
1570401 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTG-AGAAAA--A
*
1570433 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAA-A-AA
1570464 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1570485 AAAAAAGGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
30 24 0.23
31 49 0.48
32 27 0.26
33 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.24
Consensus pattern (29 bp):
TGCCACTGAGTCGTGGACTTTGAGAAAAA
Found at i:1570477 original size:93 final size:94
Alignment explanation
Indices: 1569759--1570484 Score: 315
Period size: 102 Copynumber: 7.3 Consensus size: 94
1569749 CTTTAAAAAG
* * * * * * *
1569759 GAAAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAGAAG-GTGCCACGGAGTCGTGGACTTTG-A-GACAAA-A-TGCCACGGAGTCGTGGACTT
* * * * * *
1569824 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
61 TGAAAGAAGAAG-GTGCCACGGAGTCGTGGACTTT
* * * * *
1569859 GAAGGAA-AAGAGTGCCACGTAGTTGTGGGCTTTAAGAAGA-AAAATTGTGCCACAGAGTTGTGG
1 GAA--AAGAAG-GTGCCACGGAGTCGTGGACTTT--G-AGACAAAA---TGCCACGGAGTCGTGG
* * * * * *
1569922 GCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAGAAG
57 ACTTTGAAAGAAGAAGGTGCCACGGAGTCGTGGACTT----T
* * * * * **
1569964 GAAAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGT
1 GAAAAGAAGGTGCCACGGAGTCGTGGACTTT-----GAGACAAA-A-TGCCACGGAGTCGTGGAC
* * * *
1570029 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
59 TTT-GAAAGAAGAAGGTGCCACGGAGTCGTGGACTTT
* * ** * * *
1570066 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGTTTTAAAAAGA-AAAAGGTGCCACGGAGTTGTGGG
1 GAAAAG---AAGGTGCCACGGAGTCGTGGACTTT---GAGACAAAA--TGCCACGGAGTCGTGGA
* * * * *
1570130 CTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGGC-TT
58 CTTT-GAAAGAAGAAGGTGCCACGGAGTCGTGGACTTT
* * * *
1570167 -AAAAG--GGTGCCACGGAGTCGTGGACTTTAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAGAAGGTGCCACGGAGTCGTGGACTTT---GAGACAAA-A-TGCCACGGAGTCGTGGACTT
* * * * * *
1570229 TAAAAAGAAAAATTGTGCCACAGAGTTGTGGGCTTT
61 T-GAAAGAAGAA-GGTGCCACGGAGTCGTGGACTTT
* * * *
1570265 GAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGA-A-AAGAAGGTGCCACGGAGTTGTGGGCTTTG
1 GAAAAGAAGGTGCCACGGAGTCGTGGACTTTGAGACAA-AA--TGCCACGGAGTCGTGGACTTTG
* *
1570328 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT
63 -AAAGAAGAAGGTGCCACGGAGTCGTGGACTTT
*
1570361 GAAAAGAAGGTGCCACGGAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTG-AA
1 GAAAAGAAGGTGCCACGGAGTCGTGGACTTTGAGACAAAATGCCACGGAGTCGTGGACTTTGAAA
*
1570425 GAA-AAGGATGCCACTGAGTCGTGGACTTT
66 GAAGAAGG-TGCCACGGAGTCGTGGACTTT
* * *
1570454 GAGAAG-AGATTGCCACTGAGTCGTGGACTTT
1 GAAAAGAAG-GTGCCACGGAGTCGTGGACTTT
1570485 AAAAAAGGTA
Statistics
Matches: 547, Mismatches: 44, Indels: 77
0.82 0.07 0.12
Matches are distributed among these distances:
92 6 0.01
93 48 0.09
95 44 0.08
96 91 0.17
97 53 0.10
98 5 0.01
99 5 0.01
100 9 0.02
101 72 0.13
102 92 0.17
103 31 0.06
104 3 0.01
105 49 0.09
106 38 0.07
107 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (94 bp):
GAAAAGAAGGTGCCACGGAGTCGTGGACTTTGAGACAAAATGCCACGGAGTCGTGGACTTTGAAA
GAAGAAGGTGCCACGGAGTCGTGGACTTT
Found at i:1571441 original size:9 final size:9
Alignment explanation
Indices: 1571429--1571454 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1571419 GTTTTTCCCT
1571429 TTTTTTTTG
1 TTTTTTTTG
1571438 TTTTTTTTG
1 TTTTTTTTG
1571447 TTTTTTTT
1 TTTTTTTT
1571455 TGTGAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1571441 original size:10 final size:10
Alignment explanation
Indices: 1571428--1571457 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1571418 GGTTTTTCCC
1571428 TTTTTTTTTG
1 TTTTTTTTTG
1571438 -TTTTTTTTG
1 TTTTTTTTTG
1571447 TTTTTTTTTG
1 TTTTTTTTTG
1571457 T
1 T
1571458 GAAGATTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1575499 original size:21 final size:21
Alignment explanation
Indices: 1575475--1575517 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1575465 ATCAAAATGA
1575475 CATTCATTGCATGACGAGATG
1 CATTCATTGCATGACGAGATG
1575496 CATTCATTGCATGACGAGATG
1 CATTCATTGCATGACGAGATG
1575517 C
1 C
1575518 TCCTGACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
CATTCATTGCATGACGAGATG
Found at i:1578818 original size:52 final size:52
Alignment explanation
Indices: 1578740--1578867 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
1578730 CGAAATATGA
* *
1578740 AAATTTGCCTGCATGTATCGATACA-TTTAATAGGGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AAGGTATCGATACATCTGGGC
*
1578792 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAAGGTATCGATACATCTGGGC
1578844 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1578868 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 21 0.29
52 46 0.64
53 5 0.07
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAAGGTATCGATACATCTGGGC
Found at i:1578880 original size:51 final size:50
Alignment explanation
Indices: 1578740--1578887 Score: 176
Period size: 52 Copynumber: 2.9 Consensus size: 50
1578730 CGAAATATGA
* * *
1578740 AAATTTGCCTGCATGTATCGATACATTTAATAGGGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
1578792 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
1578844 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1578888 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 45 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:1578894 original size:13 final size:13
Alignment explanation
Indices: 1578876--1578900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1578866 CAAAGATCAG
1578876 TGTATCGATACAA
1 TGTATCGATACAA
1578889 TGTATCGATACA
1 TGTATCGATACA
1578901 TTTGAGTAAT
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:1579253 original size:50 final size:51
Alignment explanation
Indices: 1579135--1579269 Score: 191
Period size: 50 Copynumber: 2.6 Consensus size: 51
1579125 ATTTGCTTGC
*
1579135 ATGTATCGATACATTGAAGAATGTATCGATACATTTAGGTCAAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTAGGT-AAAAACCCAGA
* * *
1579187 ATGTATCGATACAATGAAGAATGTATTGATACATTTGGGT-TAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTAAAAACCCAGA
* * *
1579237 ATGTATCGATAAAATGAAAAATGTATCAATACA
1 ATGTATCGATACAATGAAGAATGTATCGATACA
1579270 ATGGAAAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
50 38 0.51
52 37 0.49
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTAAAAACCCAGA
Found at i:1579261 original size:20 final size:21
Alignment explanation
Indices: 1579236--1579288 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1579226 TTAAACCCAG
1579236 AATGTATCGATAAAAT-GAAA
1 AATGTATCGATAAAATGGAAA
* *
1579256 AATGTATCAATACAATGGAAA
1 AATGTATCGATAAAATGGAAA
*
1579277 AATATATCGATA
1 AATGTATCGATA
1579289 CATTTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (21 bp):
AATGTATCGATAAAATGGAAA
Found at i:1579278 original size:21 final size:20
Alignment explanation
Indices: 1579236--1579290 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
1579226 TTAAACCCAG
*
1579236 AATGTATCGATAAAATGAAA
1 AATGTATCGATACAATGAAA
*
1579256 AATGTATCAATACAATGGAAA
1 AATGTATCGATACAAT-GAAA
*
1579277 AATATATCGATACA
1 AATGTATCGATACA
1579291 TTTTCATTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:1590242 original size:21 final size:22
Alignment explanation
Indices: 1590209--1590259 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1590199 AATTGTAGTA
1590209 TTTGATTTAATTTTAATTTAAT
1 TTTGATTTAATTTTAATTTAAT
* * *
1590231 TTTGA-TTGATTTTAGTTTGAT
1 TTTGATTTAATTTTAATTTAAT
*
1590252 TTTAATTT
1 TTTGATTT
1590260 GAATAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (22 bp):
TTTGATTTAATTTTAATTTAAT
Found at i:1590260 original size:11 final size:11
Alignment explanation
Indices: 1590213--1590261 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1590203 GTAGTATTTG
*
1590213 ATTTAATTTTA
1 ATTTGATTTTA
* *
1590224 ATTTAATTTTG
1 ATTTGATTTTA
1590235 A-TTGATTTTA
1 ATTTGATTTTA
*
1590245 GTTTGATTTTA
1 ATTTGATTTTA
1590256 ATTTGA
1 ATTTGA
1590262 ATAATAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 7 0.22
11 25 0.78
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (11 bp):
ATTTGATTTTA
Found at i:1590393 original size:23 final size:23
Alignment explanation
Indices: 1590351--1590395 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1590341 TTTATTTTTT
*
1590351 AATTTTATATTAATATAAAAATG
1 AATTTTAAATTAATATAAAAATG
1590374 AATTTCTAAATTAATA-AAAAAT
1 AATTT-TAAATTAATATAAAAAT
1590396 TAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTTTAAATTAATATAAAAATG
Found at i:1597105 original size:18 final size:18
Alignment explanation
Indices: 1597082--1597116 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1597072 GAATTTAAAA
1597082 TAGTTAATAAAACATTAG
1 TAGTTAATAAAACATTAG
1597100 TAGTTAATAAAACATTA
1 TAGTTAATAAAACATTA
1597117 TTCATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (18 bp):
TAGTTAATAAAACATTAG
Found at i:1598921 original size:13 final size:13
Alignment explanation
Indices: 1598903--1598927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1598893 CTATTTATGA
1598903 TGTATCGATACAC
1 TGTATCGATACAC
1598916 TGTATCGATACA
1 TGTATCGATACA
1598928 TGAATAGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1599016 original size:21 final size:21
Alignment explanation
Indices: 1598991--1599031 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1598981 CCTATGAACA
1598991 GTGATGTATCGATACATGAAG
1 GTGATGTATCGATACATGAAG
1599012 GTGATGTATCGATACATGAA
1 GTGATGTATCGATACATGAA
1599032 CAGTGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
GTGATGTATCGATACATGAAG
Found at i:1599054 original size:16 final size:16
Alignment explanation
Indices: 1599033--1599063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1599023 ATACATGAAC
*
1599033 AGTGATGAATAGTGAT
1 AGTGATGAACAGTGAT
1599049 AGTGATGAACAGTGA
1 AGTGATGAACAGTGA
1599064 AAATGAGATT
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:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (16 bp):
AGTGATGAACAGTGAT
Found at i:1599153 original size:53 final size:53
Alignment explanation
Indices: 1599089--1599223 Score: 216
Period size: 53 Copynumber: 2.5 Consensus size: 53
1599079 ACTACCAATG
1599089 TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACCTA
1 TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACCTA
* * * *
1599142 TATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCTAATGTCCTG
1 TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACCTA
*
1599195 TATCGATACATATTTGTGTGTATCAATAC
1 TATCGATACATATTT-TGTGTATCGATAC
1599224 TATGTAATCT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 63 0.84
54 12 0.16
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (53 bp):
TATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACCTA
Found at i:1599218 original size:20 final size:20
Alignment explanation
Indices: 1599193--1599263 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1599183 GCTAATGTCC
**
1599193 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1599213 TGTATCAATAC-TATGTAATC
1 TGTATCGATACATAT-TAATG
1599233 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1599253 TGTATCGATAC
1 TGTATCGATAC
1599264 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.10
20 37 0.88
21 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1599329 original size:21 final size:21
Alignment explanation
Indices: 1599303--1599343 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1599293 GTCAACCTTG
1599303 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1599324 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1599344 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1599719 original size:79 final size:77
Alignment explanation
Indices: 1599642--1600055 Score: 413
Period size: 79 Copynumber: 5.2 Consensus size: 77
1599632 AATAGGGTCG
* * *
1599642 GAGTACTCCCTCAGAAATAACGGGGTTGGAGTATCCTCAATAGTGAAAAATCGATGTTTT-GAAA
1 GAGTA-TCCCTCAGAAATAACGGGGTTGGAGTATCC-CAATTGTGAAAAATTGGTGTTTTGGAAA
* *
1599706 GTAAAATTGGGGTCA
64 -TAAAATCGGGGTTA
* * *
1599721 GAGTATCTCCTC-GAAAATAACGAGGTTGGAGTATCCCTAATTGTGAAAAATGGGTATTTTGGAA
1 GAGTATC-CCTCAG-AAATAACGGGGTTGGAGTATCCC-AATTGTGAAAAATTGGTGTTTTGGAA
*
1599785 ATAAAATCGGGGTTG
63 ATAAAATCGGGGTTA
* *
1599800 GAGTATCTCCTC-GAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGGAA
1 GAGTATC-CCTCAG-AAATAACGGGGTTGGAGTAT-CCCAATTGTGAAAAATTGGTGTTTTGGAA
1599864 ATAAAATCGGGGTTA
63 ATAAAATCGGGGTTA
* * * ** *
1599879 GACTATCCCCTTAGAAATAAC-GGGTTGAAGTATCCTTGATTGTAAAAAATTGGTGTTTTGGAAA
1 GAGTAT-CCCTCAGAAATAACGGGGTTGGAGTATCC-CAATTGTGAAAAATTGGTGTTTTGGAAA
* *
1599943 TAAAACCGGAGTTA
64 TAAAATCGGGGTTA
* * * * * *
1599957 GAGTATCCCTTCAAAAATAACGAGATTGGAGTATCCCTAATTGTGGAAAAGTGGTGTTTTGAAAA
1 GAGTATCCC-TCAGAAATAACGGGGTTGGAGTATCCC-AATTGTGAAAAATTGGTGTTTTGGAAA
*
1600022 TAAAATCGAGGTTA
64 TAAAATCGGGGTTA
* * *
1600036 CAGTATTCCATCGGAAATAA
1 GAGTA-TCCCTCAGAAATAA
1600056 AAACATGAAT
Statistics
Matches: 284, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
77 5 0.02
78 66 0.23
79 201 0.71
80 12 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (77 bp):
GAGTATCCCTCAGAAATAACGGGGTTGGAGTATCCCAATTGTGAAAAATTGGTGTTTTGGAAATA
AAATCGGGGTTA
Found at i:1599986 original size:157 final size:157
Alignment explanation
Indices: 1599642--1600035 Score: 461
Period size: 157 Copynumber: 2.5 Consensus size: 157
1599632 AATAGGGTCG
* * * * *
1599642 GAGTACTCCCTCAGAAATAACGGGGTTGGAGTATCCTCAATAGTGAAAAATCGATGTTTT-GAAA
1 GAGTA-TCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAA
* * * * * * *
1599706 GTAAAATTGGGGTCAGAGTATCTCCTCGAAAATAACGAGGTTGGAGTATCCCTAATTGTGAAAAA
65 -TAAAATCGGGGTTAGACTATCCCCTAGAAAATAACGAGGTTGAAGTATCCCTAATTGTAAAAAA
* * *
1599771 TGGGTATTTTGGAAATAAAATCGGGGTTG
129 TGGGTATTTTGGAAATAAAACCGGAGTTA
* * *
1599800 GAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGGAAA
1 GAGTATC-CCTCAAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAA
* *
1599865 TAAAATCGGGGTTAGACTATCCCCTTAG-AAATAACG-GGTTGAAGTATCCTTGATTGTAAAAAA
65 TAAAATCGGGGTTAGACTATCCCC-TAGAAAATAACGAGGTTGAAGTATCCCTAATTGTAAAAAA
* *
1599928 TTGGTGTTTTGGAAATAAAACCGGAGTTA
129 TGGGTATTTTGGAAATAAAACCGGAGTTA
* * * * * *
1599957 GAGTATCCCTTCAAAAATAACGAGATTGGAGTATCCCTAATTGTGGAAAAGTGGTGTTTTGAAAA
1 GAGTATCCC-TCAAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAA
*
1600022 TAAAATCGAGGTTA
65 TAAAATCGGGGTTA
1600036 CAGTATTCCA
Statistics
Matches: 200, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
156 2 0.01
157 115 0.57
158 77 0.38
159 6 0.03
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (157 bp):
GAGTATCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAAT
AAAATCGGGGTTAGACTATCCCCTAGAAAATAACGAGGTTGAAGTATCCCTAATTGTAAAAAATG
GGTATTTTGGAAATAAAACCGGAGTTA
Found at i:1602438 original size:70 final size:70
Alignment explanation
Indices: 1602338--1602492 Score: 195
Period size: 70 Copynumber: 2.2 Consensus size: 70
1602328 AAAATGCCTA
* * * * *
1602338 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAA-CTAAGAATGTATTGATATA
1 AATGTATCAATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAA-AATGTATCGATACA
1602402 ATGAAC
65 ATGAAC
* * * *
1602408 AATGTATCAATGCAATGAATAATGTCTCGATACATTTGGGTAAAACCCAAAATGTATCGATACAA
1 AATGTATCAATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCGATACAA
*
1602473 TGAAT
66 TGAAC
*
1602478 AATGTATCGATACAA
1 AATGTATCAATACAA
1602493 ATTGTGAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
70 69 0.96
71 3 0.04
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (70 bp):
AATGTATCAATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCGATACAA
TGAAC
Found at i:1603122 original size:43 final size:41
Alignment explanation
Indices: 1603092--1603203 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 41
1603082 AGAGTACGTT
1603092 TTGCTCTTTGAGGACAAAAGAAAAGAAGGAAATTAAATGTGTC
1 TTGCTCTTTGAGGACAAAAGAAAA-AAGGAAA-TAAATGTGTC
* * *
1603135 TTGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGCGTCC
1 TTGCTCTTTGAGGACAAAAGAAAAAAGGAAATAAA-TGTGT-C
* * *
1603178 CT-CTCTTTGAGGACAAAGGGAAAAAG
1 TTGCTCTTTGAGGACAAAAGAAAAAAG
1603204 AAAGGAAGCG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
41 4 0.07
42 33 0.54
43 24 0.39
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.22
Consensus pattern (41 bp):
TTGCTCTTTGAGGACAAAAGAAAAAAGGAAATAAATGTGTC
Found at i:1603184 original size:42 final size:42
Alignment explanation
Indices: 1603093--1603232 Score: 151
Period size: 41 Copynumber: 3.3 Consensus size: 42
1603083 GAGTACGTTT
* * * *
1603093 TGCTCTTTGAGGACAAAAGAAAAGAAGGAAATTAAA-TGTGTCT
1 TGCTCTTTGAGGACAAAGGAGAA-AAGGAAA-TAAAGTGCGTCC
1603136 TGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGCGTCCC
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGCGT-CC
* ** *
1603179 T-CTCTTTGAGGACAAAGG-GAAAAAGAAAGGAAGCGCGTCC
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGCGTCC
*
1603219 TGCTCTTTGGGGAC
1 TGCTCTTTGAGGAC
1603233 TAGAAGGTGC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
40 3 0.04
41 31 0.36
42 28 0.33
43 23 0.27
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (42 bp):
TGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGCGTCC
Found at i:1603769 original size:300 final size:302
Alignment explanation
Indices: 1603214--1603816 Score: 853
Period size: 300 Copynumber: 2.0 Consensus size: 302
1603204 AAAGGAAGCG
* * * * ** *
1603214 CGTCCTGCTCTTTGGGGACTAGAAGGTGCCACTAACTTGTGTGGGCTTTGCAAGGAGAAAGCGTC
1 CGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAGAAAGAGTC
* *
1603279 CTACTTTTTGAGGACTAAAAGGTGTCACCAGTTCGTGTGGGCTTTAAAAAGAAAAGGCATCCTGC
66 CTACTTTTTGAGGACTAAAAGGTGCCACCACTTCGTGTGGGCTTTAAAAAGAAAAGG-ATCCTGC
* * * *
1603344 TTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCGTCCTGCTCTT
130 TCTTTGAGAACTGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAGAAGAAAGCGTCCTGCTCTT
* *
1603409 TGAGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAAGTGTCTTGCTCTTTGAA
195 TGAGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAAGCGTCCTGCTCTTTGAA
* *
1603474 GACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
260 GACTGA-AAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAA
*
1603517 CGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGA-AAAGGAGT
1 CGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAGAAA-GAGT
* * *
1603581 CCTACTTTTTGAGGACTAGAAGGTGCCACCAACTT-GTGTGGGCTTTGAAAA-AAAATG-TCCTG
65 CCTACTTTTTGAGGACTAAAAGGTGCCACC-ACTTCGTGTGGGCTTTAAAAAGAAAAGGATCCTG
*
1603643 CTCTTTGAGAACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAA-AAAGCGTCCTGCTC
129 CTCTTTGAGAACTGAAAGGTGCCACCAACTTGTGTGGACTTTAAAA-GAAGAAAGCGTCCTGCTC
* *
1603707 TTTGGGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGGCGTCCTGCTCTT
193 TTTGAGGACTGA-AAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAA-GCGTCCTGCTCTT
* *
1603770 TGAGGACTGAAAATTGCCACCAACTTATGTGGGCTTTAAAAGGAAAA
256 TGAAGACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAA
1603817 GGCATCCTGC
Statistics
Matches: 268, Mismatches: 26, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
299 7 0.03
300 151 0.56
301 4 0.01
302 8 0.03
303 95 0.35
304 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (302 bp):
CGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAGAAAGAGTC
CTACTTTTTGAGGACTAAAAGGTGCCACCACTTCGTGTGGGCTTTAAAAAGAAAAGGATCCTGCT
CTTTGAGAACTGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAGAAGAAAGCGTCCTGCTCTTT
GAGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAAGCGTCCTGCTCTTTGAAG
ACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAA
Found at i:1603839 original size:61 final size:61
Alignment explanation
Indices: 1603213--1603841 Score: 773
Period size: 61 Copynumber: 10.4 Consensus size: 61
1603203 GAAAGGAAGC
* * **
1603213 GCGTCCTGCTCTTTGGGGACT-AGAAGGTGCCACTAACTTGTGTGGGCTTTGCAAGGAGAAA-
1 GCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAG
* * * * * *
1603274 GCGTCCTACTTTTTGAGGACTAAAAGGTGTCACC-AGTTCGTGTGGGCTTTAAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTT-GTGTGGGCTTTAAAAGGAAAAG
* *
1603335 GCATCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAGAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA-AAG
* *
1603396 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
1603457 GTGTCTTGCTCTTTGAAGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-
1 GCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
1603517 -CGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
1603577 GAGTCCTACTTTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA--AAAA-
1 GCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAG
* * * * *
1603636 -TGTCCTGCTCTTTGAGAACTGGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
1603696 GCGTCCTGCTCTTTGGGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
** *
1603757 GCGTCCTGCTCTTTGAGGACTGAAAATTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
1603818 GCATCCTGCT-TTTCGAGGACTGAA
1 GCGTCCTGCTCTTT-GAGGACTGAA
1603842 CGGATAGAAG
Statistics
Matches: 497, Mismatches: 51, Indels: 40
0.85 0.09 0.07
Matches are distributed among these distances:
57 4 0.01
58 42 0.08
59 56 0.11
60 17 0.03
61 366 0.74
62 12 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
Found at i:1604822 original size:28 final size:29
Alignment explanation
Indices: 1604791--1604846 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1604781 AGCAGGTTCT
1604791 TTTCATTTT-TTTTGGTTGTTCTTTTTTG
1 TTTCATTTTGTTTTGGTTGTTCTTTTTTG
* * *
1604819 TTTCATTTTGTTTTTGTTTTTGTTTTTT
1 TTTCATTTTGTTTTGGTTGTTCTTTTTT
1604847 TTGAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.04, C:0.05, G:0.12, T:0.79
Consensus pattern (29 bp):
TTTCATTTTGTTTTGGTTGTTCTTTTTTG
Found at i:1610522 original size:33 final size:33
Alignment explanation
Indices: 1610480--1610545 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1610470 ACACACCCAG
**
1610480 ATGTATCAATACATTATGCTTTGTATCGATACA
1 ATGTATCAATACATTATGAATTGTATCGATACA
1610513 ATGTATCAATACATTATGAATTGTATCGATACA
1 ATGTATCAATACATTATGAATTGTATCGATACA
1610546 TAGCTACGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
ATGTATCAATACATTATGAATTGTATCGATACA
Found at i:1615898 original size:4 final size:4
Alignment explanation
Indices: 1615889--1615919 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1615879 AAACAAAACA
*
1615889 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1615920 CACCTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1619559 original size:45 final size:45
Alignment explanation
Indices: 1619509--1619603 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
1619499 TATTAAAGCA
1619509 ATTTAACAATTACAAATTTCTTTCACCCCCTTAATCATAAAATTT
1 ATTTAACAATTACAAATTTCTTTCACCCCCTTAATCATAAAATTT
*
1619554 ATTTAACAATTACAAATTTCTTTCTCCCCCTTAATCATAAAATTT
1 ATTTAACAATTACAAATTTCTTTCACCCCCTTAATCATAAAATTT
1619599 ATTTA
1 ATTTA
1619604 CAGAGATTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (45 bp):
ATTTAACAATTACAAATTTCTTTCACCCCCTTAATCATAAAATTT
Found at i:1626161 original size:13 final size:13
Alignment explanation
Indices: 1626143--1626168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1626133 TACAGCAAGT
1626143 ATGTATCGATACA
1 ATGTATCGATACA
1626156 ATGTATCGATACA
1 ATGTATCGATACA
1626169 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:1630253 original size:15 final size:15
Alignment explanation
Indices: 1630233--1630271 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1630223 TAAAAATGTC
*
1630233 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1630248 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
1630263 CCAAATGAA
1 CAAAATGAA
1630272 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1632358 original size:20 final size:21
Alignment explanation
Indices: 1632280--1632357 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
1632270 ATGTCCAAAA
*
1632280 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
1632300 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
1632324 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
1632345 TGTATCGATACAT
1 TGTATCGATACAT
1632358 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:1632362 original size:13 final size:13
Alignment explanation
Indices: 1632344--1632382 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1632334 ACATTTTTTG
1632344 TTGTATCGATACA
1 TTGTATCGATACA
1632357 TTGTATCGATACA
1 TTGTATCGATACA
*
1632370 CTGTATCGATACA
1 TTGTATCGATACA
1632383 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1634229 original size:18 final size:16
Alignment explanation
Indices: 1634188--1634233 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
1634178 AATTACTTGA
1634188 TTAAGGGGGAGATTTT
1 TTAAGGGGGAGATTTT
1634204 TTAAGGGGGAGATTTT
1 TTAAGGGGGAGATTTT
1634220 TTAAACGGGGGAGA
1 TT-AA-GGGGGAGA
1634234 CAAAGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 18 0.64
17 2 0.07
18 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.39, T:0.30
Consensus pattern (16 bp):
TTAAGGGGGAGATTTT
Found at i:1634950 original size:13 final size:13
Alignment explanation
Indices: 1634932--1634957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1634922 TACAGCAAGT
1634932 ATGTATCGATACA
1 ATGTATCGATACA
1634945 ATGTATCGATACA
1 ATGTATCGATACA
1634958 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:1638097 original size:28 final size:28
Alignment explanation
Indices: 1638061--1638132 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
1638051 AATAAAATCG
*
1638061 GGGTTGGAGTATCCCCTCGAAAATAAC-
1 GGGTTGGAGTATCCCCTCAAAAATAACA
1638088 GTGGTTGGAGTATCCCCTCAAAAATAACA
1 G-GGTTGGAGTATCCCCTCAAAAATAACA
1638117 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
1638133 GATTGCGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 1 0.02
28 40 0.95
29 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCAAAAATAACA
Found at i:1638123 original size:107 final size:107
Alignment explanation
Indices: 1637980--1638211 Score: 324
Period size: 107 Copynumber: 2.2 Consensus size: 107
1637970 AAAATAAAAT
* * * * *
1637980 CGGGGTTGGAGTATCCCCTCGAAAATAATGAGGTTGGAGTATCCCTAATTGTGAAAAATTGCTAT
1 CGGGGTTGGAGTATCCCCTCAAAAATAAAGAGGTTGGAGTATCCCCAATTGCGAAAAATTGATAT
* *
1638045 TTTGAAAATAAAATCGGGGTTGGAGTATCCCCTC-GAAAATAA
66 TTTGAAAATAAAACCGAGGTTGGAGTATCCCCTCAG-AAATAA
* * *
1638087 CGTGGTTGGAGTATCCCCTCAAAAATAACAG-GGTTGGAGTATCCCCGATTGCGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTCAAAAATAA-AGAGGTTGGAGTATCCCCAATTGCGAAAAATTGATA
* *
1638151 TTTTGGAAATAAAACCGAGTTTGGAGTATCCCCTCAGAAATAA
65 TTTTGAAAATAAAACCGAGGTTGGAGTATCCCCTCAGAAATAA
1638194 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1638212 GAATGTGAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
107 108 0.98
108 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAAAGAGGTTGGAGTATCCCCAATTGCGAAAAATTGATAT
TTTGAAAATAAAACCGAGGTTGGAGTATCCCCTCAGAAATAA
Found at i:1638175 original size:79 final size:79
Alignment explanation
Indices: 1638090--1638667 Score: 707
Period size: 79 Copynumber: 7.3 Consensus size: 79
1638080 AAAATAACGT
* * *
1638090 GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGCGAAAAATTGATGTTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
1638155 GGAAATAAAACCGA
66 GGAAATAAAACCGA
* *
1638169 GTTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAATGTGAAAAATT-AGTGTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTTT
1638233 TGGAAATAAAACCGA
65 TGGAAATAAAACCGA
* * *
1638248 GGTTGAAGTATCTCCTC-GAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTT
1 GGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTT
* *
1638312 TGAAAATAAAATCGA
65 TGGAAATAAAACCGA
* * * * * *
1638327 AGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATGCTCAATTGTGAAAAATTTG-TATTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAA-TTGATGTTT
**
1638391 TGGAAATAAAA-ATA
65 TGGAAATAAAACCGA
* * * *
1638405 GGGTTGGAGTATCCCCTTAGAAATAACGGGGTTGGAGTATCCCCGATTATGGAAAAGTGATGTTT
1 -GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTT
* * *
1638470 TGGAAAAAAAATCGG
65 TGGAAATAAAACCGA
* * * * *
1638485 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATTCCCAATTGTGGAAAATTGGTGTTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
* ** *
1638550 AGAAATAAAATTGG
66 GGAAATAAAACCGA
* * * * *
1638564 GGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAAGTGGTGTTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
1638629 GGAAATAAAACCG-
66 GGAAATAAAACCGA
* *
1638642 GAGTTGGAGTATCCCTTCGGAAATAA
1 G-GTTGGAGTATCCCCTCAGAAATAA
1638668 AAACATGAAT
Statistics
Matches: 432, Mismatches: 58, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
78 6 0.01
79 422 0.98
80 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
GGAAATAAAACCGA
Found at i:1641034 original size:24 final size:20
Alignment explanation
Indices: 1640989--1641094 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
1640979 AAAAATGCCT
1640989 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
1641009 AAATGTATCGATACACTTGGGTAA
1 AAATGTATCGATACA-TT--G-AA
*
1641033 AACCTGGATTGTATCGATACAATGAA
1 AA-----A-TGTATCGATACATTGAA
* *
1641059 TAATGTATCGATACAATGAA
1 AAATGTATCGATACATTGAA
* *
1641079 TAATATATCGATACAT
1 AAATGTATCGATACAT
1641095 CTGGGTAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
20 46 0.64
21 3 0.04
23 1 0.01
24 4 0.06
26 3 0.04
27 1 0.01
29 2 0.03
30 12 0.17
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATTGAA
Found at i:1641103 original size:70 final size:70
Alignment explanation
Indices: 1640990--1641144 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
1640980 AAAATGCCTA
* * *** *
1640990 AATGTATCGATACATTGAAAAATGTATCGATACACTTGGGTAAAACCTGGATTGTATCGATACAA
1 AATGTATCGATACAATGAAAAATATATCGATACACTTGGGTAAAACCCAAAATGTATCGATACAA
1641055 TGAAT
66 TGAAT
*
1641060 AATGTATCGATACAATGAATAATATATCGATACA-TCTGGGTAAAACCCAAAATGTATCGATACA
1 AATGTATCGATACAATGAAAAATATATCGATACACT-TGGGTAAAACCCAAAATGTATCGATACA
1641124 ATGAAT
65 ATGAAT
1641130 AATGTATCGATACAA
1 AATGTATCGATACAA
1641145 ATTGTGAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
69 1 0.01
70 76 0.99
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (70 bp):
AATGTATCGATACAATGAAAAATATATCGATACACTTGGGTAAAACCCAAAATGTATCGATACAA
TGAAT
Found at i:1645778 original size:37 final size:37
Alignment explanation
Indices: 1645737--1645812 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
1645727 TTTAAGCAAT
*
1645737 TCCTTGACAAACTATGAAAACTATTCT-GTGGATGATG
1 TCCTTAACAAACTATGAAAACTATT-TAGTGGATGATG
*
1645774 TCCTTAACAAACTATGAAAACTGTTTAGTGGATGATG
1 TCCTTAACAAACTATGAAAACTATTTAGTGGATGATG
1645811 TC
1 TC
1645813 ACAATCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 35 0.97
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (37 bp):
TCCTTAACAAACTATGAAAACTATTTAGTGGATGATG
Found at i:1646650 original size:166 final size:164
Alignment explanation
Indices: 1646359--1646914 Score: 634
Period size: 167 Copynumber: 3.3 Consensus size: 164
1646349 AATTATGAGG
* * * *
1646359 TTTTCTTCTCCGTAATTTTTTTCGAGGGGTTTTTTCTTGATTTTTAATTTTTAAAATTCATAAAA
1 TTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAAAATTCATCAAA
* * * * *
1646424 TATCATTATTTATTTCATATTAATTAAATTTTCAAAAATTAATTCATTTTCAGAAGTTTTTGAAT
66 CATCATTATTTATTTCATAGTAATTTAGTTTTCAAAAATTAATTCATTTTCAG-AGTTTTTGATT
* *
1646489 TTTTCCTTCAAACTCCCATTTTTTTGAAATACTATA
130 TTTTCCTTGAAACTCCC-TTTTTTTGAAATACCATA
* *
1646525 TTTTCTACTTCGTAAATTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
1 TTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAAAATTCATCAAA
*
1646590 CATCATTATTTATTTCATAGTAATTTAGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTTATT
66 CATCATTATTTATTTCATAGTAATTTAGTTTTCAAAAATTAATTCATTTTCA-GAGTTTTTGA-T
* *** **
1646655 TTTTTCCTTGAAACTTCCCTTTCTCCAAAATACGGTA
129 TTTTTCCTTGAAAC-TCCCTTTTTTTGAAATACCATA
* * * * * * *
1646692 TTTTCTACTTCGTAAATTTTTTCAAGGGGAGTTTTCTTGGTTTTCAATTTTTAGAATCCATCAAA
1 TTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAAAATTCATCAAA
* * *
1646757 CATCATCATTTGA-TTCATAGTAATTTAGTTTTAAAAAATTAATTCATTTTCACGAGTTTTGGAT
66 CATCATTATTT-ATTTCATAGTAATTTAGTTTTCAAAAATTAATTCATTTTCA-GAGTTTTTGAT
** * * *
1646821 TTTGTTTGTTGAAATTCCCTTTTTTTTGAGACACCA-A
129 TTT-TTCCTTGAAACTCCC-TTTTTTTGAAATACCATA
* * *
1646858 GTTTTCTTCTCCATAAATTTTTTCG-GGGAGATTTTTCTT-ATTTTAAAATTTTTAAAA
1 -TTTTCTACTCCGTAAATTTTTTCGAGGG-GATTTTTCTTGATTTT-TAATTTTTAAAA
1646915 GGCTTCTAAT
Statistics
Matches: 333, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
166 131 0.39
167 197 0.59
168 5 0.02
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.50
Consensus pattern (164 bp):
TTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAAAATTCATCAAA
CATCATTATTTATTTCATAGTAATTTAGTTTTCAAAAATTAATTCATTTTCAGAGTTTTTGATTT
TTTCCTTGAAACTCCCTTTTTTTGAAATACCATA
Found at i:1647534 original size:10 final size:10
Alignment explanation
Indices: 1647519--1647546 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1647509 GAAAAGCAAG
1647519 AGAAAATAGA
1 AGAAAATAGA
1647529 AGAAAATAGA
1 AGAAAATAGA
1647539 AGAAAATA
1 AGAAAATA
1647547 TGTAGAAAAA
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:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (10 bp):
AGAAAATAGA
Found at i:1654712 original size:20 final size:20
Alignment explanation
Indices: 1654682--1654728 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1654672 CAATTTGTCA
*
1654682 ATACAATAAGTTAATGTATCG
1 ATAC-ATAAGTGAATGTATCG
*
1654703 ATACATAAGTGAATGTATTG
1 ATACATAAGTGAATGTATCG
1654723 ATACAT
1 ATACAT
1654729 GCTTGAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (20 bp):
ATACATAAGTGAATGTATCG
Found at i:1658340 original size:21 final size:22
Alignment explanation
Indices: 1658311--1658383 Score: 98
Period size: 21 Copynumber: 3.5 Consensus size: 22
1658301 GTGAACAGTG
1658311 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
1658333 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
* * *
1658354 TGAACAATGATGAATAG-TA-A
1 TGAACAGTGATGTATCGATACA
1658374 TGAACAGTGA
1 TGAACAGTGA
1658384 AAATGAGATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.22
21 23 0.50
22 13 0.28
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:1658443 original size:18 final size:19
Alignment explanation
Indices: 1658407--1658443 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1658397 CTACTACCAA
1658407 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1658426 TGTATCGATACA-ATTTTG
1 TGTATCGATACATATTTTG
1658444 GCTACTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1658471 original size:53 final size:53
Alignment explanation
Indices: 1658407--1658543 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
1658397 CTACTACCAA
* *
1658407 TGTATCGATACATATTTTGTGTATCGATACAATTTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTAGCTACTGCCAATGACC
* *
1658460 TGTATCGATACATATTGTGTGTATCGATACAAATTTAGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTAGCTACTGCCAATGACC
1658513 TGTATCGATACATATTTATGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1658544 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTAGCTACTGCCAATGACC
Found at i:1658538 original size:20 final size:20
Alignment explanation
Indices: 1658513--1658583 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1658503 GCCAATGTCC
*
1658513 TGTATCGATACATATTTATG
1 TGTATCGATACATATTAATG
* *
1658533 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1658553 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1658573 TGTATCGATAC
1 TGTATCGATAC
1658584 TTTTCAGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.07
20 39 0.91
21 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1658647 original size:21 final size:21
Alignment explanation
Indices: 1658623--1658663 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1658613 GTCAACCTTG
1658623 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1658644 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1658664 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1659184 original size:13 final size:13
Alignment explanation
Indices: 1659166--1659190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1659156 CAATTCATTA
1659166 TGTATCGATACAT
1 TGTATCGATACAT
1659179 TGTATCGATACA
1 TGTATCGATACA
1659191 ATGTGCCATG
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:1659284 original size:19 final size:19
Alignment explanation
Indices: 1659240--1659295 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1659230 CTGCCAGTTT
* **
1659240 CATGTCTCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
1659260 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1659279 CATGTATTGATACAATG
1 CATGTATCGATACAATG
1659296 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1663596 original size:13 final size:13
Alignment explanation
Indices: 1663578--1663603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1663568 TACAGCAAGT
1663578 ATGTATCGATACA
1 ATGTATCGATACA
1663591 ATGTATCGATACA
1 ATGTATCGATACA
1663604 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:1668768 original size:20 final size:20
Alignment explanation
Indices: 1668689--1668768 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1668679 AATGTCCAAA
*
1668689 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1668709 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1668734 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1668754 TTGTATCGATACATT
1 ATGTATCGATACATT
1668769 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1668772 original size:13 final size:13
Alignment explanation
Indices: 1668754--1668792 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1668744 ACATTTTTCT
1668754 TTGTATCGATACA
1 TTGTATCGATACA
1668767 TTGTATCGATACA
1 TTGTATCGATACA
*
1668780 CTGTATCGATACA
1 TTGTATCGATACA
1668793 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1671331 original size:13 final size:13
Alignment explanation
Indices: 1671313--1671338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1671303 TACAGCAAGT
1671313 ATGTATCGATACA
1 ATGTATCGATACA
1671326 ATGTATCGATACA
1 ATGTATCGATACA
1671339 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:1675193 original size:15 final size:15
Alignment explanation
Indices: 1675175--1675205 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1675165 CGAGTCAACT
1675175 TCATCATTATCATCA
1 TCATCATTATCATCA
*
1675190 TCATCATTATCTTCA
1 TCATCATTATCATCA
1675205 T
1 T
1675206 TATCTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (15 bp):
TCATCATTATCATCA
Done.