Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 9 of 24
Found at i:1293930 original size:7 final size:6
Alignment explanation
Indices: 1293863--1293942 Score: 60
Period size: 7 Copynumber: 13.0 Consensus size: 6
1293853 GCATCCTTCT
*
1293863 CAAAAA GCAAAACA AAAAAA CAAAAA -AAAAA GCAAAAA -AAAAA CAAGGAAA
1 CAAAAA -CAAAA-A CAAAAA CAAAAA CAAAAA -CAAAAA CAAAAA CAA--AAA
*
1293914 -AAAAA CAAAAA CTAAAAA -AAATA CAAAAA
1 CAAAAA CAAAAA C-AAAAA CAAAAA CAAAAA
1293943 GGAGGGGTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
5 17 0.28
6 18 0.30
7 21 0.35
8 4 0.07
ACGTcount: A:0.81, C:0.11, G:0.05, T:0.03
Consensus pattern (6 bp):
CAAAAA
Found at i:1293931 original size:13 final size:11
Alignment explanation
Indices: 1293876--1293924 Score: 71
Period size: 11 Copynumber: 4.2 Consensus size: 11
1293866 AAAGCAAAAC
1293876 AAAAAAACAAA
1 AAAAAAACAAA
1293887 AAAAAAAGCAAA
1 AAAAAAA-CAAA
1293899 AAAAAAACAAGGA
1 AAAAAAACAA--A
1293912 AAAAAAACAAA
1 AAAAAAACAAA
1293923 AA
1 AA
1293925 CTAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.37
12 11 0.31
13 11 0.31
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:1293934 original size:11 final size:10
Alignment explanation
Indices: 1293871--1293942 Score: 58
Period size: 11 Copynumber: 7.0 Consensus size: 10
1293861 CTCAAAAAGC
1293871 AAAACAAAAA
1 AAAACAAAAA
1293881 AACAA-AAAAA
1 AA-AACAAAAA
*
1293891 AAAGCAAAAAA
1 AAAAC-AAAAA
**
1293902 AAAACAAGGA
1 AAAACAAAAA
*
1293912 AAAA-AAACA
1 AAAACAAAAA
1293921 AAAACTAAAAA
1 AAAAC-AAAAA
1293932 AAATACAAAAA
1 AAA-ACAAAAA
1293943 GGAGGGGTCC
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
9 8 0.16
10 16 0.33
11 23 0.47
12 2 0.04
ACGTcount: A:0.83, C:0.10, G:0.04, T:0.03
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:1294996 original size:28 final size:28
Alignment explanation
Indices: 1294929--1295483 Score: 564
Period size: 28 Copynumber: 19.5 Consensus size: 28
1294919 TACGACACCT
* *
1294929 TTTCAAATCCCATAAGTCAGTGGCATCCC
1 TTTCAAAGCCCACAAGTCAGTGGCAT-CC
*
1294958 TTTTCAAAGCCCACAAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1294987 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
1295015 TTTTAGAGTCCATAAGTCAGTGGCAACCC
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCC
*
1295044 TTTTCAAAGCCCACAAGTCAGCGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1295073 TTTCAAAGCCCATAAGTCAGTAGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
1295101 TTTCAGAGCCCATAAGTTAGTGGCAACCC
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCC
* *
1295130 TTTTCAAAGCCCACAAGCCAGTGGC-GCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1295158 TTTCGAAGCCC-CAAGTGAGAGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1295184 TTTTCAAAGCCCACAAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1295213 TTTCAAAGCCCACAAGTCAGTGACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1295241 TTTCAAAACCTATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1295268 TTTTCAAAGCCCGCAAGTTAGTGGCA-CC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1295296 TTTTCAAAGCCCGCCAGTCGGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1295325 TTTCAAAGCCCAAAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1295353 TTTCAAAGCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1295381 TTTCAAAACCCACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1295408 TTTTCAAAGCCCACAAGTCGGTGGCAACC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1295437 TCTTCTAAAGCCCACATAGGTCAGTGGCAACC
1 T-TTC-AAAGCCCACA-A-GTCAGTGGCATCC
1295469 TTTCTAAAGCCCACA
1 TTTC-AAAGCCCACA
1295484 CAAGTTGGTG
Statistics
Matches: 444, Mismatches: 65, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.02
27 24 0.05
28 290 0.65
29 19 0.04
30 72 0.16
31 15 0.03
32 13 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:1301234 original size:27 final size:25
Alignment explanation
Indices: 1301199--1301267 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 25
1301189 GTCACAAGTA
1301199 AAAACACAAAAAAAAAGAGAAAGAAGAA-
1 AAAA-ACAAAAAAAAA-A-AAA-AAGAAC
* *
1301227 ACAAACAAAAAAAAAACAAAAGAAC
1 AAAAACAAAAAAAAAAAAAAAGAAC
1301252 AAAAACAAAAAAAAAA
1 AAAAACAAAAAAAAAA
1301268 CACAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.14
25 17 0.46
26 1 0.03
27 11 0.30
28 3 0.08
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (25 bp):
AAAAACAAAAAAAAAAAAAAAGAAC
Found at i:1301241 original size:29 final size:26
Alignment explanation
Indices: 1301198--1301279 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 26
1301188 AGTCACAAGT
* *
1301198 AAAAACACAAAAAAAAAGAGAAAGAAGA
1 AAAAACAAAAAAAAAAACA-AAAGAA-A
*
1301226 AACAAAC-AAAAAAAAAACAAAAGAAC
1 AA-AAACAAAAAAAAAAACAAAAGAAA
1301252 AAAAACAAAAAAAAAACACAAAA-AAA
1 AAAAACAAAAAAAAAA-ACAAAAGAAA
1301278 AA
1 AA
1301280 GAGAGTGCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
25 4 0.09
26 15 0.32
27 12 0.26
28 12 0.26
29 4 0.09
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (26 bp):
AAAAACAAAAAAAAAAACAAAAGAAA
Found at i:1301252 original size:8 final size:8
Alignment explanation
Indices: 1301225--1301276 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
1301215 GAGAAAGAAG
*
1301225 AAACAAAC
1 AAACAAAA
1301233 AAA-AAAA
1 AAACAAAA
1301240 AAACAAAA
1 AAACAAAA
*
1301248 GAACAAAA
1 AAACAAAA
*
1301256 ACAAAAAAA
1 A-AACAAAA
1301265 AAACACAAA
1 AAACA-AAA
1301274 AAA
1 AAA
1301277 AAAGAGAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.17
8 17 0.47
9 13 0.36
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (8 bp):
AAACAAAA
Found at i:1301254 original size:19 final size:17
Alignment explanation
Indices: 1301206--1301279 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 17
1301196 GTAAAAACAC
* * *
1301206 AAAAAAAAAGAGAAAGA
1 AAAAAAAAACAAAAAAA
* *
1301223 AGAAACAAACAAAAAAA
1 AAAAAAAAACAAAAAAA
1301240 AAACAAAAGAACAAAAACAA
1 AAA-AAAA-AACAAAAA-AA
1301260 AAAAAAAACACAAAAAAA
1 AAAAAAAA-ACAAAAAAA
1301278 AA
1 AA
1301280 GAGAGTGCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
17 14 0.30
18 8 0.17
19 19 0.41
20 5 0.11
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAA
Found at i:1301257 original size:14 final size:12
Alignment explanation
Indices: 1301198--1301279 Score: 76
Period size: 12 Copynumber: 6.4 Consensus size: 12
1301188 AGTCACAAGT
*
1301198 AAAAACACAAAA
1 AAAAAAACAAAA
* *
1301210 AAAAAGAGAAAGA
1 AAAAAAACAAA-A
1301223 AGAAACAAAC-AAA
1 A-AAA-AAACAAAA
1301236 AAAAAAACAAAA
1 AAAAAAACAAAA
1301248 GAACAAAAACAAAA
1 -AA-AAAAACAAAA
1301262 AAAAAACACAAAA
1 AAAAAA-ACAAAA
1301275 AAAAA
1 AAAAA
1301280 GAGAGTGCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
11 4 0.07
12 19 0.32
13 19 0.32
14 15 0.25
15 2 0.03
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:1301272 original size:27 final size:27
Alignment explanation
Indices: 1301198--1301274 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
1301188 AGTCACAAGT
* *
1301198 AAAAACACAAAAAAAAAGA-GAAAGAAG
1 AAAAACACAAAAAAAAA-ACAAAAGAAC
1301225 AAACAA-ACAAAAAAAAAACAAAAGAAC
1 AAA-AACACAAAAAAAAAACAAAAGAAC
1301252 AAAAACA-AAAAAAAAACACAAAA
1 AAAAACACAAAAAAAAA-ACAAAA
1301275 AAAAAGAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 12 0.27
27 30 0.68
28 2 0.05
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (27 bp):
AAAAACACAAAAAAAAAACAAAAGAAC
Found at i:1302597 original size:32 final size:31
Alignment explanation
Indices: 1302547--1302693 Score: 149
Period size: 31 Copynumber: 4.8 Consensus size: 31
1302537 AATTTTTTAA
*
1302547 ATCTTTT-TTCTAAGTCCATGACTCAGTGGC
1 ATCTTTTCTTCCAAGTCCATGACTCAGTGGC
*
1302577 ATCTTTTTCTTCCAAGTCCATGACTCGGTGGC
1 ATC-TTTTCTTCCAAGTCCATGACTCAGTGGC
* * * *
1302609 ATCTCTTC--CCAAAATCCACGACTTAGTGGC
1 ATCTTTTCTTCC-AAGTCCATGACTCAGTGGC
*
1302639 ATCTTTTCTTCAAAGTCCATGACTCAGTGGC
1 ATCTTTTCTTCCAAGTCCATGACTCAGTGGC
* * *
1302670 AATCTCTTCTT-AAAGTCCACGACT
1 -ATCTTTTCTTCCAAGTCCATGACT
1302694 TTGTGGCACC
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.02
30 25 0.26
31 36 0.37
32 34 0.35
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (31 bp):
ATCTTTTCTTCCAAGTCCATGACTCAGTGGC
Found at i:1302669 original size:61 final size:63
Alignment explanation
Indices: 1302561--1302701 Score: 196
Period size: 62 Copynumber: 2.3 Consensus size: 63
1302551 TTTTTCTAAG
* * * *
1302561 TCCATGACTCAGTGGCATCTTTTTCTTCCAAGTCCATGACTCGGTGGC-ATCTCTTCCCAAAA
1 TCCACGACTTAGTGGCATCTTTTTCTTCAAAGTCCATGACTCAGTGGCAATCTCTTCCCAAAA
** *
1302623 TCCACGACTTAGTGGCATC-TTTTCTTCAAAGTCCATGACTCAGTGGCAATCTCTTCTTAAAG
1 TCCACGACTTAGTGGCATCTTTTTCTTCAAAGTCCATGACTCAGTGGCAATCTCTTCCCAAAA
*
1302685 TCCACGACTTTGTGGCA
1 TCCACGACTTAGTGGCA
1302702 CCCTTTTAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
61 26 0.37
62 44 0.63
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (63 bp):
TCCACGACTTAGTGGCATCTTTTTCTTCAAAGTCCATGACTCAGTGGCAATCTCTTCCCAAAA
Found at i:1302721 original size:27 final size:27
Alignment explanation
Indices: 1302686--1302938 Score: 148
Period size: 27 Copynumber: 8.6 Consensus size: 27
1302676 TTCTTAAAGT
* *
1302686 CCACGACTTTGTGGCACCCTTTTAAGC
1 CCACAACTTCGTGGCACCCTTTTAAGC
* *
1302713 CCATAACTTCGTGGCACCCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGC
1302740 CCACAAC-TCTGTGGCACCCTTTTAAGC
1 CCACAACTTC-GTGGCACCCTTTTAAGC
*
1302767 CTACAACTTCGTGGCACTTTTTTTTCCTTTTAAGC
1 CCACAACTTCGTGGCAC--------CCTTTTAAGC
* *
1302802 CCACAACTCCGTGGCATTCTTCTTCCTTTTAAGT
1 CCACAACTTCGTGGCA-----C--CCTTTTAAGC
* * * *
1302836 CCACAACTCCATAGCACCCTTTTAAGA
1 CCACAACTTCGTGGCACCCTTTTAAGC
* * *
1302863 CCACAACTTTGTGACACCTTGTTCCTTTTAAGT
1 CCACAACTTCGTGGCA-C-----CCTTTTAAGC
* *
1302896 CCACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGC
*
1302923 CCACAACTACGTGGCA
1 CCACAACTTCGTGGCA
1302939 TCTTTCTCCT
Statistics
Matches: 182, Mismatches: 23, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
26 2 0.01
27 103 0.57
28 3 0.02
29 1 0.01
32 1 0.01
33 22 0.12
34 25 0.14
35 24 0.13
40 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.32
Consensus pattern (27 bp):
CCACAACTTCGTGGCACCCTTTTAAGC
Found at i:1302808 original size:35 final size:34
Alignment explanation
Indices: 1302757--1302961 Score: 129
Period size: 27 Copynumber: 6.5 Consensus size: 34
1302747 TCTGTGGCAC
* * * *
1302757 CCTTTTAAGCCTACAACTTCGTGGCACTTTTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TTCTTCTT
1302792 CCTTTTAAGCCCACAACTCCGTGGCATTCTTCTT
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTCTT
* * *
1302826 CCTTTTAAGTCCACAACTCCATAGCA-----C--
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTCTT
* ** * * *
1302853 CCTTTTAAGACCACAACTTTGTGACA-CCTTGTT
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTCTT
*
1302886 CCTTTTAAGTCCACAACTCCGTGGCA-----C--
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTCTT
* *
1302913 CCTTTTAAGTCCACAACTACGTGGCA-TCTT-TCT
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTCT-T
1302946 CCTTTTAAGCCCACAA
1 CCTTTTAAGCCCACAA
1302962 GTCAATGGCA
Statistics
Matches: 136, Mismatches: 21, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
27 45 0.33
29 1 0.01
33 37 0.27
34 29 0.21
35 24 0.18
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.34
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCATTCTTCTT
Found at i:1302860 original size:96 final size:94
Alignment explanation
Indices: 1302730--1302911 Score: 258
Period size: 96 Copynumber: 1.9 Consensus size: 94
1302720 TTCGTGGCAC
** * * * *
1302730 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAG-CCTACAACTTCGTGGCACTTTTTTTTCC
1 CCTTTTAAGTCCACAACTCCATAGCACCCTTTTAAGACC-ACAACTTCGTGACAC--CTTGTTCC
1302794 TTTTAAGCCCACAACTCCGTGGCATTCTTCTT
63 TTTTAAGCCCACAACTCCGTGGCATTCTTCTT
*
1302826 CCTTTTAAGTCCACAACTCCATAGCACCCTTTTAAGACCACAACTTTGTGACACCTTGTTCCTTT
1 CCTTTTAAGTCCACAACTCCATAGCACCCTTTTAAGACCACAACTTCGTGACACCTTGTTCCTTT
*
1302891 TAAGTCCACAACTCCGTGGCA
66 TAAGCCCACAACTCCGTGGCA
1302912 CCCTTTTAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 29 0.38
96 46 0.60
97 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (94 bp):
CCTTTTAAGTCCACAACTCCATAGCACCCTTTTAAGACCACAACTTCGTGACACCTTGTTCCTTT
TAAGCCCACAACTCCGTGGCATTCTTCTT
Found at i:1302971 original size:60 final size:60
Alignment explanation
Indices: 1302792--1302978 Score: 216
Period size: 60 Copynumber: 3.1 Consensus size: 60
1302782 ACTTTTTTTT
* * *
1302792 CCTTTTAAGCCCACAACTCCGTGGCAT-TCTTCTTCCTTTTAAGTCCACAACTCCATAGCAC
1 CCTTTTAAGACCACAACTACGTGGCATCT-TTC-TCCTTTTAAGTCCACAACTCCATGGCAC
** * * *
1302853 CCTTTTAAGACCACAACTTTGTGACACCTTGT-TCCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGACCACAACTACGTGGCATCTT-TCTCCTTTTAAGTCCACAACTCCATGGCAC
* * * * *
1302913 CCTTTTAAGTCCACAACTACGTGGCATCTTTCTCCTTTTAAGCCCACAAGTCAATGGCAT
1 CCTTTTAAGACCACAACTACGTGGCATCTTTCTCCTTTTAAGTCCACAACTCCATGGCAC
1302973 CCTTTT
1 CCTTTT
1302979 CAAAAGCCCA
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 80 0.75
61 23 0.22
62 2 0.02
ACGTcount: A:0.23, C:0.33, G:0.12, T:0.33
Consensus pattern (60 bp):
CCTTTTAAGACCACAACTACGTGGCATCTTTCTCCTTTTAAGTCCACAACTCCATGGCAC
Found at i:1303023 original size:29 final size:30
Alignment explanation
Indices: 1302952--1303105 Score: 192
Period size: 29 Copynumber: 5.3 Consensus size: 30
1302942 TTCTCCTTTT
** * *
1302952 AAGCCCACAAGTCAATGGCATCCTTTTCAA
1 AAGCCCACAAGTCGGTGGCACCCCTTTCAA
1302982 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCGGTGGCACCCCTTTCAA
1303011 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCGGTGGCACCCCTTTCAA
* *
1303040 AAGCCCACAAGTCGGTGGCA-ACC-TACAA
1 AAGCCCACAAGTCGGTGGCACCCCTTTCAA
* * *
1303068 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCGGTGGCACCCCTTTCAA
1303097 AAGCCCACA
1 AAGCCCACA
1303106 GAAGTTGGTG
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
27 5 0.05
28 19 0.17
29 62 0.56
30 24 0.22
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (30 bp):
AAGCCCACAAGTCGGTGGCACCCCTTTCAA
Found at i:1303101 original size:57 final size:59
Alignment explanation
Indices: 1302952--1303105 Score: 181
Period size: 57 Copynumber: 2.7 Consensus size: 59
1302942 TTCTCCTTTT
* ** * * * *
1302952 AAGCCCACAAGTCAATGGCATCCTTTTCAAAAGCCCACAAGTCGGTGGCACCCCTTTCA
1 AAGCACACAAGTCGGTGGCAACCCTTTCAAAAGCCCACAAGTCGGTGGCACACCTTACA
* *
1303011 AAGCCCACAAGTCGGTGGCACCCCTTTC-AAAGCCCACAAGTCGGTGGCA-ACC-TACAA
1 AAGCACACAAGTCGGTGGCAACCCTTTCAAAAGCCCACAAGTCGGTGGCACACCTTAC-A
*
1303068 AAGCACACAAGTTGGT-GCAACCCTTTCAAAAGCCCACA
1 AAGCACACAAGTCGGTGGCAACCCTTTCAAAAGCCCACA
1303106 GAAGTTGGTG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
56 12 0.14
57 27 0.32
58 21 0.25
59 24 0.29
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (59 bp):
AAGCACACAAGTCGGTGGCAACCCTTTCAAAAGCCCACAAGTCGGTGGCACACCTTACA
Found at i:1303204 original size:49 final size:49
Alignment explanation
Indices: 1303122--1303831 Score: 635
Period size: 49 Copynumber: 14.8 Consensus size: 49
1303112 GGTGGCGTCT
* * * *
1303122 TCTTCTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTCA
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
**
1303172 TCTTTAAGACCAATGTCATTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * ** *
1303221 TCTTTAAAACCGATGTCTTTGGCCTTGAATCAGCACATTGGCACTTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
1303270 TCTTTAAGTCCAA-ATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACTA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT-C-A
* * * * * *
1303321 TC-TTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGTACCTT-G
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1303368 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * * *
1303411 -C---AAGCCCAATATCGCTAGCCTTGAATTAGCATATTAGCACCTT-G
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
1303455 TCTCTGAGACCAATGCCGCTGGCCTTGAATCAGCACATT-G---C--CA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
1303498 -C---AAGCCCCATATCGCTGGCCTTGAATCAGCAAATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* **
1303543 TCTTTAAGAACAATGTCATTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
** *
1303592 TCTTTAAGACTGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CA
1303644 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * ** * * * *
1303693 TCTTTAAGTCCAATATCATTGGCCTTGAATCAGTATATTGGCATCTTTA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * ** * *
1303742 ACATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--ATCT
1 TC-TT--TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
1303792 TCTTTAAGTCTAATGTCGCTGGCCATGAATCAGCACATTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
1303832 TCATTCTTCG
Statistics
Matches: 539, Mismatches: 88, Indels: 69
0.77 0.13 0.10
Matches are distributed among these distances:
39 58 0.11
40 1 0.00
42 2 0.00
43 1 0.00
44 1 0.00
45 3 0.01
46 1 0.00
47 34 0.06
48 87 0.16
49 222 0.41
50 20 0.04
51 32 0.06
52 77 0.14
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:1303432 original size:39 final size:39
Alignment explanation
Indices: 1303377--1303537 Score: 133
Period size: 39 Copynumber: 3.9 Consensus size: 39
1303367 GTCTTTAAGA
*
1303377 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * * * * *
1303416 CCAATATCGCTAGCCTTGAATTAGCATATTAGCACCTTGTCTCTGAGA
1 CCAATATCGCTGGCCTTGAA-T--C-----AGCACATTGGCAC-AAGC
** *
1303464 CCAATGCCGCTGGCCTTGAATCAGCACATTGCCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
1303503 CCCATATCGCTGGCCTTGAATCAGCAAATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
1303538 CTTCATCTTT
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
39 50 0.54
40 11 0.12
42 1 0.01
45 1 0.01
47 11 0.12
48 19 0.20
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
Found at i:1303475 original size:87 final size:87
Alignment explanation
Indices: 1303325--1303687 Score: 393
Period size: 87 Copynumber: 4.0 Consensus size: 87
1303315 TTACTATCTT
* *
1303325 AAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGTACCTTGTCTTTAAGACCAATGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
1303390 CCTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
* * * * * *
1303412 AAGCCCAATATCGCTAGCCTTGAATTAGCATATTAGCACCTTGTCTCTGAGACCAATGCCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
*
1303477 CCTTGAATCAGCACATTGCCAC
66 CCTTGAATCAGCACATTGGCAC
* * * * **
1303499 AAGCCCCATATCGCTGGCCTTGAATCAGCAAATTGGCACCTTCATCTTTAAGAACAATGTCATTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCGCTG
1303564 GCCTTGAATCAGCACATTGGCACCTTCATC
65 GCCTTGAATCAGCACATTGG------CA-C
* ** * * * *
1303594 TTTAAGACTGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGACCAATG
1 ---AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT----GTCTTTAAGACCAATG
1303659 TCGCTGGCCTTGAATCAGCACATTGGCAC
59 TCGCTGGCCTTGAATCAGCACATTGGCAC
1303688 CTTCATCTTT
Statistics
Matches: 231, Mismatches: 31, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
87 115 0.50
88 34 0.15
94 3 0.01
95 3 0.01
98 36 0.16
101 40 0.17
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (87 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTGGCAC
Found at i:1303685 original size:101 final size:100
Alignment explanation
Indices: 1303513--1303831 Score: 396
Period size: 101 Copynumber: 3.2 Consensus size: 100
1303503 CCCATATCGC
* * **
1303513 TGGCCTTGAATCAGCAAATTGGCACCTT--CATCTTTAAGAACAATGTCATTGGCCTTGAATCAG
1 TGGCCTTGAATCAGCACATTGGCACCTTAACATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG
* *
1303576 CACATTGGCACCTTCATCTTTAAGACTGATGTCGT
66 CACATTGGCACCTTCATCTTTAAGTCTAATGTCGT
1303611 TGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
1 TGGCCTTGAATCAGCACATTGGCACCTTAA-CATCTTTAAGACCAATGTCGCTGGCCTTGAATCA
* * *
1303676 GCACATTGGCACCTTCATCTTTAAGTCCAATATCAT
65 GCACATTGGCACCTTCATCTTTAAGTCTAATGTCGT
* * * * * **
1303712 TGGCCTTGAATCAGTATATTGGCATCTTTAACAT-TCCTAAGCCCAATGTCGCTGGCCTTGTCTC
1 TGGCCTTGAATCAGCACATTGGCA-CCTTAACATCT-TTAAGACCAATGTCGCTGGCCTTGAATC
* * *
1303776 AGCACATTGGCA--ATCTTCTTTAAGTCTAATGTCGC
64 AGCACATTGGCACCTTCATCTTTAAGTCTAATGTCGT
*
1303811 TGGCCATGAATCAGCACATTG
1 TGGCCTTGAATCAGCACATTG
1303832 TCATTCTTCG
Statistics
Matches: 191, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
98 27 0.14
99 35 0.18
100 1 0.01
101 123 0.64
102 5 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (100 bp):
TGGCCTTGAATCAGCACATTGGCACCTTAACATCTTTAAGACCAATGTCGCTGGCCTTGAATCAG
CACATTGGCACCTTCATCTTTAAGTCTAATGTCGT
Found at i:1309562 original size:27 final size:27
Alignment explanation
Indices: 1309521--1309572 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1309511 TGGGATGGTC
**
1309521 GGGGATACTCGAACCTTGCTTTTCTGA
1 GGGGATACTCGAACCCCGCTTTTCTGA
* *
1309548 GGGGATATTCTAACCCCGCTTTTCT
1 GGGGATACTCGAACCCCGCTTTTCT
1309573 TCAAGATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
GGGGATACTCGAACCCCGCTTTTCTGA
Found at i:1310952 original size:2 final size:2
Alignment explanation
Indices: 1310947--1310985 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1310937 ATTTTTTTCT
1310947 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1310986 AAGAGAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1310968 original size:19 final size:19
Alignment explanation
Indices: 1310946--1310984 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1310936 AATTTTTTTC
1310946 TTATATATATATATATATA
1 TTATATATATATATATATA
1310965 TTATATATATATATATATA
1 TTATATATATATATATATA
1310984 T
1 T
1310985 AAAGAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATATATATATATA
Found at i:1310971 original size:17 final size:17
Alignment explanation
Indices: 1310949--1310982 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1310939 TTTTTTCTTA
1310949 TATATATATATATATAT
1 TATATATATATATATAT
1310966 TATATATATATATATAT
1 TATATATATATATATAT
1310983 ATAAAGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:1312120 original size:13 final size:13
Alignment explanation
Indices: 1312102--1312127 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1312092 CAATTTTTGG
1312102 TGTATCGATACAT
1 TGTATCGATACAT
1312115 TGTATCGATACAT
1 TGTATCGATACAT
1312128 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1312139 original size:32 final size:33
Alignment explanation
Indices: 1312082--1312145 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1312072 TACAAGCCAA
**
1312082 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1312115 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1312146 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1312152 original size:19 final size:18
Alignment explanation
Indices: 1312082--1312152 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1312072 TACAAGCCAA
1312082 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1312102 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1312115 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1312134 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1312153 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1314632 original size:13 final size:13
Alignment explanation
Indices: 1314614--1314639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1314604 ATAATCACCC
1314614 TGTATCGATACAA
1 TGTATCGATACAA
1314627 TGTATCGATACAA
1 TGTATCGATACAA
1314640 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1320828 original size:13 final size:13
Alignment explanation
Indices: 1320810--1320835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1320800 CAATTTTTGG
1320810 TGTATCGATACAT
1 TGTATCGATACAT
1320823 TGTATCGATACAT
1 TGTATCGATACAT
1320836 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1320847 original size:32 final size:33
Alignment explanation
Indices: 1320790--1320853 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1320780 TACAAGCCAA
**
1320790 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1320823 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1320854 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1320860 original size:19 final size:18
Alignment explanation
Indices: 1320790--1320860 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1320780 TACAAGCCAA
1320790 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1320810 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1320823 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1320842 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1320861 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1330581 original size:89 final size:89
Alignment explanation
Indices: 1330429--1330608 Score: 247
Period size: 89 Copynumber: 2.0 Consensus size: 89
1330419 GGGTTATTAG
* * *
1330429 AGGAGGTTGGTAATGTTTGGAACAATTCAGAAGTCCATGGGAGAGTTGGGTTCTGTTTTAAGTCT
1 AGGAGGTTGGTAATGTTTGGAACAATTCAGAAGTCCATGGAAGAGTTGGGTTCTATTTAAAGTCT
1330494 TAAGTAAGATT-ACAGTATCCTTAA
66 TAAGTAAGATTGA-AGTATCCTTAA
* * * *
1330518 AGGAGGTTGGTGATGTTTGGAACACTTC-GAAAGTCCATGGAAGTGTTGGGTTTTATTTAAAGTC
1 AGGAGGTTGGTAATGTTTGGAACAATTCAG-AAGTCCATGGAAGAGTTGGGTTCTATTTAAAGTC
* *
1330582 TTAATTAGGATTGAAGTATCCTTAA
65 TTAAGTAAGATTGAAGTATCCTTAA
1330607 AG
1 AG
1330609 AATTGGAATA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
88 1 0.01
89 78 0.98
90 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.34
Consensus pattern (89 bp):
AGGAGGTTGGTAATGTTTGGAACAATTCAGAAGTCCATGGAAGAGTTGGGTTCTATTTAAAGTCT
TAAGTAAGATTGAAGTATCCTTAA
Found at i:1336500 original size:13 final size:13
Alignment explanation
Indices: 1336482--1336507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1336472 TACAGCAAGT
1336482 ATGTATCGATACA
1 ATGTATCGATACA
1336495 ATGTATCGATACA
1 ATGTATCGATACA
1336508 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1338757 original size:21 final size:21
Alignment explanation
Indices: 1338724--1338768 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1338714 TTGCAAGTTG
*
1338724 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1338746 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1338766 AAA
1 AAA
1338769 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1340592 original size:15 final size:15
Alignment explanation
Indices: 1340572--1340602 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1340562 TAAAAATGTC
*
1340572 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1340587 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1340602 C
1 C
1340603 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1342687 original size:20 final size:20
Alignment explanation
Indices: 1342608--1342687 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1342598 AATGTCCAAA
*
1342608 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1342628 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1342653 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1342673 TTGTATCGATACATT
1 ATGTATCGATACATT
1342688 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1342691 original size:13 final size:13
Alignment explanation
Indices: 1342673--1342711 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1342663 ACATTTTTCT
1342673 TTGTATCGATACA
1 TTGTATCGATACA
1342686 TTGTATCGATACA
1 TTGTATCGATACA
*
1342699 CTGTATCGATACA
1 TTGTATCGATACA
1342712 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1342856 original size:21 final size:21
Alignment explanation
Indices: 1342832--1342878 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1342822 AAATCTTTTG
1342832 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1342853 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1342873 CAAAAT
1 CAAAAT
1342879 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1342875 original size:20 final size:19
Alignment explanation
Indices: 1342834--1342876 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1342824 ATCTTTTGCA
1342834 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1342854 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1342874 AAA
1 AAA
1342877 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1345279 original size:13 final size:13
Alignment explanation
Indices: 1345261--1345286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1345251 TACAGCAAGT
1345261 ATGTATCGATACA
1 ATGTATCGATACA
1345274 ATGTATCGATACA
1 ATGTATCGATACA
1345287 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1347536 original size:21 final size:21
Alignment explanation
Indices: 1347503--1347547 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1347493 TTGCAAGTTG
*
1347503 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1347525 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1347545 AAA
1 AAA
1347548 ATGAAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1351467 original size:20 final size:20
Alignment explanation
Indices: 1351388--1351467 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1351378 AATGTCCAAA
*
1351388 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1351408 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1351433 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1351453 TTGTATCGATACATT
1 ATGTATCGATACATT
1351468 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1351471 original size:13 final size:13
Alignment explanation
Indices: 1351453--1351491 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1351443 ACATTTTTCT
1351453 TTGTATCGATACA
1 TTGTATCGATACA
1351466 TTGTATCGATACA
1 TTGTATCGATACA
*
1351479 CTGTATCGATACA
1 TTGTATCGATACA
1351492 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1351655 original size:20 final size:19
Alignment explanation
Indices: 1351614--1351656 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1351604 ATCTTTTGCA
1351614 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1351634 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1351654 AAA
1 AAA
1351657 GTCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1353965 original size:20 final size:20
Alignment explanation
Indices: 1353942--1354015 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1353932 ACAATTCAAA
1353942 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1353962 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1353983 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1354003 GTATCGATACATG
1 GTATCGATACATG
1354016 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1353986 original size:21 final size:21
Alignment explanation
Indices: 1353960--1354035 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1353950 ACATGTTGCA
1353960 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1353981 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1354001 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1354022 ATGTATCGATACAT
1 ATGTATCGATACAT
1354036 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1353993 original size:41 final size:41
Alignment explanation
Indices: 1353942--1354035 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1353932 ACAATTCAAA
1353942 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1353983 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1354024 GTATCGATACAT
1 GTATCGATACAT
1354036 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1360711 original size:33 final size:33
Alignment explanation
Indices: 1360654--1360720 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1360644 TGTTTGGCAT
*
1360654 AATGTATCGATACAATTCTTCATGTAACGATAC
1 AATGTATCGATACAATTCTCCATGTAACGATAC
* *
1360687 AATGTATCGATAC-ATTGTCCCATGTATCGATAC
1 AATGTATCGATACAATTCT-CCATGTAACGATAC
1360720 A
1 A
1360721 TTTCACTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATTCTCCATGTAACGATAC
Found at i:1360797 original size:19 final size:19
Alignment explanation
Indices: 1360749--1360804 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1360739 TTGCCACTTT
*
1360749 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
1360769 TATATATCGATACAATGAA
1 CATGTATCGATACAATGAA
1360788 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1360805 TATTGATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1361510 original size:165 final size:166
Alignment explanation
Indices: 1361339--1361701 Score: 446
Period size: 166 Copynumber: 2.2 Consensus size: 166
1361329 GATAATGTTA
* * *
1361339 GATGAATTTTAAAAATTTTAAATCAAGAAAAAAAATTTCTAAAAATATTTATAGAATAGAAAAC-
1 GATGAATTTTAAAAATTATAAACCAAGAAAAAAAACTTC-AAAAATATTTATAGAATAGAAAACT
* * * ** * * *** *
1361403 TTGATTTTTC-AATAA-TAGGAGAATTTTTTA-AAAAATGAAAAACTTATGAAAATAAATGAATT
65 TTG-TATCTCGAA-AACAAAAAAAAATTCAAAGAAAAATGAAAAACATATGAAAATAAATGAATT
* * * *
1361465 TTTTAAAATTGATTTACAATGAATTAAATTATGATATTT
128 TTTCAAAACTCATTTACAATGAATTAAATGATGATATTT
*** * *
1361504 GATGAATTTTAAAAATTATAAACCAAGAAAAATCCCTTCGAAAATATTTATGGAATAGAAAACTT
1 GATGAATTTTAAAAATTATAAACCAAGAAAAAAAACTTCAAAAATATTTATAGAATAGAAAACTT
1361569 TGTATCTCGAAAACAAAAAAAAATTCAAAGAAAAATGAAAAACATATGAAAATAAATGAATTTTT
66 TGTATCTCGAAAACAAAAAAAAATTCAAAGAAAAATGAAAAACATATGAAAATAAATGAATTTTT
*
1361634 CAAAACTCATTTACTATGAATTAAATGATGATATTT
131 CAAAACTCATTTACAATGAATTAAATGATGATATTT
*
1361670 GATGAATTTTAAAAATTATAAACCTAGAAAAA
1 GATGAATTTTAAAAATTATAAACCAAGAAAAA
1361702 TCTCCTTGAA
Statistics
Matches: 169, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
164 28 0.17
165 45 0.27
166 96 0.57
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (166 bp):
GATGAATTTTAAAAATTATAAACCAAGAAAAAAAACTTCAAAAATATTTATAGAATAGAAAACTT
TGTATCTCGAAAACAAAAAAAAATTCAAAGAAAAATGAAAAACATATGAAAATAAATGAATTTTT
CAAAACTCATTTACAATGAATTAAATGATGATATTT
Found at i:1370079 original size:51 final size:50
Alignment explanation
Indices: 1370014--1370152 Score: 206
Period size: 51 Copynumber: 2.7 Consensus size: 50
1370004 TAATTTTAAC
* * *
1370014 TAGATGTATCGATACATTGAATAATGTATTGATACATCTGGGTAAAAAGA
1 TAGATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAAAGA
*
1370064 TAGAGTGTATTGATACATTGAAGAATGTATCGATACATCTAGGTAAAAAGA
1 TAGA-TGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAAAGA
* *
1370115 TAAAATGTATCGATACATTAAAGAATGTATCGATACAT
1 T-AGATGTATCGATACATTGAAGAATGTATCGATACAT
1370153 TCATACATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
50 4 0.05
51 74 0.93
52 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.31
Consensus pattern (50 bp):
TAGATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAAAGA
Found at i:1370143 original size:20 final size:20
Alignment explanation
Indices: 1370116--1370189 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
1370106 GTAAAAAGAT
1370116 AAAATGTATCGATACATT-A
1 AAAATGTATCGATACATTCA
1370135 AAGAATGTATCGATACATTCA
1 AA-AATGTATCGATACATTCA
* * * * *
1370156 TACATATATCGATGCATTGA
1 AAAATGTATCGATACATTCA
1370176 AAAATGTATCGATA
1 AAAATGTATCGATA
1370190 TATCTAGGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAATGTATCGATACATTCA
Found at i:1371168 original size:32 final size:32
Alignment explanation
Indices: 1371079--1371223 Score: 150
Period size: 32 Copynumber: 4.6 Consensus size: 32
1371069 AAAGTGGTGA
* *
1371079 TTTGAAAAGGGTTGCCACCAACTTGCGTGGGC
1 TTTGAAAAGAGTTGCCACCAACTTGTGTGGGC
* * * *
1371111 TTTTAAAAAAAGGTGCCACTAACTTGTGTGGGC
1 -TTTGAAAAGAGTTGCCACCAACTTGTGTGGGC
* *
1371144 TTTGAAAAGAGTTGCCACCGACTTGTGTGGTC
1 TTTGAAAAGAGTTGCCACCAACTTGTGTGGGC
* * **
1371176 TTTAAAAAGAGTTGGCACTGAC-T-TGTGGGC
1 TTTGAAAAGAGTTGCCACCAACTTGTGTGGGC
*
1371206 TTTGAAAAGAGTTACCAC
1 TTTGAAAAGAGTTGCCAC
1371224 TAGCTTATGC
Statistics
Matches: 93, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
30 21 0.23
31 1 0.01
32 45 0.48
33 26 0.28
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (32 bp):
TTTGAAAAGAGTTGCCACCAACTTGTGTGGGC
Found at i:1371280 original size:28 final size:28
Alignment explanation
Indices: 1371119--1371964 Score: 927
Period size: 28 Copynumber: 29.8 Consensus size: 28
1371109 GCTTTTAAAA
*
1371119 AAAGG-TGCCACTAACTTGTGTGGGCTTTG
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTG
* * *
1371148 AAAAGAGTTGCCACCGACTTGTGTGGTCTTTAA
1 -AAAG-GATGCCACTGACTTGTG-GG-CTTT-G
* *
1371181 AAAGAGTTGGCACTGACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
* * * * *
1371210 AAAAGAGTTACCACT-AGCTTATGCGCTTTAA
1 -AAAG-GATGCCACTGA-CTTGTGGGCTTT-G
* *
1371241 AAAGGGTGCCACTGACTTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
1371269 AAAGGGTACCACAGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
1371297 AAAGGATGCCACTGCCTTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
1371325 AAAGGGTGCCACTGACTTGTGGGCATTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371353 AAATGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371381 AAAGGATGCCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
1371409 AAAGGGTGCCACTGACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371437 AAAGGATGCCACTGACTTGTAGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371465 AGAAAGATGCCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* * *
1371494 AAAGGGTGCCATTGACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371522 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
1371550 AAAGGATGCCATTGACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* **
1371578 AAAGGGTGCCACTGACTTGTGGATTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371606 AAAGGAT---AC-CAC-TGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371629 AGAAGGATGCCACTGACTTGTGGGCTTTA
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* * *
1371658 AGAAGGATGCCACAGTC-AGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
*
1371686 AGAAGGATGCCACTGACTTATGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* *
1371715 AGAAGGGTGCCACTGATTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
*
1371744 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
1371772 AAATGATGCCATTGACTTGTGGGTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
1371800 AAAAGATGCCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371828 AAAGGTTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
1371856 AGAAGGGTGCCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* *
1371885 AAAGGATGCCATTGACTTGTGGGTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* **
1371913 AAAGGATGCCACTAACTTGTGGTTTTCTTG
1 AAAGGATGCCACTGACTTGTGG-GCT-TTG
1371943 -AAGAGATGCCACTGACTTGTGG
1 AAAG-GATGCCACTGACTTGTGG
1371965 TTTTTTTATT
Statistics
Matches: 700, Mismatches: 95, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
23 10 0.01
24 8 0.01
25 2 0.00
27 2 0.00
28 445 0.64
29 136 0.19
30 59 0.08
31 6 0.01
32 32 0.05
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:1371931 original size:141 final size:140
Alignment explanation
Indices: 1371139--1371964 Score: 930
Period size: 141 Copynumber: 5.8 Consensus size: 140
1371129 CTAACTTGTG
* * * * *
1371139 TGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGTCTTTAAAAAGAGTTGGCACTGACTTGTGG
1 TGGGCTTTG-AAAG-GGTGCCACTGACTTGTG-GG-CTTT-GAAAG-GATGCCACTGACTTGTGG
* * * * * * *
1371204 GCTTTGAAAAGAGTTACCACT-AGCTTATGCGCTTTAAAAAGGGTGCCACTGACTTGTAGGCTTT
60 GCTTTG-AAAG-GATGCCACTGA-CTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTT
* * * *
1371268 GAAAGGGTACCACAGACTTG
121 GAAAGGATGCCACTGACTTA
* * * * * *
1371288 TGGGCTTTGAAAGGATGCCACTGCCTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCATTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
1371353 AAATGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGGTGC
66 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGC
1371418 CACTGACTTA
131 CACTGACTTA
* * *
1371428 TGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAGAAAGATGCCACTGACTTGTGGGCTTT
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTT
* * * * *
1371493 GAAAGGGTGCCATTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATG
65 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATG
*
1371558 CCATTGACTTA
130 CCACTGACTTA
** *
1371569 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGATTTTGAAAGGAT---AC-CAC-TGTGGGCTTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * *
1371629 AGAAGGATGCCACTGACTTGTGGGCTTT-AAGAAGGATGCCACAGTC-AGTGGGCTTTGAGAAGG
66 A-AAGGATGCCACTGACTTGTGGGCTTTGAA-AA-GATGCCACTGACTTGTGGGCTTTGA-AAGG
1371692 ATGCCACTGACTTA
127 ATGCCACTGACTTA
* *
1371706 TGGGCTTTGAGAAGGGTGCCACTGATTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT
1 TGGGCTTTGA-AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT
* * * * *
1371771 GAAATGATGCCATTGACTTGTGGGTTTTGAAAAGATGCCATTGACTTGTGGGCTTTGAAAGGTTG
65 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATG
*
1371836 CCACTGACTTG
130 CCACTGACTTA
* *
1371847 TGGGCTTTGAGAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGTTTT
1 TGGGCTTTGA-AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT
* ** *
1371912 GAAAGGATGCCACTAACTTGTGGTTTTCTTGAAGAGATGCCACTGACTTGTGG
65 GAAAGGATGCCACTGACTTGTGG-GCT-TTGAAAAGATGCCACTGACTTGTGG
1371965 TTTTTTTATT
Statistics
Matches: 588, Mismatches: 73, Indels: 38
0.84 0.10 0.05
Matches are distributed among these distances:
135 14 0.02
136 37 0.06
137 38 0.06
138 31 0.05
140 79 0.13
141 252 0.43
142 44 0.07
143 57 0.10
144 4 0.01
145 4 0.01
146 2 0.00
147 13 0.02
148 4 0.01
149 9 0.02
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (140 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGC
CACTGACTTA
Found at i:1371982 original size:4 final size:4
Alignment explanation
Indices: 1371973--1372032 Score: 56
Period size: 4 Copynumber: 15.8 Consensus size: 4
1371963 GGTTTTTTTA
* * *
1371973 TTTG TTTG TTTG TTTG TTTG TTT- TTTG TTT- TTTT TTCTA TTTT TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TT-TG TTTG TTTG
1372020 TTT- TTT- TTTG TTT
1 TTTG TTTG TTTG TTT
1372033 TTTTAGTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 12 0.24
4 34 0.69
5 3 0.06
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (4 bp):
TTTG
Found at i:1371986 original size:8 final size:7
Alignment explanation
Indices: 1371973--1372025 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
1371963 GGTTTTTTTA
1371973 TTTGTTT
1 TTTGTTT
1371980 GTTTGTTT
1 -TTTGTTT
1371988 GTTTGTTT
1 -TTTGTTT
1371996 TTTGTTT
1 TTTGTTT
1372003 TTT-TTT
1 TTTGTTT
*
1372009 CTAT-TTT
1 -TTTGTTT
1372016 TTTGTTT
1 TTTGTTT
1372023 TTT
1 TTT
1372026 TTTGTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
6 5 0.12
7 21 0.51
8 15 0.37
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (7 bp):
TTTGTTT
Found at i:1371988 original size:12 final size:11
Alignment explanation
Indices: 1371973--1372036 Score: 73
Period size: 10 Copynumber: 6.1 Consensus size: 11
1371963 GGTTTTTTTA
1371973 TTTGTTTGTTT
1 TTTGTTTGTTT
1371984 GTTTGTTTGTTT
1 -TTTGTTTGTTT
1371996 TTTGTTT-TTT
1 TTTGTTTGTTT
* *
1372006 TTTCTAT-TTT
1 TTTGTTTGTTT
1372016 TTTGTTT-TTT
1 TTTGTTTGTTT
1372026 TTTGTTT-TTT
1 TTTGTTTGTTT
1372036 T
1 T
1372037 AGTATGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 30 0.62
11 7 0.15
12 11 0.23
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (11 bp):
TTTGTTTGTTT
Found at i:1371997 original size:27 final size:27
Alignment explanation
Indices: 1371966--1372032 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1371956 GACTTGTGGT
*
1371966 TTTTTTATTTGTTTGTT-TGTTTGTTTG
1 TTTTTT-TTTGTTTGTTCTATTTGTTTG
* *
1371993 TTTTTTGTTT-TTTTTTCTATTTTTTTG
1 TTTTTT-TTTGTTTGTTCTATTTGTTTG
1372020 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
1372033 TTTTAGTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.03, C:0.01, G:0.12, T:0.84
Consensus pattern (27 bp):
TTTTTTTTTGTTTGTTCTATTTGTTTG
Found at i:1372026 original size:8 final size:8
Alignment explanation
Indices: 1371968--1372036 Score: 56
Period size: 8 Copynumber: 8.9 Consensus size: 8
1371958 CTTGTGGTTT
1371968 TTTTATTTG
1 TTTT-TTTG
*
1371977 TTTGTTTG
1 TTTTTTTG
*
1371985 TTTGTTTG
1 TTTTTTTG
1371993 -TTTTTTG
1 TTTTTTTG
1372000 TTTTTTT-
1 TTTTTTTG
*
1372007 TTCTATTT-
1 TT-TTTTTG
*
1372015 TTTTGTT-
1 TTTTTTTG
1372022 TTTTTTTG
1 TTTTTTTG
1372030 TTTTTTT
1 TTTTTTT
1372037 AGTATGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
7 17 0.33
8 31 0.61
9 3 0.06
ACGTcount: A:0.03, C:0.01, G:0.12, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1378748 original size:13 final size:13
Alignment explanation
Indices: 1378727--1378756 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1378717 CGATACAAGG
*
1378727 TACATTGTATCGA
1 TACAATGTATCGA
1378740 TACAATGTATCGA
1 TACAATGTATCGA
1378753 TACA
1 TACA
1378757 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:1378776 original size:33 final size:33
Alignment explanation
Indices: 1378712--1378776 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
1378702 TACCACTGTT
* *
1378712 TGTATCGATACAAGGTACATTGTATCGATACAA
1 TGTATCGATACAAGATACATTGTATCAATACAA
* *
1378745 TGTATCGATACATGATGA-ATTGTATTAATACA
1 TGTATCGATACAAGAT-ACATTGTATCAATACA
1378777 TTGCTTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAGATACATTGTATCAATACAA
Found at i:1384286 original size:21 final size:21
Alignment explanation
Indices: 1384262--1384301 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1384252 TTCATCAAAT
* *
1384262 CTTCAAATTTCTTCATTTTCA
1 CTTCAAAATACTTCATTTTCA
1384283 CTTCAAAATACTTCATTTT
1 CTTCAAAATACTTCATTTT
1384302 TCATCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.50
Consensus pattern (21 bp):
CTTCAAAATACTTCATTTTCA
Found at i:1384310 original size:20 final size:20
Alignment explanation
Indices: 1384272--1384311 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1384262 CTTCAAATTT
1384272 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
1384293 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
1384312 TACCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:1385631 original size:150 final size:150
Alignment explanation
Indices: 1385360--1385667 Score: 598
Period size: 150 Copynumber: 2.1 Consensus size: 150
1385350 TCTTCATGGC
1385360 ATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGATATGTCATGCGAGCCGGGATTCCTATC
1 ATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGATATGTCATGCGAGCCGGGATTCCTATC
1385425 TCTTGACCATGCATCATCAGTTCCAAAACCATGGCCAAGATTAGCTATGAAGTAAGAAACCGATC
66 TCTTGACCATGCATCATCAGTTCCAAAACCATGGCCAAGATTAGCTATGAAGTAAGAAACCGATC
1385490 ATTAGTACCTCGATAGCATG
131 ATTAGTACCTCGATAGCATG
**
1385510 ATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGATATGTCATGCGAGTTGGGATTCCTATC
1 ATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGATATGTCATGCGAGCCGGGATTCCTATC
1385575 TCTTGACCATGCATCATCAGTTCCAAAACCATGGCCAAGATTAGCTATGAAGTAAGAAACCGATC
66 TCTTGACCATGCATCATCAGTTCCAAAACCATGGCCAAGATTAGCTATGAAGTAAGAAACCGATC
1385640 ATTAGTACCTCGATAGCATG
131 ATTAGTACCTCGATAGCATG
1385660 ATGATCCT
1 ATGATCCT
1385668 ACTCCCCAAG
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 156 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (150 bp):
ATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGATATGTCATGCGAGCCGGGATTCCTATC
TCTTGACCATGCATCATCAGTTCCAAAACCATGGCCAAGATTAGCTATGAAGTAAGAAACCGATC
ATTAGTACCTCGATAGCATG
Found at i:1386113 original size:13 final size:13
Alignment explanation
Indices: 1386095--1386132 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1386085 ATTACTCAAA
1386095 TGTATCGATACAT
1 TGTATCGATACAT
1386108 TGTATCGATACAT
1 TGTATCGATACAT
1386121 TGTATCGATACA
1 TGTATCGATACA
1386133 CTGATCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1398877 original size:79 final size:80
Alignment explanation
Indices: 1398653--1398908 Score: 202
Period size: 79 Copynumber: 3.2 Consensus size: 80
1398643 GAGATAATAA
* * * * ** * * *
1398653 CGGGGTTGGAGTGTTCCCTTGAAAATAAC-AGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGA-GGTTGGAGTATCCCCAATTATGAGAAAACAAT-
* * *
1398717 A--TTAGAAAAAAAAAT
64 ATTTTAGGAAATAAAAC
* *
1398732 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAAACAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAAACAATAT
*
1398797 TTTAGG-AATAAAGC
66 TTTAGGAAATAAAAC
* * * ***
1398811 CGGGGTTGGAGTAT-CCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGA-AAAATTGG
1 CGGGGTTGGAGTATCCCCTCGA--AAATAACGAGGTTGGAGTATCCCCAATTATGAGAAAA-CAA
* *
1398873 TATTTTTGGAAATAAAAT
63 TATTTTAGGAAATAAAAC
*
1398891 CGGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1398909 AATTAAAGGA
Statistics
Matches: 142, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
77 3 0.02
78 8 0.06
79 105 0.74
80 23 0.16
81 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAAACAATAT
TTTAGGAAATAAAAC
Found at i:1399013 original size:52 final size:51
Alignment explanation
Indices: 1398842--1399015 Score: 192
Period size: 52 Copynumber: 3.4 Consensus size: 51
1398832 GAAATAACGA
* *
1398842 GGTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTT-GAAATAAAACT-GG
* * ** *
1398894 AGTTGGAGTATCCCCAATTAAAGG-AAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTTG-AAATAAAACTGG
* *
1398946 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACTGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTT-GAAATAAAACTGG
1398998 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
1399016 GATTAACGGG
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
51 3 0.03
52 88 0.86
53 10 0.10
54 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAATAAAACTGG
Found at i:1399013 original size:184 final size:182
Alignment explanation
Indices: 1398760--1399153 Score: 553
Period size: 184 Copynumber: 2.1 Consensus size: 182
1398750 TCGAAAATAA
* * *
1398760 CGGGGTTGGAGTATCCCCAATTATGAGAAAACAATATTTTAGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATG-GAAAACAATATTTTAGCAATAAAACCGGGGTTGGAGTAT
*
1398825 CCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAA
65 CCCCGATG-AATAACGAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAA
*
1398888 AATCGGAGTTGGAGTATCCCCAATTA-AAGGAAAATTGGTGTTTTGAAAATAAAAC
129 AATCGGAGTTGGAGTATCCCCAATTATAA--AAAATTAGTGTTTTGAAAATAAAAC
* * *
1398943 CGGGGTTGGAGTATCCCCGATTGTGGAAAA-ATTAGTGTTTTAGCAATAAAACTGGGGTTGGAGT
1 CGGGGTTGGAGTATCCCCGATTATGGAAAACA--A-TATTTTAGCAATAAAACCGGGGTTGGAGT
* * *
1399007 ATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATA
63 ATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATA
* *
1399072 AAATCGGAGTTGGAGTATCCCCGATTATAAAAAATTAGTGTTTTGAAAATAAAAT
128 AAATCGGAGTTGGAGTATCCCCAATTATAAAAAATTAGTGTTTTGAAAATAAAAC
* * *
1399127 CGGAGTTGGAATATCCCCGATTCTGGA
1 CGGGGTTGGAGTATCCCCGATTATGGA
1399154 GAATTGAGAA
Statistics
Matches: 189, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
181 1 0.01
182 5 0.03
183 53 0.28
184 90 0.48
185 38 0.20
186 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (182 bp):
CGGGGTTGGAGTATCCCCGATTATGGAAAACAATATTTTAGCAATAAAACCGGGGTTGGAGTATC
CCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAA
TCGGAGTTGGAGTATCCCCAATTATAAAAAATTAGTGTTTTGAAAATAAAAC
Found at i:1399130 original size:51 final size:53
Alignment explanation
Indices: 1399026--1399148 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 53
1399016 GATTAACGGG
* * * *
1399026 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAAATTAGTG-TTTTTGAAAATAAAATCGGA
1399080 GTTGGAGTATCCCCGATTAT-AAAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGA
*
1399131 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1399149 CTGGAGAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
51 35 0.55
53 10 0.16
54 19 0.30
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:1401525 original size:13 final size:13
Alignment explanation
Indices: 1401507--1401532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1401497 ACAAAGATCC
1401507 ATGTATCGATACA
1 ATGTATCGATACA
1401520 ATGTATCGATACA
1 ATGTATCGATACA
1401533 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:1401528 original size:33 final size:33
Alignment explanation
Indices: 1401486--1401552 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1401476 AAAATTTCCA
***
1401486 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1401519 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1401552 A
1 A
1401553 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:1401596 original size:19 final size:19
Alignment explanation
Indices: 1401572--1401626 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1401562 CAGTAGCTAA
*
1401572 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
1401591 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1401610 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1401627 TTGTTGACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1402735 original size:61 final size:59
Alignment explanation
Indices: 1402417--1402785 Score: 408
Period size: 55 Copynumber: 6.4 Consensus size: 59
1402407 ATAAAGTGTA
* ** *
1402417 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT---G-AAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
* * *
1402472 TCCTGCTCTTTAAGGACT-GAAAGGTGCCACCAACTTGTGTAGGCTTT-AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
* * *
1402527 TCCTGCTCTTTGAGGACTGGAAAATGTCACCAACTTGTGTGGGCTTTGAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCG
* *
1402587 TCCCGCTCTTTGAGGACTGG-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCG
* * *
1402646 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAGGCG
* *
1402707 TCCTGCGT-TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT----AAAAGGGG
1 TCCTGC-TCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
* *
1402762 TCCTACTCTTTGAGGACTGAAAAG
1 TCCTGCTCTTTGAGGACTGGAAAG
1402786 CGGAAGGAGA
Statistics
Matches: 272, Mismatches: 29, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
54 4 0.01
55 105 0.39
56 4 0.01
57 3 0.01
59 54 0.20
60 51 0.19
61 50 0.18
62 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
Found at i:1405419 original size:15 final size:14
Alignment explanation
Indices: 1405397--1405456 Score: 77
Period size: 14 Copynumber: 4.2 Consensus size: 14
1405387 AAGAAAGAAG
1405397 AAAAAAAACAAACA
1 AAAAAAAACAAACA
*
1405411 AACAAAAAAAAAACA
1 AA-AAAAAACAAACA
*
1405426 AAGAAAAA-AAACAA
1 AAAAAAAACAAAC-A
1405440 AAAAAAAACAAACA
1 AAAAAAAACAAACA
1405454 AAA
1 AAA
1405457 TAGAAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.10
14 19 0.47
15 17 0.43
ACGTcount: A:0.87, C:0.12, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAACA
Found at i:1405429 original size:35 final size:34
Alignment explanation
Indices: 1405368--1405484 Score: 102
Period size: 35 Copynumber: 3.5 Consensus size: 34
1405358 CATCCTCCGT
* *
1405368 AAAA-AAA-AAACAAAAGAAGAAGAAAGAAGAAAA
1 AAAACAAACAAACAAAA-AAAAAAAAAGAAGAAAA
1405401 AAAACAAACAAACAAAAAAAAAACAAAGAA-AAAA
1 AAAACAAACAAACAAAAAAAAAA-AAAGAAGAAAA
* * * * *
1405435 AACAAAAAAAAAACAAACAAAATAGAA-AAGAAAA
1 AA-AACAAACAAACAAAAAAAAAAAAAGAAGAAAA
1405469 AAAAC-AAC-AACAAAAA
1 AAAACAAACAAACAAAAA
1405485 GGGTCCGGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
31 7 0.10
32 2 0.03
33 8 0.12
34 21 0.30
35 31 0.45
ACGTcount: A:0.83, C:0.09, G:0.07, T:0.01
Consensus pattern (34 bp):
AAAACAAACAAACAAAAAAAAAAAAAGAAGAAAA
Found at i:1405442 original size:39 final size:42
Alignment explanation
Indices: 1405398--1405484 Score: 117
Period size: 40 Copynumber: 2.1 Consensus size: 42
1405388 AGAAAGAAGA
*
1405398 AAAAAAACAAACAAACAAAA-AAAAAACAAAGAAAA-AA-AAC
1 AAAAAAA-AAACAAACAAAATAAAAAACAAAAAAAACAACAAC
* *
1405438 AAAAAAAAAACAAACAAAATAGAAAAGAAAAAAAACAACAAC
1 AAAAAAAAAACAAACAAAATAAAAAACAAAAAAAACAACAAC
1405480 AAAAA
1 AAAAA
1405485 GGGTCCGGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
39 12 0.29
40 19 0.46
41 2 0.05
42 8 0.20
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.01
Consensus pattern (42 bp):
AAAAAAAAAACAAACAAAATAAAAAACAAAAAAAACAACAAC
Found at i:1405445 original size:28 final size:27
Alignment explanation
Indices: 1405368--1405484 Score: 108
Period size: 28 Copynumber: 4.1 Consensus size: 27
1405358 CATCCTCCGT
* *
1405368 AAAAAAAAAACAAAAGAAGAAGAAAGAAGA
1 AAAAAAAAAACAAAA-AA-AA-AAAAAACA
*
1405398 AAAAAAACAAACAAACAAAAAAAAAACA
1 AAAAAAA-AAACAAAAAAAAAAAAAACA
*
1405426 AAGAAAAAAAACAAAAAAAAAACAAACA
1 AA-AAAAAAAACAAAAAAAAAAAAAACA
* * * * *
1405454 AAATAGAAAAGAAAAAAAACAACAACA
1 AAAAAAAAAACAAAAAAAAAAAAAACA
1405481 AAAA
1 AAAA
1405485 GGGTCCGGAT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 22 0.30
28 28 0.38
29 7 0.10
30 9 0.12
31 7 0.10
ACGTcount: A:0.83, C:0.09, G:0.07, T:0.01
Consensus pattern (27 bp):
AAAAAAAAAACAAAAAAAAAAAAAACA
Found at i:1405484 original size:1 final size:1
Alignment explanation
Indices: 1405368--1405472 Score: 57
Period size: 1 Copynumber: 105.0 Consensus size: 1
1405358 CATCCTCCGT
* * * * * * * * * * *
1405368 AAAAAAAAAACAAAAGAAGAAGAAAGAAGAAAAAAAACAAACAAACAAAAAAAAAACAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
1405433 AAAACAAAAAAAAAACAAACAAAATAGAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1405473 CAACAACAAA
Statistics
Matches: 70, Mismatches: 34, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.01
Consensus pattern (1 bp):
A
Found at i:1407062 original size:34 final size:34
Alignment explanation
Indices: 1406954--1407114 Score: 171
Period size: 34 Copynumber: 4.7 Consensus size: 34
1406944 CTTCTAAAGT
*
1406954 CCACAACTCCGTGGCACCTTTTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACC--TTTTTTCCTTTT-AAGC
** * * *
1406991 CCACAACTCTTTGGCA-CTCTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
* *
1407024 CCACAACTCCATGGCACCTTTCTTCCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
* *
1407058 CCACAACTCCGTGGCACTTTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
* * *
1407092 CCATAACTCTGTGGCACCCTTTT
1 CCACAACTCCGTGGCACCTTTTT
1407115 AAGCCCACAA
Statistics
Matches: 103, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
33 17 0.17
34 71 0.69
36 1 0.01
37 14 0.14
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.38
Consensus pattern (34 bp):
CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
Found at i:1407100 original size:68 final size:69
Alignment explanation
Indices: 1406943--1407114 Score: 213
Period size: 68 Copynumber: 2.5 Consensus size: 69
1406933 CTAGTGGCAA
* * **
1406943 CCTTCTAAAGTCCACAACTCCGTGGCACCTTTTTTTTCTTTTTAAAGCCCACAACTCTTTGGCAC
1 CCTTCT-AAGTCCACAACTCCGTGGCACC-TTTTCTTCCTTTTAAAGCCCACAACTCCGTGGCAC
1407008 TCTTTT
64 TCTTTT
*
1407014 CCTTCTAAGTCCACAACTCCATGGCACC-TTTCTTCCTTTT-AAGCCCACAACTCCGTGGCACTT
1 CCTTCTAAGTCCACAACTCCGTGGCACCTTTTCTTCCTTTTAAAGCCCACAACTCCGTGGCAC-T
*
1407077 TTTTT
65 CTTTT
* * *
1407082 CCTTTTAAGTCCATAACTCTGTGGCACCCTTTT
1 CCTTCTAAGTCCACAACTCCGTGGCA-CCTTTT
1407115 AAGCCCACAA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
67 19 0.22
68 37 0.42
69 2 0.02
70 24 0.27
71 6 0.07
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (69 bp):
CCTTCTAAGTCCACAACTCCGTGGCACCTTTTCTTCCTTTTAAAGCCCACAACTCCGTGGCACTC
TTTT
Found at i:1407132 original size:27 final size:29
Alignment explanation
Indices: 1407102--1407163 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1407092 CCATAACTCT
*
1407102 GTGGCA-CCCTTTT-AAGCCCACAAGTTG
1 GTGGCACCCCTTTTAAAGCCCACAAGTTA
*
1407129 GTGGCACCCCTTTTAAAGCCCACGAGTTA
1 GTGGCACCCCTTTTAAAGCCCACAAGTTA
1407158 GTGGCA
1 GTGGCA
1407164 ACTTTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 6 0.19
28 7 0.23
29 18 0.58
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (29 bp):
GTGGCACCCCTTTTAAAGCCCACAAGTTA
Found at i:1407513 original size:98 final size:101
Alignment explanation
Indices: 1407337--1407564 Score: 266
Period size: 100 Copynumber: 2.3 Consensus size: 101
1407327 GACCAACGTC
* *
1407337 GCTAGCCTTGGATCAGCACATTGGCACCTTAACCATCTTTAAGACCAATGTTGTTGGCCTAGAAT
1 GCTAGCCTTGAATCAGCACATTGGCACCTTAACCA-CTTTAAGACCAATGTTGCTGGCCTAGAAT
1407402 CAAAACATTGGCACCCTCAT-C-TTTAAGTCCAATGTA
65 CAAAACATTGGCA-CCTCATCCGTTTAAGTCCAATGTA
* * * * *
1407438 GCTGGCCTTGAATCAGCACATTGGCATCTTTA-C-CTTTAAGTCCAATGTTGCTGGCCTTGAATC
1 GCTAGCCTTGAATCAGCACATTGGCACCTTAACCACTTTAAGACCAATGTTGCTGGCCTAGAATC
** * ** *
1407501 AGCATATTGGCACCTTTTCCGTTTTGAGTCCAATGTA
66 AAAACATTGGCACCTCATCCG-TTTAAGTCCAATGTA
* *
1407538 GCTAGCCTTGAGTCAGCACATTAGCAC
1 GCTAGCCTTGAATCAGCACATTGGCAC
1407565 AAGTCCAATA
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
97 4 0.04
98 37 0.35
100 38 0.36
101 28 0.26
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (101 bp):
GCTAGCCTTGAATCAGCACATTGGCACCTTAACCACTTTAAGACCAATGTTGCTGGCCTAGAATC
AAAACATTGGCACCTCATCCGTTTAAGTCCAATGTA
Found at i:1407554 original size:51 final size:49
Alignment explanation
Indices: 1407231--1407564 Score: 239
Period size: 49 Copynumber: 6.8 Consensus size: 49
1407221 CGTCTTCTTC
* * * * * * *
1407231 TAAGTCCAATATCGCTGGCCTAGAACCAACATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTT
** * * * *
1407280 TAAAACTCAATATCGCTGGCCTTGAATTAGCATATT-G-A-C---ACCTT
1 TAAGTC-CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTT
* * * * * * *
1407324 GAAGACCAACGTCGCTAGCCTTGGATCAGCACATTGGCACCTTAACCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTA-C--CTT
* * * * ** * * *
1407376 TAAGACCAATGTTGTTGGCCTAGAATCAAAACATTGGCACCCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTT
*
1407425 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTT
* * *
1407474 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCGTTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTACC--TT
* * * *
1407525 TGAGTCCAATGTAGCTAGCCTTGAGTCAGCACATTAGCAC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1407565 AAGTCCAATA
Statistics
Matches: 226, Mismatches: 47, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
43 23 0.10
44 9 0.04
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 91 0.40
50 26 0.12
51 36 0.16
52 37 0.16
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTT
Found at i:1407755 original size:157 final size:157
Alignment explanation
Indices: 1407469--1407874 Score: 632
Period size: 157 Copynumber: 2.6 Consensus size: 157
1407459 TGGCATCTTT
* *
1407469 ACCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCGTTTTGAGTCCAA
1 ACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATTTTGAGTCCAA
* *
1407534 TGTAGCTAGCCTTGAGTCAGCACATTAGCACAAGTCCAATATCGTTGGCCGTGAATCAGCATATT
66 TGTAGTTGGCCTTGAGTCAGCACATTAGCACAAGTCCAATATCGTTGGCCGTGAATCAGCATATT
1407599 AGCATCTTTATCACTTTTCTCACCTTC
131 AGCATCTTTATCACTTTTCTCACCTTC
*
1407626 ACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCACCTTTTCCATTTTGAGTCCAA
1 ACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATTTTGAGTCCAA
*
1407691 TGTAGTTGGCCTTGAGTCAGCACATTAGCACAAGTCCAATATCGTTGGTCGTGAATCAGCATATT
66 TGTAGTTGGCCTTGAGTCAGCACATTAGCACAAGTCCAATATCGTTGGCCGTGAATCAGCATATT
*
1407756 GGCATCTTTATCACTTTTCTCACCTTC
131 AGCATCTTTATCACTTTTCTCACCTTC
* * * * ** ** * *
1407783 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATCCCTAAGCCCA
1 ACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT-TTTGAGTCCA
**
1407848 ATGTAGTTGGCCTTGTCTCAGCACATT
65 ATGTAGTTGGCCTTGAGTCAGCACATT
1407875 GACATTCTTC
Statistics
Matches: 228, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
157 197 0.86
158 31 0.14
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (157 bp):
ACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATTTTGAGTCCAA
TGTAGTTGGCCTTGAGTCAGCACATTAGCACAAGTCCAATATCGTTGGCCGTGAATCAGCATATT
AGCATCTTTATCACTTTTCTCACCTTC
Found at i:1407963 original size:154 final size:154
Alignment explanation
Indices: 1407781--1408139 Score: 596
Period size: 154 Copynumber: 2.3 Consensus size: 154
1407771 TTTCTCACCT
* *
1407781 TCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATCCCTAAGCC
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATCCCTAAGCA
*
1407846 CAATGT-AGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGT-
66 CAATGTCA-TTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTAACCGTG
1407909 AAGTCAGCACATTGACATCCTTTTTC
130 AA-TCAGCACATTGACATCCTTTTTC
*
1407935 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCA
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATCCCTAAGCA
* *
1408000 CAATGTCATTGGCCTTGTCTCAGCACATTGACATTCTTTTCCAAGTCTAATGCTGCTAACCGTGA
66 CAATGTCATTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTAACCGTGA
1408065 ATCAGCACATTGACATCCTTTTTC
131 ATCAGCACATTGACATCCTTTTTC
* * * *
1408089 TTATCTTTAAGCCCAATATCGTTGACCGTGAATCAGCATATTGGTATCTTT
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTT
1408140 CTCACTCTTC
Statistics
Matches: 192, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
154 189 0.98
155 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (154 bp):
TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATCCCTAAGCA
CAATGTCATTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTAACCGTGA
ATCAGCACATTGACATCCTTTTTC
Found at i:1408802 original size:32 final size:32
Alignment explanation
Indices: 1408766--1408833 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
1408756 TTCAACGATT
1408766 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
* * *
1408798 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
1408830 TGTA
1 TGTA
1408834 CAGTTACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:1408803 original size:13 final size:13
Alignment explanation
Indices: 1408785--1408809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1408775 ACATAAGTGT
1408785 TGTATCGATACAA
1 TGTATCGATACAA
1408798 TGTATCGATACA
1 TGTATCGATACA
1408810 TAAGTTTTGT
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:1408899 original size:13 final size:13
Alignment explanation
Indices: 1408881--1408905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1408871 ATTACTCAAA
1408881 TGTATCGATACAT
1 TGTATCGATACAT
1408894 TGTATCGATACA
1 TGTATCGATACA
1408906 CTGATCTTTG
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:1412606 original size:19 final size:19
Alignment explanation
Indices: 1412582--1412637 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1412572 GTATTGATAC
***
1412582 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATGACA
*
1412601 ATTGTATCGATATATGGACA
1 ATTGTATCGATACAT-GACA
1412621 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
1412638 AACTGGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:1412709 original size:33 final size:33
Alignment explanation
Indices: 1412666--1412728 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1412656 TACTACTTTT
*
1412666 TGTATCGATACATGGT-ACATTGTATCGATAAAA
1 TGTATCGATACATGATGA-ATTGTATCGATAAAA
*
1412699 TGTATTGATACATGATGAATTGTATCGATA
1 TGTATCGATACATGATGAATTGTATCGATA
1412729 CATTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATAAAA
Found at i:1419846 original size:165 final size:165
Alignment explanation
Indices: 1419521--1419864 Score: 374
Period size: 165 Copynumber: 2.1 Consensus size: 165
1419511 TTTTTCTTAG
* ** * *
1419521 TTTAAAATTCATCAAGTATTATCATTTGATTCGTAGCAAATCAGTTTTTAAAAATTCATTCATTT
1 TTTAAAATTCATCAAATATTATCATTTGATTCACAGCAAATCAGTTTTGAAAAATTCAATCATTT
* ** * *
1419586 CCATAAGTTTTGAATTTTTTCCTTAAAATTCCCATGTTTCCAAAATATGGAGTTTTTTACTCCGT
66 CCATAAGTTTTGAATTTTTTCCTTAAAATTCCCATGTTTCCAAAAAATCAAGTTTTCTACTCCAT
*
1419651 AAATGTTTTCATGGCGATTTTCCCTGGTTTAAAATT
131 AAATATTTT-ATGGCGATTTTCCCTGGTTTAAAATT
* * *
1419687 TTTAAAATTCATTAAATATTATCCTTTGATTCACA-TAAATCAGTTTTGAAAGAA-TCAATCATT
1 TTTAAAATTCATCAAATATTATCATTTGATTCACAGCAAATCAGTTTTGAAA-AATTCAATCATT
* * * * * * *
1419750 TTCATGAGTTTTGAATTTTTTCTTTGAAATTTTTCTAT-TTT-CAAAAAATCAAGTTTTCTATTC
65 TCCATAAGTTTTGAATTTTTTCCTT-AAA-ATTCCCATGTTTCCAAAAAATCAAGTTTTCTACTC
* **
1419813 CATAAATATTTT-TGGGGGAATTTTCTGTGGTTTAAAATT
128 CATAAATATTTTAT-GGCG-ATTTTCCCTGGTTTAAAATT
*
1419852 TTTGAAATTCATC
1 TTTAAAATTCATC
1419865 TAACATTGTT
Statistics
Matches: 147, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
163 1 0.01
164 3 0.02
165 100 0.68
166 38 0.26
167 5 0.03
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (165 bp):
TTTAAAATTCATCAAATATTATCATTTGATTCACAGCAAATCAGTTTTGAAAAATTCAATCATTT
CCATAAGTTTTGAATTTTTTCCTTAAAATTCCCATGTTTCCAAAAAATCAAGTTTTCTACTCCAT
AAATATTTTATGGCGATTTTCCCTGGTTTAAAATT
Found at i:1421864 original size:21 final size:21
Alignment explanation
Indices: 1421840--1421888 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1421830 ACTACTATTG
* *
1421840 GTGGATGCTGCTGCTATGCTC
1 GTGGAAGCTACTGCTATGCTC
1421861 GTGGAAGCTACTGCTATGCTC
1 GTGGAAGCTACTGCTATGCTC
1421882 GTGGAAG
1 GTGGAAG
1421889 AGGCTCGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.29
Consensus pattern (21 bp):
GTGGAAGCTACTGCTATGCTC
Found at i:1421976 original size:54 final size:54
Alignment explanation
Indices: 1421883--1421992 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
1421873 GCTATGCTCG
* * * * *
1421883 TGGAAGAGGCTCGAGTTGTTGGTTCATGGAGACTGCTGCTATGCTCGTGGAAGC
1 TGGAAAAGGCTCGAGCTGCTGGTTCATGGAGACTACTGCTATGCTCGTAGAAGC
* * *
1421937 TGGAAAAGGCTCGAGCTGCTGGTTCGTGGATG-TTACTGCTGTGCTCGTAGAAGC
1 TGGAAAAGGCTCGAGCTGCTGGTTCATGGA-GACTACTGCTATGCTCGTAGAAGC
1421991 TG
1 TG
1421993 CTGTTGTGCT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.36, T:0.28
Consensus pattern (54 bp):
TGGAAAAGGCTCGAGCTGCTGGTTCATGGAGACTACTGCTATGCTCGTAGAAGC
Found at i:1422422 original size:107 final size:105
Alignment explanation
Indices: 1422308--1422511 Score: 318
Period size: 107 Copynumber: 1.9 Consensus size: 105
1422298 TGCACGTTGC
* * *
1422308 TTTGCCCTCCACTTCTTCTCGTTGCCATACTTCACATGTTGTCCACTTTCCTTCACATTGGCTTC
1 TTTGCCCTCCACTTCTTCCCGTTGCAATACTTCACATGCTGTCCACTTTCCTTCACATTGGCTTC
* *
1422373 CTTTCTTTTTCTTCTTTTTTGTGTTCTAGCTCTTTACATTGT
66 CTTTC-TTTT-TTCTTTTTTATGTTCCAGCTCTTTACATTGT
* * *
1422415 TTTGCCCTCCACTTCTTCCCGTTGCAATGCTTCACATGCTGTCCACTTTCTTTCACGTTGGCTTC
1 TTTGCCCTCCACTTCTTCCCGTTGCAATACTTCACATGCTGTCCACTTTCCTTCACATTGGCTTC
1422480 CTTTCTTTTTTCTTTTTTATGTTCCAGCTCTT
66 CTTTCTTTTTTCTTTTTTATGTTCCAGCTCTT
1422512 CACGTCATGC
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 21 0.24
106 4 0.04
107 64 0.72
ACGTcount: A:0.10, C:0.30, G:0.11, T:0.50
Consensus pattern (105 bp):
TTTGCCCTCCACTTCTTCCCGTTGCAATACTTCACATGCTGTCCACTTTCCTTCACATTGGCTTC
CTTTCTTTTTTCTTTTTTATGTTCCAGCTCTTTACATTGT
Found at i:1422734 original size:16 final size:17
Alignment explanation
Indices: 1422713--1422751 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1422703 ATGTCGTTTC
1422713 TTCATTCATTT-TTTTT
1 TTCATTCATTTCTTTTT
**
1422729 TTCATTTTTTTCTTTTT
1 TTCATTCATTTCTTTTT
1422746 TTCATT
1 TTCATT
1422752 ATGTGCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCATTCATTTCTTTTT
Found at i:1422857 original size:23 final size:22
Alignment explanation
Indices: 1422813--1422915 Score: 68
Period size: 23 Copynumber: 4.4 Consensus size: 22
1422803 TGATTTCTAA
*
1422813 TTTTATTTTTTTGATGGTTTT-AT
1 TTTTA-TTTTTTGAT-TTTTTAAT
1422836 TTTTATTTCTTTGATTTCTTTAAT
1 TTTTATTT-TTTGATTT-TTTAAT
* *
1422860 TTTTAATTTTTTAATTTTTTTGATT
1 TTTT-ATTTTTTGA-TTTTTT-AAT
*
1422885 TTTTATATTTTTG-TTATTTTGAT
1 TTTTAT-TTTTTGATT-TTTTAAT
1422908 TTTT-TTTT
1 TTTTATTTT
1422916 AATTTTTGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
21 3 0.05
22 5 0.08
23 21 0.32
24 19 0.29
25 18 0.27
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTATTTTTTGATTTTTTAAT
Found at i:1422874 original size:15 final size:15
Alignment explanation
Indices: 1422835--1422878 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1422825 GATGGTTTTA
* *
1422835 TTTTTATTTCTTTGAT
1 TTTTTAATT-TTTAAT
1422851 TTCTTTAATTTTTAAT
1 TT-TTTAATTTTTAAT
1422867 TTTTTAATTTTT
1 TTTTTAATTTTT
1422879 TTGATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTTAATTTTTAAT
Found at i:1422876 original size:24 final size:23
Alignment explanation
Indices: 1422834--1422896 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
1422824 TGATGGTTTT
*
1422834 ATTTTTATTTCTTTGATTTCTTTA
1 ATTTTTATTT-TTTAATTTCTTTA
*
1422858 ATTTTTAATTTTTTAATTTTTTTGA
1 ATTTTT-ATTTTTTAATTTCTTT-A
*
1422883 TTTTTTATATTTTT
1 ATTTTTAT-TTTTT
1422897 GTTATTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (23 bp):
ATTTTTATTTTTTAATTTCTTTA
Found at i:1422883 original size:33 final size:31
Alignment explanation
Indices: 1422830--1422913 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 31
1422820 TTTTTGATGG
*
1422830 TTTTA-TTTTTATTTCTTTGATTTCTTTA-AT
1 TTTTATTTTTTATTTTTTTGATTT-TTTATAT
1422860 TTTTAATTTTTTAATTTTTTTGATTTTTTATAT
1 TTTT-ATTTTTT-ATTTTTTTGATTTTTTATAT
*
1422893 TTTTGTTATTTTGATTTTTTT
1 TTTTATT-TTTT-ATTTTTTT
1422914 TTAATTTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 4 0.09
31 1 0.02
32 11 0.24
33 30 0.65
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (31 bp):
TTTTATTTTTTATTTTTTTGATTTTTTATAT
Found at i:1422895 original size:9 final size:8
Alignment explanation
Indices: 1422835--1422927 Score: 57
Period size: 9 Copynumber: 11.1 Consensus size: 8
1422825 GATGGTTTTA
1422835 TTTTT-AT
1 TTTTTAAT
*
1422842 TTCTTTGAT
1 TT-TTTAAT
1422851 TTCTTTAA-
1 TT-TTTAAT
1422859 TTTTTAAT
1 TTTTTAAT
1422867 TTTTTAATT
1 TTTTTAA-T
*
1422876 TTTTTGAT
1 TTTTTAAT
1422884 TTTTTATAT
1 TTTTTA-AT
*
1422893 TTTTGTTAT
1 TTTT-TAAT
*
1422902 TTTGATT-TT
1 TTT--TTAAT
1422911 TTTTTAAT
1 TTTTTAAT
*
1422919 TTTTGAAT
1 TTTTTAAT
1422927 T
1 T
1422928 GATTTATTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
7 9 0.13
8 27 0.39
9 31 0.44
10 2 0.03
11 1 0.01
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.74
Consensus pattern (8 bp):
TTTTTAAT
Found at i:1422904 original size:17 final size:17
Alignment explanation
Indices: 1422859--1422922 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
1422849 ATTTCTTTAA
1422859 TTTTTAATTTTT-TAATT
1 TTTTTAATTTTTAT-ATT
*
1422876 TTTTTGATTTTTTATATT
1 TTTTT-AATTTTTATATT
* *
1422894 TTTGTT-ATTTTGATTTT
1 TTT-TTAATTTTTATATT
1422911 TTTTTAATTTTT
1 TTTTTAATTTTT
1422923 GAATTGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.55
18 12 0.32
19 3 0.08
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTAATTTTTATATT
Found at i:1423526 original size:42 final size:42
Alignment explanation
Indices: 1423439--1423983 Score: 331
Period size: 42 Copynumber: 12.6 Consensus size: 42
1423429 CAATCTTCAA
* * * *
1423439 GGTCAAAGCCGATAAGCAGACTGAAGGATAGAAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACT-AAGGGTAGAAAAGTCTCCAG
*
1423482 GGTCAAAACCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* * ** * * * *
1423524 GGTCAAAGTCAACAGTTAGACTTAGGGAAGGAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* * * * *
1423566 GATCAAAGCTGACAAGCAAACTGAGGGATAGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGG-TAGAAAAGTCTCCAG
* * * * * * * *
1423609 GGTCAAAGCTGATAGGTAGACTGA-GGAAGGAAAGTTTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* * ** * **
1423650 GGTGAAAACTAACAAGCAGACTGGGGGATAGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGG-TAGAAAAGTCTCCAG
* * * * *
1423693 GGTCAAAACTGACAGGTAGACTAAGGATAGAAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* * * * * * *
1423735 GGTTAAAGCTGATAGGGAGACTTAGGGAAGGAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* * * * *
1423777 GGTCAAAGTCGACAGGCAGATTGAGGGAAGAAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* * * * *
1423819 GGTCAAAGCCGATAGGCAAACTAAGGGTAGGAAAGTCTCTAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
* ** * *
1423861 GGTC-AAGTCTTCAGGGTCAAAGCTGATAGGTAGACTAAGGGAGGAAAGTCTCCAA
1 GGTCAAAGCCGACA-GG-CAGA-CT-A-AGG--G--T-A--GA--AAAGTCTCCAG
* * *
1423916 GCTCAAAGCCGACAGGCAGACTAAGGG-AGGAAAAGTTTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGTA-GAAAAGTCTCCAG
*
1423958 GGTCAAAGCCGACAGGTAGACTAAGG
1 GGTCAAAGCCGACAGGCAGACTAAGG
1423984 AAAAAAAGGC
Statistics
Matches: 388, Mismatches: 96, Indels: 37
0.74 0.18 0.07
Matches are distributed among these distances:
41 33 0.09
42 225 0.58
43 85 0.22
44 5 0.01
45 2 0.01
46 3 0.01
48 1 0.00
49 1 0.00
50 1 0.00
51 4 0.01
52 1 0.00
53 3 0.01
54 3 0.01
55 15 0.04
56 6 0.02
ACGTcount: A:0.37, C:0.16, G:0.30, T:0.17
Consensus pattern (42 bp):
GGTCAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCCAG
Found at i:1423743 original size:126 final size:126
Alignment explanation
Indices: 1423439--1423866 Score: 403
Period size: 126 Copynumber: 3.4 Consensus size: 126
1423429 CAATCTTCAA
* * * * * * * * * *
1423439 GGTCAAAGCCGATAAGCAGACTGAAGGATAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACT
1 GGTCAAAGCTGACAGGCAAACT-AAGGATAGAAAAGTCTCCAAGGTCAAAGCTGATAGGGAGACT
* * * * * * * * *
1423504 AAGGGTAGAAAAGTCTCCAGGGTCAAAGTCAAC-AGTTAGACTTAGGGAAGGAAAGTCTCCAA
65 GAGGGAAGGAAAGTCTCCAGGGTAAAACTCAACAAG-CAGACTGAGGGAAGAAAAGTCTCCAG
* * * * *
1423566 GATCAAAGCTGACAAGCAAACTGAGGGATAGAAAAGTCTCCAGGGTCAAAGCTGATAGGTAGACT
1 GGTCAAAGCTGACAGGCAAACT-AAGGATAGAAAAGTCTCCAAGGTCAAAGCTGATAGGGAGACT
* * *
1423631 GA-GGAAGGAAAGTTTCTAGGGTGAAAACT-AACAAGCAGACTGGGGGATAGAAAAGTCTCCAG
65 GAGGGAAGGAAAGTCTCCAGGGT-AAAACTCAACAAGCAGACTGAGGGA-AGAAAAGTCTCCAG
* * * * *
1423693 GGTCAAAACTGACAGGTAGACTAAGGATAGAAAAGTCTCCAAGGTTAAAGCTGATAGGGAGACTT
1 GGTCAAAGCTGACAGGCAAACTAAGGATAGAAAAGTCTCCAAGGTCAAAGCTGATAGGGAGACTG
* * * * * *
1423758 AGGGAAGGAAAGTCTCCAGGGTCAAAGTCGACAGGCAGATTGAGGGAAGAAAAGTCTCTAG
66 AGGGAAGGAAAGTCTCCAGGGTAAAACTCAACAAGCAGACTGAGGGAAGAAAAGTCTCCAG
* * * * *
1423819 GGTCAAAGCCGATAGGCAAACTAAGGGTAGGAAAGTCTCTAAGGTCAA
1 GGTCAAAGCTGACAGGCAAACTAAGGATAGAAAAGTCTCCAAGGTCAA
1423867 GTCTTCAGGG
Statistics
Matches: 246, Mismatches: 50, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
126 123 0.50
127 123 0.50
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.17
Consensus pattern (126 bp):
GGTCAAAGCTGACAGGCAAACTAAGGATAGAAAAGTCTCCAAGGTCAAAGCTGATAGGGAGACTG
AGGGAAGGAAAGTCTCCAGGGTAAAACTCAACAAGCAGACTGAGGGAAGAAAAGTCTCCAG
Found at i:1423827 original size:84 final size:84
Alignment explanation
Indices: 1423456--1423998 Score: 378
Period size: 84 Copynumber: 6.3 Consensus size: 84
1423446 GCCGATAAGC
* * *
1423456 AGACTGAAGGATAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACTAAGGGTAGAAAAGTCTC
1 AGACTGAAGGA-AGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTC
* *
1423521 CAGGGTCAAAGTCAACAGTT
65 CAGGGTCAAAGTCGACAGGT
* * * * * * * * *
1423541 AGACTTAGGGAAGGAAAGTCTCCAAGATCAAAGCTGACAAGCAAACTGAGGGATAGAAAAGTCTC
1 AGACTGAAGGAAGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGA-AGAAAAGTCTC
*
1423606 CAGGGTCAAAG-CTGATAGGT
65 CAGGGTCAAAGTC-GACAGGT
* * * * * * **
1423626 AGACTG-AGGAAGGAAAGTTTCTAGGGTGAAAACTAACAAGCAGACTGGGGGATAGAAAAGTCTC
1 AGACTGAAGGAAGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGA-AGAAAAGTCTC
*
1423690 CAGGGTCAAA-ACTGACAGGT
65 CAGGGTCAAAGTC-GACAGGT
* * * * * * *
1423710 AGACT-AAGGATAGAAAAGTCTCCAAGGTTAAAGCTGATAGGGAGACTTAGGGAAGGAAAGTCTC
1 AGACTGAAGGA-AGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTC
*
1423774 CAGGGTCAAAGTCGACAGGC
65 CAGGGTCAAAGTCGACAGGT
* * * * * * * *
1423794 AGATTGAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGATAGGCAAACTAAGGGTAGGAAAGTCTCT
1 AGACTGAAGGAAGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTCC
* **
1423859 AAGGTC-AAGTCTTCAGGGT
66 AGGGTCAAAGTCGACA-GGT
* * * * *
1423878 CAAAGCTGATAGGTAGACTAAGGGAGGAAAGTCTCCAAGCTCAAAGCCGACAGGCAGACTAAGGG
1 -AGA-CTGA-A-G--G---AA--GA--AAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGG
* * * *
1423943 AGGAAAAGTTTCTAGGGTCAAAGCCGACAGGT
53 AAGAAAAGTCTCCAGGGTCAAAGTCGACAGGT
* *
1423975 AGACT-AAGGAAAAAAAGGCTCTAG
1 AGACTGAAGGAAGAAAAGTCTCTAG
1423999 AAGTTTAATG
Statistics
Matches: 358, Mismatches: 78, Indels: 46
0.74 0.16 0.10
Matches are distributed among these distances:
83 15 0.04
84 190 0.53
85 78 0.22
86 3 0.01
87 2 0.01
88 1 0.00
90 2 0.01
92 1 0.00
93 3 0.01
94 1 0.00
95 4 0.01
96 2 0.01
97 50 0.14
98 6 0.02
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.17
Consensus pattern (84 bp):
AGACTGAAGGAAGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTCC
AGGGTCAAAGTCGACAGGT
Found at i:1423853 original size:211 final size:211
Alignment explanation
Indices: 1423452--1423859 Score: 552
Period size: 211 Copynumber: 1.9 Consensus size: 211
1423442 CAAAGCCGAT
* *
1423452 AAGCAGACTGAAGGATAGAAAAGTCTCTAGGGTCAAAACCGACAGGCAGACTAAGGGTAGAAAAG
1 AAGCAGACTGAAGGATAGAAAAGTCTCCAGGGTCAAAACCGACAGGCAGACTAAGGATAGAAAAG
* **
1423517 TCTCCAGGGTCAAAGTCAACAGTTAGACTTAGGGAAGGAAAGTCTCCAAGATCAAAGCTGACAAG
66 TCTCCAAGGTCAAAGTCAACAGGGAGACTTAGGGAAGGAAAGTCTCCAAGATCAAAGCTGACAAG
* * * * *
1423582 CAAACTGAGGGATAGAAAAGTCTCCAGGGTCAAAGCTGATAGGTAGACTGAGGAAGGAAAGTTTC
131 CAAACTGAGGGATAGAAAAGTCTCCAGGGTCAAAGCCGATAGGCAAACTAAGGAAGGAAAGTCTC
1423647 TAGGGTGAAAACTAAC
196 TAGGGTGAAAACTAAC
** * *
1423663 AAGCAGACTGGGGGATAGAAAAGTCTCCAGGGTCAAAACTGACAGGTAGACTAAGGATAGAAAAG
1 AAGCAGACTGAAGGATAGAAAAGTCTCCAGGGTCAAAACCGACAGGCAGACTAAGGATAGAAAAG
* * * * *
1423728 TCTCCAAGGTTAAAG-CTGATAGGGAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAG-TCGACA
66 TCTCCAAGGTCAAAGTC-AACAGGGAGACTTAGGGAAGGAAAGTCTCCAAGATCAAAGCT-GACA
* * * * *
1423791 GGCAGATTGAGGGA-AGAAAAGTCTCTAGGGTCAAAGCCGATAGGCAAACTAAGGGTAGGAAAGT
129 AGCAAACTGAGGGATAGAAAAGTCTCCAGGGTCAAAGCCGATAGGCAAACTAA-GGAAGGAAAGT
1423855 CTCTA
193 CTCTA
1423860 AGGTCAAGTC
Statistics
Matches: 170, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
210 35 0.21
211 135 0.79
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.17
Consensus pattern (211 bp):
AAGCAGACTGAAGGATAGAAAAGTCTCCAGGGTCAAAACCGACAGGCAGACTAAGGATAGAAAAG
TCTCCAAGGTCAAAGTCAACAGGGAGACTTAGGGAAGGAAAGTCTCCAAGATCAAAGCTGACAAG
CAAACTGAGGGATAGAAAAGTCTCCAGGGTCAAAGCCGATAGGCAAACTAAGGAAGGAAAGTCTC
TAGGGTGAAAACTAAC
Found at i:1423878 original size:56 final size:55
Alignment explanation
Indices: 1423809--1423921 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 55
1423799 GAGGGAAGAA
* *
1423809 AAGTCTCTAGGGTCAAAGCCGATAGGCAAACTAAGGGTAGGAAAGTCTCTAAGGTC
1 AAGTCTCTAGGGTCAAAGCCGATAGGCAAACTAAGGG-AGGAAAGTCTCCAAGCTC
* * *
1423865 AAGTCT-TCAGGGTCAAAGCTGATAGGTAGACTAAGGGAGGAAAGTCTCCAAGCTC
1 AAGTCTCT-AGGGTCAAAGCCGATAGGCAAACTAAGGGAGGAAAGTCTCCAAGCTC
1423920 AA
1 AA
1423922 AGCCGACAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
55 19 0.37
56 32 0.63
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (55 bp):
AAGTCTCTAGGGTCAAAGCCGATAGGCAAACTAAGGGAGGAAAGTCTCCAAGCTC
Found at i:1423911 original size:41 final size:42
Alignment explanation
Indices: 1423865--1423983 Score: 161
Period size: 41 Copynumber: 2.9 Consensus size: 42
1423855 CTCTAAGGTC
* *
1423865 AAGTCTTCAGGGTCAAAGCTGATAGGTAGACTAAGGGAGG-A
1 AAGTCTTCAGGGTCAAAGCCGACAGGTAGACTAAGGGAGGAA
* * * *
1423906 AAGTCTCCAAGCTCAAAGCCGACAGGCAGACTAAGGGAGGAA
1 AAGTCTTCAGGGTCAAAGCCGACAGGTAGACTAAGGGAGGAA
1423948 AAGT-TTCTAGGGTCAAAGCCGACAGGTAGACTAAGG
1 AAGTCTTC-AGGGTCAAAGCCGACAGGTAGACTAAGG
1423984 AAAAAAAGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
41 36 0.55
42 30 0.45
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (42 bp):
AAGTCTTCAGGGTCAAAGCCGACAGGTAGACTAAGGGAGGAA
Found at i:1423939 original size:97 final size:98
Alignment explanation
Indices: 1423767--1423963 Score: 238
Period size: 97 Copynumber: 2.0 Consensus size: 98
1423757 TAGGGAAGGA
* * * * * *
1423767 AAGTCTCCAGGGTCAAAGTCGACAGGCAGATTGAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGAT
1 AAGTCTCCAGGGTCAAAGTCGACAGGCAGACTAAGGGAAGAAAAGTCTCCAAGCTCAAAGCCGAC
1423832 AGGCAAACTAAGGGTAGG-AAAGTCTCTAAGGTC
66 AGGCAAACTAAGGG-AGGAAAAGTCTCTAAGGTC
* * * *
1423865 AAGTCTTCAGGGTCAAAG-CTGATAGGTAGACTAAGGG-AGGAAAGTCTCCAAGCTCAAAGCCGA
1 AAGTCTCCAGGGTCAAAGTC-GACAGGCAGACTAAGGGAAGAAAAGTCTCCAAGCTCAAAGCCGA
* * *
1423928 CAGGCAGACTAAGGGAGGAAAAGTTTCTAGGGTC
65 CAGGCAAACTAAGGGAGGAAAAGTCTCTAAGGTC
1423962 AA
1 AA
1423964 AGCCGACAGG
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
96 3 0.04
97 51 0.61
98 30 0.36
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.17
Consensus pattern (98 bp):
AAGTCTCCAGGGTCAAAGTCGACAGGCAGACTAAGGGAAGAAAAGTCTCCAAGCTCAAAGCCGAC
AGGCAAACTAAGGGAGGAAAAGTCTCTAAGGTC
Found at i:1423981 original size:139 final size:140
Alignment explanation
Indices: 1423725--1423983 Score: 376
Period size: 139 Copynumber: 1.9 Consensus size: 140
1423715 AAGGATAGAA
* * * * *
1423725 AAGTCTCCAAGGTTAAAGCTGATAGGGAGACTTAGGGAAGGAAAGTCTCCAGGGTCAAAGTCGAC
1 AAGTCTCCAAGGTCAAAGCTGATAGGGAGACTAAGGGAAGGAAAGTCTCCAAGCTCAAAGCCGAC
* * *
1423790 AGGCAGATTGAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGATAGGCAAACTAAGGGTAGGAAAGT
66 AGGCAGACTAAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTAAGGGTAGGAAAGT
1423855 CTCTAAGGTC
131 CTCTAAGGTC
* * *
1423865 AAGTCTTCAGGGTCAAAGCTGATAGGTAGACTAAGGG-AGGAAAGTCTCCAAGCTCAAAGCCGAC
1 AAGTCTCCAAGGTCAAAGCTGATAGGGAGACTAAGGGAAGGAAAGTCTCCAAGCTCAAAGCCGAC
* * * *
1423929 AGGCAGACTAAGGGAGGAAAAGTTTCTAGGGTCAAAGCCGACAGGTAGACTAAGG
66 AGGCAGACTAAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTAAGG
1423984 AAAAAAAGGC
Statistics
Matches: 104, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
139 72 0.69
140 32 0.31
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (140 bp):
AAGTCTCCAAGGTCAAAGCTGATAGGGAGACTAAGGGAAGGAAAGTCTCCAAGCTCAAAGCCGAC
AGGCAGACTAAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTAAGGGTAGGAAAGT
CTCTAAGGTC
Found at i:1423998 original size:41 final size:41
Alignment explanation
Indices: 1423865--1423998 Score: 135
Period size: 41 Copynumber: 3.2 Consensus size: 41
1423855 CTCTAAGGTC
* * * *
1423865 AAGTCT-TCAGGGTCAAAGCTGATAGGTAGACTAAGGGAGGA
1 AAGTCTCT-AGGGTCAAAGCCGACAGGTAGACTAAGGAAGAA
* * * * *
1423906 AAGTCTCCAAGCTCAAAGCCGACAGGCAGACTAAGGGAGGAA
1 AAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAA-GGAAGAA
* *
1423948 AAGTTTCTAGGGTCAAAGCCGACAGGTAGACTAAGGAAAAA
1 AAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGAAGAA
*
1423989 AAGGCTCTAG
1 AAGTCTCTAG
1423999 AAGTTTAATG
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
41 40 0.55
42 33 0.45
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.16
Consensus pattern (41 bp):
AAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGAAGAA
Found at i:1427686 original size:19 final size:18
Alignment explanation
Indices: 1427661--1427725 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
1427651 ATTTCAACGA
1427661 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1427679 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
1427695 --TGTATCGATACATTAG
1 TTTGTATCGATACATAAG
1427711 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1427726 ATGTACAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
17 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1427699 original size:32 final size:32
Alignment explanation
Indices: 1427663--1427730 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1427653 TTCAACGATT
1427663 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1427695 TGTATCGATACATTAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1427727 TGTA
1 TGTA
1427731 CAGTTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1427700 original size:13 final size:13
Alignment explanation
Indices: 1427682--1427706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1427672 ACATAAGTGT
1427682 TGTATCGATACAA
1 TGTATCGATACAA
1427695 TGTATCGATACA
1 TGTATCGATACA
1427707 TTAGTTTTGT
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:1427775 original size:13 final size:12
Alignment explanation
Indices: 1427756--1427815 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 12
1427746 TGCCAAGAAA
1427756 ATGTATCGATAC
1 ATGTATCGATAC
1427768 ATTGTATCGATAC
1 A-TGTATCGATAC
1427781 AT-TACTC-A-A-
1 ATGTA-TCGATAC
1427790 ATGTATCGATAC
1 ATGTATCGATAC
1427802 ATTGTATCGATAC
1 A-TGTATCGATAC
1427815 A
1 A
1427816 CTGATCTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
9 4 0.10
10 4 0.10
11 4 0.10
12 5 0.12
13 24 0.59
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1427869 original size:52 final size:52
Alignment explanation
Indices: 1427824--1427952 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1427814 CACTGATCTT
1427824 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
1427876 TGTATTGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
1427928 TGTATCGATACATGTAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1427953 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1433139 original size:79 final size:77
Alignment explanation
Indices: 1433003--1433221 Score: 224
Period size: 79 Copynumber: 2.8 Consensus size: 77
1432993 ACAACAGGGC
* * * * * *
1433003 TGGAGTATCCCCGATTATGAAAAATCGATATTTTGGAAATAAAATCTGGGTTGGAGTAT-CCCTT
1 TGGAGTATCCCCGATTGTG-GAAATCGATATTTTAGAAAT-AAAGCTGGGTTAGAGTATCCCCGT
1433067 CAGAAATAACGGGGT
64 CA-AAATAACGGGGT
** *
1433082 TGGAGTATCCCCGATTGTGGACAATCGATGCTTTAGAAATAAGGCTAGGGTTAGAGTATCCCCGT
1 TGGAGTATCCCCGATTGTGGA-AATCGATATTTTAGAAATAAAGCT-GGGTTAGAGTATCCCCGT
* *
1433147 GAAAATAATGGGGT
64 CAAAATAACGGGGT
* * * * *
1433161 TGGAGTATCTCCGATTGTGAGAAATCGGTATTTTAGAAATAAAATCAGAGTTAGAGTATCC
1 TGGAGTATCCCCGATTGTG-GAAATCGATATTTTAGAAAT-AAAGCTGGGTTAGAGTATCC
1433222 TCGATTGTGA
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 5 0.04
79 101 0.87
80 10 0.09
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (77 bp):
TGGAGTATCCCCGATTGTGGAAATCGATATTTTAGAAATAAAGCTGGGTTAGAGTATCCCCGTCA
AAATAACGGGGT
Found at i:1433269 original size:51 final size:52
Alignment explanation
Indices: 1433155--1433272 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 52
1433145 GTGAAAATAA
*
1433155 TGGGGTTGGAGTAT-CTCCGATTGTGAGAAATCGGTATTTTAGAAATAAAAT
1 TGGGGTTGGAGTATCCTCCGATTGTGAAAAATCGGTATTTTAGAAATAAAAT
** * *
1433206 CAGAGTTAGAGTATCCT-CGATTGTGAAAAAAT-GGTATTTTAGAAATAAAAT
1 TGGGGTTGGAGTATCCTCCGATTGTG-AAAAATCGGTATTTTAGAAATAAAAT
1433257 TGGGGTTGGAGTATCC
1 TGGGGTTGGAGTATCC
1433273 CCTCGAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 49 0.88
52 7 0.12
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.32
Consensus pattern (52 bp):
TGGGGTTGGAGTATCCTCCGATTGTGAAAAATCGGTATTTTAGAAATAAAAT
Done.