Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold198
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: 1648337
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:1239202 original size:142 final size:143
Alignment explanation
Indices: 1239045--1239301 Score: 399
Period size: 143 Copynumber: 1.8 Consensus size: 143
1239035 TTAATGTTTT
* * * *
1239045 TTTTTTAAAAAGCCCAACTAGCTAAATGGTAAGGTATTTTTAGAAATGTTAGA-TTTTTTAATGG
1 TTTTTTAAAAAGCCCAACTAGCTAAATGGCAAGGCATTTTTAGAAATATTAGATTTTTTTAAGGG
* * *
1239109 CATTCTTGATAATGTACCATTATTTGGTACAATGAAGGCACTATAACCAACTAGCAAAATGGTTA
66 CATTCTTGATAATCTACAATTATTTAGTACAATGAAGGCACTATAACCAACTAGCAAAATGGTTA
1239174 TAGTTTTTTTAGA
131 TAGTTTTTTTAGA
* *
1239187 TTTTTTAAAAGGCCCAACTAGCTAAATGGCCAGGCATTTTTAGAAATATTAGATTTTTTTAAGGG
1 TTTTTTAAAAAGCCCAACTAGCTAAATGGCAAGGCATTTTTAGAAATATTAGATTTTTTTAAGGG
* * *
1239252 CATTCTTGATAATCTAGAATTATTTAGTATAATGAAGGTACTATAACCAA
66 CATTCTTGATAATCTACAATTATTTAGTACAATGAAGGCACTATAACCAA
1239302 TAAAATTTGT
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
142 48 0.47
143 54 0.53
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (143 bp):
TTTTTTAAAAAGCCCAACTAGCTAAATGGCAAGGCATTTTTAGAAATATTAGATTTTTTTAAGGG
CATTCTTGATAATCTACAATTATTTAGTACAATGAAGGCACTATAACCAACTAGCAAAATGGTTA
TAGTTTTTTTAGA
Found at i:1240403 original size:20 final size:20
Alignment explanation
Indices: 1240378--1240433 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1240368 ACTACCAAGG
*
1240378 AAATGTATTGACACATTGGT
1 AAATGTATCGACACATTGGT
*
1240398 AAATGTATCGATACATTGGT
1 AAATGTATCGACACATTGGT
*
1240418 AAATGTATCGATACAT
1 AAATGTATCGACACAT
1240434 GCTTACAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATGTATCGACACATTGGT
Found at i:1248946 original size:30 final size:30
Alignment explanation
Indices: 1248912--1249049 Score: 120
Period size: 30 Copynumber: 4.5 Consensus size: 30
1248902 CCTAAACTCA
1248912 ATGACTTAGTGGCATCTCTTCTCCAAGTCC
1 ATGACTTAGTGGCATCTCTTCTCCAAGTCC
* * *
1248942 ATGACCTAGTGGCATTCTTTTTCTTCCAAAAGCCC
1 ATGACTTAGTGGCA-TC-TCTTC-TCC--AAGTCC
*
1248977 ATGACTTTA-TGGCA-CTCTTC-CTAAAGTCC
1 ATGAC-TTAGTGGCATCTCTTCTC-CAAGTCC
* * *
1249006 ACGACTCAATGGCATCTCTTCTCCAAGTCC
1 ATGACTTAGTGGCATCTCTTCTCCAAGTCC
*
1249036 CTGACTTAGTGGCA
1 ATGACTTAGTGGCA
1249050 ACCTTTCTTA
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
28 2 0.02
29 14 0.17
30 36 0.43
31 3 0.04
32 8 0.10
33 4 0.05
35 15 0.18
36 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (30 bp):
ATGACTTAGTGGCATCTCTTCTCCAAGTCC
Found at i:1249011 original size:29 final size:30
Alignment explanation
Indices: 1248963--1249026 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
1248953 GCATTCTTTT
* **
1248963 TCTTCCAAAAGCCCATGACTTTATGGCA-C
1 TCTTCCAAAAGCCCACGACTCAATGGCATC
* *
1248992 TCTTCCTAAAGTCCACGACTCAATGGCATC
1 TCTTCCAAAAGCCCACGACTCAATGGCATC
1249022 TCTTC
1 TCTTC
1249027 TCCAAGTCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (30 bp):
TCTTCCAAAAGCCCACGACTCAATGGCATC
Found at i:1249027 original size:94 final size:94
Alignment explanation
Indices: 1248866--1249049 Score: 269
Period size: 94 Copynumber: 2.0 Consensus size: 94
1248856 GTCTTTCAAA
* * * *
1248866 TTTTCTTCCAAAAGCCCATGACTCCCTAGCACTCTTCCTAAACTCAATGACTTAGTGGCATCTCT
1 TTTTCTTCCAAAAGCCCATGACTCCATAGCACTCTTCCTAAACTCAACGACTCAATGGCATCTCT
1248931 TCTCCAAGTCCATGACCTAGTGGCATTCT
66 TCTCCAAGTCCATGACCTAGTGGCATTCT
** * * *
1248960 TTTTCTTCCAAAAGCCCATGACTTTATGGCACTCTTCCTAAAGTCCACGACTCAATGGCATCTCT
1 TTTTCTTCCAAAAGCCCATGACTCCATAGCACTCTTCCTAAACTCAACGACTCAATGGCATCTCT
* *
1249025 TCTCCAAGTCCCTGACTTAGTGGCA
66 TCTCCAAGTCCATGACCTAGTGGCA
1249050 ACCTTTCTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 79 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (94 bp):
TTTTCTTCCAAAAGCCCATGACTCCATAGCACTCTTCCTAAACTCAACGACTCAATGGCATCTCT
TCTCCAAGTCCATGACCTAGTGGCATTCT
Found at i:1249165 original size:32 final size:33
Alignment explanation
Indices: 1249083--1249360 Score: 305
Period size: 33 Copynumber: 8.5 Consensus size: 33
1249073 CCGTGGTACA
* *
1249083 TTTTCCCTTTTAAGTCCACAACTCAATGGCACC
1 TTTTTCCTTTTAAGTCCACAACTCTATGGCACC
* * *
1249116 TTTTTCTTTTTTAAGTCCACAACTTTGTGGCA-C
1 TTTTTC-CTTTTAAGTCCACAACTCTATGGCACC
1249149 TTTTTCCTTTTAAGTCCACAACT-TCATGGCACC
1 TTTTTCCTTTTAAGTCCACAACTCT-ATGGCACC
* * *
1249182 TTTTCCCTTTTAAGTTCACAACTCTGTGGCA-C
1 TTTTTCCTTTTAAGTCCACAACTCTATGGCACC
* * * * **
1249214 ATTTTCTTTTTAAGTCTATAACTCCGTGGCACC
1 TTTTTCCTTTTAAGTCCACAACTCTATGGCACC
*
1249247 TTTTTCTTTTTGAAGTCCACAACTCTATGGCACC
1 TTTTTCCTTTT-AAGTCCACAACTCTATGGCACC
* * *
1249281 TTTTCCCTTTTAAGTCCACAA-TTTCGTGGCACC
1 TTTTTCCTTTTAAGTCCACAACTCT-ATGGCACC
1249314 -TTTTCCTTTTAAGTCCACAACTCTATGGCACC
1 TTTTTCCTTTTAAGTCCACAACTCTATGGCACC
**
1249346 TTTTTTTTTTTAAGT
1 TTTTTCCTTTTAAGT
1249361 TTGCAACTTC
Statistics
Matches: 205, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.00
32 74 0.36
33 81 0.40
34 49 0.24
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (33 bp):
TTTTTCCTTTTAAGTCCACAACTCTATGGCACC
Found at i:1249195 original size:99 final size:97
Alignment explanation
Indices: 1249083--1249360 Score: 371
Period size: 99 Copynumber: 2.8 Consensus size: 97
1249073 CCGTGGTACA
* *
1249083 TTTTCCCTTTTAAGTCCACAACTCAATGGCACCTTTTTCTTTTTTAAGTCCACAACTTTGTGGCA
1 TTTTCCCTTTTAAGTCCACAACTC-GTGGCACC-TTTTC-TTTTTAAGTCCACAACTCTGTGGCA
*
1249148 -CTTTTTCCTTTTAAGTCCACAACT-TCATGGCACC
63 CCTTTTTCTTTTTAAGTCCACAACTCT-ATGGCACC
* * * * *
1249182 TTTTCCCTTTTAAGTTCACAACTCTGTGGCACATTTTCTTTTTAAGTCTATAACTCCGTGGCACC
1 TTTTCCCTTTTAAGTCCACAACTC-GTGGCACCTTTTCTTTTTAAGTCCACAACTCTGTGGCACC
1249247 TTTTTCTTTTTGAAGTCCACAACTCTATGGCACC
65 TTTTTCTTTTT-AAGTCCACAACTCTATGGCACC
* * *
1249281 TTTTCCCTTTTAAGTCCACAATTTCGTGGCACCTTTTCCTTTTAAGTCCACAACTCTATGGCACC
1 TTTTCCCTTTTAAGTCCACAA-CTCGTGGCACCTTTTCTTTTTAAGTCCACAACTCTGTGGCACC
*
1249346 TTTTTTTTTTTAAGT
65 TTTTTCTTTTTAAGT
1249361 TTGCAACTTC
Statistics
Matches: 157, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
97 21 0.13
98 20 0.13
99 113 0.72
100 3 0.02
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (97 bp):
TTTTCCCTTTTAAGTCCACAACTCGTGGCACCTTTTCTTTTTAAGTCCACAACTCTGTGGCACCT
TTTTCTTTTTAAGTCCACAACTCTATGGCACC
Found at i:1249372 original size:65 final size:65
Alignment explanation
Indices: 1249083--1249374 Score: 327
Period size: 65 Copynumber: 4.4 Consensus size: 65
1249073 CCGTGGTACA
* * * * *
1249083 TTTTCCCTTTTAAGTCCACAAC-TCAATGGCACCTTTTTCTTTTTTAAGTCCACAACTTTGTGGC
1 TTTTTCCTTTTAAGTCCACAACTTC-GTGGCACCTTTTTC-CTTTTAAGTCCACAACTCTATGGC
1249147 AC
64 AC
* * * *
1249149 TTTTTCCTTTTAAGTCCACAACTTCATGGCACCTTTTCCCTTTTAAGTTCACAACTCTGTGGCAC
1 TTTTTCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCTATGGCAC
* * * * * *
1249214 ATTTTCTTTTTAAGTCTATAACTCCGTGGCACCTTTTTCTTTTTGAAGTCCACAACTCTATGGCA
1 TTTTTCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCTATGGCA
1249279 CC
65 -C
* *
1249281 TTTTCCCTTTTAAGTCCACAATTTCGTGGCACC-TTTTCCTTTTAAGTCCACAACTCTATGGCAC
1 TTTTTCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCTATGGCA-
1249345 C
65 C
** ***
1249346 TTTTTTTTTTTAAGTTTGCAACTTCGTGG
1 TTTTTCCTTTTAAGTCCACAACTTCGTGG
1249375 TACTTTTACC
Statistics
Matches: 193, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
65 103 0.53
66 61 0.32
67 29 0.15
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (65 bp):
TTTTTCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCTATGGCAC
Found at i:1249421 original size:31 final size:31
Alignment explanation
Indices: 1249385--1249901 Score: 226
Period size: 32 Copynumber: 16.3 Consensus size: 31
1249375 TACTTTTACC
* *
1249385 CTTCTAAAGCCCACACAAGTCAGTGACAATT
1 CTTCTAAAGCCCACACAAGTCGGTGACAACT
* * * *
1249416 CTTCTAAAGTCCATACAAGTTGGTGGCAAC-
1 CTTCTAAAGCCCACACAAGTCGGTGACAACT
* * **
1249446 CATTCTAAAGCCTATACAAGTCAATGACAACACT
1 C-TTCTAAAGCCCACACAAGTCGGTGAC-A-ACT
* * * *
1249480 CCTCCAAAGCCCACACAAGTGGGT-AGC-ACC
1 CTTCTAAAGCCCACACAAGTCGGTGA-CAACT
* * *
1249510 CCTCTAAAGCCCACACAAGTCAGTGACAACCC
1 CTTCTAAAGCCCACACAAGTCGGTGACAA-CT
* *
1249542 CTT-TAAAGCCCACACAAGTTGGTGGCAACCT
1 CTTCTAAAGCCCACACAAGTCGGTGACAA-CT
* * *
1249573 TTTCTAAAGCCCACACAAGTTGGTGGCAA-T
1 CTTCTAAAGCCCACACAAGTCGGTGACAACT
* * *
1249603 CTTTCTAAAGCCCATACAAGTCGATGGCAACCCT
1 C-TTCTAAAGCCCACACAAGTCGGTGACAA--CT
* * * * *
1249637 CTTTTAAAGCCCATACATA-TCAGTGGC-ACC
1 CTTCTAAAGCCCACACA-AGTCGGTGACAACT
* * * *
1249667 CCTCTAAAGCCCATACAAG-CTGGTGGCAACCC
1 CTTCTAAAGCCCACACAAGTC-GGTGACAA-CT
* * ** *
1249699 CTTCAAAAGCCCACACAAATTAGTGGCAACTT
1 CTTCTAAAGCCCACACAAGTCGGTGACAAC-T
*** * * *
1249731 CTTCTCAAAGTTGACATAAGTTGGT-AGTAACTT
1 CTTCT-AAAGCCCACACAAGTCGGTGA-CAAC-T
* * * *
1249764 CTTCTCAAAGCCCAGACAAGTTGGTGGCAACC
1 CTTCT-AAAGCCCACACAAGTCGGTGACAACT
* *
1249796 CTTCTTAAAGCCCACACAAGTTGGTGGCAACCCT
1 CTTC-TAAAGCCCACACAAGTCGGTGACAA--CT
* * *
1249830 CTT-TAAAAGCCCACACAAGTGGGTGGCAACC
1 CTTCT-AAAGCCCACACAAGTCGGTGACAACT
* * * * *
1249861 CTCTCAAAAGCCTACACAAGTTGGTGGCATCT
1 CT-TCTAAAGCCCACACAAGTCGGTGACAACT
1249893 CCTTCTAAA
1 -CTTCTAAA
1249902 CCTAATGTCG
Statistics
Matches: 382, Mismatches: 74, Indels: 59
0.74 0.14 0.11
Matches are distributed among these distances:
29 2 0.01
30 47 0.12
31 102 0.27
32 116 0.30
33 107 0.28
34 8 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (31 bp):
CTTCTAAAGCCCACACAAGTCGGTGACAACT
Found at i:1249559 original size:94 final size:95
Alignment explanation
Indices: 1249451--1249889 Score: 286
Period size: 94 Copynumber: 4.6 Consensus size: 95
1249441 GCAACCATTC
* * * * *
1249451 TAAAGCCTATACAAGTCAATGACAACACTCCTCCAAAGCCCACACAAGTGGGTAGC-ACCCCTCT
1 TAAAGCCCATACAAGTCAGTGGCAAC-CTCCTCTAAAGCCCACACAAGT-GGTGGCAACCCCTCT
1249515 AAAGCCCACACAAGTC-AGTGACAACCC-C-TT
64 AAAGCCCACACAAGTCGA-TGACAACCCTCTTT
* ** ** * **
1249545 TAAAGCCCACACAAGTTGGTGGCAACCTTTTCTAAAGCCCACACAAGTTGGTGGCAATCTTTCTA
1 TAAAGCCCATACAAGTCAGTGGCAACCTCCTCTAAAGCCCACACAAG-TGGTGGCAACCCCTCTA
* *
1249610 AAGCCCATACAAGTCGATGGCAACCCTCTTT
65 AAGCCCACACAAGTCGATGACAACCCTCTTT
*
1249641 TAAAGCCCATACATA-TCAGTGGC-ACC-CCTCTAAAGCCCATACAAGCTGGTGGCAACCCCTTC
1 TAAAGCCCATACA-AGTCAGTGGCAACCTCCTCTAAAGCCCACACAAG-TGGTGGCAACCCC-TC
* * * * *
1249703 AAAAGCCCACACAAAT-TAGTGGCAA-CTTCTTCT
63 TAAAGCCCACACAAGTCGA-TGACAACCCTCTT-T
* *** * * ** * * * * * *
1249736 CAAAGTTGACATAAGTTGGTAGTAACTTCTTCTCAAAGCCCAGACAAGTTGGTGGCAACCCTTCT
1 TAAAGCCCATACAAGTCAGTGGCAACCTCCTCT-AAAGCCCACACAAG-TGGTGGCAACCCCTC-
* * *
1249801 TAAAGCCCACACAAGTTGGTGGCAACCCTCTTT
63 TAAAGCCCACACAAGTCGATGACAACCCTCTTT
* * ** * *
1249834 AAAAGCCCACACAAGTGGGTGGCAACC-CTCTCAAAAGCCTACACAAGTTGGTGGCA
1 TAAAGCCCATACAAGTCAGTGGCAACCTC-CTCTAAAGCCCACACAAG-TGGTGGCA
1249890 TCTCCTTCTA
Statistics
Matches: 265, Mismatches: 63, Indels: 31
0.74 0.18 0.09
Matches are distributed among these distances:
93 23 0.09
94 82 0.31
95 38 0.14
96 22 0.08
97 29 0.11
98 66 0.25
99 5 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (95 bp):
TAAAGCCCATACAAGTCAGTGGCAACCTCCTCTAAAGCCCACACAAGTGGTGGCAACCCCTCTAA
AGCCCACACAAGTCGATGACAACCCTCTTT
Found at i:1249584 original size:32 final size:32
Alignment explanation
Indices: 1249386--1249889 Score: 309
Period size: 31 Copynumber: 15.8 Consensus size: 32
1249376 ACTTTTACCC
** *
1249386 TTCTAAAGCCCACACAAGTCAGTGACAA--TT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* * *
1249416 CTTCTAAAGTCCATACAAGTTGGTGGCAACC-A
1 -TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* * *** * *
1249448 TTCTAAAGCCTATACAAGTCAATGACAACACTC
1 TTCTAAAGCCCACACAAGTTGGTGGCAAC-CTT
* * * * *
1249481 CTCCAAAGCCCACACAAGTGGGTAGC-ACC-C
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* ** * **
1249511 CTCTAAAGCCCACACAAGTCAGTGACAACCCC
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
1249543 TT-TAAAGCCCACACAAGTTGGTGGCAACCTT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
*
1249574 TTCTAAAGCCCACACAAGTTGGTGGCAATC-T
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* * *
1249605 TTCTAAAGCCCATACAAGTCGATGGCAACCCTCT
1 TTCTAAAGCCCACACAAGTTGGTGGCAA-CCT-T
* ** *
1249639 TT-TAAAGCCCATACATA-TCAGTGGC-ACC-C
1 TTCTAAAGCCCACACA-AGTTGGTGGCAACCTT
* * * **
1249668 CTCTAAAGCCCATACAAGCTGGTGGCAACCCC
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* * *
1249700 TTCAAAAGCCCACACAAATTAGTGGCAA-CTT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
*** * * *
1249731 CTTCTCAAAGTTGACATAAGTTGGTAGTAA-CTT
1 -TTCT-AAAGCCCACACAAGTTGGTGGCAACCTT
* *
1249764 CTTCTCAAAGCCCAGACAAGTTGGTGGCAACC-C
1 -TTCT-AAAGCCCACACAAGTTGGTGGCAACCTT
1249797 TTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCT
1 TTC-TAAAGCCCACACAAGTTGGTGGCAA-CCT-T
* * *
1249832 TT-AAAAGCCCACACAAGTGGGTGGCAACCCT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
* * *
1249863 CTCAAAAGCCTACACAAGTTGGTGGCA
1 TTCTAAAGCCCACACAAGTTGGTGGCA
1249890 TCTCCTTCTA
Statistics
Matches: 372, Mismatches: 78, Indels: 45
0.75 0.16 0.09
Matches are distributed among these distances:
29 2 0.01
30 40 0.11
31 110 0.30
32 109 0.29
33 104 0.28
34 5 0.01
35 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.22
Consensus pattern (32 bp):
TTCTAAAGCCCACACAAGTTGGTGGCAACCTT
Found at i:1249645 original size:33 final size:33
Alignment explanation
Indices: 1249485--1249889 Score: 308
Period size: 32 Copynumber: 12.7 Consensus size: 33
1249475 ACACTCCTCC
* * *
1249485 AAAGCCCACACAAGTGGGTAGC-ACCC-C-TCT
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
** *
1249515 AAAGCCCACACAAGTCAGTGACAACCC-C-TTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
1249546 AAAGCCCACACAAGTTGGTGGCAA-CCT-TTTCT
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTT-T
1249578 AAAGCCCACACAAGTTGGTGGCAA---TCTTTCT
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTT-T
* * *
1249609 AAAGCCCATACAAGTCGATGGCAACCCTCTTTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
* ** *
1249642 AAAGCCCATACATA-TCAGTGGC-ACCC-C-TCT
1 AAAGCCCACACA-AGTTGGTGGCAACCCTCTTTT
* * **
1249672 AAAGCCCATACAAGCTGGTGGCAACCC-CTTCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
* * * *
1249704 AAAGCCCACACAAATTAGTGGCAA-CTTCTTCTC
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTT-TT
*** * * * * *
1249737 AAAGTTGACATAAGTTGGTAGTAA-CTTCTTCTC
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTT-TT
* *
1249770 AAAGCCCAGACAAGTTGGTGGCAACCCT-TCTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
*
1249802 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTA
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
* **
1249835 AAAGCCCACACAAGTGGGTGGCAACCCTC-TCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
*
1249867 AAAGCCTACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTTGGTGGCA
1249890 TCTCCTTCTA
Statistics
Matches: 309, Mismatches: 50, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.00
30 40 0.13
31 63 0.20
32 105 0.34
33 92 0.30
34 8 0.03
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (33 bp):
AAAGCCCACACAAGTTGGTGGCAACCCTCTTTT
Found at i:1249839 original size:65 final size:65
Alignment explanation
Indices: 1249390--1249889 Score: 357
Period size: 63 Copynumber: 7.8 Consensus size: 65
1249380 TTACCCTTCT
* * ** * * * *
1249390 AAAGCCCACACAAGTCAGTGACAATTCTTC-TAAAGTCCATACAAGTTGGTGGCAACCAT-TCT-
1 AAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTTA
* * * * * * * * * * *
1249452 AAAGCCTATACAAGTCAATGACAACACTCCTCCAAAGCCCACACAAGTGGGTAGC-ACCC-CTCT
1 AAAGCCCACACAAGTTAGTGGCAACCCTTCT-TAAAGCCCACACAAGTTGGTGGCAACCCTCTTT
1249515 -
65 A
* * *
1249515 AAAGCCCACACAAGTCAGTGACAACCCCT-TTAAAGCCCACACAAGTTGGTGGCAA-CCT-TTTC
1 AAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTT-
*
1249577 T
65 A
* * * * * * *
1249578 AAAGCCCACACAAGTTGGTGGCAATCTTTC-TAAAGCCCATACAAGTCGATGGCAACCCTCTTTT
1 AAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTTA
* * * * * *
1249642 AAAGCCCATACATA-TCAGTGGC-ACCCCTC-TAAAGCCCATACAAGCTGGTGGCAACCC-CTTC
1 AAAGCCCACACA-AGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTT
1249703 A
65 A
* * * *** * * * *
1249704 AAAGCCCACACAAATTAGTGGCAACTTCTTCTCAAAGTTGACATAAGTTGGTAGTAA-CTTCTTC
1 AAAGCCCACACAAGTTAGTGGCAAC-CCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTT-
*
1249768 TC
64 TA
* *
1249770 AAAGCCCAGACAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTTA
1 AAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTTA
** * *
1249835 AAAGCCCACACAAGTGGGTGGCAACCC-TCTCAAAAGCCTACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTTAGTGGCAACCCTTCT-TAAAGCCCACACAAGTTGGTGGCA
1249890 TCTCCTTCTA
Statistics
Matches: 344, Mismatches: 75, Indels: 35
0.76 0.17 0.08
Matches are distributed among these distances:
61 25 0.07
62 47 0.14
63 105 0.31
64 46 0.13
65 94 0.27
66 27 0.08
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (65 bp):
AAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAACCCTCTTTA
Found at i:1250045 original size:52 final size:52
Alignment explanation
Indices: 1249981--1250156 Score: 205
Period size: 52 Copynumber: 3.4 Consensus size: 52
1249971 CTAGCCTAGG
* * *
1249981 ATCAGCACATTGGCACCTTTTTCTTTCTTAA-CTCCAATATCGTTGGCCTTGA
1 ATCAGCATATTGGCACCTTTGTCTTTCTTAAGC-CCAATATCGCTGGCCTTGA
* * * * *
1250033 ATCAACATATTGGCACCTTTGTCATTT-TTAAGCCCAATGTTGCTAGCTTTGA
1 ATCAGCATATTGGCACCTTTGTC-TTTCTTAAGCCCAATATCGCTGGCCTTGA
* *
1250085 ATCAGCACATTGGCACCTTTGTC-ATCTTTAAGCCCAATATCGCTGGCCTTGA
1 ATCAGCATATTGGCACCTTTGTCTTTC-TTAAGCCCAATATCGCTGGCCTTGA
*
1250137 ATCAGCATATTAGCACCTTT
1 ATCAGCATATTGGCACCTTT
1250157 ATCATTTTTC
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
50 1 0.01
52 98 0.95
53 4 0.04
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (52 bp):
ATCAGCATATTGGCACCTTTGTCTTTCTTAAGCCCAATATCGCTGGCCTTGA
Found at i:1250201 original size:61 final size:61
Alignment explanation
Indices: 1250106--1250310 Score: 238
Period size: 61 Copynumber: 3.4 Consensus size: 61
1250096 GGCACCTTTG
* *
1250106 TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTATCATTTTTC
1 TCATCTTTAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTTTTC
* * *
1250167 TCATCTTTAAGCCTAATATCGCTGGCCTTAAATCAACATTTTGGCACCTTTATCATTTTT-
1 TCATCTTTAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTTTTC
* * * * * * *
1250227 TCATATTCAAGCCTGATATCACTAG-TTGTGAATCAGCATATTGGCACCTTTATCATTCTTC
1 TCATCTTTAAGCCTAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTTATCATTTTTC
*
1250288 GT-ATCCTTAAGTCC-AATATCGCT
1 -TCATCTTTAAG-CCTAATATCGCT
1250311 CACCTGGAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 48 0.40
61 68 0.57
62 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (61 bp):
TCATCTTTAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTTTTC
Found at i:1252355 original size:21 final size:19
Alignment explanation
Indices: 1252286--1252359 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
1252276 CACACCCAGA
*
1252286 TGTATCGATACATGCTG-CTT
1 TGTATCGATACATG--GACAT
**
1252306 TGTATCGATACATGTTCAT
1 TGTATCGATACATGGACAT
* *
1252325 CGTATTGATACATGGACAAAT
1 TGTATCGATACATGGAC--AT
1252346 TGTATCGATACATG
1 TGTATCGATACATG
1252360 AAACTAGCAG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 15 0.35
20 14 0.33
21 14 0.33
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGGACAT
Found at i:1252418 original size:20 final size:18
Alignment explanation
Indices: 1252389--1252443 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 18
1252379 TATCACTATT
*
1252389 TGTATTGATACATGGTACAA
1 TGTATCGATACATGG-A-AA
1252409 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG--GAAA
1252429 TGTATCGATACATGG
1 TGTATCGATACATGG
1252444 CTTGTAATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.03
20 29 0.91
21 1 0.03
22 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
TGTATCGATACATGGAAA
Found at i:1261076 original size:19 final size:20
Alignment explanation
Indices: 1261052--1261106 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1261042 TATTGATACT
**
1261052 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
1261071 TTGTATCGATACATGGACAAA
1 TTGTATCGATACATGGAC-AA
1261092 TTGTATCGATACATG
1 TTGTATCGATACATG
1261107 AAACTAGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:1266116 original size:105 final size:104
Alignment explanation
Indices: 1265747--1266999 Score: 891
Period size: 105 Copynumber: 11.9 Consensus size: 104
1265737 AACATCAAGA
* * * *
1265747 GGATACTCCAA-TGCCGTTGTTCATAAAAAAATAAAATATTCTCTTTGTTCCTAAATATTGTT-T
1 GGATACTCTAACT-CCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATT-TTCT
*
1265810 AAAATCTTTCACTTT--GGAGAACTCCAACCCCACCACTCCAAGG
64 -AAATCTTT-ACTTTGAGGA-AACTCCAACCCCACCACTTC-AGG
* *
1265853 GGATACTCTAAC-CC---CTT-AT-AAAAAATCAAATTTTCTCTTTGTTCCTAAAAAATTTCTAA
1 GGATACTCTAACTCCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCT-A
* * * * *
1265912 AATCTTTGACTTTGGGGAAATTCCAGCCCCACTACTCTGAGGG
65 AATCTTT-ACTTTGAGGAAACTCCAACCCCACCACT-TCA-GG
* * * *
1265955 GGATAATCCAAC-CTCGTTCTTCATAAAAAAAATCAAATTTTCTCTTTGTTTCTAAATGTTTTCA
1 GGATACTCTAACTC-CGTTCTTCAT-AAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTC-
* * * * *
1266019 TAACTCTTTACCTCGAGGAAACTCCAACCCCACCATTATCAGA
63 TAAATCTTTACTTTGAGGAAACTCCAACCCCACCACT-TCAGG
* * * *
1266062 GGATACTCTAACTACGTTCTTCATAAAAAAA-CAAATTTTATCTTTGTTCTTAAATTTTTTTCTA
1 GGATACTCTAACTCCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAA-TATTTTCTA
* * *
1266126 ATATCTTTGACTTTG-GGTAAACTCCAAGCCCGCCACTCCGAGG
65 A-ATCTTT-ACTTTGAGG-AAACTCCAACCCCACCACTTC-AGG
* ** * * *
1266169 GGA-ACTCCAAC-CTTATTCTTTAT-AAAAAATCAAATTTTTTTCTTTGTTCTTAAATATTTTCT
1 GGATACTCTAACTC-CGTTCTTCATAAAAAAATCAAA-TTTTCTCTTTGTTCCTAAATATTTTCT
* * *
1266231 AAAATTTTTGATTTTGAGGAAACTCCAA-CCCACTACTTCGAGG
64 -AAATCTTT-ACTTTGAGGAAACTCCAACCCCACCACTTC-AGG
* * * * *
1266274 GGATACTCTAAC-CCATTCTTTATAAAAAAATCAAATTTTCTATTGGTTCCTAAATGTTTT-TAT
1 GGATACTCTAACTCCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCTA-
* * * *
1266337 AAGTCTTGACCTT-AGGAAACTCCAACCTCACTACTTCGAGG
65 AA-TCTTTACTTTGAGGAAACTCCAACCCCACCACTTC-AGG
* * * *
1266378 GGATACTTTAACCCCGTTCTTCATAAAAAAATCAAATTTTTTCTTAGTTCCTAAAT-TTTT-TAA
1 GGATACTCTAACTCCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCTAA
* * *
1266441 ATCTTTGATTTTG-GGAAAACTCCAACCCCACCACTCTGAAG
66 ATCTTT-ACTTTGAGG-AAACTCCAACCCCACCACT-TCAGG
* * * * * * *
1266482 GAATACTCCAAC-CCTGTTCTTCATAAAAAAATTAAAATTTCTATTTTTTCCTAAATATTTTTTA
1 GGATACTCTAACTCC-GTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCT-
* * * * *
1266546 AAATCTTGGACTTT-AGGGATACTCCAGCCCTACTA-TTCCGAGG
64 AAATCTT-TACTTTGA-GGAAACTCCAACCCCACCACTT-C-AGG
* * * * **
1266589 GGATAGTCTAAC-CCTGTTCTTCAAAAAAAAAATCAATTTTTCTCTTTGTTTCTAAATGGTTTCA
1 GGATACTCTAACTCC-GTTCTTC-ATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTC-
* * ** * * *
1266653 TAATTCTTGACTTCAAGGAAACTTCAACCCCACCACTATGAGA
63 TAAATCTTTACTTTGAGGAAACTCCAACCCCACCACT-TCAGG
* * * *
1266696 GGATACTCTAACTACTTTCTTCATAGAAAAA-CAAATTTTATCTTTGTTCCTAAATATTTTCTAC
1 GGATACTCTAACTCCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCTA-
* * * * * *
1266760 TATCTTCGACTTTG-GGAAAACTCCAGCCCTACCACTCCGACG
65 AATCTT-TACTTTGAGG-AAACTCCAACCCCACCACTTC-AGG
* * *
1266802 GGA-ACTCCAAC-CCTATTCTTCAT-AAAAAATCAAATTTTCTCCTTGTTCCTAAATATTTTCTA
1 GGATACTCTAACTCC-GTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCT-
* * *
1266864 AAATCTTTGACTTTGGGGAAACTCCAACCCCACTACTTAGAGG
64 AAATCTTT-ACTTTGAGGAAACTCCAACCCCACCACTT-CAGG
* * * *
1266907 GGATACTCTAA-TCCTGTTCTTTATAAAAAAATCAAATTTTCTCTTGGATCCTAAATGTTTTCAT
1 GGATACTCTAACTCC-GTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTC-T
* * * *
1266971 GATTCTTGACTTTTG-GGAAAATCCAACCC
64 AAATCTTTAC-TTTGAGGAAACTCCAACCC
1267000 TATCCTTCAC
Statistics
Matches: 916, Mismatches: 166, Indels: 130
0.76 0.14 0.11
Matches are distributed among these distances:
99 2 0.00
100 45 0.05
101 18 0.02
102 22 0.02
103 23 0.03
104 108 0.12
105 229 0.25
106 166 0.18
107 195 0.21
108 65 0.07
109 42 0.05
110 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (104 bp):
GGATACTCTAACTCCGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCCTAAATATTTTCTAA
ATCTTTACTTTGAGGAAACTCCAACCCCACCACTTCAGG
Found at i:1270340 original size:33 final size:33
Alignment explanation
Indices: 1270299--1270365 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1270289 TTTTTAAGTT
1270299 AGTTTATTCTGACACTGGCAACATATGTGGGGA
1 AGTTTATTCTGACACTGGCAACATATGTGGGGA
*
1270332 AGTTTATTCTGACGCTGGCAACATATGTGGGGA
1 AGTTTATTCTGACACTGGCAACATATGTGGGGA
1270365 A
1 A
1270366 AAACAAATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (33 bp):
AGTTTATTCTGACACTGGCAACATATGTGGGGA
Found at i:1270479 original size:23 final size:23
Alignment explanation
Indices: 1270447--1270498 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
1270437 GAAATGAAGT
*
1270447 TTTGTAAAATTTTTGAGAAAAATA-
1 TTTG-AAAATTTTAGA-AAAAATAG
1270471 TTTGAAAATTTTAGAAAAAATAG
1 TTTGAAAATTTTAGAAAAAATAG
1270494 TTTGA
1 TTTGA
1270499 TGGGCCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.27
23 15 0.58
24 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.40
Consensus pattern (23 bp):
TTTGAAAATTTTAGAAAAAATAG
Found at i:1270892 original size:219 final size:219
Alignment explanation
Indices: 1270625--1271065 Score: 749
Period size: 219 Copynumber: 2.0 Consensus size: 219
1270615 TTTTAGAAAG
* * *
1270625 GTATTTTGATGCCCGTTAAGGAAAAAAAATCAAAAAAATCAAAGGAAATATTTTGTAGTACGAAA
1 GTATTTCGATGCCCGTTAAGGAAAAAAAATCAAAAAAATCAAAGGAAATATTTTGCAGTACAAAA
* * * *
1270690 ATGATTTTTCAATCTCAAGTTGTGCTGTTATTAGAGTAAAATAGGGGGTTATTTGATGTTTTCAT
66 ATGATTTTTCAATCTCAAGTTATGCTGCTATTAGAGTAAAATAGGGGGTCATTTGATATTTTCAT
**
1270755 GCTCCTTGAGATTAGTTCAAGTTTAGGATGTTAGAACATCAGTGATGGAAATTAACATGGGTGTC
131 GCTCCTTGAGAAAAGTTCAAGTTTAGGATGTTAGAACATCAGTGATGGAAATTAACATGGGTGTC
1270820 ATGAGTTCATTCCATAATCTTGAA
196 ATGAGTTCATTCCATAATCTTGAA
** *
1270844 GTATTTCGATGCCTTTTAAGG-AAAAAAATCAAAAAAAATCAAAGGAAATATTTTGCAGTTCAAA
1 GTATTTCGATGCCCGTTAAGGAAAAAAAATC-AAAAAAATCAAAGGAAATATTTTGCAGTACAAA
*
1270908 AATGATTTTTCAATCTCAAGTTATGTTGCTATTAGAGTAAAATAGGGGGTCATTTGATATTTTCA
65 AATGATTTTTCAATCTCAAGTTATGCTGCTATTAGAGTAAAATAGGGGGTCATTTGATATTTTCA
1270973 TGCTCCTTGAGAAAAGTTCAAGTTTAGGATGTTAGAACATCAGTGATGGAAATTAACATGGGTGT
130 TGCTCCTTGAGAAAAGTTCAAGTTTAGGATGTTAGAACATCAGTGATGGAAATTAACATGGGTGT
1271038 CATGAGTTCATTCCATAATCTTGAA
195 CATGAGTTCATTCCATAATCTTGAA
1271063 GTA
1 GTA
1271066 GGTTGGGATG
Statistics
Matches: 208, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 9 0.04
219 199 0.96
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (219 bp):
GTATTTCGATGCCCGTTAAGGAAAAAAAATCAAAAAAATCAAAGGAAATATTTTGCAGTACAAAA
ATGATTTTTCAATCTCAAGTTATGCTGCTATTAGAGTAAAATAGGGGGTCATTTGATATTTTCAT
GCTCCTTGAGAAAAGTTCAAGTTTAGGATGTTAGAACATCAGTGATGGAAATTAACATGGGTGTC
ATGAGTTCATTCCATAATCTTGAA
Found at i:1273702 original size:20 final size:20
Alignment explanation
Indices: 1273651--1273707 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1273641 AGCTACCTTA
1273651 AGTGAAATGTATCGATACAT
1 AGTGAAATGTATCGATACAT
* *
1273671 GGT-ACATTGTATCGATACAT
1 AGTGA-AATGTATCGATACAT
*
1273691 AGTGAAAAGTATCGATA
1 AGTGAAATGTATCGATA
1273708 TATTGTGCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTGAAATGTATCGATACAT
Found at i:1274136 original size:23 final size:23
Alignment explanation
Indices: 1274106--1274149 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1274096 TGAATTCAAC
1274106 TTGGGTTACAATCTCTT-AAGAAT
1 TTGGGTTACAAT-TCTTGAAGAAT
1274129 TTGGGTTACAATTCTTGAAGA
1 TTGGGTTACAATTCTTGAAGA
1274150 GATTGAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (23 bp):
TTGGGTTACAATTCTTGAAGAAT
Found at i:1284956 original size:13 final size:13
Alignment explanation
Indices: 1284938--1284964 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1284928 ACATTATGCT
1284938 TTGTATCGATACA
1 TTGTATCGATACA
1284951 TTGTATCGATACA
1 TTGTATCGATACA
1284964 T
1 T
1284965 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1284973 original size:19 final size:19
Alignment explanation
Indices: 1284949--1285004 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1284939 TGTATCGATA
*
1284949 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* **
1284968 CATTGTATCGATGCACACT
1 CATTGTATCGATACATGCT
1284987 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1285005 AAATTGGCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1286674 original size:10 final size:10
Alignment explanation
Indices: 1286656--1286697 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1286646 GATGAAGGTG
1286656 ATTGATACCA
1 ATTGATACCA
*
1286666 ATTGTTACCA
1 ATTGATACCA
1286676 ATTGATA--A
1 ATTGATACCA
*
1286684 AATGATACCA
1 ATTGATACCA
1286694 ATTG
1 ATTG
1286698 TTGAAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.27
10 19 0.73
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (10 bp):
ATTGATACCA
Found at i:1287759 original size:13 final size:13
Alignment explanation
Indices: 1287741--1287765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1287731 TTTTACAATT
1287741 TGTATCGATACAA
1 TGTATCGATACAA
1287754 TGTATCGATACA
1 TGTATCGATACA
1287766 TTTATCATTG
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:1291807 original size:21 final size:21
Alignment explanation
Indices: 1291765--1291807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1291755 AAGAGAGCAT
* * *
1291765 GAAATATTTTATTAAGGGGGA
1 GAAAAATTTTATTAAAGAGGA
1291786 GAAAAATTTTATTAAAGAGGA
1 GAAAAATTTTATTAAAGAGGA
1291807 G
1 G
1291808 TTACAAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (21 bp):
GAAAAATTTTATTAAAGAGGA
Found at i:1293141 original size:89 final size:89
Alignment explanation
Indices: 1292990--1293169 Score: 342
Period size: 89 Copynumber: 2.0 Consensus size: 89
1292980 ACAATCTTTT
1292990 AAGAATTTGGGGTATAATTCTTGAAGAGATTGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGT
1 AAGAATTTGGGGTATAATTCTTGAAGAGATTGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGT
* *
1293055 GTTGTAAGGTTATACCTTTGCTTG
66 GTTGTAAGGTTATAACTTTGCCTG
1293079 AAGAATTTGGGGTATAATTCTTGAAGAGATTGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGT
1 AAGAATTTGGGGTATAATTCTTGAAGAGATTGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGT
1293144 GTTGTAAGGTTATAACTTTGCCTG
66 GTTGTAAGGTTATAACTTTGCCTG
1293168 AA
1 AA
1293170 AGGTAAACAA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (89 bp):
AAGAATTTGGGGTATAATTCTTGAAGAGATTGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGT
GTTGTAAGGTTATAACTTTGCCTG
Found at i:1293764 original size:73 final size:71
Alignment explanation
Indices: 1293633--1294163 Score: 312
Period size: 73 Copynumber: 7.3 Consensus size: 71
1293623 AGGGTTTGAA
* * * * *
1293633 GTAGGTAAGAAAAGCATC-GTATTCTTTGACAACT-GGTAGATAGGTGTCACCAGCTTGTGTGGC
1 GTAGGTAAGAAAAGCATCTG-ACTCTTTAAGAACTAGGTAGATAGGTGCCACCAGCTTGTGTGGG
1293696 CTTTAAG
65 CTTTAAG
* * * ** *
1293703 GTAGGTAAGAAAAGCGTCTGATTTTTTGAA-AACTAGAGGTAGATAGGTGCCATTAGCTTGTGTA
1 GTAGGTAAGAAAAGCATCTGACTCTTT-AAGAACT--AGGTAGATAGGTGCCACCAGCTTGTGTG
1293767 GGCTTTAAG
63 GGCTTTAAG
* * * *
1293776 GTAGGCAAGAAAAGCATCTTACTCTTTAAGGACTAAGGGTAGATAGGTGCCACCTGCTTGTGTGG
1 GTAGGTAAGAAAAGCATCTGACTCTTTAAGAACT-A-GGTAGATAGGTGCCACCAGCTTGTGTGG
*
1293841 GCTTTGAG
64 GCTTTAAG
* * * * * *
1293849 GTAGGTAAAAAAAACGTCCTG-CTTTTTAAGGACTGAAGGTAGCTAGGTGCCACCAGCTT-TGTG
1 GTAGGTAAGAAAAGCAT-CTGACTCTTTAAGAACT--AGGTAGATAGGTGCCACCAGCTTGTGTG
1293912 GGCTTTAAG
63 GGCTTTAAG
* * * * * * *
1293921 GTAAGT-AGAAAAAGCATCCT-ACTCTTTGAGGA-TTGGAAATAGATAAGTGCCACTAGCTTATG
1 GTAGGTAAG-AAAAGCAT-CTGACTCTTTAAGAACTAGG---TAGATAGGTGCCACCAGCTTGTG
1293983 TGGGCTTTACA-
61 TGGGCTTTA-AG
* * * *** * * * * ** *
1293994 ATAAGTACGAAAAATGTCTAACTCTTTGAGGACTGAAGGTAGATAAGTGCCACCAATTTGTGTAG
1 GTAGGTAAGAAAAGCATCTGACTCTTTAAGAACT--AGGTAGATAGGTGCCACCAGCTTGTGTGG
*
1294059 CCTTTGCAA-
64 GCTTT--AAG
* * * * * *
1294068 -TAGGTAAGAAAAGCAT-TTAGGTCTTTGAGGACTAATGGTAGATAAGTGCCACCAGCTTGTATG
1 GTAGGTAAGAAAAGCATCTGA-CTCTTTAAGAACT-A-GGTAGATAGGTGCCACCAGCTTGTGTG
1294131 GGCTTTAAG
63 GGCTTTAAG
* * *
1294140 ATAGGTTAGAAAAGCATCTTACTC
1 GTAGGTAAGAAAAGCATCTGACTC
1294164 CTAGAGAGTT
Statistics
Matches: 368, Mismatches: 65, Indels: 53
0.76 0.13 0.11
Matches are distributed among these distances:
69 2 0.01
70 27 0.07
71 6 0.02
72 61 0.17
73 258 0.70
74 11 0.03
75 1 0.00
76 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (71 bp):
GTAGGTAAGAAAAGCATCTGACTCTTTAAGAACTAGGTAGATAGGTGCCACCAGCTTGTGTGGGC
TTTAAG
Found at i:1294152 original size:146 final size:144
Alignment explanation
Indices: 1293621--1294152 Score: 453
Period size: 146 Copynumber: 3.7 Consensus size: 144
1293611 ATAAGCTTGC
* * * * *
1293621 GTAGGGTTTGAAGTAGGTAAGAAAAGCATCGTATTCTTT---GAC-AACTGGTAGATAGGTGTCA
1 GTAGGCTTT-AAGTAGGTAAGAAAAGCATCTTACTCTTTGAGGACTAA-TGGTAGATAAGTGCCA
* * * * **
1293682 CCAGCTTGTGTGGCCTTTAAGGTAGGTAAGAAAAGCGTCTGATTTTTTGAAAACT-AGAGGTAGA
64 CCAGCTTGTGTGGGCTTTAAGATAGGTAAGAAAAACGTCT-ACTTTTTGAGGACTGA-AGGTAGA
** **
1293746 TAGGTGCCATTAGCTTGT
127 TAGGTGCCACCAATTTGT
* * * *
1293764 GTAGGCTTTAAGGTAGGCAAGAAAAGCATCTTACTCTTTAAGGACTAAGGGTAGATAGGTGCCAC
1 GTAGGCTTTAA-GTAGGTAAGAAAAGCATCTTACTCTTTGAGGACTAATGGTAGATAAGTGCCAC
* * * * * * *
1293829 CTGCTTGTGTGGGCTTTGAGGTAGGTAAAAAAAACGTCCTGCTTTTTAAGGACTGAAGGTAGCTA
65 CAGCTTGTGTGGGCTTTAAGATAGGTAAGAAAAACGT-CTACTTTTTGAGGACTGAAGGTAGATA
*
1293894 GGTGCCACCAGCTTTGT
129 GGTGCCACCA-ATTTGT
* *
1293911 G--GGCTTTAAGGTAAGT-AGAAAAAGCATCCTACTCTTTGAGGA-T--TGGAAATAGATAAGTG
1 GTAGGCTTTAA-GTAGGTAAG-AAAAGCATCTTACTCTTTGAGGACTAATGG---TAGATAAGTG
* * * * * *
1293970 CCACTAGCTTATGTGGGCTTTACA-ATAAGTACGAAAAATGTCTAACTCTTTGAGGACTGAAGGT
61 CCACCAGCTTGTGTGGGCTTTA-AGATAGGTAAGAAAAACGTCT-ACTTTTTGAGGACTGAAGGT
*
1294034 AGATAAGTGCCACCAATTTGT
124 AGATAGGTGCCACCAATTTGT
* *
1294055 GTAGCCTTTGCAA-TAGGTAAGAAAAGCAT-TTAGGTCTTTGAGGACTAATGGTAGATAAGTGCC
1 GTAGGCTTT--AAGTAGGTAAGAAAAGCATCTTA-CTCTTTGAGGACTAATGGTAGATAAGTGCC
* *
1294118 ACCAGCTTGTATGGGCTTTAAGATAGGTTAGAAAA
63 ACCAGCTTGTGTGGGCTTTAAGATAGGTAAGAAAA
1294153 GCATCTTACT
Statistics
Matches: 313, Mismatches: 52, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
142 4 0.01
143 32 0.10
144 11 0.04
145 106 0.34
146 142 0.45
147 13 0.04
148 2 0.01
149 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (144 bp):
GTAGGCTTTAAGTAGGTAAGAAAAGCATCTTACTCTTTGAGGACTAATGGTAGATAAGTGCCACC
AGCTTGTGTGGGCTTTAAGATAGGTAAGAAAAACGTCTACTTTTTGAGGACTGAAGGTAGATAGG
TGCCACCAATTTGT
Found at i:1295689 original size:157 final size:155
Alignment explanation
Indices: 1295405--1295980 Score: 593
Period size: 158 Copynumber: 3.7 Consensus size: 155
1295395 AGAAAATGAT
* * * ** * * *
1295405 AAAAATGCCCTTA-GGGGATACCTTCGACAT-AGAAGTA-CCCAATACCCCTACAGGACTTAAAA
1 AAAAATGCCTTTATGGGTATACCTTCGACGTGA-AAGTATCCCGGTAACCCTAAAAGACTT-AAA
** * * * * *
1295467 AGGACTATAAAAGGGACAAACCTATCCTAAATACCCACATTCGGCATAAAAACAAACCTAGTGAC
64 AGGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCGA-TGAC
* *
1295532 AACCTACGACTCGCTTCTAAAAGAAATAT
128 AACCTAAGACTCGCTTCTAAAA-AAATAC
* **
1295561 GAAAATGCCTTTATGGGTATACCTTCGACGTGAAAGTGCCCCGGTAACCCTAAAAGACTTAAAAG
1 AAAAATGCCTTTATGGGTATACCTTCGACGTGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAG
* * * *
1295626 GACTATAAAAGGGGTGAACCTATCCTAAATACCTACCTTTAGCATAAAAGCGGATCCGATGACAA
66 GACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGC-GAACCGATGACAA
* * *
1295691 CCTAGGACTCAGTTTTTAAAAAAATTAC
130 CCTAAGACTC-GCTTCTAAAAAAA-TAC
* * * * ** *
1295719 AAAAATG-CTTGTATGGGTATACTTTCGATGTAAAAGTATTCTTGTAACCCTAAAGGACTTAAAA
1 AAAAATGCCTT-TATGGGTATACCTTCGACGTGAAAGTATCCCGGTAACCCTAAAAGACTTAAAA
* * * *
1295783 GGACTATAAAAAGGTTGAACCTATCCTAAATACCCACCTTTGGCATAAAAGTGAACTCGGTGACA
65 GGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAAC-CGATGACA
* * *
1295848 ACCTAAGACTTGGTTCTAAAAAAGTAC
129 ACCTAAGACTCGCTTCTAAAAAAATAC
* * * *
1295875 AAAAATACCTCTATGGGTATACCTTCGACGTGAAAGTATCCCGGTACCCCTAAAAAACTTAAAAT
1 AAAAATGCCTTTATGGGTATACCTTCGACGTGAAAGTATCCCGGTAACCCTAAAAGACTTAAAA-
* * *
1295940 GGATTTTAAAAAGGAATGAACCTATCCTAAATACCCACCTT
65 GGACTAT-AAAAGGGATGAACCTATCCTAAATACCCACCTT
1295981 CGACGTAAAA
Statistics
Matches: 346, Mismatches: 63, Indels: 20
0.81 0.15 0.05
Matches are distributed among these distances:
156 64 0.18
157 108 0.31
158 174 0.50
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (155 bp):
AAAAATGCCTTTATGGGTATACCTTCGACGTGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAG
GACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCGATGACAAC
CTAAGACTCGCTTCTAAAAAAATAC
Found at i:1297042 original size:165 final size:162
Alignment explanation
Indices: 1296643--1297067 Score: 604
Period size: 161 Copynumber: 2.6 Consensus size: 162
1296633 TTTTGTGCAT
* * *
1296643 TAATGGATACCCGAAAAGATACGAAAAGTTTTTCGAAATCTTTTCTACCCGTACGGATACCCATA
1 TAATGGATA-CCGAAAAGATACGAAAAATTTTT-GAAATCTTTTATACCCCTACGGATACCCATA
* * * *
1296708 GGAATATAAAAGACTTGAAAATAATTGATATTTATTGTAATTAATGAGGAATGAATTTAATATTA
64 GGAATATAAAAGATTTAAAAATGATTAATATTTATTGTAATTAATGAGGAATGAATTTAATATTA
*
1296773 TTTATTTAATTTTTAAAAAAATCATTTCGTACCT
129 TTTATTTAATTTTTAAAAAAATCATTTCGTACCA
* * * * **
1296807 TAATGGATACCTGAAAAGAT--GGAAAAGTTTTGAAATCCTTTATACCCTTACGGATACTTATAG
1 TAATGGATACC-GAAAAGATACGAAAAATTTTTGAAATCTTTTATACCCCTACGGATACCCATAG
* *
1296870 GAATATAAAAGATTTAAAAATGATTAATATTTGTTGTAATTAACT-AGGAGTGAATTTAATATTA
65 GAATATAAAAGATTTAAAAATGATTAATATTTATTGTAATTAA-TGAGGAATGAATTTAATATTA
*
1296934 TTTATTTATTTTTTTAAAAAAAATCATTTCGTACCA
129 TTTATTTA-ATTTTT-AAAAAAATCATTTCGTACCA
*
1296970 TAATGGATACTCGAAAAGATACGAAAAATTTTTGAAATCTTTTATACCCCTACGGATACCCATAA
1 TAATGGATAC-CGAAAAGATACGAAAAATTTTTGAAATCTTTTATACCCCTACGGATACCCATAG
1297035 GAATATAAAAGATTTAAAAATGATTAATATTTA
65 GAATATAAAAGATTTAAAAATGATTAATATTTA
1297068 AAATATATAT
Statistics
Matches: 230, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
161 91 0.40
162 14 0.06
163 39 0.17
164 18 0.08
165 68 0.30
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (162 bp):
TAATGGATACCGAAAAGATACGAAAAATTTTTGAAATCTTTTATACCCCTACGGATACCCATAGG
AATATAAAAGATTTAAAAATGATTAATATTTATTGTAATTAATGAGGAATGAATTTAATATTATT
TATTTAATTTTTAAAAAAATCATTTCGTACCA
Found at i:1298865 original size:159 final size:162
Alignment explanation
Indices: 1298579--1298872 Score: 368
Period size: 161 Copynumber: 1.8 Consensus size: 162
1298569 AAAAAAATTT
*
1298579 AAAAACTCATGAAAATGAATAAATTTTTGAAAACTGAATTATTATGAAATAGATAATGATATTTG
1 AAAAACTCATGAAAATGAATAAATTTTTGAAAAC---ATTATTATGAAATAAATAATGATATTTG
*
1298644 ATGGATTTTAAAAATTGAAAATCAAGAAAAATCCCCTCGAAAAAAATTATGAAGTAGAAAACACC
63 ATGGATTTTAAAAATTGAAAATCAAGAAAAATCCCCTCGAAAAAAATTACGAAGTAGAAAACACC
*
1298709 GTATTGTAGAAAAAAGGAAGTTTTAAGGAAAAATC
128 ATATTGTAGAAAAAAGGAAGTTTTAAGGAAAAATC
* * * * * * *
1298744 AAAAACTCATGAAAATGGATGAATTTTTTGAAAAC-TTA-TGTGATATAAATGATGGTATTTGGT
1 AAAAACTCATGAAAATGAAT-AAATTTTTGAAAACATTATTATGAAATAAATAATGATATTTGAT
* *
1298807 GGATTTTAAAAATT-AAAA-CTAAGAAAAA-CCCACT-G-AAAAAATTCACGGAGTAGCAAACAC
65 GGATTTTAAAAATTGAAAATC-AAGAAAAATCCC-CTCGAAAAAAATT-ACGAAGTAGAAAACAC
1298867 CATATT
127 CATATT
1298873 TTGAAAACTA
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
158 8 0.07
159 23 0.20
160 14 0.12
161 33 0.29
162 3 0.03
165 19 0.17
166 13 0.12
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (162 bp):
AAAAACTCATGAAAATGAATAAATTTTTGAAAACATTATTATGAAATAAATAATGATATTTGATG
GATTTTAAAAATTGAAAATCAAGAAAAATCCCCTCGAAAAAAATTACGAAGTAGAAAACACCATA
TTGTAGAAAAAAGGAAGTTTTAAGGAAAAATC
Found at i:1301772 original size:41 final size:41
Alignment explanation
Indices: 1301540--1302023 Score: 205
Period size: 42 Copynumber: 11.5 Consensus size: 41
1301530 GCCGGCAGGT
* *
1301540 AAACGAAAGAT-AAAGAAGTCTCCTAGGTCTAAGCCGACGGGC
1 AAACAAAAGATGAAA-AAGTCTCCCAGGTCTAAG-CGACGGGC
* * * * *
1301582 AAATAAAAGATAAAAGAAGTCTCCTAGGTCTAAGCCGATGGGT
1 AAACAAAAGATGAAA-AAGTCTCCCAGGTCTAAG-CGACGGGC
* * *
1301625 AGACAAATGAT-AAAGGAAGTCTCCC-GTGTCTGAGCGACGGGC
1 AAACAAAAGATGAAA--AAGTCTCCCAG-GTCTAAGCGACGGGC
* * * * *
1301667 AAACGAATGAT-AAAGGAA-TCTCTCAAGTCTAAGCTGACGGGT
1 AAACAAAAGATGAAA--AAGTCTCCCAGGTCTAAGC-GACGGGC
* ** * * **
1301709 AGACAATGGATGAAGAAGTCTCCCAGGTCTAAGTGATTGGC
1 AAACAAAAGATGAAAAAGTCTCCCAGGTCTAAGCGACGGGC
*
1301750 AAACAAAAGATGAAAAAATCTCCCGAGGTCTAAGCGACGGGC
1 AAACAAAAGATGAAAAAGTCTCCC-AGGTCTAAGCGACGGGC
** * * *
1301792 AAATGAAA-ATGAAAAAGTCCCCCAGGTCTAAGCCAACAGGC
1 AAACAAAAGATGAAAAAGTCTCCCAGGTCTAAG-CGACGGGC
* * * * * * * *
1301833 AGATAAAAAAT-AAAGAAGTCTTCCGGGTCTAAGTTGATGGGT
1 AAACAAAAGATGAAA-AAGTCTCCCAGGTCTAAG-CGACGGGC
* ***** * * * * *
1301875 AGATGGTTGATGAAGAAGTCTCTCAGGTCTGAGCCGATGGGA
1 AAACAAAAGATGAAAAAGTCTCCCAGGTCTAAG-CGACGGGC
*
1301917 AAATGAAAA-ATGAAAAAGTCTCCC-GAGTCTAAGTCGACGGGC
1 AAA-CAAAAGATGAAAAAGTCTCCCAG-GTCTAAG-CGACGGGC
* * * * *
1301959 AAACAAAGGGTGAAGAAGTCTCCAAGGTC-AATGCCGACAGGC
1 AAACAAAAGATGAAAAAGTCTCCCAGGTCTAA-G-CGACGGGC
* * *
1302001 AAACTTAAGGGTGAAAAAGTCTC
1 AAAC-AAAAGATGAAAAAGTCTC
1302024 TAAGGTCAAA
Statistics
Matches: 337, Mismatches: 87, Indels: 35
0.73 0.19 0.08
Matches are distributed among these distances:
40 9 0.03
41 71 0.21
42 184 0.55
43 73 0.22
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (41 bp):
AAACAAAAGATGAAAAAGTCTCCCAGGTCTAAGCGACGGGC
Found at i:1301781 original size:84 final size:81
Alignment explanation
Indices: 1301548--1301790 Score: 247
Period size: 83 Copynumber: 2.9 Consensus size: 81
1301538 GTAAACGAAA
* * *
1301548 GATAAAGAAGTCTCCTAGGTCTAAGCCGACGGGCAAATAAAAGATAAAAGAAGTCTCCTAGGTCT
1 GATAAAGAAGTCTCCCAGGTCTAAG-CGACGGGCAAACAAAAGATAAAA-AA-TCTCCCAGGTCT
*
1301613 AAGCCGATGGGTAGACAAAT
63 AAG-CGACGGGTAGACAAAT
* * * * * *
1301633 GATAAAGGAAGTCTCCC-GTGTCTGAGCGACGGGCAAACGAATGATAAAGGAATCTCTCAAGTCT
1 GATAAA-GAAGTCTCCCAG-GTCTAAGCGACGGGCAAACAAAAGATAAA-AAATCTCCCAGGTCT
1301697 AAGCTGACGGGTAGAC-AAT
63 AAGC-GACGGGTAGACAAAT
* * **
1301716 GGATGAAGAAGTCTCCCAGGTCTAAGTGATTGGCAAACAAAAGATGAAAAAATCTCCCGAGGTCT
1 -GATAAAGAAGTCTCCCAGGTCTAAGCGACGGGCAAACAAAAGAT-AAAAAATCTCCC-AGGTCT
1301781 AAGCGACGGG
63 AAGCGACGGG
1301791 CAAATGAAAA
Statistics
Matches: 130, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
83 47 0.36
84 40 0.31
85 28 0.22
86 15 0.12
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (81 bp):
GATAAAGAAGTCTCCCAGGTCTAAGCGACGGGCAAACAAAAGATAAAAAATCTCCCAGGTCTAAG
CGACGGGTAGACAAAT
Found at i:1302022 original size:43 final size:43
Alignment explanation
Indices: 1301951--1302108 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 43
1301941 GAGTCTAAGT
* * * * *
1301951 CGACGGGCAAAC-AAAGGGTGAAGAAGTCTCCAAGGTCAATGC
1 CGACAGGCAAACTTAAGGGCGAAGAAGTCTCTAAGGTCAAAGC
* *
1301993 CGACAGGCAAACTTAAGGGTGAAAAAGTCTCTAAGGTCAAAGC
1 CGACAGGCAAACTTAAGGGCGAAGAAGTCTCTAAGGTCAAAGC
* * * * * *
1302036 TGACAAGCAGACTTAAGGGCGAAGAGGTCTCTAGGGTCAAAGT
1 CGACAGGCAAACTTAAGGGCGAAGAAGTCTCTAAGGTCAAAGC
*
1302079 CGATAGGCAAACTTAAGGGCGAAGAAGTCT
1 CGACAGGCAAACTTAAGGGCGAAGAAGTCT
1302109 AGACTTAAGG
Statistics
Matches: 97, Mismatches: 18, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
42 11 0.11
43 86 0.89
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.16
Consensus pattern (43 bp):
CGACAGGCAAACTTAAGGGCGAAGAAGTCTCTAAGGTCAAAGC
Found at i:1302133 original size:65 final size:65
Alignment explanation
Indices: 1302044--1302367 Score: 226
Period size: 65 Copynumber: 5.0 Consensus size: 65
1302034 GCTGACAAGC
** * *
1302044 AGACTTAAGGGCGAAGAGGTCTCTAGGGTCAAAGTCGATAGGCAAACTTAAGGGCGAAGAAGTCT
1 AGACTTAAGGATGAAGAAGTCTCTAGGGTCAAAGTCGATAGGCAGACTTAAGGGCGAAGAAGTCT
* *
1302109 AGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAG-CAGATAGGCAGACTTAAAGGCGAAGAAGTC
1 AGACTTAAGGATGAAGAAGTCTCTAGGGTCAAAGTC-GATAGGCAGACTTAAGGGCGAAGAAGTC
1302173 TT
65 -T
* * * * * * ** ** * * *
1302175 CA-AGGTCAAAGCTGACAGGCAGACT-TAAGGGGGAAAAAGTCTCTATG--G--TCAA-AGCTGA
1 -AGA-CTTAAGGATGA-A-GAAGTCTCT-A--GGGTCAAAGTCGATAGGCAGACTTAAGGGC-GA
1302233 CAG--G--T
58 -AGAAGTCT
* * *
1302238 AGACTTAAGGGTGAAGAAGTCTCCT-GGGTCATAGTCGACAGGCAGACTTAAGGGCGAAGAAGTC
1 AGACTTAAGGATGAAGAAGTCT-CTAGGGTCAAAGTCGATAGGCAGACTTAAGGGCGAAGAAGTC
1302302 T
65 T
*
1302303 AGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAG-CAGATAGGCAGACTTAAGGGCGAAGAAGTC
1 AGACTTAAGGATGAAGAAGTCTCTAGGGTCAAAGTC-GATAGGCAGACTTAAGGGCGAAGAAGTC
1302367 T
65 T
1302368 TTAAGGTTAA
Statistics
Matches: 194, Mismatches: 39, Indels: 52
0.68 0.14 0.18
Matches are distributed among these distances:
58 10 0.05
60 6 0.03
61 3 0.02
62 14 0.07
63 5 0.03
64 4 0.02
65 113 0.58
66 5 0.03
67 12 0.06
68 4 0.02
69 7 0.04
71 10 0.05
72 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.19
Consensus pattern (65 bp):
AGACTTAAGGATGAAGAAGTCTCTAGGGTCAAAGTCGATAGGCAGACTTAAGGGCGAAGAAGTCT
Found at i:1302170 original size:43 final size:43
Alignment explanation
Indices: 1302122--1302302 Score: 224
Period size: 43 Copynumber: 4.2 Consensus size: 43
1302112 CTTAAGGATT
* * *
1302122 AAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGCG
1 AAGAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTTAAGGGCG
* *
1302165 AAGAAGTCT-TCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGG
1 AAGAAGTCTCT-AGGGTCAAAGCTGACAGGCAGACTTAAGGGCG
* * * *
1302208 AAAAAGTCTCTATGGTCAAAGCTGACAGGTAGACTTAAGGGTG
1 AAGAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTTAAGGGCG
*
1302251 AAGAAGTCTCCT-GGGTCATAG-TCGACAGGCAGACTTAAGGGCG
1 AAGAAGTCT-CTAGGGTCAAAGCT-GACAGGCAGACTTAAGGGCG
1302294 AAGAAGTCT
1 AAGAAGTCT
1302303 AGACTTAAGG
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
42 2 0.02
43 115 0.96
44 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (43 bp):
AAGAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTTAAGGGCG
Found at i:1302195 original size:108 final size:108
Alignment explanation
Indices: 1302003--1302216 Score: 270
Period size: 108 Copynumber: 2.0 Consensus size: 108
1301993 CGACAGGCAA
* * * *
1302003 ACTTAAGGGTGAAAAAGTCTCTAAGGTCAAAGCTGACAAGCAGACTTAAGGGCGAAGAGGTCTCT
1 ACTTAAGGATGAAAAAGTCTCTAAGGTCAAAGCAGACAAGCAGACTTAAAGGCGAAGAAGTCTCT
* * *
1302068 AGGGTCAAAGTCGATAGGCAAACTTAAGGGCGAAGAAGTCTAG
66 AAGGTCAAAGTCGACAGGCAAACTTAAGGGCGAAAAAGTCTAG
* * * * *
1302111 ACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGCGAAGAAGTCT-T
1 ACTTAAGGATGAAAAAGTCTCTAAGGTCAAAGCAGACAAGCAGACTTAAAGGCGAAGAAGTCTCT
* *
1302175 CAAGGTCAAAG-CTGACAGGCAGACTTAAGGGGGAAAAAGTCT
66 -AAGGTCAAAGTC-GACAGGCAAACTTAAGGGCGAAAAAGTCT
1302217 CTATGGTCAA
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 2 0.02
108 88 0.98
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19
Consensus pattern (108 bp):
ACTTAAGGATGAAAAAGTCTCTAAGGTCAAAGCAGACAAGCAGACTTAAAGGCGAAGAAGTCTCT
AAGGTCAAAGTCGACAGGCAAACTTAAGGGCGAAAAAGTCTAG
Found at i:1302245 original size:151 final size:151
Alignment explanation
Indices: 1301971--1302259 Score: 384
Period size: 151 Copynumber: 1.9 Consensus size: 151
1301961 ACAAAGGGTG
* * * *
1301971 AAGAAGTCTCCAAGGTCAATGCCGACAGGCAAACTTAAGGGTGAAAAAGTCTCTAAGGTCAAAGC
1 AAGAAGTCTCCAAGGTCAAAGCAGACAGGCAAACTTAAAGGCGAAAAAGTCTCTAAGGTCAAAGC
* * *
1302036 TGACAAGCAGACTTAAGGGCGAAGAGGTCTCTAGGGTCAAAGTCGATAGGCAAACTTAAGGGCGA
66 TGACAAGCAGACTTAAGGGCGAAAAAGTCTCTAGGGTCAAAGTCGACAGGCAAACTTAAGGGCGA
1302101 AGAAGTCTAGACTTAAGGATT
131 AGAAGTCTAGACTTAAGGATT
* * * * *
1302122 AAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGCGAAGAAGTCT-TCAAGGTCAAAG
1 AAGAAGTCTCCAAGGTCAAAGCAGACAGGCAAACTTAAAGGCGAAAAAGTCTCT-AAGGTCAAAG
* * * * * *
1302186 CTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAG-CTGACAGGTAGACTTAAGGGT
65 CTGACAAGCAGACTTAAGGGCGAAAAAGTCTCTAGGGTCAAAGTC-GACAGGCAAACTTAAGGGC
1302250 GAAGAAGTCT
129 GAAGAAGTCT
1302260 CCTGGGTCAT
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
150 2 0.02
151 116 0.98
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (151 bp):
AAGAAGTCTCCAAGGTCAAAGCAGACAGGCAAACTTAAAGGCGAAAAAGTCTCTAAGGTCAAAGC
TGACAAGCAGACTTAAGGGCGAAAAAGTCTCTAGGGTCAAAGTCGACAGGCAAACTTAAGGGCGA
AGAAGTCTAGACTTAAGGATT
Found at i:1302299 original size:194 final size:194
Alignment explanation
Indices: 1301970--1302496 Score: 804
Period size: 194 Copynumber: 2.7 Consensus size: 194
1301960 AACAAAGGGT
* * * * * *
1301970 GAAGAAGTCTCCAAGGTCAATGCCGACAGGCAAACTTAAGGGTGAAAAAGTCTCTAAGGTCAAAG
1 GAAGAAGTCTTCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAG
* * * * * *
1302035 CTGACAAGCAGACTTAAGGGCGAAGAGGTCT-CTAGGGTCAAAGTCGATAGGCAAACTTAAGGGC
66 CTGACAGGTAGACTTAAGGGTGAAGAAGTCTCCT-GGGTCAAAGTCGACAGGCAGACTTAAGGGC
1302099 GAAGAAGTCTAGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGC
130 GAAGAAGTCTAGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGC
1302164 GAAGAAGTCTTCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAG
1 GAAGAAGTCTTCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAG
*
1302229 CTGACAGGTAGACTTAAGGGTGAAGAAGTCTCCTGGGTCATAGTCGACAGGCAGACTTAAGGGCG
66 CTGACAGGTAGACTTAAGGGTGAAGAAGTCTCCTGGGTCAAAGTCGACAGGCAGACTTAAGGGCG
*
1302294 AAGAAGTCTAGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAGGGC
131 AAGAAGTCTAGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGC
* * * * * * *
1302358 GAAGAAGTCTTTAAGGTTAAAGTTGATAGGCAGACTTAAGAGGGAAGAAGTCTCTATTGTCAAAG
1 GAAGAAGTCTTCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAG
* * * * *
1302423 CTGATAGGTAAACTTAAAGGTGAAGAAGTCTCTTGGGTCAAAGTCGACAGGCAGACTTAAGGGTG
66 CTGACAGGTAGACTTAAGGGTGAAGAAGTCTCCTGGGTCAAAGTCGACAGGCAGACTTAAGGGCG
1302488 AAGAAGTCT
131 AAGAAGTCT
1302497 CCTAGGTCAA
Statistics
Matches: 305, Mismatches: 27, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
194 303 0.99
195 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.20
Consensus pattern (194 bp):
GAAGAAGTCTTCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAG
CTGACAGGTAGACTTAAGGGTGAAGAAGTCTCCTGGGTCAAAGTCGACAGGCAGACTTAAGGGCG
AAGAAGTCTAGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAAGGC
Found at i:1302364 original size:43 final size:43
Alignment explanation
Indices: 1302303--1302523 Score: 259
Period size: 43 Copynumber: 5.1 Consensus size: 43
1302293 GAAGAAGTCT
* * *
1302303 AGACTTAAGGATTAAGAAGTCTCTAGGGTCAAAGCAGATAGGC
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAGCTGATAGGC
* * * * *
1302346 AGACTTAAGGGCGAAGAAGTCTTTAAGGTTAAAGTTGATAGGC
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAGCTGATAGGC
** *
1302389 AGACTTAAGAGG-GAAGAAGTCTCTATTGTCAAAGCTGATAGGT
1 AGACTTAAG-GGTGAAGAAGTCTCTAGGGTCAAAGCTGATAGGC
* * * *
1302432 AAACTTAAAGGTGAAGAAGTCTCTTGGGTCAAAG-TCGACAGGC
1 AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAGCT-GATAGGC
1302475 AGACTTAAGGGTGAAGAAGTCTCCTA-GGTCAAAGCTGATAGGC
1 AGACTTAAGGGTGAAGAAGTCT-CTAGGGTCAAAGCTGATAGGC
1302518 AGACTT
1 AGACTT
1302524 GAGATGAAGT
Statistics
Matches: 148, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.02
43 140 0.95
44 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.23
Consensus pattern (43 bp):
AGACTTAAGGGTGAAGAAGTCTCTAGGGTCAAAGCTGATAGGC
Found at i:1302389 original size:108 final size:108
Alignment explanation
Indices: 1302211--1302410 Score: 269
Period size: 108 Copynumber: 1.9 Consensus size: 108
1302201 AAGGGGGAAA
* * * * * *
1302211 AAGTCTCTATGGTCAAAGCTGACAGGTAGACTTAAGGGTGAAGAAGTCTCCTGGGTCATAGTCGA
1 AAGTCTCTAGGGTCAAAGCAGACAGGCAGACTTAAGGGCGAAGAAGTCTCCTAGGTCAAAGTCGA
1302276 CAGGCAGACTTAAG-GGCGAAGAAGTCTAGACTTAAGGATTAAG
66 CAGGCAGACTTAAGAGG-GAAGAAGTCTAGACTTAAGGATTAAG
* * * *
1302319 AAGTCTCTAGGGTCAAAGCAGATAGGCAGACTTAAGGGCGAAGAAGTCT-TTAAGGTTAAAGTTG
1 AAGTCTCTAGGGTCAAAGCAGACAGGCAGACTTAAGGGCGAAGAAGTCTCCT-AGGTCAAAGTCG
*
1302383 ATAGGCAGACTTAAGAGGGAAGAAGTCT
65 ACAGGCAGACTTAAGAGGGAAGAAGTCT
1302411 CTATTGTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 1 0.01
108 76 0.96
109 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (108 bp):
AAGTCTCTAGGGTCAAAGCAGACAGGCAGACTTAAGGGCGAAGAAGTCTCCTAGGTCAAAGTCGA
CAGGCAGACTTAAGAGGGAAGAAGTCTAGACTTAAGGATTAAG
Found at i:1302438 original size:151 final size:151
Alignment explanation
Indices: 1302165--1302453 Score: 343
Period size: 151 Copynumber: 1.9 Consensus size: 151
1302155 CTTAAAGGCG
* * *
1302165 AAGAAGTCTTCAAGGTCAAAGCTGACAGGCAGACTTAAGGGGGAAAAAGTCTCTATGGTCAAAGC
1 AAGAAGTCTTCAAGGTCAAAGCAGACAGGCAGACTTAAGGGCGAAAAAGTCTCTAAGGTCAAAGC
* * * *
1302230 TGACAGGTAGACTTAAGGGTGAAGAAGTCTCCTGGGTCATAGTCGACAGGCAGACTTAAGGGCGA
66 TGACAGGCAGACTTAAGGGTGAAGAAGTCTCCTGGGTCAAAGTCGACAGGCAAACTTAAAGGCGA
1302295 AGAAGTCTAGACTTAAGGATT
131 AGAAGTCTAGACTTAAGGATT
* * * * *
1302316 AAGAAGTC-TCTAGGGTCAAAGCAGATAGGCAGACTTAAGGGCGAAGAAGTCTTTAAGGTTAAAG
1 AAGAAGTCTTC-AAGGTCAAAGCAGACAGGCAGACTTAAGGGCGAAAAAGTCTCTAAGGTCAAAG
* * ** * *
1302380 TTGATAGGCAGACTTAAGAGG-GAAGAAGTCT-CTATTGTCAAAG-CTGATAGGTAAACTTAAAG
65 CTGACAGGCAGACTTAAG-GGTGAAGAAGTCTCCT-GGGTCAAAGTC-GACAGGCAAACTTAAAG
*
1302442 GTGAAGAAGTCT
127 GCGAAGAAGTCT
1302454 CTTGGGTCAA
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
150 5 0.04
151 108 0.94
152 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (151 bp):
AAGAAGTCTTCAAGGTCAAAGCAGACAGGCAGACTTAAGGGCGAAAAAGTCTCTAAGGTCAAAGC
TGACAGGCAGACTTAAGGGTGAAGAAGTCTCCTGGGTCAAAGTCGACAGGCAAACTTAAAGGCGA
AGAAGTCTAGACTTAAGGATT
Found at i:1302551 original size:42 final size:41
Alignment explanation
Indices: 1302303--1302554 Score: 170
Period size: 43 Copynumber: 5.9 Consensus size: 41
1302293 GAAGAAGTCT
* *
1302303 AGACTTAAGGATTAAGAAGTCT-CTAGGGTCAAAGCAGATAGGC
1 AGACTTAA-GATGAAGAAGTCTCCT-GGGT-AAAGCTGATAGGC
** * * *
1302346 AGACTTAAGGGCGAAGAAGTCT-TTAAGGTTAAAGTTGATAGGC
1 AGACTTAA-GATGAAGAAGTCTCCT--GGGTAAAGCTGATAGGC
* ** *
1302389 AGACTTAAGAGGGAAGAAGTCT-CTATTGTCAAAGCTGATAGGT
1 AGACTTAAGA-TGAAGAAGTCTCCT-GGGT-AAAGCTGATAGGC
* * * *
1302432 AAACTTAAAGGTGAAGAAGTCTCTTGGGTCAAAG-TCGACAGGC
1 AGACTT-AAGATGAAGAAGTCTCCTGGGT-AAAGCT-GATAGGC
* *
1302475 AGACTTAAGGGTGAAGAAGTCTCCTAGGTCAAAGCTGATAGGC
1 AGACTTAA-GATGAAGAAGTCTCCTGGGT-AAAGCTGATAGGC
* *
1302518 AGACTTGAGATGAAGTAGTCTCCTGGGCTAAAGCTGA
1 AGACTTAAGATGAAGAAGTCTCCTGGG-TAAAGCTGA
1302555 CGAGTAAACA
Statistics
Matches: 169, Mismatches: 31, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
42 30 0.18
43 130 0.77
44 9 0.05
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (41 bp):
AGACTTAAGATGAAGAAGTCTCCTGGGTAAAGCTGATAGGC
Found at i:1302757 original size:42 final size:41
Alignment explanation
Indices: 1302576--1302779 Score: 121
Period size: 42 Copynumber: 4.9 Consensus size: 41
1302566 AGGGCGAAGG
* ** *
1302576 AGTCTCCTAGGTCAAAG-TCGATGGGCAGATGAAGGATAAAGA
1 AGTCTCCTAGGTCTAAGCT-GATGGGCAGACAAAAGATAAA-A
* * * * *
1302618 AGTCTTCCGA-GCCTAAG-TCGACGGGTAGACAAAGGATAAAA
1 AGTC-TCCTAGGTCTAAGCT-GATGGGCAGACAAAAGATAAAA
* * * * *
1302659 ACGTCTCCTAAGCCTAAGCTGATAGGTAGAAAAAAGATAGAGAA
1 A-GTCTCCTAGGTCTAAGCTGATGGGCAGACAAAAGATA-A-AA
*
1302703 A-TCT-CTCGGGTCTAAGCTGATGGGCAGACAAAAGATAGAAA
1 AGTCTCCT-AGGTCTAAGCTGATGGGCAGACAAAAGATA-AAA
** * *
1302744 AGTCTCCTAGGTCTAAGCCAATAGGCAAACAAAAGA
1 AGTCTCCTAGGTCTAAGCTGATGGGCAGACAAAAGA
1302780 CCAAAGGATC
Statistics
Matches: 130, Mismatches: 23, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
41 11 0.08
42 108 0.83
43 8 0.06
44 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (41 bp):
AGTCTCCTAGGTCTAAGCTGATGGGCAGACAAAAGATAAAA
Found at i:1302948 original size:44 final size:42
Alignment explanation
Indices: 1302855--1302948 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 42
1302845 AATGTAAATT
* ** *
1302855 GTTTGACTAGGGTGGTAACCATACGTCAAATTGGAATGAAAA
1 GTTTGACTAAGGTGGTAACCATACGTCAAACAGGAAAGAAAA
*
1302897 GAATTTGACTAAGGTGGTAACCATACGTCAGACAGGAAAGAGGAAA
1 G--TTTGACTAAGGTGGTAACCATACGTCAAACAGGAAAGA--AAA
1302943 GTTTGA
1 GTTTGA
1302949 GTAGGCCTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
42 1 0.02
44 38 0.88
46 4 0.09
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (42 bp):
GTTTGACTAAGGTGGTAACCATACGTCAAACAGGAAAGAAAA
Found at i:1303423 original size:89 final size:88
Alignment explanation
Indices: 1303264--1303431 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 88
1303254 TAAGATATCC
* * *
1303264 TTGCCCCAAGAAAATCAGGTTTTGTGATGCATCAATACCATCTAGTGGTTGGATGAAGGAAATGT
1 TTGCCCCAAGAAAATCAGGCTTAGTGATGCATCAATACCATCTAGTGGTTGGAAGAAGGAAATGT
*
1303329 GATTGGGAATATGTGGGCTGCACT
66 AATTGGGAA-ATGTGGGCTGCACT
** * *
1303353 TTGCCCCAAGGGAATTAGGCTTAGTGATGCATCAATACCATGTAGTGGTTGAGAAAGAA-GAAAT
1 TTGCCCCAAGAAAATCAGGCTTAGTGATGCATCAATACCATCTAGTGGTTG-G-AAGAAGGAAAT
1303417 -TAATTGGGAAATGTG
64 GTAATTGGGAAATGTG
1303432 TGCTTTCCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 5 0.07
89 54 0.78
90 6 0.09
91 4 0.06
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (88 bp):
TTGCCCCAAGAAAATCAGGCTTAGTGATGCATCAATACCATCTAGTGGTTGGAAGAAGGAAATGT
AATTGGGAAATGTGGGCTGCACT
Found at i:1304829 original size:18 final size:18
Alignment explanation
Indices: 1304806--1304855 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1304796 TAGAGCCTCA
1304806 TTCTTTTCTTTT-TTCCAT
1 TTCTTTT-TTTTCTTCCAT
*
1304824 TTCTTTTTTTTCTTCCTT
1 TTCTTTTTTTTCTTCCAT
*
1304842 TTC-ATTTTTTCTTC
1 TTCTTTTTTTTCTTC
1304856 TCTTTCACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTTTTTTTTCTTCCAT
Found at i:1305853 original size:20 final size:20
Alignment explanation
Indices: 1305828--1305895 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1305818 ATTACAAGCA
1305828 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
1305848 ATGTATCGAT---A--CA--
1 ATGTATCGATACAATTCATC
1305861 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
1305881 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1305896 GTATCGATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
16 1 0.02
17 1 0.02
18 2 0.05
20 25 0.61
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:1305866 original size:13 final size:13
Alignment explanation
Indices: 1305826--1305907 Score: 80
Period size: 13 Copynumber: 7.2 Consensus size: 13
1305816 CCATTACAAG
1305826 CAATGTATCGATA
1 CAATGTATCGATA
1305839 CAA--T-TC-AT-
1 CAATGTATCGATA
1305847 C-ATGTATCGATA
1 CAATGTATCGATA
1305859 CAATGTATCGATA
1 CAATGTATCGATA
1305872 CAA--T-TC-AT-
1 CAATGTATCGATA
1305880 C-ATGTATCGATA
1 CAATGTATCGATA
1305892 CAATGTATCGATA
1 CAATGTATCGATA
1305905 CAA
1 CAA
1305908 ACAGTGGTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
9 6 0.11
10 8 0.14
11 6 0.11
12 2 0.04
13 31 0.54
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1305866 original size:33 final size:33
Alignment explanation
Indices: 1305826--1305907 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
1305816 CCATTACAAG
1305826 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGTATCGATACAATTCATCATGTATCGATA
1305859 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGTATCGATACAATTCATCATGTATCGATA
1305892 CAATGTATCGATACAA
1 CAATGTATCGATACAA
1305908 ACAGTGGTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATTCATCATGTATCGATA
Found at i:1305975 original size:13 final size:13
Alignment explanation
Indices: 1305957--1305982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1305947 ACAATTGTCC
1305957 ATGTATCGATACA
1 ATGTATCGATACA
1305970 ATGTATCGATACA
1 ATGTATCGATACA
1305983 TCTGGGTGTG
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:1306535 original size:22 final size:22
Alignment explanation
Indices: 1306507--1306585 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
1306497 AGTTTTCGTT
*
1306507 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATAAAAGAA
* * *
1306529 TTTCTCCCCTTTAGTCAAAAAAA
1 TTTCTCCCCCTTAAT-AAAAGAA
* * * *
1306552 TTTCTCGCTCTTAATCAAAGCA
1 TTTCTCCCCCTTAATAAAAGAA
1306574 TTTCTCCCCCTT
1 TTTCTCCCCCTT
1306586 TGTTAAATCT
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
22 27 0.63
23 16 0.37
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (22 bp):
TTTCTCCCCCTTAATAAAAGAA
Found at i:1310270 original size:78 final size:78
Alignment explanation
Indices: 1310154--1310359 Score: 216
Period size: 78 Copynumber: 2.6 Consensus size: 78
1310144 GAGATAATAA
* * * * ** * * *
1310154 CGGGGTTGGAGTGTTCCCTTGAAAAAAACGGGACTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
1310219 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* *
1310232 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
1310297 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* * *
1310311 CGGGGTTGGAGTATCCCCTCGGAAGTAACAGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1310360 GAAATAACGA
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 52 0.50
79 52 0.50
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:1310353 original size:28 final size:27
Alignment explanation
Indices: 1310313--1310382 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
1310303 AATAAAGCCG
** *
1310313 GGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGTTGGAGTATCCCCGAGGAAATAAC
*
1310340 AGGGTTGGAGTATCCCCGATGAAATAAC
1 -GGGTTGGAGTATCCCCGAGGAAATAAC
1310368 GAGGTTGGAGTATCC
1 G-GGTTGGAGTATCC
1310383 TCGACTGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:1312810 original size:13 final size:13
Alignment explanation
Indices: 1312792--1312817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1312782 CATTACTCAC
1312792 ATGTATCGATACA
1 ATGTATCGATACA
1312805 ATGTATCGATACA
1 ATGTATCGATACA
1312818 CTGATCTTTG
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:1316368 original size:13 final size:13
Alignment explanation
Indices: 1316350--1316375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1316340 ACAAAGATCC
1316350 ATGTATCGATACA
1 ATGTATCGATACA
1316363 ATGTATCGATACA
1 ATGTATCGATACA
1316376 CAGAAAAATG
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:1316371 original size:33 final size:33
Alignment explanation
Indices: 1316329--1316395 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1316319 AAAATTTCCA
***
1316329 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1316362 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1316395 A
1 A
1316396 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1316512 original size:21 final size:21
Alignment explanation
Indices: 1316486--1316564 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
1316476 GTTGGGACCC
*
1316486 TGTATCAATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
*
1316507 TGTATCGATACATTTGTGGAA
1 TGTATCGATACATTTGTAGAA
* *
1316528 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
1316549 TGTATCGATACATTTG
1 TGTATCGATACATTTG
1316565 GATAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 3 0.06
21 45 0.90
22 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:1322203 original size:33 final size:32
Alignment explanation
Indices: 1322165--1322229 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1322155 TACAAGCAAT
*
1322165 GTATCGATACAATTCAT-GATGTATCGATACAAG
1 GTATCGATAC-ATT-ATACATGTATCGATACAAG
1322198 GTATCGATACATTATACCATGTATCGATACAA
1 GTATCGATACATTATA-CATGTATCGATACAA
1322230 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 3 0.10
33 24 0.83
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (32 bp):
GTATCGATACATTATACATGTATCGATACAAG
Found at i:1322214 original size:20 final size:20
Alignment explanation
Indices: 1322191--1322228 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1322181 TGATGTATCG
1322191 ATACAAGGTATCGATACATT
1 ATACAAGGTATCGATACATT
* *
1322211 ATACCATGTATCGATACA
1 ATACAAGGTATCGATACA
1322229 AACAGTGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (20 bp):
ATACAAGGTATCGATACATT
Found at i:1322302 original size:19 final size:19
Alignment explanation
Indices: 1322258--1322313 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1322248 CTACCAATCT
* **
1322258 CATGTATGGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1322278 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1322297 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1322314 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1322316 original size:13 final size:13
Alignment explanation
Indices: 1322298--1322323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1322288 TACAATGAAC
1322298 ATGTATCGATACA
1 ATGTATCGATACA
1322311 ATGTATCGATACA
1 ATGTATCGATACA
1322324 GAGCATTATG
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:1327439 original size:167 final size:166
Alignment explanation
Indices: 1327239--1327888 Score: 503
Period size: 167 Copynumber: 3.9 Consensus size: 166
1327229 TAGAACAAAG
* * * *
1327239 AAAATCCTCCCGAAAATATTTATGGAATAGAAAACTCGATTTTTCGAGAAAATAGGGA-TTTCAA
1 AAAATCCTCTCGAAAAAATTTATGGAGTAGAAAACTCG-TATTTCGAGAAAATA-GGACTTTCAA
* * *
1327303 AGAAAAAATTCAAAAACTCATGAAGATAAATGAATTTTTGAAAACTAAATTAATATGAAATAAAT
64 AGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAAT
1327368 AATGATGTTTGATGGATTTTAAAAATTGAAAACCAAGA
129 AATGATGTTTGATGGATTTTAAAAATTGAAAACCAAGA
** * * * *
1327406 AAAATCCTCTCGAAAAAATTTATGGAGTAGAAAA-TACCGTATTTAAAAAAAAAAGAAGTTTCAA
1 AAAATCCTCTCGAAAAAATTTATGGAGTAGAAAACT--CGTATTTCGAGAAAATAGGACTTTCAA
* * * * * *
1327470 GGAAGAAAA-TCAAAAACTCATAAAAATGGATGAATTTTTGTAAACTGAATTAATGTGATATAAA
64 AGAA-AAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAA
*** * * *
1327534 TAATGGCATTTGGTGGATTTTAAAAATTAAAAACTAAGA
128 TAATGATGTTTGATGGATTTTAAAAATTGAAAACCAAGA
* * * *** * * *
1327573 AAAA-CGCACT--AAAAAAATCACAAAGTAGAAAACACTGTATTTCGGGAAAAATAAGACTTTC-
1 AAAATC-CTCTCGAAAAAATTTATGGAGTAGAAAACTC-GTATTTCGAG-AAAATAGGACTTTCA
* * * ** * * *
1327634 AAGGAAAAATTCAAACATTTTTGAAAATGAATGAAATTTTGAAAA-TGGAATTACTATGGAATAA
63 AAGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAACT-GAATTAATATGAAATAA
* * *
1327698 ATGATAATGTTTGATGAATTTTAAAAATTGAAAACCAAGA
127 ATAATGATGTTTGATGGATTTTAAAAATTGAAAACCAAGA
* *** * * * * * * * *
1327738 AAAATCC-CTTTGAAAAAATTTACAAAGCATAAAACACCGTACTTT-AAAAAAAAAGGGATTTTT
1 AAAATCCTC-TCGAAAAAATTTATGGAGTAGAAAAC-TCGTA-TTTCGAGAAAATA-GGACTTTC
* * * * * *
1327801 AAGGAAAAAATTAAAAAAAT-GTAAAAACGAATGAATTTTTGAAAACTGAATTAATATGAAATAA
62 AAAGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAA
** * *
1327865 ATAAAAATATTTGATGAATTTTAA
127 ATAATGATGTTTGATGGATTTTAA
1327889 TGCTTGAAAC
Statistics
Matches: 376, Mismatches: 88, Indels: 38
0.75 0.18 0.08
Matches are distributed among these distances:
164 7 0.02
165 103 0.27
166 20 0.05
167 221 0.59
168 25 0.07
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (166 bp):
AAAATCCTCTCGAAAAAATTTATGGAGTAGAAAACTCGTATTTCGAGAAAATAGGACTTTCAAAG
AAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAA
TGATGTTTGATGGATTTTAAAAATTGAAAACCAAGA
Found at i:1339046 original size:13 final size:13
Alignment explanation
Indices: 1339028--1339084 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1339018 TATATTGCTT
1339028 TGTATCGATACAA
1 TGTATCGATACAA
1339041 TGTATCGATACATATTCA
1 TGTATCGATAC--A---A
1339059 TTGTATCGATACAA
1 -TGTATCGATACAA
1339073 TGTATCGATACA
1 TGTATCGATACA
1339085 TATTCATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1339065 original size:19 final size:19
Alignment explanation
Indices: 1339041--1339103 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1339031 ATCGATACAA
1339041 TGTATCGATACATATTCAT
1 TGTATCGATACATATTCAT
1339060 TGTATCGATAC--A---A-
1 TGTATCGATACATATTCAT
1339073 TGTATCGATACATATTCAT
1 TGTATCGATACATATTCAT
1339092 TGTATCGATACA
1 TGTATCGATACA
1339104 CAAAGAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 23 0.61
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATATTCAT
Found at i:1339068 original size:32 final size:32
Alignment explanation
Indices: 1339013--1339103 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
1339003 CCAGAAGTAC
* *
1339013 CGATATATATTGCTTTGTATCGATACAATGTAT
1 CGATACATATT-CATTGTATCGATACAATGTAT
1339046 CGATACATATTCATTGTATCGATACAATGTAT
1 CGATACATATTCATTGTATCGATACAATGTAT
1339078 CGATACATATTCATTGTATCGATACA
1 CGATACATATTCATTGTATCGATACA
1339104 CAAAGAATTG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 46 0.82
33 10 0.18
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (32 bp):
CGATACATATTCATTGTATCGATACAATGTAT
Found at i:1340706 original size:21 final size:21
Alignment explanation
Indices: 1340659--1340714 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1340649 AAAATTTATC
*
1340659 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
1340680 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
*
1340701 CAAATGTATTGATA
1 CAAATGTATCGATA
1340715 TAGGGTCCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:1340870 original size:34 final size:33
Alignment explanation
Indices: 1340807--1340873 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1340797 GCCAAGAGAA
* *
1340807 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCAATACATTATTCTGTGTATCGATACAT
*
1340840 TGTATCAATACATCTATTCTTTGTATCGATACAT
1 TGTATCAATACAT-TATTCTGTGTATCGATACAT
1340874 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (33 bp):
TGTATCAATACATTATTCTGTGTATCGATACAT
Found at i:1343279 original size:51 final size:51
Alignment explanation
Indices: 1343219--1343335 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
1343209 AATTCTCCGC
1343219 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCGAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCGAT
1343270 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTT---T
1 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCGAT
*
1343318 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
1343336 CCCGTTAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
48 18 0.29
51 41 0.66
52 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCGAT
Found at i:1343357 original size:27 final size:27
Alignment explanation
Indices: 1343319--1343393 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
1343309 TCAATTTTTC
1343319 ATCGGGGATACTCCAACCCCGTTAATT
1 ATCGGGGATACTCCAACCCCGTTAATT
* *
1343346 ATCGGGGATACTCCAAACCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTAATT
* *
1343373 TTGAGGGGATACTCCAACCCC
1 AT-CGGGGATACTCCAACCCC
1343394 CGGCTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATT
Found at i:1343516 original size:79 final size:80
Alignment explanation
Indices: 1343346--1343525 Score: 231
Period size: 80 Copynumber: 2.3 Consensus size: 80
1343336 CCCGTTAATT
* * **
1343346 ATCGGGGATACTCCAAACCCGTTATTTTTGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
* *
1343411 TATTAATTTCTCATA
66 TATGAATTTCTCACA
* *
1343426 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCCCGGTTTTATTT-TCAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
*
1343489 TCATCGATTTTC-CACA
66 T-AT-GAATTTCTCACA
*
1343505 ATCGGGAATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1343526 GCTTTATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.06
79 38 0.43
80 45 0.51
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
TATGAATTTCTCACA
Found at i:1343592 original size:52 final size:50
Alignment explanation
Indices: 1343458--1343626 Score: 187
Period size: 52 Copynumber: 3.3 Consensus size: 50
1343448 TATCTCCGAG
* * *
1343458 GGGATACTCCAACCCCGGTTTTATTTTCAAATCATCGATTTTCCACAATC
1 GGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACAATC
* **
1343508 GGGAATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGG-ATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCC-ACAATC
* * * *
1343560 AGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT-CACAATT
1 -GGGATACTCCAACCCCGGTTTTATTTTC-AAAACACC-AATTTTCCACAATC
1343612 GAGGATACTCCAACC
1 G-GGATACTCCAACC
1343627 TCGTTATTTC
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
50 3 0.03
51 38 0.38
52 40 0.40
53 12 0.12
54 6 0.06
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (50 bp):
GGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACAATC
Found at i:1343646 original size:28 final size:28
Alignment explanation
Indices: 1343614--1343684 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1343604 TCACAATTGA
* **
1343614 GGATACTCCAA-CCTCGTTATTTCATCGG
1 GGATACTCCAACCCT-GTTACTTCAGAGG
*
1343642 GGATACTCCAACCCTGTTACTTCCGAGG
1 GGATACTCCAACCCTGTTACTTCAGAGG
1343670 GGATACTCCAACCCT
1 GGATACTCCAACCCT
1343685 AGCTTTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCTGTTACTTCAGAGG
Found at i:1343733 original size:290 final size:284
Alignment explanation
Indices: 1343246--1343814 Score: 766
Period size: 290 Copynumber: 2.0 Consensus size: 284
1343236 CTCCGATTTC
* * * *
1343246 ATTTTCAAAACACTAATTTTCGATAATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATC
1 ATTTTCAAAACACCAATTTTCGATAATCAGGGATACTCCAACTCCGATTTCATTTCAAAAACACC
* * * **
1343311 AATTTTTCATCGGGGATACTCCAACCCCGTTAATTATCGGGGATACTCCAAACCCGTTATTTTTG
66 AATTTTACATCGAGGATACTCCAACCCCGTTAATTATCGGGGATACTCCAAACCCGTTACTTCCG
* * *
1343376 AGGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCA
131 AGGGGATACTCCAACCCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCA
*
1343441 ACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTTTATTTTCAAATCATCGATTT-TCCACA
196 ACCCCGTTATCTCCGAGGGGATACTCCAACCCCGATTTT-TTTTCAAATCATCGATTTCT-CACA
*
1343505 ATCGGGAATACTCCAACCCCGGCTTT
259 ACCGGGAATACTCCAACCCCGGCTTT
** *
1343531 ATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAACA
1 ATTTTCAAAACACCAATTTT-CGATAATCAGGGATACTCCAACTCCGATTTCATTT-CAAAAACA
* * *
1343596 CCAAATTTTCACAATTGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCC-AACCCTGTT
64 CC-AATTTT-AC-ATCGAGGATACTCCAACCCCGTTAATT-ATCGGGGATACTCCAAACCC-GTT
* * *
1343660 ACTTCCGAGGGGATACTCCAA-CCCTAGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGA
124 ACTTCCGAGGGGATACTCCAACCCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGA
* * * * *
1343724 TACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCTGATTTTTTTTCTAATCATCGATTTC
189 TACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGATTTTTTTTCAAATCATCGATTTC
* *
1343789 TCACAACCGGGGATACTCCAGCCCCG
254 TCACAACCGGGAATACTCCAACCCCG
1343815 TTATTTTCAA
Statistics
Matches: 246, Mismatches: 30, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
285 19 0.08
286 31 0.13
287 8 0.03
288 6 0.02
289 40 0.16
290 107 0.43
291 35 0.14
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (284 bp):
ATTTTCAAAACACCAATTTTCGATAATCAGGGATACTCCAACTCCGATTTCATTTCAAAAACACC
AATTTTACATCGAGGATACTCCAACCCCGTTAATTATCGGGGATACTCCAAACCCGTTACTTCCG
AGGGGATACTCCAACCCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCA
ACCCCGTTATCTCCGAGGGGATACTCCAACCCCGATTTTTTTTCAAATCATCGATTTCTCACAAC
CGGGAATACTCCAACCCCGGCTTT
Found at i:1343814 original size:78 final size:78
Alignment explanation
Indices: 1343639--1343842 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 78
1343629 GTTATTTCAT
* * * *
1343639 CGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAACCCTAGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCT-GATTTATTCCCAAAATAT
* * *
1343704 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * ** *
1343718 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCTGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTATTCCCAAAAT-AT
1343782 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
1343796 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCTG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTG
1343843 TTATTATCTC
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 3 0.03
78 61 0.58
79 41 0.39
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:1353110 original size:12 final size:12
Alignment explanation
Indices: 1353093--1353117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1353083 TACAATGAAT
1353093 ATGTATCGATAC
1 ATGTATCGATAC
1353105 ATGTATCGATAC
1 ATGTATCGATAC
1353117 A
1 A
1353118 AAGCAATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1353110 original size:31 final size:32
Alignment explanation
Indices: 1353075--1353136 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1353065 TAATTCTTTG
*
1353075 TGTATCGATACAATG-AATATGTATCGATACA
1 TGTATCGATACAAAGCAATATGTATCGATACA
1353106 TGTATCGATACAAAGCAATATGTATCGATAC
1 TGTATCGATACAAAGCAATATGTATCGATAC
1353137 TTCTGGGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGCAATATGTATCGATACA
Found at i:1353166 original size:21 final size:20
Alignment explanation
Indices: 1353126--1353166 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1353116 CAAAGCAATA
*
1353126 TGTATCGATACTTCTGGGCT
1 TGTATCGATACTTCTAGGCT
1353146 TGTATCGATACTTTCTAGGCT
1 TGTATCGATAC-TTCTAGGCT
1353167 CTTGACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
TGTATCGATACTTCTAGGCT
Found at i:1353730 original size:23 final size:22
Alignment explanation
Indices: 1353689--1353739 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
1353679 TTTGTTTTTG
1353689 ATAAAAAATTTTCTCCCCCTTA
1 ATAAAAAATTTTCTCCCCCTTA
* *
1353711 ATAAGAAATTTTTCTTCCCCTTA
1 ATAA-AAAATTTTCTCCCCCTTA
1353734 ATAAAA
1 ATAAAA
1353740 TTCCTTCCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAAAAAATTTTCTCCCCCTTA
Found at i:1360294 original size:13 final size:13
Alignment explanation
Indices: 1360276--1360300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1360266 CAAAGATCAG
1360276 TGTATCGATACAA
1 TGTATCGATACAA
1360289 TGTATCGATACA
1 TGTATCGATACA
1360301 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:1360373 original size:32 final size:32
Alignment explanation
Indices: 1360337--1360502 Score: 305
Period size: 32 Copynumber: 5.1 Consensus size: 32
1360327 GGCAGTAGCT
*
1360337 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1360369 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1360401 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1360433 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1360466 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1360499 TACA
1 TACA
1360503 AATCGTTAAA
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
32 84 0.64
33 48 0.36
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1360379 original size:13 final size:13
Alignment explanation
Indices: 1360361--1360482 Score: 73
Period size: 13 Copynumber: 7.9 Consensus size: 13
1360351 ACAAAACTTA
1360361 TGTATCGATACAT
1 TGTATCGATACAT
1360374 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1360392 ATGTATCGATACAT
1 -TGTATCGATACAT
1360406 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1360424 ATGTATCGATACAT
1 -TGTATCGATACAT
1360438 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
1360457 ATGTATCGATACAT
1 -TGTATCGATACAT
1360471 TGTATCGATACA
1 TGTATCGATACA
1360483 ACACTTTATG
Statistics
Matches: 90, Mismatches: 0, Indels: 38
0.70 0.00 0.30
Matches are distributed among these distances:
13 39 0.43
14 3 0.03
16 15 0.17
17 3 0.03
18 2 0.02
19 19 0.21
20 9 0.10
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1361061 original size:7 final size:7
Alignment explanation
Indices: 1361049--1361102 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
1361039 CAATTTTTTG
1361049 AAAAAAT
1 AAAAAAT
1361056 AAAAAAT
1 AAAAAAT
1361063 -AAAAAT
1 AAAAAAT
* *
1361069 AATACAT
1 AAAAAAT
1361076 AAAAAAT
1 AAAAAAT
*
1361083 AAAAAGT
1 AAAAAAT
1361090 AAAAAAAT
1 -AAAAAAT
1361098 AAAAA
1 AAAAA
1361103 TAATATGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 6 0.15
7 27 0.69
8 6 0.15
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:1361081 original size:15 final size:14
Alignment explanation
Indices: 1361049--1361102 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
1361039 CAATTTTTTG
*
1361049 AAAAAATAAAAAAT
1 AAAAAATAAAAAGT
*
1361063 -AAAAATAATACA-T
1 AAAAAATAA-AAAGT
1361076 AAAAAATAAAAAGT
1 AAAAAATAAAAAGT
1361090 AAAAAAATAAAAA
1 -AAAAAATAAAAA
1361103 TAATATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.32
14 11 0.32
15 12 0.35
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAAATAAAAAGT
Found at i:1361171 original size:6 final size:6
Alignment explanation
Indices: 1361160--1361217 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
1361150 GGTTTCTTGA
* * ** *
1361160 AAAAAT AAAAAT ATAAAT ATAAAT AATACGT AAAAAT AAAAAAT ATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT -AAAAAT AAAAAT
1361210 AAAAAT AA
1 AAAAAT AA
1361218 TATGTATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 32 0.76
7 10 0.24
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:1361209 original size:13 final size:13
Alignment explanation
Indices: 1361159--1361214 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
1361149 TGGTTTCTTG
1361159 AAAAAATAAAAAT
1 AAAAAATAAAAAT
* *
1361172 -ATAAATATAAAT
1 AAAAAATAAAAAT
* **
1361184 AATACGTAAAAAT
1 AAAAAATAAAAAT
*
1361197 AAAAAATATAAAT
1 AAAAAATAAAAAT
1361210 AAAAA
1 AAAAA
1361215 TAATATGTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
12 10 0.30
13 23 0.70
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1361234 original size:32 final size:32
Alignment explanation
Indices: 1361159--1361236 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
1361149 TGGTTTCTTG
* *
1361159 AAAAAATAAAAATATAAATATAAATAATACGT
1 AAAAATTAAAAATATAAATAAAAATAATACGT
* *
1361191 AAAAATAAAAAATATAAATAAAAATAATATGT
1 AAAAATTAAAAATATAAATAAAAATAATACGT
* *
1361223 ATATATTAAAAATA
1 AAAAATTAAAAATA
1361237 ATATTTTGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (32 bp):
AAAAATTAAAAATATAAATAAAAATAATACGT
Found at i:1361398 original size:22 final size:22
Alignment explanation
Indices: 1361357--1361415 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1361347 TCTTTCGAAT
* * *
1361357 ATATAATTATAATAGTATATAC
1 ATATAATTTTAATTGGATATAC
*
1361379 ATATAATTTTAATTGGATATAT
1 ATATAATTTTAATTGGATATAC
* *
1361401 ATATGATGTTAATTG
1 ATATAATTTTAATTG
1361416 AACGTGTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (22 bp):
ATATAATTTTAATTGGATATAC
Found at i:1362256 original size:67 final size:68
Alignment explanation
Indices: 1362134--1362260 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
1362124 ATTGGGTTTT
* * * *
1362134 AAAGATGATGAAGGTGCCAATATGCTGATTCAATGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1362199 AGA
66 AGA
* * * *
1362202 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
1362261 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:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1362310 original size:55 final size:52
Alignment explanation
Indices: 1362250--1362814 Score: 292
Period size: 43 Copynumber: 12.0 Consensus size: 52
1362240 CGATATTGGG
* *
1362250 CTTAAAGATGAGAAAAAGGATGTCAAGGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAAGATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
1362305 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCCAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCTACATTGAA
*
1362357 C-T-----T---AAAGGTGCCAATG-TGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAA-GATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
1362400 CTTAAAGAT--AAAA-ATGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCTACATTGAA
*
1362449 C-T-----T---AAAGGTGCCAATG-TGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAA-GATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
1362492 CTTAAAGA---ATAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCTACATTGAA
* *
1362541 C-T-----T---AAAGGTGCCAATG-TGCTGATTCAAGGCTAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAA-GATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
1362584 CTTAAAGA---AGAAGGTGCCAATATGCTGATTCAAGGCCAG-TGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCT-ACATTGAA
*
1362633 C-T-----T-G-AAA-GTGCCAATG-TGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAA-GATGCTGATTCAAGGCCAGCTACATTGAA
* * *
1362676 CTTAAAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAG-TGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCT-ACATTGAA
* *
1362725 C-T-----T-G-AAA-GTGCCATTG-TGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCA-AGATGCTGATTCAAGGCCAGCTACATTGAA
* * *
1362768 CTTAAAGA---AGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCTACATTG
1362815 GGCTTAGAAG
Statistics
Matches: 417, Mismatches: 38, Indels: 116
0.73 0.07 0.20
Matches are distributed among these distances:
42 3 0.01
43 172 0.41
44 11 0.03
46 1 0.00
48 10 0.02
49 169 0.41
50 3 0.01
51 1 0.00
52 30 0.07
53 6 0.01
54 1 0.00
55 10 0.02
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAAGATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:1362450 original size:92 final size:92
Alignment explanation
Indices: 1362277--1362825 Score: 892
Period size: 92 Copynumber: 5.9 Consensus size: 92
1362267 GGATGTCAAG
* * *
1362277 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCCAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATTCAAG
1362342 GCCAGCTATATTGGACTTAAAGGTGCCAAT
63 GCCAGCTATATTGGACTTAAAGGTGCCAAT
**
1362372 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAAATGCCAATATGCTGATTCAAGGC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGC
1362436 CAGCTATATTGGACTTAAAGGTGCCAAT
65 CAGCTATATTGGACTTAAAGGTGCCAAT
*
1362464 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAATAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
1362529 AGCTATATTGGACTTAAAGGTGCCAAT
66 AGCTATATTGGACTTAAAGGTGCCAAT
*
1362556 GTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
1362621 AG-TGATATTGGACTTGAAA-GTGCCAAT
66 AGCT-ATATTGGACTT-AAAGGTGCCAAT
*
1362648 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
*
1362713 AG-TGATATTGGACTTGAAA-GTGCCATT
66 AGCT-ATATTGGACTT-AAAGGTGCCAAT
1362740 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
*
1362805 AGCTATATTGGGCTTAGAAGG
66 AGCTATATTGGACTTA-AAGG
1362826 GTTGCCACCG
Statistics
Matches: 434, Mismatches: 14, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
91 3 0.01
92 390 0.90
93 6 0.01
95 35 0.08
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCC
AGCTATATTGGACTTAAAGGTGCCAAT
Found at i:1362862 original size:33 final size:33
Alignment explanation
Indices: 1362820--1362989 Score: 222
Period size: 32 Copynumber: 5.2 Consensus size: 33
1362810 TATTGGGCTT
* *
1362820 AGAAGGGTTGCCACCGATTTGTGTTGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1362853 AGAATGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1362886 AG--GGGATTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
* * * *
1362918 AAAAAGGTTGCCACCGACTTGTATAGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1362951 A-AAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1362982 AGAAGGGT
1 AGAAGGGT
1362990 GAAAGATGCC
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
31 4 0.03
32 57 0.48
33 55 0.47
34 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1362915 original size:65 final size:63
Alignment explanation
Indices: 1362813--1362985 Score: 231
Period size: 65 Copynumber: 2.7 Consensus size: 63
1362803 CCAGCTATAT
* * * *
1362813 TGGGC-TTAGAAGGGTTGCCACCGATTTGTGTTGGCTTTAGAGAATGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAAGGTTGCCACCGACTTGTA
* * *
1362876 TGGGCTTTAGAGGGGATTGCCACCAACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCGACTTGTA
1 TGGGCTTTAGAAGGG-TTGCCACCGACTTGTGTGGGCTTT-GAGAAAGGTTGCCACCGACTTGTA
*
1362941 TAGGCTTTAGAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAA
1 TGGGCTTTAG-AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAA
1362986 GGGTGAAAGA
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
63 5 0.05
64 12 0.13
65 74 0.78
66 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (63 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCGACTTGTA
Found at i:1363201 original size:34 final size:34
Alignment explanation
Indices: 1362991--1363649 Score: 522
Period size: 34 Copynumber: 20.8 Consensus size: 34
1362981 GAGAAGGGTG
* *
1362991 AAAGA-TGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
1363024 CAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAGAA-GGAA
* *
1363059 AAAGAGTGCCACGGAGTTGTGGCCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
1363091 GAAG-GTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * * * * *
1363124 CAAG-GTGCCACGGGGTTATGGAATTTAAAAGGGGA
1 AAAGAGTGCCACGGAGTTGTGG-ACTTAGAA-GGAA
*
1363159 AAAGAGTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
1363193 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAGAAGGAA
1363228 AAAG-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
1363261 AAAGAGTGTCATGGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
1363288 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
1363322 AAAGAGTGCCACAGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
1363349 AAAGGGTACCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
** *
1363383 AAAGAGTGCCATAGAGTTGTGGGCTTA-AAGG--
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1363414 ---G-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
1363444 AAAGAGTGCCACGGAGTTGTGGGCTTA-AACG--
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1363475 ---G-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
1363505 AAAGAATGCCACGGAGTTATGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
1363532 AAAGTGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* *
1363566 AAAGAGTGCCACAGAGTTGTGGGCTT------AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
1363594 AAA-AGTGCCACGCAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
1363625 GAAG-GTGCCACGGAGTTGTGGACTT
1 AAAGAGTGCCACGGAGTTGTGGACTT
1363650 TAAGAAGGTA
Statistics
Matches: 503, Mismatches: 72, Indels: 104
0.74 0.11 0.15
Matches are distributed among these distances:
27 129 0.26
28 14 0.03
31 44 0.09
32 5 0.01
33 61 0.12
34 184 0.37
35 35 0.07
36 31 0.06
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
Found at i:1363290 original size:27 final size:27
Alignment explanation
Indices: 1363260--1363649 Score: 204
Period size: 27 Copynumber: 13.0 Consensus size: 27
1363250 CTTAGAAGGA
* * *
1363260 AAAAGAGTGTCATGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
*
1363287 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
* *
1363314 AGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
* *
1363348 AAAAGGGTACCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
** *
1363375 AGAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
* *
1363409 AAAGGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
*
1363436 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
* *
1363470 AAACGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
* * *
1363497 AGAAGGAAAAAGAATGCCACGGAGTTATGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
*
1363531 AAAAGTGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
* *
1363558 AGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
* * *
1363592 AAAAAAGTGCCACGCAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGAC-TT
1363620 GAAAAGAAGGTGCCACGGAGTTGTGGACTT
1 -AAAAG-A-GTGCCACGGAGTTGTGGACTT
1363650 TAAGAAGGTA
Statistics
Matches: 279, Mismatches: 45, Indels: 75
0.70 0.11 0.19
Matches are distributed among these distances:
27 137 0.49
28 2 0.01
29 4 0.01
30 3 0.01
31 17 0.06
34 116 0.42
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.21
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:1363326 original size:61 final size:61
Alignment explanation
Indices: 1363226--1363645 Score: 639
Period size: 61 Copynumber: 6.9 Consensus size: 61
1363216 CTTTAAAAAG
* * **
1363226 AAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGTCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1363287 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
* *
1363348 AAAAGGGTACCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
* *
1363409 AAAGGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
* * * *
1363470 AAACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAATGCCACGGAGTTATGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
*
1363531 AAAAGTGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
** * * * * *
1363592 AAAAAAGTGCCACGCAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGGAGTTGTGG
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGG
1363646 ACTTTAAGAA
Statistics
Matches: 334, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
58 16 0.05
59 5 0.01
61 313 0.94
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
Found at i:1363420 original size:122 final size:122
Alignment explanation
Indices: 1363027--1363645 Score: 733
Period size: 122 Copynumber: 4.9 Consensus size: 122
1363017 AAAGGAACAA
* * * *
1363027 GGTGCCACGAAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGCCTTTGAAAAG
1 GGTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAGAGTGCCACAGAGTTGTGGGC-TT-AAAAG
* * * * * * **
1363092 AAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAG-GTGCCACGGGGTTATGGAATTTAAAAGG
62 --GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGG-GCTTAAAA--
1363156 GG
122 -G
* *
1363158 AAAAGAGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 ----G-GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TT-AA
*
1363223 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGTCATGGAGTTGTGGGCTTA
59 AAG-----GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTA
1363288 AAAG
119 AAAG
*
1363292 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGTA
1 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGTG
* *
1363357 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTTAAAGG
66 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAG
* *
1363414 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
1 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGTG
* * *
1363479 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAATGCCACGGAGTTATGGGCTTAAAAG
66 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAG
* **
1363536 TGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAAAGTG
1 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGTG
* * * * *
1363601 CCACGCAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGGAGTTGTGG
66 CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGG
1363646 ACTTTAAGAA
Statistics
Matches: 440, Mismatches: 39, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
119 15 0.03
120 5 0.01
122 250 0.57
127 5 0.01
128 2 0.00
129 51 0.12
130 1 0.00
134 36 0.08
135 6 0.01
136 17 0.04
137 39 0.09
138 13 0.03
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (122 bp):
GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGTG
CCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAG
Found at i:1363487 original size:183 final size:183
Alignment explanation
Indices: 1363026--1363645 Score: 771
Period size: 183 Copynumber: 3.3 Consensus size: 183
1363016 AAAAGGAACA
* * *
1363026 AGGTGCCACGAAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGCCTTTGAAAA
1 AGGTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA
* * * * **
1363091 GAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAG-GTGCCACGGGGTTATGGAATTTAAAAG
62 G--GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTATGG-GCTTAAAA-
* *
1363155 GGGAAAAGAGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
123 --G----G-GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TT
1363220 AAAAAG
180 --AAAG
* *
1363226 AAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGTCATGGAGTTGTGGGCTTAAAA
1 ----AGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
* *
1363291 GGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGT
62 GGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTATGGGCTTAAAAGGGT
* *
1363356 ACCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTTAAAG
127 GCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAG
* *
1363413 GGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGT
1 AGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGT
* *
1363478 GCCACGGAGTTGTGGACTTAGAAGGAAAAAGAATGCCACGGAGTTATGGGCTTAAAAGTGTGCCA
66 GCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTATGGGCTTAAAAGGGTGCCA
*
1363543 CGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAA
131 CGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAG
* * * * *
1363596 AAGTGCCACGCAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGGAGTTGTGG
1 AGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGG
1363646 ACTTTAAGAA
Statistics
Matches: 381, Mismatches: 34, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
180 17 0.04
181 5 0.01
183 194 0.51
187 4 0.01
189 2 0.01
190 49 0.13
191 1 0.00
195 1 0.00
198 37 0.10
199 14 0.04
200 5 0.01
201 2 0.01
202 25 0.07
203 5 0.01
204 20 0.05
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (183 bp):
AGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGT
GCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTATGGGCTTAAAAGGGTGCCA
CGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAG
Found at i:1364543 original size:8 final size:8
Alignment explanation
Indices: 1364523--1364595 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
1364513 GAAAAAGAGG
*
1364523 TTTTTCCT
1 TTTTTCTT
1364531 TTTTTCTT
1 TTTTTCTT
*
1364539 TTTTTGTT
1 TTTTTCTT
1364547 TGTTTGT-TT
1 T-TTT-TCTT
1364556 GTTTCTTCTT
1 -TTT-TTCTT
*
1364566 TTTTTCCT
1 TTTTTCTT
*
1364574 TTTTTGTT
1 TTTTTCTT
1364582 TTGTTTCTT
1 TT-TTTCTT
1364591 TTTTT
1 TTTTT
1364596 GGAAAAAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
8 30 0.57
9 18 0.34
10 5 0.09
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1364566 original size:27 final size:28
Alignment explanation
Indices: 1364534--1364595 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
1364524 TTTTCCTTTT
*
1364534 TTCTTTTTTT-GTTTGTTTG-TTTGTTTC
1 TTCTTTTTTTCCTTT-TTTGTTTTGTTTC
1364561 TTCTTTTTTTCCTTTTTTGTTTTGTTTC
1 TTCTTTTTTTCCTTTTTTGTTTTGTTTC
1364589 TT-TTTTT
1 TTCTTTTT
1364596 GGAAAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (28 bp):
TTCTTTTTTTCCTTTTTTGTTTTGTTTC
Found at i:1364874 original size:17 final size:17
Alignment explanation
Indices: 1364834--1364875 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1364824 ACTTTGCACC
*
1364834 TTTTTTCTGTGTTTGTT
1 TTTTTTTTGTGTTTGTT
1364851 TTTTTTTTGT-TTTGTT
1 TTTTTTTTGTGTTTGTT
1364867 TTGTTTTTT
1 TT-TTTTTT
1364876 TTCTTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.83
Consensus pattern (17 bp):
TTTTTTTTGTGTTTGTT
Found at i:1376115 original size:3 final size:3
Alignment explanation
Indices: 1376107--1376141 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1376097 CCAAGAGAAA
1376107 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1376142 AGAGCAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:1381068 original size:13 final size:13
Alignment explanation
Indices: 1381050--1381075 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1381040 TCACTCCTTG
1381050 CACCCTAGGTAGC
1 CACCCTAGGTAGC
1381063 CACCCTAGGTAGC
1 CACCCTAGGTAGC
1381076 TCACTACTCA
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:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
CACCCTAGGTAGC
Found at i:1383194 original size:19 final size:20
Alignment explanation
Indices: 1383151--1383206 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
1383141 CACACCCAGA
*
1383151 TGTATCGATACATATTGCTT
1 TGTATCGATACATATTGCAT
* *
1383171 TGTATAGATACATGTT-CAT
1 TGTATCGATACATATTGCAT
*
1383190 TGTATCGATACACATTG
1 TGTATCGATACATATTG
1383207 AAATGTATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTGCAT
Found at i:1390768 original size:13 final size:13
Alignment explanation
Indices: 1390750--1390774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1390740 ACAAAACTTA
1390750 TGTATCGATACAT
1 TGTATCGATACAT
1390763 TGTATCGATACA
1 TGTATCGATACA
1390775 ACACTTTATG
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:1390770 original size:32 final size:33
Alignment explanation
Indices: 1390729--1390794 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1390719 AGTAGCTTAA
1390729 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1390761 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1390794 A
1 A
1390795 AATCATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1392337 original size:51 final size:52
Alignment explanation
Indices: 1392228--1392355 Score: 222
Period size: 51 Copynumber: 2.5 Consensus size: 52
1392218 CGAAATATGA
* * *
1392228 AAATTTGCCTGCTTGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
1392280 AAATTTGCCTGCATGTATCGATACATTT-ATAATGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
1392331 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1392356 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 46 0.63
52 27 0.37
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
Found at i:1392382 original size:13 final size:13
Alignment explanation
Indices: 1392364--1392388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1392354 CAAAGATCAG
1392364 TGTATCGATACAA
1 TGTATCGATACAA
1392377 TGTATCGATACA
1 TGTATCGATACA
1392389 TTTTTTGGCA
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:1392447 original size:13 final size:13
Alignment explanation
Indices: 1392429--1392453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1392419 ACAAAACTTA
1392429 TGTATCGATACAT
1 TGTATCGATACAT
1392442 TGTATCGATACA
1 TGTATCGATACA
1392454 ACACTTTATG
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:1392453 original size:32 final size:33
Alignment explanation
Indices: 1392408--1392473 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1392398 AGTAGCTTAA
1392408 ATTGTATCAATACAAAAC-TTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
* *
1392440 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
1392473 A
1 A
1392474 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (33 bp):
ATTGTATCAATACAAAACTTTATGTATCGATAC
Found at i:1393997 original size:13 final size:13
Alignment explanation
Indices: 1393979--1394003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1393969 CAAAGATCAG
1393979 TGTATCGATACAA
1 TGTATCGATACAA
1393992 TGTATCGATACA
1 TGTATCGATACA
1394004 TTTTTTGGCA
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:1394062 original size:13 final size:13
Alignment explanation
Indices: 1394044--1394068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1394034 ACAAAACTTA
1394044 TGTATCGATACAT
1 TGTATCGATACAT
1394057 TGTATCGATACA
1 TGTATCGATACA
1394069 ACACTTTATG
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:1394068 original size:32 final size:33
Alignment explanation
Indices: 1394023--1394088 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1394013 AGTAGCTTAA
1394023 ATTGTATCAATACAAAAC-TTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
* *
1394055 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
1394088 A
1 A
1394089 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (33 bp):
ATTGTATCAATACAAAACTTTATGTATCGATAC
Found at i:1394843 original size:23 final size:23
Alignment explanation
Indices: 1394816--1394859 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1394806 TTGGTATAGG
1394816 TATCTAAATAATTATGGGTATTA
1 TATCTAAATAATTATGGGTATTA
1394839 TATCTAAATAATTATGGGTAT
1 TATCTAAATAATTATGGGTAT
1394860 AGGAAAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (23 bp):
TATCTAAATAATTATGGGTATTA
Found at i:1396193 original size:84 final size:81
Alignment explanation
Indices: 1396083--1396314 Score: 245
Period size: 84 Copynumber: 2.8 Consensus size: 81
1396073 AAAATTTAAA
* * * *
1396083 TTTTTTAAAGATCAAGGTTA-ATGTATCCCCTCGAAAGAGTGGAGATGAAGTTTCCCTAAAAATT
1 TTTTTTGAAGATCGAGGTTAGA-GTATCCCCTTG-AGGAGTGGAGATGAAGTTTCCC-AAAAATT
*
1396147 ATATGAAAGAAAAGTTTATG
63 ATATGAAAAAAAAGTTTA-G
*
1396167 TTTTTTGAAGATCGAGGTTAGAGTATCCCCTATGAGGAATGG-GAAT-AGAGTTTTCCCAAAAAT
1 TTTTTTGAAGATCGAGGTTAGAGTATCCCCT-TGAGGAGTGGAG-ATGA-AG-TTTCCCAAAAAT
*
1396230 TATTTGAAAAAAAAGTTTAG
62 TATATGAAAAAAAAGTTTAG
* * * *
1396250 TTTTTCTGAAGATTGGGGTTAGAGTATCCCCCTTGGAGGAGCGGAGATGGAGTTTCCCAAAAATT
1 TTTTT-TGAAGATCGAGGTTAGAGTAT-CCCCTT-GAGGAGTGGAGATGAAGTTTCCCAAAAATT
1396315 GAGAATTTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 20
0.80 0.08 0.13
Matches are distributed among these distances:
83 8 0.06
84 93 0.74
85 24 0.19
86 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (81 bp):
TTTTTTGAAGATCGAGGTTAGAGTATCCCCTTGAGGAGTGGAGATGAAGTTTCCCAAAAATTATA
TGAAAAAAAAGTTTAG
Found at i:1400777 original size:21 final size:21
Alignment explanation
Indices: 1400751--1400804 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1400741 TTCAACAATT
*
1400751 TGTATCTATACAATAAG-GTAA
1 TGTATCGATACAATAAGTG-AA
*
1400772 TGTATCGACAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
1400792 TGTATCGATACAA
1 TGTATCGATACAA
1400805 GCTTGAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Done.