Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_pilon, whole genome shotgun sequence
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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1360732 original size:49 final size:49
Alignment explanation
Indices: 1360657--1360751 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
1360647 AGTCCTTAAG
1360657 CAGGGGCGGACCTCCATGGTGCTCGGGGTATCTCAAGCAACCCCTCATC
1 CAGGGGCGGACCTCCATGGTGCTCGGGGTATCTCAAGCAACCCCTCATC
* *
1360706 CAGGGGCGGACCTCCATGGTGTTCGGGGTATCTCAGGCAACCCCTC
1 CAGGGGCGGACCTCCATGGTGCTCGGGGTATCTCAAGCAACCCCTC
1360752 CACAAGTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.19
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGGTGCTCGGGGTATCTCAAGCAACCCCTCATC
Found at i:1360798 original size:16 final size:16
Alignment explanation
Indices: 1360745--1360799 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
1360735 ATCTCAGGCA
*
1360745 ACCCCTCCACAAGTGTC
1 ACCCCT-CAAAAGTGTC
*
1360762 ACCCCTAATACAAGTGTC
1 ACCCCTCA-A-AAGTGTC
*
1360780 ACCCCTCAAAAGTGCC
1 ACCCCTCAAAAGTGTC
1360796 ACCC
1 ACCC
1360800 TGGGGCTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 11 0.34
17 7 0.22
18 14 0.44
ACGTcount: A:0.29, C:0.44, G:0.11, T:0.16
Consensus pattern (16 bp):
ACCCCTCAAAAGTGTC
Found at i:1362941 original size:3 final size:3
Alignment explanation
Indices: 1362909--1362969 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
1362899 TCTACAAAAA
1362909 TAT T-T TAT TA- TAT TAT ATATT TATT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT -TA-T TA-T TAT TAT TAT TAT TAT TA-T TAT
*
1362956 T-T TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT
1362970 AGGCCCCACA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 6 0.12
3 32 0.64
4 11 0.22
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1362964 original size:21 final size:22
Alignment explanation
Indices: 1362909--1362970 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 22
1362899 TCTACAAAAA
1362909 TATTTTATTA-TATTATATATT
1 TATTTTATTATTATTATATATT
1362930 TA-TTTATTATTATTATTATTATT
1 TATTTTATTATTATTA-TA-TATT
*
1362953 TATTTTATTATTTTTATA
1 TATTTTATTATTATTATA
1362971 GGCCCCACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 7 0.19
21 7 0.19
22 2 0.06
23 8 0.22
24 12 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTATTATTATTATATATT
Found at i:1369539 original size:20 final size:21
Alignment explanation
Indices: 1369506--1369559 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1369496 TCCCAATCCC
* *
1369506 CTTAAATCTATAAATCTAA-A
1 CTTAAATCTCTAAACCTAATA
*
1369526 CTTAAATCCCTAAACCTAATA
1 CTTAAATCTCTAAACCTAATA
*
1369547 CATAAATCTCTAA
1 CTTAAATCTCTAA
1369560 CTTTAATTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (21 bp):
CTTAAATCTCTAAACCTAATA
Found at i:1370140 original size:13 final size:13
Alignment explanation
Indices: 1370109--1370152 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1370099 TAAGAAATAA
1370109 TATTT-TTATTTT
1 TATTTATTATTTT
* *
1370121 TACTTATTACTTT
1 TATTTATTATTTT
1370134 TATTTATTATTTAT
1 TATTTATTATTT-T
1370148 TATTT
1 TATTT
1370153 TTAATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 4 0.15
13 16 0.62
14 6 0.23
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTATTATTTT
Found at i:1370147 original size:20 final size:19
Alignment explanation
Indices: 1370112--1370155 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1370102 GAAATAATAT
1370112 TTTTATTTTTACTTATTAC
1 TTTTATTTTTACTTATTAC
* *
1370131 TTTTATTTATTATTTATTAT
1 TTTTATTT-TTACTTATTAC
1370151 TTTTA
1 TTTTA
1370156 ATATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTACTTATTAC
Found at i:1370273 original size:18 final size:19
Alignment explanation
Indices: 1370252--1370312 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
1370242 TAAACTTCAT
1370252 TTAAAA-TAATATATATTA
1 TTAAAAGTAATATATATTA
* *
1370270 TTAATTAAGTAAAAGATATT-
1 TTAA--AAGTAATATATATTA
* *
1370290 CTAAAATTAATATATATTA
1 TTAAAAGTAATATATATTA
1370309 TTAA
1 TTAA
1370313 TTAAGTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 15 0.47
19 3 0.09
20 5 0.16
21 9 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (19 bp):
TTAAAAGTAATATATATTA
Found at i:1374522 original size:30 final size:30
Alignment explanation
Indices: 1374434--1374522 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
1374424 ATTTTAAATT
* *
1374434 AATAATAAAAT-TAATTTATATCATT-TTAA
1 AATAATTAAATATAATTT-TATTATTATTAA
* *
1374463 ATTTAAATAAA-ATAATTATT-TTAATTATTAA
1 A-ATAATTAAATATAATT-TTATT-ATTATTAA
1374494 AATAATTAAATATAATTTTATTATTATTA
1 AATAATTAAATATAATTTTATTATTATTA
1374523 TTATTATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
29 2 0.04
30 31 0.66
31 14 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AATAATTAAATATAATTTTATTATTATTAA
Found at i:1376114 original size:332 final size:335
Alignment explanation
Indices: 1375504--1376164 Score: 1078
Period size: 332 Copynumber: 2.0 Consensus size: 335
1375494 TAAAATATGG
* * * *
1375504 GTAAAGTACACAAATGGTTCCCCGATTATCGGATGTTGTTTTGTTGAGTTTCCTAATTATTAAAA
1 GTAAAGTACACAAATGGTTCCCCGATTATCGAACGCTGCTTTGTTGAGTTTCCTAATTATTAAAA
*
1375569 ATTACAAAATGATCCCCGACTATAGAGAGTTGCTTTGTTGAGTCCCTCGAGTACTATTAAAGGTT
66 ATTACAAAATGATCCCCGACTATAGAGAGTCGCTTTGTTGAGTCCCTCGAGTACTATTAAAGGTT
*
1375634 AGAAAATGGTAACTCGACTATTCATTATGTTCCAAACTTGTCATTTTTCATTAAAAAACAGTCTA
131 ACAAAATGGTAACTCGACTATTCATTATGTTCCAAACTTGTCATTTTTCATTAAAAAACAGTCTA
*
1375699 AGCTGGACGTTAACATGTTAATTGAGATATCATAAAATCTGATCGCATAATCTCAAACACTATCA
196 AGCTGGACGTTAACATGTTAACTGAGATATCATAAAATCTGATCGCATAATCTCAAACACTATCA
* * * *
1375764 TACCTCAGCCAACATGTTAACTTCCAATCCATACGGTTGTTAATATTTTAACTGAAAATGACGAG
261 TACCTCAGCCAACATGTTAACGTCCAACCCAGACAGTTGTTAATATTTTAACTGAAAATGACGAG
1375829 TTTGTAACTT
326 TTTGTAACTT
* *
1375839 GTAAAGTACACAAATGGTTCCTCGATTATCGAACGCTGCTTTGTTGAGTTTCCTGATTATTAAAA
1 GTAAAGTACACAAATGGTTCCCCGATTATCGAACGCTGCTTTGTTGAGTTTCCTAATTATTAAAA
1375904 ATTACAAAATGAT-CCCGACTATATG-GAGTCGCTTTGTTGAGTCCCTCGAGTACTATTAAAGGT
66 ATTACAAAATGATCCCCGACTATA-GAGAGTCGCTTTGTTGAGTCCCTCGAGTACTATTAAAGGT
* *
1375967 TACAAAATGGTCAC-CGACTATTCATTATGTTCCAAACTTGTCATTTTTCGTT-AAAAACAGTCT
130 TACAAAATGGTAACTCGACTATTCATTATGTTCCAAACTTGTCATTTTTCATTAAAAAACAGTCT
* * * *
1376030 AAGCTGGACGTTAACATGTTGACTGATATATCATAAAATCTGATCTCATAATCTCAAACGCTATC
195 AAGCTGGACGTTAACATGTTAACTGAGATATCATAAAATCTGATCGCATAATCTCAAACACTATC
* * * *
1376095 ATACCTCAGCCAGCATGTTAACGTCCAGCCCAGACAGTTGTTAGTTTTTTAACTGAAAATGACGA
260 ATACCTCAGCCAACATGTTAACGTCCAACCCAGACAGTTGTTAATATTTTAACTGAAAATGACGA
1376160 GTTTG
325 GTTTG
1376165 AAACATAATA
Statistics
Matches: 302, Mismatches: 23, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
332 133 0.44
333 37 0.12
334 59 0.20
335 73 0.24
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (335 bp):
GTAAAGTACACAAATGGTTCCCCGATTATCGAACGCTGCTTTGTTGAGTTTCCTAATTATTAAAA
ATTACAAAATGATCCCCGACTATAGAGAGTCGCTTTGTTGAGTCCCTCGAGTACTATTAAAGGTT
ACAAAATGGTAACTCGACTATTCATTATGTTCCAAACTTGTCATTTTTCATTAAAAAACAGTCTA
AGCTGGACGTTAACATGTTAACTGAGATATCATAAAATCTGATCGCATAATCTCAAACACTATCA
TACCTCAGCCAACATGTTAACGTCCAACCCAGACAGTTGTTAATATTTTAACTGAAAATGACGAG
TTTGTAACTT
Found at i:1376522 original size:21 final size:20
Alignment explanation
Indices: 1376498--1376536 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1376488 AAAAAGGAAA
1376498 AATAATAAAATAATAAAAATT
1 AATAATAAAA-AATAAAAATT
* *
1376519 AATAGTAATAAATAAAAA
1 AATAATAAAAAATAAAAA
1376537 GAGTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAATAAAAAATAAAAATT
Found at i:1377342 original size:25 final size:24
Alignment explanation
Indices: 1377295--1377342 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1377285 AAATACTAAT
* *
1377295 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
1377319 TAAAATACATAAAACAAATATAAA
1 TAAAATAC-TAAAACAAATATAAA
1377343 ATATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:1377355 original size:25 final size:25
Alignment explanation
Indices: 1377295--1377357 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1377285 AAATACTAAT
* * *
1377295 TAAAATACTAAAACATATTTAAACTA
1 TAAAATA-TAAAACAAATATAAAATA
*
1377321 -AAATACATAAAACAAATATAAAATA
1 TAAA-ATATAAAACAAATATAAAATA
1377346 TAAAATATAAAA
1 TAAAATATAAAA
1377358 ATAATATCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (25 bp):
TAAAATATAAAACAAATATAAAATA
Found at i:1379826 original size:17 final size:18
Alignment explanation
Indices: 1379789--1379829 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1379779 ATATTATGTA
*
1379789 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1379807 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1379824 TTTACT
1 TTTACT
1379830 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1381530 original size:18 final size:18
Alignment explanation
Indices: 1381507--1381542 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1381497 CACAGCAGCC
* *
1381507 ACCGCAGCCATTTATGAT
1 ACCGCAACCATATATGAT
1381525 ACCGCAACCATATATGAT
1 ACCGCAACCATATATGAT
1381543 GTCGCCGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (18 bp):
ACCGCAACCATATATGAT
Found at i:1382310 original size:21 final size:21
Alignment explanation
Indices: 1382284--1382328 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1382274 GATTTCTGGG
* *
1382284 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1382305 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1382326 CAA
1 CAA
1382329 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1382926 original size:18 final size:18
Alignment explanation
Indices: 1382903--1382937 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1382893 CTAGGAGATT
1382903 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1382921 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1382938 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1383022 original size:21 final size:22
Alignment explanation
Indices: 1382993--1383036 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1382983 GTTGTATGAT
1382993 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1383014 AGAATATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1383036 A
1 A
1383037 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.34
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1383266 original size:2 final size:2
Alignment explanation
Indices: 1383259--1383308 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1383249 GAACATGTGA
1383259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1383301 AT AT AT AT
1 AT AT AT AT
1383309 GTCTAAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1384020 original size:23 final size:23
Alignment explanation
Indices: 1383976--1384020 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1383966 ATCATTATAT
* *
1383976 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGATGCAATTATACGG
* *
1383999 GGCACTTCGATGCATTTATACG
1 GGCACTACGATGCAATTATACG
1384021 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGG
Found at i:1388665 original size:12 final size:12
Alignment explanation
Indices: 1388627--1388672 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1388617 AATCATAATA
*
1388627 AACAATAATTAT
1 AACAAAAATTAT
*
1388639 AAAAAAAATTAT
1 AACAAAAATTAT
*
1388651 AACAAAATTTAT
1 AACAAAAATTAT
1388663 AACGAAAAAT
1 AAC-AAAAAT
1388673 CGCACGAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (12 bp):
AACAAAAATTAT
Found at i:1389052 original size:51 final size:51
Alignment explanation
Indices: 1388952--1389063 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
1388942 CTAGGTGGCG
* * * **
1388952 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGTAAGTCATGTCAGCA
1 TATAGCGCGGATCAAGGGGCGCGCTATACCCACGTGGAACTCAAATCAGCA
*
1389003 TATAGCGCGG-TACAAGGGGCGCGCTATACCCCACGTGGCACT-AAATCAGCA
1 TATAGCGCGGAT-CAAGGGGCGCGCTATA-CCCACGTGGAACTCAAATCAGCA
1389054 TATAGCGCGG
1 TATAGCGCGG
1389064 GACAGAGAGC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.02
51 42 0.79
52 10 0.19
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (51 bp):
TATAGCGCGGATCAAGGGGCGCGCTATACCCACGTGGAACTCAAATCAGCA
Found at i:1390083 original size:36 final size:36
Alignment explanation
Indices: 1390031--1390101 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1390021 TTGATGCTAA
*
1390031 TAATAAGTCATATTACTT-GATGAATACACTTATTAG
1 TAATAAGTCATATTACTTGGA-GAATAAACTTATTAG
*
1390067 TAATAAGTCATGTTACTTGGAGAATAAACTTATTA
1 TAATAAGTCATATTACTTGGAGAATAAACTTATTA
1390102 CTTTTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (36 bp):
TAATAAGTCATATTACTTGGAGAATAAACTTATTAG
Found at i:1402531 original size:20 final size:19
Alignment explanation
Indices: 1402508--1402546 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1402498 TTTCTTTTAT
1402508 TAAAATAATATGTTGAAATA
1 TAAAAT-ATATGTTGAAATA
* *
1402528 TAAAATTTATTTTGAAATA
1 TAAAATATATGTTGAAATA
1402547 AAATATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
TAAAATATATGTTGAAATA
Found at i:1402544 original size:19 final size:19
Alignment explanation
Indices: 1402520--1402556 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1402510 AAATAATATG
1402520 TTGAAATATAAA-ATTTATT
1 TTGAAATA-AAATATTTATT
1402539 TTGAAATAAAATATTTAT
1 TTGAAATAAAATATTTAT
1402557 ATAATCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TTGAAATAAAATATTTATT
Found at i:1405146 original size:17 final size:17
Alignment explanation
Indices: 1405108--1405146 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1405098 AACTAAAACT
1405108 AAAATTAGGAAAACTAC
1 AAAATTAGGAAAACTAC
* * *
1405125 GAAATTAGGACAATTAC
1 AAAATTAGGAAAACTAC
1405142 AAAAT
1 AAAAT
1405147 GGCAGAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (17 bp):
AAAATTAGGAAAACTAC
Found at i:1405885 original size:55 final size:54
Alignment explanation
Indices: 1405814--1406274 Score: 467
Period size: 55 Copynumber: 8.6 Consensus size: 54
1405804 TGACGGGTCC
* * * * * *
1405814 GCTCACTATTTCTTCAGGGAGTATAAGACTCGCACAATGTTCAGCAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCG-ACAATCTTCAACAAACGTGTCT
* * * * *
1405869 GCTCCCTATTCGTTCAGGGAGTATAAGATTCGAACAATCTTCAGCAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCG-ACAATCTTCAACAAACGTGTCT
* * * * *
1405924 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTTAACAAACGGGTCA
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCG-ACAATCTTCAACAAACGTGTCT
* ** * * * *
1405979 GTTCCCTATTTGTTCAGAGAGTATAGGACTCGATCAATCTTCGTA-AAACGGGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGA-CAATCTTC-AACAAACGTGTCT
* * *
1406034 GCTCTCTATTCCTTCAGAGTGTAT-AGAACTCGAACAATCTTCAACAAACGAGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCG-ACAATCTTCAACAAACGTGTCT
* * *
1406089 GCTCCCTATTCCTTCATAGAGTATAGGACT---CAATCTTTAACAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGACAATCTTCAACAAACGTGTCT
* *
1406140 GCTCCCTATTCCTACAGAGAGTATAAGACTCG---ATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGACAATCTTCAACAAACGTGTCT
* * *
1406191 GCTCCCTATTCCTTCTGAGAGTATAAGACTCG---ATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGACAATCTTCAACAAACGTGTCT
*
1406242 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGA
1406275 TCTTCATAAA
Statistics
Matches: 352, Mismatches: 45, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
51 141 0.40
54 3 0.01
55 205 0.58
56 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGACAATCTTCAACAAACGTGTCT
Found at i:1406309 original size:102 final size:102
Alignment explanation
Indices: 1406070--1406280 Score: 289
Period size: 102 Copynumber: 2.1 Consensus size: 102
1406060 AACTCGAACA
* * * * *
1406070 ATCTTCAACAAACGAGTCTGCTCCCTATTCCTTCAT-AGAGTATAGGACTCAATCTTTAACAAAC
1 ATCTTCAACAAACGAGTCCGCTCACTACTCCTTC-TGAGAGTATAAGACTCAATCTTCAACAAAC
*
1406134 GTGTCTGCTCCCTATTCCTACAGAGAGTATAAGACTCG
65 GTGTCCGCTCCCTATTCCTACAGAGAGTATAAGACTCG
* * * * *
1406172 ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCTGAGAGTATAAGACTCGATCTTCAATAAACG
1 ATCTTCAACAAACGAGTCCGCTCACTACTCCTTCTGAGAGTATAAGACTCAATCTTCAACAAACG
* *
1406237 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
66 TGTCCGCTCCCTATTCCTACAGAGAGTATAAGACTCG
1406274 ATCTTCA
1 ATCTTCA
1406281 TAAAATGAGT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 1 0.01
102 98 0.99
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (102 bp):
ATCTTCAACAAACGAGTCCGCTCACTACTCCTTCTGAGAGTATAAGACTCAATCTTCAACAAACG
TGTCCGCTCCCTATTCCTACAGAGAGTATAAGACTCG
Found at i:1406335 original size:37 final size:36
Alignment explanation
Indices: 1406285--1406359 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
1406275 TCTTCATAAA
* *
1406285 ATGAGTTTGCTTCACTACTCTTCTGTGAAGGCTTATAG
1 ATGAGTTTACTTCACCACTCTTC-GTGAAGGCTTA-AG
1406323 ATGA-TTTACTTCACCACTCTTCGTGAAGGCTTAAG
1 ATGAGTTTACTTCACCACTCTTCGTGAAGGCTTAAG
1406358 AT
1 AT
1406360 TGACTTGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 4 0.11
36 11 0.31
37 16 0.46
38 4 0.11
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (36 bp):
ATGAGTTTACTTCACCACTCTTCGTGAAGGCTTAAG
Found at i:1407675 original size:16 final size:15
Alignment explanation
Indices: 1407639--1407734 Score: 90
Period size: 16 Copynumber: 6.1 Consensus size: 15
1407629 CCCCCTTTTA
1407639 TTTTCTTTTTTTCAT
1 TTTTCTTTTTTTCAT
*
1407654 TTTTC-ATTTTTC-T
1 TTTTCTTTTTTTCAT
1407667 TTTTCTTCATTTTTCACT
1 TTTTCTT--TTTTTCA-T
1407685 TTTTCATTTTTTTCAT
1 TTTTC-TTTTTTTCAT
*
1407701 TTTT-TATTTTTCATTT
1 TTTTCTTTTTTTCA--T
1407717 TTTTCATTTTTTTCAT
1 TTTTC-TTTTTTTCAT
1407733 TT
1 TT
1407735 CATTTTTTCA
Statistics
Matches: 67, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
13 6 0.09
14 14 0.21
15 5 0.07
16 19 0.28
17 7 0.10
18 14 0.21
19 2 0.03
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTTTCAT
Found at i:1407675 original size:23 final size:23
Alignment explanation
Indices: 1407639--1407727 Score: 137
Period size: 23 Copynumber: 3.9 Consensus size: 23
1407629 CCCCCTTTTA
1407639 TTTTC-TTTTTTTCATTTTTCAT
1 TTTTCATTTTTTTCATTTTTCAT
1407661 TTTTC-TTTTTCTTCATTTTTCACT
1 TTTTCATTTTT-TTCATTTTTCA-T
*
1407685 TTTTCATTTTTTTCATTTTTTAT
1 TTTTCATTTTTTTCATTTTTCAT
1407708 TTTTCATTTTTTTCATTTTT
1 TTTTCATTTTTTTCATTTTT
1407728 TTCATTTCAT
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
22 10 0.16
23 32 0.51
24 16 0.25
25 5 0.08
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCATTTTTTTCATTTTTCAT
Found at i:1407688 original size:9 final size:9
Alignment explanation
Indices: 1407639--1407734 Score: 83
Period size: 9 Copynumber: 12.0 Consensus size: 9
1407629 CCCCCTTTTA
1407639 TTTTC-TTT
1 TTTTCATTT
1407647 TTTTCA--T
1 TTTTCATTT
1407654 TTTTCA--T
1 TTTTCATTT
1407661 TTTTC-TTT
1 TTTTCATTT
1407669 TTCTTCA--T
1 TT-TTCATTT
*
1407677 TTTTCA-CT
1 TTTTCATTT
1407685 TTTTCATTT
1 TTTTCATTT
1407694 TTTTCA-TT
1 TTTTCATTT
1407702 TTTT-A--T
1 TTTTCATTT
1407708 TTTTCATTT
1 TTTTCATTT
1407717 TTTTCATTT
1 TTTTCATTT
1407726 TTTTCATTT
1 TTTTCATTT
1407735 CATTTTTTCA
Statistics
Matches: 77, Mismatches: 1, Indels: 19
0.79 0.01 0.20
Matches are distributed among these distances:
6 5 0.06
7 19 0.25
8 24 0.31
9 29 0.38
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCATTT
Found at i:1407698 original size:47 final size:46
Alignment explanation
Indices: 1407639--1407727 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 46
1407629 CCCCCTTTTA
1407639 TTTTCTTTTTTTCATTTTTCATTTTTC-TTTTTCTTCATTTTTCACT
1 TTTTCTTTTTTTCATTTTTCATTTTTCATTTTT-TTCATTTTTCACT
*
1407685 TTTTCATTTTTTTCATTTTTTATTTTTCATTTTTTTCATTTTT
1 TTTTC-TTTTTTTCATTTTTCATTTTTCATTTTTTTCATTTTT
1407728 TTCATTTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
46 5 0.12
47 30 0.75
48 5 0.12
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.76
Consensus pattern (46 bp):
TTTTCTTTTTTTCATTTTTCATTTTTCATTTTTTTCATTTTTCACT
Found at i:1407727 original size:7 final size:7
Alignment explanation
Indices: 1407646--1407718 Score: 83
Period size: 7 Copynumber: 9.7 Consensus size: 7
1407636 TTATTTTCTT
1407646 TTTTTCA
1 TTTTTCA
1407653 TTTTTCA
1 TTTTTCA
*
1407660 TTTTTCTT
1 TTTTTC-A
1407668 TTTCTTCA
1 TTT-TTCA
1407676 TTTTTCA
1 TTTTTCA
1407683 CTTTTTCA
1 -TTTTTCA
1407691 TTTTTTTCA
1 --TTTTTCA
*
1407700 TTTTTTA
1 TTTTTCA
1407707 TTTTTCA
1 TTTTTCA
1407714 TTTTT
1 TTTTT
1407719 TTCATTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
7 34 0.60
8 13 0.23
9 10 0.18
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:1407728 original size:23 final size:23
Alignment explanation
Indices: 1407634--1407742 Score: 136
Period size: 23 Copynumber: 4.8 Consensus size: 23
1407624 TGAACCCCCC
1407634 TTTTA-TTTTC-TTTTTTTCATT
1 TTTTATTTTTCATTTTTTTCATT
*
1407655 TTTCATTTTTC-TTTTTCTTCATT
1 TTTTATTTTTCATTTTT-TTCATT
*
1407678 TTTCACTTTTTCATTTTTTTCATT
1 TTTTA-TTTTTCATTTTTTTCATT
1407702 TTTTATTTTTCATTTTTTTCATT
1 TTTTATTTTTCATTTTTTTCATT
*
1407725 TTTT-TCATTTCATTTTTT
1 TTTTAT-TTTTCATTTTTT
1407743 CATCTATTCT
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.05
22 11 0.14
23 44 0.55
24 16 0.20
25 5 0.06
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTATTTTTCATTTTTTTCATT
Found at i:1407742 original size:47 final size:47
Alignment explanation
Indices: 1407640--1407742 Score: 140
Period size: 47 Copynumber: 2.2 Consensus size: 47
1407630 CCCCTTTTAT
*
1407640 TTTC-TTTTTTTCATTTTTCATTTTTCTTTTTCTTCATTTTTCACTT
1 TTTCATTTTTTTCATTTTTCATTTTTCTTTTTCTTCATTTTTCACTA
* **
1407686 TTTCATTTTTTTCATTTTTTATTTTTCATTTTT-TTCATTTTTTTC-A
1 TTTCATTTTTTTCATTTTTCATTTTTC-TTTTTCTTCATTTTTCACTA
1407732 TTTCATTTTTT
1 TTTCATTTTTT
1407743 CATCTATTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 15 0.29
47 31 0.61
48 5 0.10
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (47 bp):
TTTCATTTTTTTCATTTTTCATTTTTCTTTTTCTTCATTTTTCACTA
Found at i:1407745 original size:13 final size:14
Alignment explanation
Indices: 1407686--1407742 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
1407676 TTTTTCACTT
1407686 TTTCATTTTTTTCA
1 TTTCATTTTTTTCA
*
1407700 TTT-TTTATTTTTCA
1 TTTCATT-TTTTTCA
1407714 TTTTTTTCATTTTTTTCA
1 ----TTTCATTTTTTTCA
1407732 TTTCATTTTTT
1 TTTCATTTTTT
1407743 CATCTATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 2 0.06
14 21 0.60
18 10 0.29
19 2 0.06
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCATTTTTTTCA
Found at i:1417207 original size:32 final size:32
Alignment explanation
Indices: 1417148--1417208 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1417138 CTGTTAATTT
*
1417148 TAAAAATTAATAGTTGAGTGATCAAAATAAAA
1 TAAAAATTAATAGTTGAGTGATAAAAATAAAA
1417180 TAAAAA-TAATAGTTAGAGT-ACTAAAAATA
1 TAAAAATTAATAGTT-GAGTGA-TAAAAATA
1417209 TAATTTATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.28
Consensus pattern (32 bp):
TAAAAATTAATAGTTGAGTGATAAAAATAAAA
Found at i:1417456 original size:2 final size:2
Alignment explanation
Indices: 1417451--1417483 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1417441 TTTAAAAAAT
1417451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1417484 TAAAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1417866 original size:60 final size:59
Alignment explanation
Indices: 1417800--1417922 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 59
1417790 TCAGGTGACT
* * * *
1417800 ATTTTATAAATTGTAATAGTCATGTGACTTAACAAAGCAACACCCTATAGTCGGAAGACC
1 ATTTTATAAATTGTAATAATCA-GAGACTCAAAAAAGCAACACCCTATAGTCGGAAGACC
* * * * * * *
1417860 ATTTTATAACTTTTAATAATCAGAGACTCAAAAAAGTAGCATCCTATGGTCGGAGGACC
1 ATTTTATAAATTGTAATAATCAGAGACTCAAAAAAGCAACACCCTATAGTCGGAAGACC
1417919 ATTT
1 ATTT
1417923 ATGTAGTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 33 0.63
60 19 0.37
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (59 bp):
ATTTTATAAATTGTAATAATCAGAGACTCAAAAAAGCAACACCCTATAGTCGGAAGACC
Found at i:1418944 original size:60 final size:60
Alignment explanation
Indices: 1418848--1418963 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
1418838 AGTATATACG
* * *
1418848 TATAGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTGAGGACTAATTTAGAATGAAGGT
1 TATAGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTAAAGACTAAGTTAGAATGAAGGT
* *
1418908 TATAGTTTGGGGATGGAATTGAAATG-TCCAAAAGTTTAAAGACTAAGTTAGAATGA
1 TATAGTTT-GGGATGAAATTGAAATGTTCAAAAAGTTTAAAGACTAAGTTAGAATGA
1418964 TAGTCATAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 34 0.68
61 16 0.32
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (60 bp):
TATAGTTTGGGATGAAATTGAAATGTTCAAAAAGTTTAAAGACTAAGTTAGAATGAAGGT
Found at i:1420049 original size:35 final size:35
Alignment explanation
Indices: 1419996--1420085 Score: 137
Period size: 35 Copynumber: 2.6 Consensus size: 35
1419986 GAATTATGAA
* *
1419996 TTTGGGGTGAGCATGTAATTGAAGTATTTTGGAA-
1 TTTGGGTTGAGAATGTAATTGAAGTATTTTGGAAT
*
1420030 TTTGAGGTTTAGAATGTAATTGAAGTATTTTGGAAT
1 TTTG-GGTTGAGAATGTAATTGAAGTATTTTGGAAT
1420066 TTTGGGTTGAGAATGTAATT
1 TTTGGGTTGAGAATGTAATT
1420086 AATGACTGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 4 0.08
35 42 0.84
36 4 0.08
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.42
Consensus pattern (35 bp):
TTTGGGTTGAGAATGTAATTGAAGTATTTTGGAAT
Found at i:1420825 original size:35 final size:35
Alignment explanation
Indices: 1420786--1420854 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
1420776 AATTAACTAT
*
1420786 GAATTT-AGGGTTGAGCATGTAATTGAAGTATTTTG
1 GAATTTGA-GGTTGAGAATGTAATTGAAGTATTTTG
*
1420821 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTT
1 GAATTTGAGGTTGAGAATGTAATTGAAGTATTTT
1420855 ACCCTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.42
Consensus pattern (35 bp):
GAATTTGAGGTTGAGAATGTAATTGAAGTATTTTG
Found at i:1428328 original size:31 final size:32
Alignment explanation
Indices: 1428286--1428354 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1428276 GTTATAATAA
* *
1428286 GTGTAAAAGTTCAAT-AATTTTAATGATCATT
1 GTGTAAAAGTTCAATAAAATTTAATGACCATT
* * *
1428317 TTGTAATAGTTCTATAAAATTTAATGACCATT
1 GTGTAAAAGTTCAATAAAATTTAATGACCATT
1428349 GTGTAA
1 GTGTAA
1428355 CTTTTGAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (32 bp):
GTGTAAAAGTTCAATAAAATTTAATGACCATT
Found at i:1430997 original size:30 final size:31
Alignment explanation
Indices: 1430941--1431016 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 31
1430931 CACTATTCTA
1430941 AGCTTTGCTAAGCTTTACCCTTTCTCTCTAAT
1 AGCTTTGCTAAGCTTTACCC-TTCTCTCTAAT
1430973 AGCTTTGCTAAGCTTTACCC-TCTCTCTAAT
1 AGCTTTGCTAAGCTTTACCCTTCTCTCTAAT
* *
1431003 ATCTTTGATAAGCT
1 AGCTTTGCTAAGCT
1431017 ATTATTCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 22 0.52
32 20 0.48
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (31 bp):
AGCTTTGCTAAGCTTTACCCTTCTCTCTAAT
Found at i:1434022 original size:23 final size:23
Alignment explanation
Indices: 1433996--1434105 Score: 150
Period size: 23 Copynumber: 4.8 Consensus size: 23
1433986 AGCTCATATA
*
1433996 AATTGCACCGAAGTGCCAAGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1434019 AATTGCACC-ATAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACGTAG
*
1434042 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1434065 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1434088 AAATGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
1434106 TATAAGGTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
22 1 0.01
23 73 0.97
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1434052 original size:46 final size:46
Alignment explanation
Indices: 1433999--1434105 Score: 196
Period size: 46 Copynumber: 2.3 Consensus size: 46
1433989 TCATATAAAT
1433999 TGCACCGAAGTGCCAAGTAGAATTGCACCATAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCAAGTAGAATTGCACCATAGTGCCGCGTAGAAA
* *
1434045 TGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCAAGTAGAATTGCACCATAGTGCCGCGTAGAAA
1434091 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1434106 TATAAGGTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (46 bp):
TGCACCGAAGTGCCAAGTAGAATTGCACCATAGTGCCGCGTAGAAA
Found at i:1439224 original size:23 final size:22
Alignment explanation
Indices: 1439198--1439261 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
1439188 AGCTCATATA
1439198 AATTGCACCGAAGTGCCAAGTAG
1 AATTGCACCGAAGTGCCAA-TAG
*
1439221 AATTGCACC-ATAGTGCCGCATAG
1 AATTGCACCGA-AGTGCC-AATAG
*
1439244 AAATGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
1439262 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 1 0.03
23 32 0.91
24 2 0.06
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (22 bp):
AATTGCACCGAAGTGCCAATAG
Found at i:1440289 original size:2 final size:2
Alignment explanation
Indices: 1440282--1440311 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1440272 ACATCTCCTA
1440282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1440312 TAATCTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1457320 original size:16 final size:16
Alignment explanation
Indices: 1457301--1457334 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1457291 TCATATTTTG
*
1457301 TTATTATTTTATTTAA
1 TTATTATATTATTTAA
*
1457317 TTATTGTATTATTTAA
1 TTATTATATTATTTAA
1457333 TT
1 TT
1457335 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTATATTATTTAA
Found at i:1457479 original size:80 final size:80
Alignment explanation
Indices: 1457346--1457505 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
1457336 TTTTATTTTT
*
1457346 TTGCAGTTATAAAATGGAAAGTGGTCATTGAATAATTATATTCGGATTTCTCGGTTTTTAAACTT
1 TTGCAGTTATAAAATGGAAAGTGGTCATTGAATAATTATATTCGGATTTCTCGGCTTTTAAACTT
1457411 TTCTCTCGGCTATAA
66 TTCTCTCGGCTATAA
1457426 TTGCAGTTATAAAATGGAAAGTGGTCATTGAATAATTATATTCGGATTTCTCGGCTTTTAAACTT
1 TTGCAGTTATAAAATGGAAAGTGGTCATTGAATAATTATATTCGGATTTCTCGGCTTTTAAACTT
1457491 TTCTCTCGGCTATAA
66 TTCTCTCGGCTATAA
1457506 ATACGCTCTC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (80 bp):
TTGCAGTTATAAAATGGAAAGTGGTCATTGAATAATTATATTCGGATTTCTCGGCTTTTAAACTT
TTCTCTCGGCTATAA
Found at i:1457696 original size:8 final size:8
Alignment explanation
Indices: 1457685--1457729 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
1457675 TAAAAAAATA
1457685 AAATAATT
1 AAATAATT
1457693 AAAT-A--
1 AAATAATT
*
1457698 AAATAATA
1 AAATAATT
*
1457706 AAAAAATT
1 AAATAATT
1457714 AAATAATT
1 AAATAATT
1457722 AAATAATT
1 AAATAATT
1457730 TAAAAAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.13
6 1 0.03
7 1 0.03
8 25 0.81
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATT
Found at i:1457698 original size:13 final size:13
Alignment explanation
Indices: 1457680--1457738 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
1457670 AACTGTAAAA
1457680 AAATAAAATAATT
1 AAATAAAATAATT
1457693 AAATAAAATAA-T
1 AAATAAAATAATT
*
1457705 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
1457718 -AATTAAATAATT
1 AAATAAAATAATT
*
1457730 TAA-AAAATA
1 AAATAAAATA
1457739 CTAACAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.10
12 18 0.46
13 17 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1457699 original size:21 final size:21
Alignment explanation
Indices: 1457675--1457719 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1457665 TTTATAACTG
*
1457675 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAAAAATTAAA
*
1457696 TAAAATAATAAAAAAATTAAA
1 TAAAAAAATAAAAAAATTAAA
1457717 TAA
1 TAA
1457720 TTAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATTAAA
Found at i:1458355 original size:10 final size:10
Alignment explanation
Indices: 1458340--1458370 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1458330 TTTAGATTCA
1458340 GGTCGAGTCG
1 GGTCGAGTCG
*
1458350 GGTCGAGTAG
1 GGTCGAGTCG
1458360 GGTCGAGTCG
1 GGTCGAGTCG
1458370 G
1 G
1458371 ATCAGACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.16, G:0.52, T:0.19
Consensus pattern (10 bp):
GGTCGAGTCG
Found at i:1481502 original size:25 final size:25
Alignment explanation
Indices: 1481474--1481524 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1481464 TTTTTTATTA
* *
1481474 ATAA-TATATTTTTCTTTATAATTTT
1 ATAAGTATA-TTTTCTATAAAATTTT
*
1481499 ATAAGTTTATTTTCTATAAAATTTT
1 ATAAGTATATTTTCTATAAAATTTT
1481524 A
1 A
1481525 AAAATCCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (25 bp):
ATAAGTATATTTTCTATAAAATTTT
Found at i:1483428 original size:2 final size:2
Alignment explanation
Indices: 1483421--1483455 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1483411 GTTTATTAAG
1483421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1483456 AAGTGAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1484600 original size:120 final size:121
Alignment explanation
Indices: 1484343--1484705 Score: 281
Period size: 120 Copynumber: 3.0 Consensus size: 121
1484333 GAATAAATGA
* * * * ** *
1484343 TTACTTGCATGATTCAACTTATAGACAGATCTGAATAGAGACATCATTTATTAACTTAAATTTTA
1 TTACTTGCATGATTCAACTTATAAACAGATCTAAACAGAGACAACATCCACTAACTTAAATTTTA
* *** * **
1484408 CGATATTTTTTTTTAAAATTTGTCAAATCACATCAAACTTTGCATAAATAATTACT
66 CGAGATACCTTTTTAAAATTTGTCAAATCACACCAAACTTTAAATAAATAATTACT
* *
1484464 TTA-TT-TATTCGATTCAA-TTCATAAATAGATCTAAACAGAGACAACATCCACTAACTTAAATT
1 TTACTTGCA-T-GATTCAACTT-ATAAACAGATCTAAACAGAGACAACATCCACTAACTTAAATT
* * **
1484526 TTACGAGA-ACCTTTTTAAAA-TTGATCAAATCATACCAAACTTTAAATAGATTGTTACT
63 TTACGAGATACCTTTTTAAAATTTG-TCAAATCACACCAAACTTTAAATAAATAATTACT
* * * * * * ** ** * *
1484584 TTACTTGCATGATTCAACTTATAGATATATCTGAATAGATACATTATTTATTAACTTAAATTTTG
1 TTACTTGCATGATTCAACTTATAAACAGATCTAAACAGAGACAACATCCACTAACTTAAATTTTA
** * * * * * *
1484649 C-A-ATAATTTTTTAAAATTGGTCAAGTCATATCAAACTTTGAGTAAATAATTACT
66 CGAGATACCTTTTTAAAATTTGTCAAATCACACCAAACTTTAAATAAATAATTACT
1484703 TTA
1 TTA
1484706 TTTAACCGAT
Statistics
Matches: 191, Mismatches: 42, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
118 1 0.01
119 45 0.24
120 88 0.46
121 56 0.29
122 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (121 bp):
TTACTTGCATGATTCAACTTATAAACAGATCTAAACAGAGACAACATCCACTAACTTAAATTTTA
CGAGATACCTTTTTAAAATTTGTCAAATCACACCAAACTTTAAATAAATAATTACT
Found at i:1485674 original size:27 final size:27
Alignment explanation
Indices: 1485640--1485702 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1485630 CACTTTATCA
1485640 TAAAATTTTATTAGTCCATCCTTTAAT
1 TAAAATTTTATTAGTCCATCCTTTAAT
1485667 TAAAATTTTATTAGTCCATCCTTTAAT
1 TAAAATTTTATTAGTCCATCCTTTAAT
1485694 TAAAATTTT
1 TAAAATTTT
1485703 GTATTTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (27 bp):
TAAAATTTTATTAGTCCATCCTTTAAT
Found at i:1494688 original size:218 final size:218
Alignment explanation
Indices: 1494309--1494968 Score: 1275
Period size: 218 Copynumber: 3.0 Consensus size: 218
1494299 CCATCTGTAC
1494309 ACCAAAATATAGTCCCATACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
1 ACCAAAATATAGTCCCATACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
*
1494374 AGGTTTGTAAGGAATTACAAACTTGATCAGAGTTAAACCTCCATACTCCAAAATCCTACCTAGAC
66 AGGTTTGTAAGGAATTACAAACTTGATCAGAGTTGAACCTCCATACTCCAAAATCCTACCTAGAC
1494439 AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
131 AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
1494504 ATATTTTCCAGTGAAAACAGGTA
196 ATATTTTCCAGTGAAAACAGGTA
*
1494527 TCCAAAATATAGTCCCATACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
1 ACCAAAATATAGTCCCATACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
1494592 AGGTTTGTAAGGAATTACAAACTTGATCAGAGTTGAACCTCCATACTCCAAAATCCTACCTAGAC
66 AGGTTTGTAAGGAATTACAAACTTGATCAGAGTTGAACCTCCATACTCCAAAATCCTACCTAGAC
1494657 AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
131 AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
1494722 ATATTTTCCAGTGAAAACAGGTA
196 ATATTTTCCAGTGAAAACAGGTA
*
1494745 ACCAAAATATAGTCCCACACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
1 ACCAAAATATAGTCCCATACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
* *
1494810 AGGTCTGTAAGGAATTACAAACTTGATCAGAGTTGAACCTTCATACTCCAAAATCCTACCTAGAC
66 AGGTTTGTAAGGAATTACAAACTTGATCAGAGTTGAACCTCCATACTCCAAAATCCTACCTAGAC
1494875 AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
131 AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
1494940 ATATTTTCCAGTGAAAACAGGTA
196 ATATTTTCCAGTGAAAACAGGTA
1494963 ACCAAA
1 ACCAAA
1494969 GAGCACATAT
Statistics
Matches: 436, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 436 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (218 bp):
ACCAAAATATAGTCCCATACTAAGGGAGTGCCTTGGGGCCTTAGAGCCTACCCAAGGAATACCTT
AGGTTTGTAAGGAATTACAAACTTGATCAGAGTTGAACCTCCATACTCCAAAATCCTACCTAGAC
AATATTCTAATAATCGGTTCATATAGTAAATAGTTGATTCCATGATCCATAAATCATGAATGATT
ATATTTTCCAGTGAAAACAGGTA
Found at i:1496799 original size:22 final size:22
Alignment explanation
Indices: 1496767--1496815 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1496757 AGACTTTTTG
*
1496767 GTCAAAGTCAA-TGTTTGTCAAA
1 GTCAAAGTCAACT-CTTGTCAAA
*
1496789 GTCAAATTCAACTCTTGTCAAA
1 GTCAAAGTCAACTCTTGTCAAA
1496811 GTCAA
1 GTCAA
1496816 CGGTCATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (22 bp):
GTCAAAGTCAACTCTTGTCAAA
Found at i:1496866 original size:13 final size:13
Alignment explanation
Indices: 1496848--1496896 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
1496838 AAGTCAACGG
1496848 GTTGACTCATTGA
1 GTTGACTCATTGA
* *
1496861 GTTGACTCAATCGG
1 GTTGACTC-ATTGA
*
1496875 GTAGACTCATTGA
1 GTTGACTCATTGA
1496888 GTTGACTCA
1 GTTGACTCA
1496897 GGTCGACTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (13 bp):
GTTGACTCATTGA
Found at i:1496881 original size:27 final size:26
Alignment explanation
Indices: 1496841--1496896 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
1496831 TCAGTCAAAG
*
1496841 TCAACGGGTTGACTCATTGAGTTGAC
1 TCAACGGGTAGACTCATTGAGTTGAC
1496867 TCAATCGGGTAGACTCATTGAGTTGAC
1 TCAA-CGGGTAGACTCATTGAGTTGAC
1496894 TCA
1 TCA
1496897 GGTCGACTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (26 bp):
TCAACGGGTAGACTCATTGAGTTGAC
Found at i:1502215 original size:21 final size:21
Alignment explanation
Indices: 1502189--1502228 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1502179 TACGAAAGTT
1502189 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
*
1502210 ACTGTAGCATTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
1502229 ACACAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:1507579 original size:30 final size:30
Alignment explanation
Indices: 1507543--1507662 Score: 140
Period size: 30 Copynumber: 4.1 Consensus size: 30
1507533 TTAAAGGGTC
1507543 AAAATAGAAAAAATAGAAACTTT-AAGGACT
1 AAAATAGAAAAAATAGAAA-TTTAAAGGACT
* * * * *
1507573 ACAATAGCAAAAACAAAAATTTAAAGGGCT
1 AAAATAGAAAAAATAGAAATTTAAAGGACT
**
1507603 AAAATAGTTAAAATAGAAATTTAAAGGACT
1 AAAATAGAAAAAATAGAAATTTAAAGGACT
1507633 AAAATAG-AAAAA-A-AAATTTAAAGGACT
1 AAAATAGAAAAAATAGAAATTTAAAGGACT
1507660 AAA
1 AAA
1507663 CAATAATTAC
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
27 17 0.22
28 1 0.01
29 7 0.09
30 52 0.68
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (30 bp):
AAAATAGAAAAAATAGAAATTTAAAGGACT
Found at i:1507607 original size:60 final size:57
Alignment explanation
Indices: 1507531--1507662 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 57
1507521 ATCCTATTCG
*
1507531 ATTTAAAGGG-TCAAAATAGAAAAAATAGAAACTTT-AAGGACTACAATAGCAAAAACAAAA
1 ATTTAAAGGGCT-AAAATAGAAAAAATAGAAA-TTTAAAGGACTAAAATAG--AAAA-AAAA
**
1507591 ATTTAAAGGGCTAAAATAGTTAAAATAGAAATTTAAAGGACTAAAATAGAAAAAAAA
1 ATTTAAAGGGCTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGAAAAAAAA
*
1507648 ATTTAAAGGACTAAA
1 ATTTAAAGGGCTAAA
1507663 CAATAATTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
57 18 0.27
58 4 0.06
59 3 0.05
60 40 0.61
61 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (57 bp):
ATTTAAAGGGCTAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGAAAAAAAA
Found at i:1507677 original size:60 final size:59
Alignment explanation
Indices: 1507552--1507677 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 59
1507542 CAAAATAGAA
* * *
1507552 AAAATAGAAACTTTAAGGACTACAATAGCAAAAACAAAAATTTAAAGGGCTAAAATAGTT
1 AAAATAGAAACTTTAAGGACTAAAATAG-AAAAACAAAAATTTAAAGGACTAAAATAATT
1507612 AAAATAGAAA-TTTAAAGGACTAAAATAG-AAAA-AAAAATTTAAAGGACTAAACAATAATT
1 AAAATAGAAACTTT-AAGGACTAAAATAGAAAAACAAAAATTTAAAGGACT-AA-AATAATT
1507671 ACAAATA
1 A-AAATA
1507678 AACCAGAGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
57 15 0.25
58 6 0.10
59 10 0.17
60 28 0.47
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (59 bp):
AAAATAGAAACTTTAAGGACTAAAATAGAAAAACAAAAATTTAAAGGACTAAAATAATT
Found at i:1507939 original size:20 final size:20
Alignment explanation
Indices: 1507910--1508124 Score: 171
Period size: 20 Copynumber: 10.9 Consensus size: 20
1507900 TAATTGAAAA
*
1507910 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
1507930 TCGTGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
1507950 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
1507970 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
1507992 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
**
1508013 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAGT
*
1508025 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
* *
1508045 TCGCGTTGCGATTTACCATT
1 TCGCGTTGCGATTTTCCAGT
*
1508065 TCGCGTTACGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* * *
1508085 TCGTGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
1508107 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
1508125 AATTCATTGC
Statistics
Matches: 158, Mismatches: 22, Indels: 30
0.75 0.10 0.14
Matches are distributed among these distances:
12 3 0.02
14 8 0.05
19 8 0.05
20 103 0.65
21 5 0.03
22 31 0.20
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:1507964 original size:40 final size:40
Alignment explanation
Indices: 1507910--1508165 Score: 205
Period size: 40 Copynumber: 6.5 Consensus size: 40
1507900 TAATTGAAAA
* * * *
1507910 TCGCGTTGCGATTTTCCATTTCGTGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTACAGT
1507950 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGAT--TCTACAGT
* *
1507992 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGA----A-A-A
1 TCG-CGTTGCGATTTTCC-AGTTCGCGTTGCGATTCTACAGT
* *
1508025 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATT-TACCATT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTA-CAGT
* *
1508065 TCGCGTTACGATTTTCCAGTTCGTGTTGCGATAGTCTACAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGAT--TCTACAGT
* *
1508107 T-GTCGTTGCGATTTTCCAAATT--CATTGCGATAGTCTACAGT
1 TCG-CGTTGCGATTTTCC-AGTTCGCGTTGCGAT--TCTACAGT
*
1508148 TCTCGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCA
1508166 AATTCGTTGC
Statistics
Matches: 180, Mismatches: 17, Indels: 38
0.77 0.07 0.16
Matches are distributed among these distances:
32 3 0.02
33 15 0.08
34 10 0.06
35 1 0.01
37 1 0.01
39 1 0.01
40 60 0.33
41 42 0.23
42 39 0.22
43 8 0.04
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (40 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTACAGT
Found at i:1508082 original size:115 final size:115
Alignment explanation
Indices: 1507905--1508136 Score: 410
Period size: 115 Copynumber: 2.0 Consensus size: 115
1507895 TGCGATAATT
* * *
1507905 GAAAATCGCGTTGCGATTTTCCATTTCGTGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCAGT
1 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTACCAGTTCGCGTTACGATTTTCCAGT
*
1507970 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
66 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCATTGC
*
1508020 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTACCATTTCGCGTTACGATTTTCCAGT
1 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTACCAGTTCGCGTTACGATTTTCCAGT
*
1508085 TCGTGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCATTGC
66 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCATTGC
1508135 GA
1 GA
1508137 TAGTCTACAG
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (115 bp):
GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTACCAGTTCGCGTTACGATTTTCCAGT
TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCATTGC
Found at i:1508107 original size:22 final size:22
Alignment explanation
Indices: 1508081--1508159 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
1508071 TACGATTTTC
1508081 CAGTTCGT-GTTGCGATAGTCTA
1 CAGTTC-TCGTTGCGATAGTCTA
* * *
1508103 CAGTTGTCGTTGCGAT--TTTC
1 CAGTTCTCGTTGCGATAGTCTA
** *
1508123 CAAAT-TCATTGCGATAGTCTA
1 CAGTTCTCGTTGCGATAGTCTA
1508144 CAGTTCTCGTTGCGAT
1 CAGTTCTCGTTGCGAT
1508160 TTTCCAAATT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 9 0.21
20 5 0.12
21 6 0.14
22 22 0.52
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (22 bp):
CAGTTCTCGTTGCGATAGTCTA
Found at i:1508140 original size:41 final size:41
Alignment explanation
Indices: 1508090--1508177 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
1508080 CCAGTTCGTG
*
1508090 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCA
1 TTGCGATAGTCTACAGTTCTCGTTGCGATTTTCCAAATTCA
*
1508131 TTGCGATAGTCTACAGTTCTCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCTACAGTTCTCGTTGCGATTTTCCAAATTCA
1508172 TTGCGA
1 TTGCGA
1508178 AAATTCGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (41 bp):
TTGCGATAGTCTACAGTTCTCGTTGCGATTTTCCAAATTCA
Found at i:1508174 original size:19 final size:19
Alignment explanation
Indices: 1508109--1508177 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1508099 TCTACAGTTG
1508109 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
1508128 TCATTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1508149 CTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1508169 TCGTTGCGA
1 TCGTTGCGA
1508178 AAATTCGTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 18 0.49
20 5 0.14
21 5 0.14
22 9 0.24
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1508292 original size:5 final size:5
Alignment explanation
Indices: 1508276--1508309 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
1508266 CGTATTACCA
1508276 CGACC ACGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGA
1508310 GATGAGACGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.24, C:0.56, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1508836 original size:6 final size:5
Alignment explanation
Indices: 1508799--1508832 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1508789 TCCGTCCGTC
*
1508799 TCGGG TCGGG TCGGG TCGGG TCGTG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
1508833 TGGTAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:1508953 original size:41 final size:41
Alignment explanation
Indices: 1508918--1509033 Score: 214
Period size: 41 Copynumber: 2.8 Consensus size: 41
1508908 CGATTGTAGG
* *
1508918 CTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCAA
1 CTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAA
1508959 CTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAA
1 CTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAA
1509000 CTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 CTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1509034 AATAGAAAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
CTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAA
Found at i:1509032 original size:61 final size:61
Alignment explanation
Indices: 1508961--1509094 Score: 259
Period size: 61 Copynumber: 2.2 Consensus size: 61
1508951 ATTTTCAACT
*
1508961 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1509022 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1509083 ATCGCAACGCGA
1 ATCGCAACGCGA
1509095 TTTTCAACTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (61 bp):
ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1509067 original size:41 final size:41
Alignment explanation
Indices: 1509022--1509156 Score: 252
Period size: 41 Copynumber: 3.3 Consensus size: 41
1509012 GAAATGGAAA
*
1509022 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1509063 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*
1509104 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1509145 ATCGCAACGCGA
1 ATCGCAACGCGA
1509157 TTTCCAACTA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:1509096 original size:102 final size:101
Alignment explanation
Indices: 1508920--1509178 Score: 428
Period size: 102 Copynumber: 2.5 Consensus size: 101
1508910 ATTGTAGGCT
*
1508920 ATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGAAATG-AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCG
1508985 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
65 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1509022 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGAAAT-GAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCG
1509087 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
65 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
** * * *
1509124 ATCGCAACGCGATTTCCAACTATCGCAACGCGATTTCCAACTATCGCAACGCGAA
1 ATCGCAACGCGAAAT-GAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGAA
1509179 TTTGCGATAG
Statistics
Matches: 148, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
102 114 0.77
103 34 0.23
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (101 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGC
AACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1509713 original size:9 final size:9
Alignment explanation
Indices: 1509699--1509735 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
1509689 ATAGAGAGAG
1509699 AACTCTCTC
1 AACTCTCTC
1509708 AACTCTCTC
1 AACTCTCTC
1509717 AACTCTCTC
1 AACTCTCTC
1509726 AACTCTCTC
1 AACTCTCTC
1509735 A
1 A
1509736 TCAGTGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.32
Consensus pattern (9 bp):
AACTCTCTC
Found at i:1513826 original size:2 final size:2
Alignment explanation
Indices: 1513767--1513812 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1513757 TTGAAAATAA
1513767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1513809 AT AT
1 AT AT
1513813 TTCTAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1514899 original size:100 final size:95
Alignment explanation
Indices: 1514692--1515013 Score: 445
Period size: 94 Copynumber: 3.3 Consensus size: 95
1514682 GACATAAATT
*
1514692 AAGAAATTCAATGAAAATATATAGGAAATACAAAGATGTTTCTCCATCTTCGATTTACGTCG-GA
1 AAGAAATTCAATGAAAATATATAGGAAATGCAAAGATGTTTCTCCATCTTCGATTTACGTCGAGA
* *
1514756 AGATAGAGATGCATATGGCATTATAAGTAG
66 AGATGGAGATGCAAATGGCATTATAAGTAG
* *
1514786 AAGAAATTCAATGAAAATATATAGGAAATGCAGAGATGTTTC-CCATCTTCGATATACGTCCGAA
1 AAGAAATTCAATGAAAATATATAGGAAATGCAAAGATGTTTCTCCATCTTCGATTTACGT-C---
1514850 GACGAAAGATGGAGATGCAAATGGCATTATAAGTAG
62 GA-G-AAGATGGAGATGCAAATGGCATTATAAGTAG
* **
1514886 AAGAAATTCAATGAAAATATATAGGAAATGCAAAGAAGTTTCTGAATCTTCGATTTACGT--ATG
1 AAGAAATTCAATGAAAATATATAGGAAATGCAAAGATGTTTCTCCATCTTCGATTTACGTCGA-G
*
1514949 AAGATGGAGATGCAAATTGCATTATAAGTAG
65 AAGATGGAGATGCAAATGGCATTATAAGTAG
*
1514980 AACAAATTCAATGAAAATATATAAAGGAAATGCA
1 AAGAAATTCAATGAAAATATAT--AGGAAATGCA
1515014 CATGATCTGC
Statistics
Matches: 205, Mismatches: 13, Indels: 18
0.87 0.06 0.08
Matches are distributed among these distances:
93 16 0.08
94 92 0.45
95 2 0.01
96 10 0.05
97 1 0.00
99 1 0.00
100 69 0.34
101 14 0.07
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (95 bp):
AAGAAATTCAATGAAAATATATAGGAAATGCAAAGATGTTTCTCCATCTTCGATTTACGTCGAGA
AGATGGAGATGCAAATGGCATTATAAGTAG
Found at i:1522794 original size:57 final size:57
Alignment explanation
Indices: 1522725--1522833 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
1522715 CATACAAACT
* *
1522725 CGTCACGAACAGTAAGGCCCTGATCACAAAGCCAAGGAACCTACAAGTATTCAACCC
1 CGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGGAACCTACAAGTATTCAACCC
* * *
1522782 CGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATTC
1 CGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGGAACCTACAAGTATTC
1522834 TTCCTCCAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (57 bp):
CGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGGAACCTACAAGTATTCAACCC
Found at i:1525364 original size:17 final size:17
Alignment explanation
Indices: 1525325--1525367 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1525315 TGGTCAACAG
*
1525325 TGGTCAACACCGGTCAA
1 TGGTCAACACAGGTCAA
** *
1525342 CAGTCAACGCAGGTCAA
1 TGGTCAACACAGGTCAA
1525359 TGGTCAACA
1 TGGTCAACA
1525368 GTCGACCGTT
Statistics
Matches: 19, Mismatches: 7, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (17 bp):
TGGTCAACACAGGTCAA
Found at i:1528278 original size:23 final size:23
Alignment explanation
Indices: 1528251--1528311 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1528241 CATTATTATA
1528251 TGGCACTATGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
*
1528274 TGGCACTACGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
*
1528297 CGGCACT-TCGGTGCA
1 TGGCACTAT-GGTGCA
1528312 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTCTACG
Found at i:1528426 original size:2 final size:2
Alignment explanation
Indices: 1528419--1528454 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1528409 AACAAATACA
1528419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1528455 GATGGATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1531865 original size:20 final size:20
Alignment explanation
Indices: 1531840--1531896 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
1531830 GAATATCATG
1531840 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
1531860 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
1531880 AGGGTATCGATACCCCC
1 AGGGTATCGATACCCCC
1531897 TAAAGGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (20 bp):
AGGGTATCGATACCCCCAGT
Found at i:1533445 original size:23 final size:23
Alignment explanation
Indices: 1533415--1533496 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
1533405 CATTATTATA
1533415 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
**
1533438 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
*
1533461 TGGCACTACGTTGTAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
* *
1533484 CGGCACTTCGGTG
1 TGGCACTACGGTG
1533497 CATTTATACG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGTAATTCTACG
Found at i:1534593 original size:20 final size:20
Alignment explanation
Indices: 1534568--1534610 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1534558 TCTAAAGGCC
1534568 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
1534588 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
1534608 CAT
1 CAT
1534611 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1544246 original size:20 final size:20
Alignment explanation
Indices: 1544221--1544263 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1544211 TCTAAAGGCC
1544221 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
1544241 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
1544261 CAT
1 CAT
1544264 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1547437 original size:57 final size:56
Alignment explanation
Indices: 1547302--1547467 Score: 217
Period size: 57 Copynumber: 3.0 Consensus size: 56
1547292 ACCATACAAC
* * * * * *
1547302 CCCGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACATGCAAGTATT-TA
1 CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTCAA
* * * *
1547357 CCCGTCACGAACAGTACGACTCTCAGCACAAAGCCGAGGAGCCTATAAGTATTCAA
1 CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTCAA
*
1547413 CCCTGTCACGAACAGTAAGGCTCTCAGCACAAAGCTGAGGAACCTACAAGTATTC
1 CCC-GTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTC
1547468 TTCCTCCAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
55 44 0.47
56 4 0.04
57 46 0.49
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.16
Consensus pattern (56 bp):
CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTCAA
Found at i:1550003 original size:24 final size:24
Alignment explanation
Indices: 1549969--1550019 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1549959 GGTCAACGCC
* *
1549969 GGTCAATGGTCAACGCCGGTCAAT
1 GGTCAACGGTCAACGCAGGTCAAT
1549993 GGTCAACGGTCAACGCAGGTCAAT
1 GGTCAACGGTCAACGCAGGTCAAT
1550017 GGT
1 GGT
1550020 AAATAGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (24 bp):
GGTCAACGGTCAACGCAGGTCAAT
Found at i:1550015 original size:17 final size:17
Alignment explanation
Indices: 1549958--1550000 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
1549948 TGGTCAACAG
1549958 TGGTCAACGCCGGTCAA
1 TGGTCAACGCCGGTCAA
1549975 TGGTCAACGCCGGTCAA
1 TGGTCAACGCCGGTCAA
1549992 TGGTCAACG
1 TGGTCAACG
1550001 GTCAACGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (17 bp):
TGGTCAACGCCGGTCAA
Found at i:1552101 original size:57 final size:57
Alignment explanation
Indices: 1552034--1552196 Score: 236
Period size: 57 Copynumber: 2.9 Consensus size: 57
1552024 TACAACCCTG
* *
1552034 TCACAAATAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
1 TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
* * * **
1552091 TCACAGATAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGTAAGTATTCAACCCTG
1 TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
** *
1552148 TCACAAACGGTAAGGCTCTCAGCACAAAGCCAAGAAACCTGCAAGTATT
1 TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATT
1552197 ATTCCTCTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 93 1.00
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (57 bp):
TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
Found at i:1557216 original size:59 final size:59
Alignment explanation
Indices: 1557109--1557221 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
1557099 TCTAGTAAAT
** * * * *
1557109 TAATAATTATTAAATAATAATTTAGTATTTTGTTGTTTATTCAAAAATTAATAAATTAG
1 TAATAATTATTAAATAATAATTTAACATTTTATTATCTACTCAAAAATTAATAAATTAG
* *
1557168 TAATAATTATTAATTAATAATTTAACATTTTATTATCTACT-AGTAAATTAATAA
1 TAATAATTATTAAATAATAATTTAACATTTTATTATCTACTCA-AAAATTAATAA
1557222 TTTAATTAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
58 1 0.02
59 44 0.98
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (59 bp):
TAATAATTATTAAATAATAATTTAACATTTTATTATCTACTCAAAAATTAATAAATTAG
Found at i:1560658 original size:16 final size:17
Alignment explanation
Indices: 1560626--1560662 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1560616 TATATTACAT
*
1560626 GTGTCATAGATATTAAA
1 GTGTCATAGAAATTAAA
1560643 GTGTCAT-GAAATTAAA
1 GTGTCATAGAAATTAAA
1560659 GTGT
1 GTGT
1560663 ATATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (17 bp):
GTGTCATAGAAATTAAA
Found at i:1561950 original size:18 final size:18
Alignment explanation
Indices: 1561923--1562011 Score: 69
Period size: 18 Copynumber: 4.9 Consensus size: 18
1561913 TATTTTAAAA
1561923 ATTT-AAAAAATAATTAT
1 ATTTAAAAAAATAATTAT
1561940 ATTTAAAAAAAT-ATTAT
1 ATTTAAAAAAATAATTAT
* * *
1561957 TTTATAAAAAAATAA-CAA
1 ATT-TAAAAAAATAATTAT
*
1561975 ATTTTAAAACTAA-AATTAT
1 A-TTTAAAA-AAATAATTAT
*
1561994 ATTTTAAAAAATGAATTA
1 ATTTAAAAAAAT-AATTA
1562012 AAAAAATTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
17 13 0.24
18 30 0.55
19 12 0.22
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (18 bp):
ATTTAAAAAAATAATTAT
Found at i:1561965 original size:15 final size:17
Alignment explanation
Indices: 1561923--1562011 Score: 58
Period size: 19 Copynumber: 4.9 Consensus size: 17
1561913 TATTTTAAAA
1561923 ATTTAAAAAATAATTAT
1 ATTTAAAAAATAATTAT
1561940 ATTTAAAAAA-ATATTAT
1 ATTTAAAAAATA-ATTAT
* * *
1561957 TTTATAAAAAAATAA-CAA
1 ATT-T-AAAAAATAATTAT
1561975 ATTTTAAAACTAA-AATTAT
1 A-TTTAAAA--AATAATTAT
1561994 ATTTTAAAAAATGAATTA
1 A-TTTAAAAAAT-AATTA
1562012 AAAAAATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.02
17 23 0.41
18 5 0.09
19 26 0.46
20 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (17 bp):
ATTTAAAAAATAATTAT
Found at i:1562368 original size:23 final size:23
Alignment explanation
Indices: 1562324--1562377 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1562314 TAGATTAAGT
* *
1562324 TTAATTTATTTAATATTTTAATC
1 TTAATTTATTTAAAATTATAATC
*
1562347 TTAATTT-TTATAAAATTATAATA
1 TTAATTTATT-TAAAATTATAATC
*
1562370 ATAATTTA
1 TTAATTTA
1562378 AATAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATTTATTTAAAATTATAATC
Found at i:1562948 original size:34 final size:35
Alignment explanation
Indices: 1562903--1562979 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
1562893 ACAACACATT
1562903 CATCAATTACATTCTAAACC-CAAATTCCAAAATA
1 CATCAATTACATTCTAAACCTCAAATTCCAAAATA
* *
1562937 CTTCAATTACATTTTAAACCTCAAATTCCAAAATA
1 CATCAATTACATTCTAAACCTCAAATTCCAAAATA
1562972 CATCAATT
1 CATCAATT
1562980 GCATACCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 18 0.46
35 21 0.54
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
CATCAATTACATTCTAAACCTCAAATTCCAAAATA
Found at i:1562997 original size:35 final size:34
Alignment explanation
Indices: 1562903--1563008 Score: 106
Period size: 35 Copynumber: 3.1 Consensus size: 34
1562893 ACAACACATT
* *
1562903 CATCAATTACATTCTAAACCCAAATTCCAAAATA
1 CATCAATTACATACCAAACCCAAATTCCAAAATA
* ***
1562937 CTTCAATTACATTTTAAACCTCAAATTCCAAAATA
1 CATCAATTACATACCAAACC-CAAATTCCAAAATA
* * *
1562972 CATCAATTGCATACCCAACTCCAAATT-CATAATA
1 CATCAATTACATACCAAAC-CCAAATTCCAAAATA
1563006 CAT
1 CAT
1563009 TCTCAAAATC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
34 27 0.44
35 33 0.54
36 1 0.02
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.29
Consensus pattern (34 bp):
CATCAATTACATACCAAACCCAAATTCCAAAATA
Found at i:1563787 original size:147 final size:139
Alignment explanation
Indices: 1563481--1563770 Score: 400
Period size: 141 Copynumber: 2.0 Consensus size: 139
1563471 AAACTATTTA
* * * *
1563481 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTAAACAGAAACTCAAAA
1 AATTAGAAT--AACAATATTATAATATGATAAATATTTATAATTAAATTAAACAGAAACTAAAAA
* * * *
1563546 ATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAATTTTTGAGTCAACTATTTTAT
64 ATTAAATTCGACTTGATTTAAATTTTATAAACTCAAATAGAAAAATTTCGAGTCAACTATTTTAT
1563611 AAACTGAATTG
129 AAACTGAATTG
*
1563622 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
1 AATTAGAAT--AACAATATTATAATATGATAAATATTTATAATTAAA-TTAAACAGAAAC-T--A
1563687 AATTAAATTAAATTCGACTTGATTTAAATTTTATAAACTCAAATAGAAAAAATTTCGAGTCAACT
60 AA--AAATTAAATTCGACTTGATTTAAATTTTATAAACTCAAATAG-AAAAATTTCGAGTCAACT
1563752 ATTTTATAAACTGAATTG
122 ATTTTATAAACTGAATTG
1563770 A
1 A
1563771 GTATTTAGGT
Statistics
Matches: 134, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
141 44 0.33
142 12 0.09
143 1 0.01
145 2 0.01
147 40 0.30
148 35 0.26
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (139 bp):
AATTAGAATAACAATATTATAATATGATAAATATTTATAATTAAATTAAACAGAAACTAAAAAAT
TAAATTCGACTTGATTTAAATTTTATAAACTCAAATAGAAAAATTTCGAGTCAACTATTTTATAA
ACTGAATTG
Found at i:1563996 original size:35 final size:35
Alignment explanation
Indices: 1563950--1564029 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
1563940 GGGGTTAGGC
*
1563950 ATGTAATTGAAGTATTTTAGAATCTAAGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATCTAAGGTTTAGA
* * * **
1563985 ATGTAATTGAAGCATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATCTAAGGTTTAGA
*
1564020 ATATAATTGA
1 ATGTAATTGA
1564030 TGAATGTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTAGAATCTAAGGTTTAGA
Found at i:1565559 original size:44 final size:44
Alignment explanation
Indices: 1565469--1565674 Score: 190
Period size: 44 Copynumber: 4.8 Consensus size: 44
1565459 AGATTTAAGC
* * * **
1565469 CGCAAAATGTCGATATTTATAGCG--GTATTTTGGAACAAACAC
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
*
1565511 CGCAAAAGGTCGATATCTATATCGACGTTTTTTGGAACAAACGT
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
** *
1565555 CGCAAAAGGTCGAGCTCTATAGCGACATTTTTTGGATACAAACGT
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGA-ACAAACGT
* * * *
1565600 CGCAAAAGGTTAGATA--TATAGCGGC-ATTTTTGGAATAAACG-
1 CGCAAAAGG-TCGATATCTATAGCGACGTTTTTTGGAACAAACGT
* * **
1565641 CAGCAAAAGGTCAAAATCTATAGCGGTGTTTTTT
1 C-GCAAAAGGTCGATATCTATAGCGACGTTTTTT
1565675 TAGATACAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
41 4 0.03
42 35 0.26
43 16 0.12
44 60 0.44
45 17 0.13
46 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
Found at i:1565602 original size:45 final size:44
Alignment explanation
Indices: 1565496--1565665 Score: 193
Period size: 44 Copynumber: 3.9 Consensus size: 44
1565486 TATAGCGGTA
** * * *
1565496 TTTTGGAACAAACACCGCAAAAGGTCGATATCTATATCGACGTT
1 TTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATAGCGACATT
*
1565540 TTTTGGAACAAACGTCGCAAAAGGTCGAGCTCTATAGCGACATT
1 TTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATAGCGACATT
* * *
1565584 TTTTGGATACAAACGTCGCAAAAGGT-TAGATATATAGCGGCA-T
1 TTTTGGA-ACAAACGTCGCAAAAGGTCGAGATCTATAGCGACATT
* * *
1565627 TTTTGGAATAAACG-CAGCAAAAGGTCAAAATCTATAGCG
1 TTTTGGAACAAACGTC-GCAAAAGGTCGAGATCTATAGCG
1565666 GTGTTTTTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 15 0.14
43 18 0.17
44 57 0.52
45 18 0.17
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (44 bp):
TTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATAGCGACATT
Found at i:1565650 original size:87 final size:87
Alignment explanation
Indices: 1565539--1565729 Score: 231
Period size: 88 Copynumber: 2.2 Consensus size: 87
1565529 ATATCGACGT
* * ** * **
1565539 TTTTTGGAACAAACGTCGCAAAAGGTCGAGCTCTATAGC-GACATTTTTTGGATACAAACGTCGC
1 TTTTTGGAATAAACG-CGCAAAAGGTCAAAATCTATAGCGGACATTTTTTAGATACAAACACCGC
**
1565603 AAAAGGTTAGATATATAGCGGCA
65 AAAAGGAAAGATATATAGCGGCA
***
1565626 TTTTTGGAATAAACGCAGCAAAAGGTCAAAATCTATAGCGGTGTTTTTTTAGATACAAACACCGC
1 TTTTTGGAATAAACGC-GCAAAAGGTCAAAATCTATAGCGGACATTTTTTAGATACAAACACCGC
*
1565691 AAAAGGAAAGATCTATAGCGGCA
65 AAAAGGAAAGATATATAGCGGCA
*
1565714 TTTTCGGAATAAACGC
1 TTTTTGGAATAAACGC
1565730 CACAAATTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
86 1 0.01
87 33 0.38
88 54 0.61
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (87 bp):
TTTTTGGAATAAACGCGCAAAAGGTCAAAATCTATAGCGGACATTTTTTAGATACAAACACCGCA
AAAGGAAAGATATATAGCGGCA
Found at i:1565708 original size:88 final size:86
Alignment explanation
Indices: 1565503--1565729 Score: 229
Period size: 88 Copynumber: 2.6 Consensus size: 86
1565493 GTATTTTGGA
** * * * * * *
1565503 ACAAACACCGCAAAAGGTCGATATCTATATCGACGTTTTTTGGAACAAACGTCGCAAAAGGTCGA
1 ACAAACACCGCAAAAGG-AAAGATCTATAGCGGC-ATTTTTGGAATAAACG-CGCAAAAGGTCAA
** *
1565568 GCTCTATAGCGACATTTTTTGGAT
63 AATCTATAGCGACATTTTTTAGAT
** ** *
1565592 ACAAACGTCGCAAAAGGTTAGATATATAGCGGCATTTTTGGAATAAACGCAGCAAAAGGTCAAAA
1 ACAAACACCGCAAAAGGAAAGATCTATAGCGGCATTTTTGGAATAAACGC-GCAAAAGGTCAAAA
***
1565657 TCTATAGCGGTGTTTTTTTAGAT
65 TCTATAGC-GACATTTTTTAGAT
*
1565680 ACAAACACCGCAAAAGGAAAGATCTATAGCGGCATTTTCGGAATAAACGC
1 ACAAACACCGCAAAAGGAAAGATCTATAGCGGCATTTTTGGAATAAACGC
1565730 CACAAATTAT
Statistics
Matches: 113, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
86 1 0.01
87 33 0.29
88 64 0.57
89 15 0.13
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (86 bp):
ACAAACACCGCAAAAGGAAAGATCTATAGCGGCATTTTTGGAATAAACGCGCAAAAGGTCAAAAT
CTATAGCGACATTTTTTAGAT
Found at i:1565955 original size:21 final size:21
Alignment explanation
Indices: 1565915--1565956 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1565905 ATGACATGAC
* *
1565915 AACAACAAACTTTAATTCCAT
1 AACAACAAACTTCAAATCCAT
*
1565936 AACAACAATCTTCAAATCCAT
1 AACAACAAACTTCAAATCCAT
1565957 TATATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (21 bp):
AACAACAAACTTCAAATCCAT
Found at i:1569244 original size:42 final size:42
Alignment explanation
Indices: 1569192--1569277 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
1569182 CATGTCACTT
1569192 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
1 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
1569234 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
1 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
1569276 GA
1 GA
1569278 ACTTAACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (42 bp):
GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
Found at i:1574956 original size:10 final size:10
Alignment explanation
Indices: 1574941--1574968 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1574931 ATTAGAAGAC
1574941 AACTAGTTGG
1 AACTAGTTGG
1574951 AACTAGTTGG
1 AACTAGTTGG
1574961 AACTAGTT
1 AACTAGTT
1574969 TTACAAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (10 bp):
AACTAGTTGG
Found at i:1576893 original size:2 final size:2
Alignment explanation
Indices: 1576886--1576911 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1576876 GAAAAACATG
1576886 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1576912 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1577781 original size:13 final size:13
Alignment explanation
Indices: 1577765--1577794 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1577755 ATTATACTTT
1577765 TAAAAAATACGTA
1 TAAAAAATACGTA
*
1577778 TAAAAAATACGTG
1 TAAAAAATACGTA
1577791 TAAA
1 TAAA
1577795 CAGAAGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (13 bp):
TAAAAAATACGTA
Found at i:1580885 original size:21 final size:21
Alignment explanation
Indices: 1580861--1580900 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1580851 TTCCTGCACC
1580861 ACTTATCTA-ATATCCTTTTAT
1 ACTTATCTATATA-CCTTTTAT
1580882 ACTTATCTATATACCTTTT
1 ACTTATCTATATACCTTTT
1580901 CCTTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.53
Consensus pattern (21 bp):
ACTTATCTATATACCTTTTAT
Found at i:1581311 original size:18 final size:18
Alignment explanation
Indices: 1581288--1581358 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
1581278 ACTATATATT
1581288 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
1581306 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
1581324 TGTCCCGAATGACTACTA
1 TGTCCCGAATGACCACTA
*
1581342 TGTCTCGAATGACCACT
1 TGTCCCGAATGACCACT
1581359 CCTTAAGAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:1582229 original size:21 final size:21
Alignment explanation
Indices: 1582203--1582248 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1582193 TGCATTGATA
1582203 CACATTAAAGATACATCGATG
1 CACATTAAAGATACATCGATG
*
1582224 CACATTAAAGATGCATCGATG
1 CACATTAAAGATACATCGATG
1582245 CACA
1 CACA
1582249 CAACCCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
CACATTAAAGATACATCGATG
Found at i:1584519 original size:27 final size:27
Alignment explanation
Indices: 1584467--1584519 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1584457 AAATTTCTTT
*
1584467 ATAAAATTAATATAAATTTTAAAAAAA
1 ATAAAATTAACATAAATTTTAAAAAAA
* *
1584494 ATAAAATTAACA-CAATTTTAATAAAA
1 ATAAAATTAACATAAATTTTAAAAAAA
1584520 TATTGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAATTAACATAAATTTTAAAAAAA
Found at i:1587615 original size:24 final size:24
Alignment explanation
Indices: 1587588--1587647 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
1587578 GTTCACGAAC
1587588 AAACTCGTTTATGAGTTCGTTTAT
1 AAACTCGTTTATGAGTTCGTTTAT
1587612 AAACTCGTTTATGAGTTCGTTTAT
1 AAACTCGTTTATGAGTTCGTTTAT
1587636 AAACTCGTTTAT
1 AAACTCGTTTAT
1587648 TGATTTATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (24 bp):
AAACTCGTTTATGAGTTCGTTTAT
Found at i:1587643 original size:12 final size:12
Alignment explanation
Indices: 1587588--1587647 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
1587578 GTTCACGAAC
1587588 AAACTCGTTTAT
1 AAACTCGTTTAT
* **
1587600 GAGTTCGTTTAT
1 AAACTCGTTTAT
1587612 AAACTCGTTTAT
1 AAACTCGTTTAT
* **
1587624 GAGTTCGTTTAT
1 AAACTCGTTTAT
1587636 AAACTCGTTTAT
1 AAACTCGTTTAT
1587648 TGATTTATTC
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (12 bp):
AAACTCGTTTAT
Found at i:1590219 original size:209 final size:209
Alignment explanation
Indices: 1589859--1590280 Score: 826
Period size: 209 Copynumber: 2.0 Consensus size: 209
1589849 TTGTTGTTTA
1589859 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTCTGCTTGTTTCATGCTTGG
1 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTCTGCTTGTTTCATGCTTGG
1589924 ACCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCCT
66 ACCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCCT
*
1589989 CGACGAGGTGGTCTACTGAGGTTGTCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
131 CGACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
1590054 CCTCTCACTTCATG
196 CCTCTCACTTCATG
*
1590068 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTTTATTGTCTGCTTGTTTCATGCTTGG
1 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTCTGCTTGTTTCATGCTTGG
1590133 ACCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCCT
66 ACCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCCT
1590198 CGACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
131 CGACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
1590263 CCTCTCACTTCATG
196 CCTCTCACTTCATG
1590277 TTCT
1 TTCT
1590281 AAGCCTAAGA
Statistics
Matches: 211, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 211 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (209 bp):
TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTCTGCTTGTTTCATGCTTGG
ACCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCCT
CGACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
CCTCTCACTTCATG
Found at i:1591679 original size:23 final size:23
Alignment explanation
Indices: 1591653--1591706 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1591643 GTTAGTGTTC
1591653 GTTCATTT-AGGATTC-TCGAACAT
1 GTTCATTTAAGG-TTCGT-GAACAT
1591676 GTTCATTTAAGGTTCGTGAACAT
1 GTTCATTTAAGGTTCGTGAACAT
*
1591699 GTTTATTT
1 GTTCATTT
1591707 GCAAGCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (23 bp):
GTTCATTTAAGGTTCGTGAACAT
Done.