Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold129
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: 3652842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 48564 characters in sequence are not A, C, G, or T
File 7 of 23
Found at i:923819 original size:90 final size:90
Alignment explanation
Indices: 923664--923878 Score: 272
Period size: 90 Copynumber: 2.4 Consensus size: 90
923654 TTTTAACTAG
** * * *
923664 ATGTATCGATACATTATTCAATGTATCGATACATCTGGGTAAAAAGACAGAACGTATCGATACAT
1 ATGTATCGATACATTA-AAAATGTATCGATACATCTAGGTAAAAAGACAGAACGTATCAACACAT
**
923729 TGAAGAATGTATCGATAA-ATTCACGT
65 TGAAGAATGTATCGA-AACATTCACAC
* * *
923755 ATGTATCGATACATTGAAAAATGTATTGAT-CATCTAGGTAAAAAGATAGAATGTATCAACACAT
1 ATGTATCGATACATT-AAAAATGTATCGATACATCTAGGTAAAAAGACAGAACGTATCAACACAT
*
923819 TGAAGAATGTATCGAAACATTCATAC
65 TGAAGAATGTATCGAAACATTCACAC
*
923845 ATGTACCGATACATTAAAAAATGTATCGATACAT
1 ATGTATCGATACATT-AAAAATGTATCGATACAT
923879 TCATACATGT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
89 2 0.02
90 76 0.71
91 28 0.26
92 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (90 bp):
ATGTATCGATACATTAAAAATGTATCGATACATCTAGGTAAAAAGACAGAACGTATCAACACATT
GAAGAATGTATCGAAACATTCACAC
Found at i:923895 original size:40 final size:40
Alignment explanation
Indices: 923805--923899 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
923795 AAAAGATAGA
* * * *
923805 ATGTATCAACACATTGAAGAATGTATCGAAACATTCATAC
1 ATGTATCGATACATTAAAAAATGTATCGAAACATTCATAC
* *
923845 ATGTACCGATACATTAAAAAATGTATCGATACATTCATAC
1 ATGTATCGATACATTAAAAAATGTATCGAAACATTCATAC
923885 ATGTATCGATACATT
1 ATGTATCGATACATT
923900 TTTCAATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (40 bp):
ATGTATCGATACATTAAAAAATGTATCGAAACATTCATAC
Found at i:923908 original size:20 final size:19
Alignment explanation
Indices: 923824--923918 Score: 91
Period size: 20 Copynumber: 4.8 Consensus size: 19
923814 CACATTGAAG
*
923824 AATGTATCGAAACATTCAT
1 AATGTATCGATACATTCAT
* * *
923843 ACATGTACCGATACATTAAAA
1 A-ATGTATCGATACATT-CAT
923864 AATGTATCGATACATTCAT
1 AATGTATCGATACATTCAT
**
923883 ACATGTATCGATACATTTTT
1 A-ATGTATCGATACATTCAT
*
923903 CAATGTTTCGATACAT
1 -AATGTATCGATACAT
923919 CTGGGTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.05
20 56 0.90
21 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTCAT
Found at i:924881 original size:32 final size:32
Alignment explanation
Indices: 924835--924901 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
924825 AAAGTGATGA
*
924835 TTTGAAAAGGGTTGCCACCGACTTGCGTGGCC
1 TTTGAAAAGAGTTGCCACCGACTTGCGTGGCC
*
924867 TTTGAAAAGAGTTGCCACCGACTTGCGTGGGC
1 TTTGAAAAGAGTTGCCACCGACTTGCGTGGCC
924899 TTT
1 TTT
924902 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.28
Consensus pattern (32 bp):
TTTGAAAAGAGTTGCCACCGACTTGCGTGGCC
Found at i:925403 original size:28 final size:28
Alignment explanation
Indices: 924932--925397 Score: 547
Period size: 28 Copynumber: 16.5 Consensus size: 28
924922 TACTAACTTG
* *
924932 TGTGGGCTTTGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
924960 TGTGGGCTTTGAAAGGGTATGCCACTAACT
1 TGTGGGCTTTGAAA-GG-ATGCCACTGACT
* * *
924990 TGTGAGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
925018 TGTGGGCTTTGAAGGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* **
925046 TGTAGGCTTTGAAAGCTTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
925074 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * * *
925102 TGTATGCTTTGGAAGGGTATACTACTGACT
1 TGTGGGCTTT-GAAAGG-ATGCCACTGACT
* *
925132 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
925160 TGTGGGCTTTGAAAGAATGCCACGGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
925188 TGTGGTCTTTCG-AAGAGATGCCACTGACT
1 TGTGGGCTTT-GAAAG-GATGCCACTGACT
*
925217 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
925245 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
925273 TGTAGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
925301 TATGGGCTTTGAAAGGATACCACTAACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
925329 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
925357 TGTGGGCTTTGAAAGGATGCCGCTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
925385 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
925398 GAGATGAACG
Statistics
Matches: 373, Mismatches: 58, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
28 298 0.80
29 36 0.10
30 39 0.10
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:926682 original size:8 final size:8
Alignment explanation
Indices: 926654--926715 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
926644 TCTGGACCCC
926654 TTTTTTGT
1 TTTTTTGT
*
926662 TTGGTTT-T
1 TT-TTTTGT
926670 TTTTTTGT
1 TTTTTTGT
926678 TTTTTTG-
1 TTTTTTGT
* *
926685 TTATTGGT
1 TTTTTTGT
926693 TTTTTATGT
1 TTTTT-TGT
926702 TTTTTTGT
1 TTTTTTGT
926710 TTTTTT
1 TTTTTT
926716 TAGTATAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 8 0.18
8 26 0.59
9 10 0.23
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (8 bp):
TTTTTTGT
Found at i:937887 original size:13 final size:13
Alignment explanation
Indices: 937869--937925 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
937859 CATAAAGTGT
937869 TGTATCGATACAA
1 TGTATCGATACAA
937882 TGTATCGATACATAAA
1 TGTATCGATAC---AA
937898 TGTTGTATCGATACAA
1 ---TGTATCGATACAA
937914 TGTATCGATACA
1 TGTATCGATACA
937926 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
16 4 0.11
19 11 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:937906 original size:19 final size:18
Alignment explanation
Indices: 937846--937944 Score: 83
Period size: 19 Copynumber: 5.8 Consensus size: 18
937836 AATTTCAACG
937846 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
937864 AGTGTTGTATCGATAC---A
1 A-T-TTGTATCGATACATAA
937881 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
937897 ATGTTGTATCGATAC---A
1 AT-TTGTATCGATACATAA
937913 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
937929 GTTTTGTATCGATACA
1 -ATTTGTATCGATACA
937945 ATGTAAGCTA
Statistics
Matches: 66, Mismatches: 1, Indels: 27
0.70 0.01 0.29
Matches are distributed among these distances:
13 22 0.33
16 5 0.08
17 2 0.03
18 1 0.02
19 24 0.36
20 12 0.18
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:937907 original size:32 final size:32
Alignment explanation
Indices: 937849--937949 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
937839 TTCAACGATT
937849 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAA-TGTTGTATCGATACAA
937882 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
* *
937914 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
937946 TGTA
1 TGTA
937950 AGCTACTGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 50 0.76
33 16 0.24
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:937970 original size:65 final size:65
Alignment explanation
Indices: 937849--937977 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 65
937839 TTCAACGATT
* ***
937849 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACATAAAAAATGTATCGATACAA
* *
937914 TGTATCGATACAT-AAGTTTTGTATCGATACAATGTA-AGCTAC-TGCCAAAAAATGTATCGATA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACAT---AAAAAATGTATCGATA
937976 CA
63 CA
937978 TTACTCAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.02
63 4 0.07
64 22 0.40
65 28 0.51
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (65 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACATAAAAAATGTATCGATACAA
Found at i:938005 original size:13 final size:13
Alignment explanation
Indices: 937987--938011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
937977 ATTACTCAAA
937987 TGTATCAATACAT
1 TGTATCAATACAT
938000 TGTATCAATACA
1 TGTATCAATACA
938012 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:943839 original size:52 final size:51
Alignment explanation
Indices: 943761--943909 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
943751 CGAAATATGA
943761 AAATTTGCCTGCATGTATCGATACATTGCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
943813 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
943865 AAATTTGCCTACATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
943910 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:943916 original size:13 final size:13
Alignment explanation
Indices: 943898--943922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
943888 CAAAGATCAG
943898 TGTATCGATACAA
1 TGTATCGATACAA
943911 TGTATCGATACA
1 TGTATCGATACA
943923 TTTAAGTGAT
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:944000 original size:33 final size:33
Alignment explanation
Indices: 943963--944029 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
943953 AGTAGCTTGA
943963 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
943996 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
944029 A
1 A
944030 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:944003 original size:13 final size:13
Alignment explanation
Indices: 943985--944009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
943975 CAAAAAAATA
943985 TGTATCGATACAT
1 TGTATCGATACAT
943998 TGTATCGATACA
1 TGTATCGATACA
944010 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:944250 original size:9 final size:9
Alignment explanation
Indices: 944236--944264 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
944226 GCTAGGCCTC
944236 AAAAATCTA
1 AAAAATCTA
944245 AAAAATCT-
1 AAAAATCTA
944253 AAAAATCTA
1 AAAAATCTA
944262 AAA
1 AAA
944265 TTCGTCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATCTA
Found at i:945580 original size:15 final size:15
Alignment explanation
Indices: 945560--945591 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
945550 AGAAAAAGAT
945560 TTAAACTTTGATGGG
1 TTAAACTTTGATGGG
945575 TTAAACTTTGATGGG
1 TTAAACTTTGATGGG
945590 TT
1 TT
945592 TAAAGCGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (15 bp):
TTAAACTTTGATGGG
Found at i:947968 original size:13 final size:13
Alignment explanation
Indices: 947950--947975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
947940 ATATTTTTTG
947950 TGTATCGATACAT
1 TGTATCGATACAT
947963 TGTATCGATACAT
1 TGTATCGATACAT
947976 ATTTTGTGTA
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:947986 original size:32 final size:33
Alignment explanation
Indices: 947929--947993 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
947919 TACAAGCTAA
*
947929 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCAATACAT
947963 TGTATCGATACATA-TTTTGTGTATCAATACA
1 TGTATCGATACATATTTTTGTGTATCAATACA
947994 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCAATACAT
Found at i:947987 original size:19 final size:19
Alignment explanation
Indices: 947929--947993 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
947919 TACAAGCTAA
947929 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
947950 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
947963 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
*
947982 TGTATCAATACA
1 TGTATCGATACA
947994 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
21 11 0.30
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:950538 original size:13 final size:13
Alignment explanation
Indices: 950520--950557 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
950510 ATAATCCCCC
950520 TGTATCGATACAG
1 TGTATCGATACAG
*
950533 TGTATCGATACAT
1 TGTATCGATACAG
950546 TGTATCGATACA
1 TGTATCGATACA
950558 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:952658 original size:15 final size:15
Alignment explanation
Indices: 952638--952668 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
952628 ATTTCGTTTG
*
952638 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
952653 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
952668 G
1 G
952669 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:954501 original size:147 final size:147
Alignment explanation
Indices: 954234--954529 Score: 592
Period size: 147 Copynumber: 2.0 Consensus size: 147
954224 ATTTTGCCTC
954234 TAAATTTATTTATTTTAGAGTTGCACGTGTGAAATGTGTGACCATGTTTATGACATAAAGAACAC
1 TAAATTTATTTATTTTAGAGTTGCACGTGTGAAATGTGTGACCATGTTTATGACATAAAGAACAC
954299 ACATATGAGGCATTTTTGTGTTTTACAAAGAAATTTTTAAATTTCGTTTCTTTCTCAAGGGCATT
66 ACATATGAGGCATTTTTGTGTTTTACAAAGAAATTTTTAAATTTCGTTTCTTTCTCAAGGGCATT
954364 ATATCCTACACCATTTT
131 ATATCCTACACCATTTT
954381 TAAATTTATTTATTTTAGAGTTGCACGTGTGAAATGTGTGACCATGTTTATGACATAAAGAACAC
1 TAAATTTATTTATTTTAGAGTTGCACGTGTGAAATGTGTGACCATGTTTATGACATAAAGAACAC
954446 ACATATGAGGCATTTTTGTGTTTTACAAAGAAATTTTTAAATTTCGTTTCTTTCTCAAGGGCATT
66 ACATATGAGGCATTTTTGTGTTTTACAAAGAAATTTTTAAATTTCGTTTCTTTCTCAAGGGCATT
954511 ATATCCTACACCATTTT
131 ATATCCTACACCATTTT
954528 TA
1 TA
954530 TCGAAAAATG
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (147 bp):
TAAATTTATTTATTTTAGAGTTGCACGTGTGAAATGTGTGACCATGTTTATGACATAAAGAACAC
ACATATGAGGCATTTTTGTGTTTTACAAAGAAATTTTTAAATTTCGTTTCTTTCTCAAGGGCATT
ATATCCTACACCATTTT
Found at i:954647 original size:21 final size:21
Alignment explanation
Indices: 954618--954662 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
954608 AAGTTTTTAT
*
954618 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
954638 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
954660 TTT
1 TTT
954663 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:956899 original size:13 final size:13
Alignment explanation
Indices: 956881--956906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
956871 ATATTTTTTG
956881 TGTATCGATACAT
1 TGTATCGATACAT
956894 TGTATCGATACAT
1 TGTATCGATACAT
956907 ATTTTGTGTA
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:956917 original size:32 final size:33
Alignment explanation
Indices: 956860--956924 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
956850 TACAAGCCAA
956860 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
956894 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
956925 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:956918 original size:19 final size:19
Alignment explanation
Indices: 956860--956924 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
956850 TACAAGCCAA
956860 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
956881 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
956894 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
956913 TGTATCGATACA
1 TGTATCGATACA
956925 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:957984 original size:51 final size:51
Alignment explanation
Indices: 957898--958124 Score: 253
Period size: 51 Copynumber: 4.7 Consensus size: 51
957888 TTTTAACTAG
* * * *
957898 ATGTATCGATACATTGAATAATGTATCAATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
* *
957949 ATGTATCGATACATTGAAAAATATATCGATTCATCTAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
* *
958000 ATGTATCGACACATTGAAGAATGTATCGATACAT-TCA--T------AC--A
1 ATGTATCGATACATTGAAAAATGTATCGATACATCT-AGGTAAAAAGACAGA
* *
958041 A-GCACCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
* *
958091 ATGTATCGACACATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
958125 TCATATGTGA
Statistics
Matches: 145, Mismatches: 18, Indels: 26
0.77 0.10 0.14
Matches are distributed among these distances:
40 29 0.20
41 3 0.02
42 1 0.01
43 2 0.01
48 2 0.01
49 1 0.01
50 3 0.02
51 104 0.72
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
Found at i:958069 original size:20 final size:20
Alignment explanation
Indices: 957999--958073 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
957989 AAAAAGACAG
* *
957999 AATGTATCGACACATTGAAG
1 AATGTATCGATACATTGAAA
* *
958019 AATGTATCGATACATTCATAC
1 AATGTATCGATACATTGA-AA
* *
958040 AA-GCACCGATACATTGAAA
1 AATGTATCGATACATTGAAA
958059 AATGTATCGATACAT
1 AATGTATCGATACAT
958074 CTAGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:958110 original size:91 final size:91
Alignment explanation
Indices: 957955--958129 Score: 332
Period size: 91 Copynumber: 1.9 Consensus size: 91
957945 TAGAATGTAT
*
957955 CGATACATTGAAAAATATATCGATTCATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAGA
1 CGATACATTGAAAAATATATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAGA
958020 ATGTATCGATACATTCATACAAGCAC
66 ATGTATCGATACATTCATACAAGCAC
*
958046 CGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAGA
1 CGATACATTGAAAAATATATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAGA
958111 ATGTATCGATACATTCATA
66 ATGTATCGATACATTCATA
958130 TGTGACTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (91 bp):
CGATACATTGAAAAATATATCGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTGAAGA
ATGTATCGATACATTCATACAAGCAC
Found at i:958113 original size:20 final size:20
Alignment explanation
Indices: 958088--958125 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
958078 GTAAAAAGAC
958088 AGAATGTATCGACACATTGA
1 AGAATGTATCGACACATTGA
*
958108 AGAATGTATCGATACATT
1 AGAATGTATCGACACATT
958126 CATATGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGACACATTGA
Found at i:963223 original size:20 final size:20
Alignment explanation
Indices: 963190--963244 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
963180 CTACTAGTTT
*
963190 CATGTATC-ATTACAATTGAG
1 CATGTATCGA-TACAATTGAA
*
963210 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
963229 CATGTATCGATACAAT
1 CATGTATCGATACAAT
963245 GTATCAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 17 0.57
20 12 0.40
21 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:965513 original size:13 final size:13
Alignment explanation
Indices: 965495--965520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
965485 TACACCAAGT
965495 ATGTATCGATACA
1 ATGTATCGATACA
965508 ATGTATCGATACA
1 ATGTATCGATACA
965521 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:965518 original size:32 final size:33
Alignment explanation
Indices: 965477--965540 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
965467 TAGCCAAACT
* **
965477 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
965509 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
965541 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:967783 original size:21 final size:22
Alignment explanation
Indices: 967737--967781 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
967727 TTGCAAGTTG
967737 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
967759 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
967779 AAA
1 AAA
967782 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:969606 original size:15 final size:15
Alignment explanation
Indices: 969586--969616 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
969576 TAAAAATGTC
*
969586 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
969601 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
969616 C
1 C
969617 CAAACAAAAT
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:971884 original size:20 final size:20
Alignment explanation
Indices: 971841--971886 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
971831 AAATCTTTTG
971841 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
971862 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
971882 CAAAA
1 CAAAA
971887 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:974283 original size:13 final size:13
Alignment explanation
Indices: 974265--974290 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
974255 TACACCAAGT
974265 ATGTATCGATACA
1 ATGTATCGATACA
974278 ATGTATCGATACA
1 ATGTATCGATACA
974291 TTGGCTTGTA
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:976532 original size:21 final size:22
Alignment explanation
Indices: 976486--976530 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
976476 TTGCAAGTTG
976486 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
976508 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
976528 AAA
1 AAA
976531 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:981826 original size:29 final size:28
Alignment explanation
Indices: 981779--981837 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
981769 CTTTTGCCTT
* * * *
981779 ATTTGCAATTTGATCCTAAATTTTCAAA
1 ATTTGCAATTTCACCCTAAATATCCAAA
981807 ATTTGCAATTTCACCCCTAAATATCCAAA
1 ATTTGCAATTTCA-CCCTAAATATCCAAA
981836 AT
1 AT
981838 ACCATTCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (28 bp):
ATTTGCAATTTCACCCTAAATATCCAAA
Found at i:982522 original size:11 final size:12
Alignment explanation
Indices: 982506--982536 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
982496 GTTTTCACTA
982506 TTTTTCTTTCT-
1 TTTTTCTTTCTC
982517 TTTTTCTTTCTC
1 TTTTTCTTTCTC
982529 TTTTTCTT
1 TTTTTCTT
982537 CTCACTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:983081 original size:165 final size:165
Alignment explanation
Indices: 982895--983785 Score: 700
Period size: 165 Copynumber: 5.5 Consensus size: 165
982885 TTATTGGAGT
* * * * ** * *
982895 TAAATAACAACATTAGATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCC-CTGAAAGAATTT
1 TAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCCTC-AAAAAAATTT
* * * *
982959 ACGAAGAAAAAAACTCGGT-TTCCCGAAAAAAAGAGAATTTCAA-CAAAAAATCCAAAACTCATG
65 ACGAAGAAGAAAACTCGGTATT-TCG-AAAAAAGAGAATTTCAAGAAAAAAATCAAAAACTCATG
* * * * *
983022 AAAATTAATTAATTTTTTAAAACTGACTTAATAT-AAA
128 AAAATGAATGAATTTTTGAAAACTAATTTAATATGAAA
* * * * * * * *
983059 TCAAATAATGATGTTTGATGAATTTTGAAAATTGAAAACCGAGAAAAATCTCCTTC-AAAACATT
1 T-AAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATC-CCCTCAAAAAAATT
* * * * * *
983123 TACGAAGTAGAAAACACCGTATTTC-AGAAAA-A-AA--TC----AAAAACTCATGAAA---ATG
64 TACGAAGAAGAAAACTCGGTATTTCGAAAAAAGAGAATTTCAAGAAAAAAATCA-AAAACTCATG
* * * ** *
983176 --AATTAAT--TTTTTTAAAGTGATTTAATATGAA-AT-AAA
128 AAAATGAATGAATTTTTGAA---AACTAAT-TTAATATGAAA
* * * * *
983212 T-GATAAT-ATT--TGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCGAAAAAATTTA
1 TAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTA
* * * * * *
983273 C-AACGTAGAAAACTTC-GTATTTTGGAAAAAGGAGAGTTTTAAGGAAAAAAATCAAAAA-TGAA
66 CGAA-GAAGAAAAC-TCGGTA-TTTCGAAAAAAGAGAATTTCAA-GAAAAAAATCAAAAACT-CA
* * *
983335 TGAAAATGAATGAATTCTTGAAGACTAATTTAATATGATA
126 TGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAAA
* *
983375 TAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCCTCAAAAAAATTTA
1 TAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTA
* * * * *
983440 CGGAGTAGAAAACT-GCGTATTT-AAAAAAAAAGGAATTTCAAGAAAAAAATCAAAAACTTATGA
66 CGAAGAAGAAAACTCG-GTATTTCGAAAAAAGA-GAATTTCAAGAAAAAAATCAAAAACTCATGA
*
983503 AAATGAATGAATTTTTGAAAACTAATTTAATATGAAT
129 AAATGAATGAATTTTTGAAAACTAATTTAATATGAAA
* *
983540 TAAATAATAATATTTTATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCTTCAAAAAAATTTA
1 TAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTA
* * * *
983605 CGGAA-TAGAAAACACAGTATTTCGAAAAAAGAGGAATTTCAAGGAAAAAATCAAAAACTCATGA
66 C-GAAGAAGAAAACTCGGTATTTCGAAAAAAGA-GAATTTCAAGAAAAAAATCAAAAACTCATGA
*
983669 AAATGAATGAATTTTTGAAAACTCATTTAATATGAAA
129 AAATGAATGAATTTTTGAAAACTAATTTAATATGAAA
* **
983706 TAAATAATAATATTTAATG-AATTTAAAAAAAATTAAAAATGAAGAAAAATCCTCCT-AAAAAAA
1 TAAATAATAATATTTGATGAAATTT---AAAAATTAAAAACCAAGAAAAATCC-CCTCAAAAAAA
*
983769 TTTACGGAGAAGAAAAC
62 TTTACGAAGAAGAAAAC
983786 CCATAATTTG
Statistics
Matches: 590, Mismatches: 88, Indels: 94
0.76 0.11 0.12
Matches are distributed among these distances:
147 6 0.01
148 53 0.09
149 4 0.01
150 13 0.02
151 6 0.01
152 8 0.01
153 9 0.02
154 7 0.01
156 7 0.01
157 3 0.01
158 3 0.01
159 10 0.02
161 8 0.01
162 7 0.01
163 14 0.02
164 5 0.01
165 209 0.35
166 108 0.18
167 65 0.11
168 43 0.07
169 2 0.00
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.28
Consensus pattern (165 bp):
TAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTA
CGAAGAAGAAAACTCGGTATTTCGAAAAAAGAGAATTTCAAGAAAAAAATCAAAAACTCATGAAA
ATGAATGAATTTTTGAAAACTAATTTAATATGAAA
Found at i:983301 original size:148 final size:147
Alignment explanation
Indices: 982995--983470 Score: 438
Period size: 148 Copynumber: 3.1 Consensus size: 147
982985 AAAAAAGAGA
* * *
982995 ATTTCA-ACAAAAAATCCAAAACTCATGAAAATTAATTAATTTTTTAAAACTGACTTAATAT-AA
1 ATTTCAGA-AAAAAATCAAAAACTCATGAAAATGAATTAATTTTTTAAAACTGATTTAATATGAA
* * * * * * * *
983058 ATCAAATAATGATGTTTGATGAATTTTGAAAATTGAAAACCGAGAAAAATCTCCTTCAAAACATT
65 AT-AAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCT-CTTCAAAAAATT
*
983123 TACGAAGTAGAAAACACCGT
128 TACGAAGTAGAAAACTCCGT
* *
983143 ATTTCAGAAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTTTAAAGTGATTTAATATGAAA
1 ATTTCAGAAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTTAAAACTGATTTAATATGAAA
983208 TAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCGAAAAAATTTA
66 TAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTC-AAAAAATTTA
*
983273 C-AACGTAGAAAACTTCGT
130 CGAA-GTAGAAAACTCCGT
** * * * * *
983291 ATTTTGGAAAAAGGAGAGTTTTAAGGAAAAAAATCAAAAATGAATGAAAATGAATGAATTCTTGA
1 ATTTCAGAAAAA--A-A----T----CAAAAACTC----ATG----AAAATGAATTAATTTTTTA
* * *
983356 AGACTAATTTAATATGATATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAA
47 AAACTGATTTAATATGAAATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAA
* * *
983421 ATCTCCTCAAAAAAATTTACGGAGTAGAAAACTGCGT
112 ATCTCTTC-AAAAAATTTACGAAGTAGAAAACTCCGT
*
983458 ATTT-AAAAAAAAA
1 ATTTCAGAAAAAAA
983471 GGAATTTCAA
Statistics
Matches: 271, Mismatches: 33, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
147 6 0.02
148 128 0.47
149 5 0.02
150 1 0.00
151 1 0.00
155 1 0.00
159 7 0.03
163 4 0.01
164 1 0.00
166 5 0.02
167 111 0.41
168 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.29
Consensus pattern (147 bp):
ATTTCAGAAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTTAAAACTGATTTAATATGAAA
TAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCAAAAAATTTAC
GAAGTAGAAAACTCCGT
Found at i:983425 original size:167 final size:166
Alignment explanation
Indices: 983149--983785 Score: 799
Period size: 167 Copynumber: 3.8 Consensus size: 166
983139 CCGTATTTCA
* ** * * *
983149 GAAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTTTAAAGTGATTTAATATGAAATAAATG
1 GAAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAAATAAATA
*
983214 ATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCGAAAAAATTTAC-AACG
66 ATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCAAAAAAATTTACGAA-G
* * *
983278 TAGAAAACTTCGTATTTTGGAAAAAGGAGAGTTTTAAG
130 TAGAAAACTACGTATTTTAGAAAAAGGAGA-TTTCAAG
* * * *
983316 GAAAAAAATCAAAAA-TGAATGAAAATGAATGAATTCTTGAAGACTAATTTAATATGATATAAAT
1 GAAAAAAATCAAAAACT-CATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAAATAAAT
* * *
983380 GATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCCTCAAAAAAATTTACGGAG
65 AATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCAAAAAAATTTACGAAG
* * *
983445 TAGAAAACTGCGTATTTAAAAAAAAAGGA-ATTTCAA-
130 TAGAAAACTACGTATTT-TAGAAAAAGGAGATTTCAAG
* *
983481 GAAAAAAATCAAAAACTTATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAATTAAATA
1 GAAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAAATAAATA
* *
983546 ATAATATTTTATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCTTCAAAAAAATTTACGGAA-
66 ATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCAAAAAAATTTAC-GAAG
* *
983610 TAGAAAAC-ACAGTA-TTTCGAAAAAAGAGGAATTTCAAG
130 TAGAAAACTAC-GTATTTTAGAAAAAGGA-G-ATTTCAAG
*
983648 G-AAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTCATTTAATATGAAATAAATA
1 GAAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAAATAAATA
* ** *
983712 ATAATATTTAATG-AATTTAAAAAAAATTAAAAATGAAGAAAAATC-CTCCTAAAAAAATTTACG
66 ATAATATTTGATGAAATTT---AAAAATTAAAAACCAAGAAAAATCTCTTC-AAAAAAATTTACG
* *
983775 GAGAAGAAAAC
127 AAGTAGAAAAC
983786 CCATAATTTG
Statistics
Matches: 414, Mismatches: 41, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
163 7 0.02
164 3 0.01
165 130 0.31
166 88 0.21
167 136 0.33
168 50 0.12
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (166 bp):
GAAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGAAATAAATA
ATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTTCAAAAAAATTTACGAAGT
AGAAAACTACGTATTTTAGAAAAAGGAGATTTCAAG
Found at i:983672 original size:166 final size:165
Alignment explanation
Indices: 983195--983785 Score: 768
Period size: 165 Copynumber: 3.6 Consensus size: 165
983185 TTTTAAAGTG
* *
983195 ATTTAATATGAAATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCT
1 ATTTAATATGAAATAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCT
* * * * *
983260 TCGAAAAAATTTAC--AACGTAGAAAACTTCGTATTTTGGAAAAAG-GAGAGTTTTAAGGAAAAA
66 TCAAAAAAATTTACGGAA--TAGAAAACTACGTA-TTTGAAAAAAGAG-GAATTTCAAGG-AAAA
* *
983322 AATCAAAAA-TGAATGAAAATGAATGAATTCTTGAAGACTA
126 AATCAAAAACT-AATGAAAATGAATGAATTTTTGAAAACTA
* *
983362 ATTTAATATGATATAAATGATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCC
1 ATTTAATATGAAATAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATC-CC
* * * * *
983427 -TCAAAAAAATTTACGGAGTAGAAAACTGCGTATTTAAAAAAAAAGGAATTTCAAGAAAAAAATC
65 TTCAAAAAAATTTACGGAATAGAAAACTACGTATTTGAAAAAAGAGGAATTTCAAGGAAAAAATC
*
983491 AAAAACTTATGAAAATGAATGAATTTTTGAAAACTA
130 AAAAACTAATGAAAATGAATGAATTTTTGAAAACTA
* *
983527 ATTTAATATGAATTAAATAATAATATTTTATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCT
1 ATTTAATATGAAATAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCT
983592 TCAAAAAAATTTACGGAATAGAAAAC-ACAGTATTTCGAAAAAAGAGGAATTTCAAGGAAAAAAT
66 TCAAAAAAATTTACGGAATAGAAAACTAC-GTATTT-GAAAAAAGAGGAATTTCAAGGAAAAAAT
* *
983656 CAAAAACTCATGAAAATGAATGAATTTTTGAAAACTC
129 CAAAAACTAATGAAAATGAATGAATTTTTGAAAACTA
* **
983693 ATTTAATATGAAATAAATAATAATATTTAATG-AATTTAAAAAAAATTAAAAATGAAGAAAAAT-
1 ATTTAATATGAAATAAATAATAATATTTGATGAAATTT---AAAAATTAAAAACCAAGAAAAATC
*
983756 CCTCCTAAAAAAATTTACGGAGA-AGAAAAC
63 CCTTC-AAAAAAATTTACGGA-ATAGAAAAC
983786 CCATAATTTG
Statistics
Matches: 381, Mismatches: 30, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
164 3 0.01
165 133 0.35
166 107 0.28
167 92 0.24
168 44 0.12
169 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (165 bp):
ATTTAATATGAAATAAATAATAATATTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCCCT
TCAAAAAAATTTACGGAATAGAAAACTACGTATTTGAAAAAAGAGGAATTTCAAGGAAAAAATCA
AAAACTAATGAAAATGAATGAATTTTTGAAAACTA
Found at i:987514 original size:60 final size:60
Alignment explanation
Indices: 987450--987640 Score: 165
Period size: 60 Copynumber: 3.2 Consensus size: 60
987440 CTAGTTGGTA
** *
987450 AAGTGGAAGACTGGCAGAGTTGGCATTTTTATTTTTCTATTAAGTCTTCTTTATCAAGTT
1 AAGTGGAAGACTGATAGAGTTGGCATTTTTATTTTTCTATTAAGTCTACTTTATCAAGTT
* * * * * * * *
987510 AAGTGGAAAAC-CATTACAGTTGACATTTTTAGTTTT-TAGTTAAGACTGCTTGATCAAGTT
1 AAGTGGAAGACTGA-TAGAGTTGGCATTTTTATTTTTCTA-TTAAGTCTACTTTATCAAGTT
* * * * *
987570 AAGTGGAAGAATGATAGAG-AGGCGACATTTTAGTTTTTC-ATTAAGTCCAGTTTATCAAGTT
1 AAGTGGAAGACTGATAGAGTTGGC-A-TTTTTA-TTTTTCTATTAAGTCTACTTTATCAAGTT
987631 AAGTGGAAGA
1 AAGTGGAAGA
987641 AGGTAGAATT
Statistics
Matches: 101, Mismatches: 23, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
59 4 0.04
60 60 0.59
61 32 0.32
62 5 0.05
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (60 bp):
AAGTGGAAGACTGATAGAGTTGGCATTTTTATTTTTCTATTAAGTCTACTTTATCAAGTT
Found at i:988833 original size:2 final size:2
Alignment explanation
Indices: 988826--988858 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
988816 ATCTAATGTT
988826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
988859 GAGGTGGCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:989580 original size:21 final size:21
Alignment explanation
Indices: 989556--989605 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
989546 ATTTAAGCTT
989556 TGAATGTTGAAATATTGATTA
1 TGAATGTTGAAATATTGATTA
*
989577 TGAATGTTGAAATCTTGATTA
1 TGAATGTTGAAATATTGATTA
989598 TGAATGTT
1 TGAATGTT
989606 AATCATATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (21 bp):
TGAATGTTGAAATATTGATTA
Found at i:998054 original size:13 final size:13
Alignment explanation
Indices: 998036--998060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
998026 CAATTCTTCA
998036 TGTATCAATACAT
1 TGTATCAATACAT
998049 TGTATCAATACA
1 TGTATCAATACA
998061 ATATGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:998154 original size:19 final size:18
Alignment explanation
Indices: 998109--998166 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
998099 ACTGCAAGTT
998109 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
998128 TGCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
998147 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
998166 T
1 T
998167 ATCGATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:998168 original size:13 final size:13
Alignment explanation
Indices: 998150--998176 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
998140 TACAATGATC
998150 ATGTATCGATACA
1 ATGTATCGATACA
998163 ATGTATCGATACA
1 ATGTATCGATACA
998176 A
1 A
998177 AGCGTAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1000246 original size:20 final size:20
Alignment explanation
Indices: 1000207--1000246 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1000197 TGAGAGCTAT
* *
1000207 CCGATTGCGACCTAGGAGTG
1 CCGATCGCGACCTAGAAGTG
*
1000227 CCGATCGCGACTTAGAAGTG
1 CCGATCGCGACCTAGAAGTG
1000247 GCTGTCTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
CCGATCGCGACCTAGAAGTG
Found at i:1010393 original size:13 final size:13
Alignment explanation
Indices: 1010375--1010400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1010365 ACATAAGTTT
1010375 TGTATCGATACAA
1 TGTATCGATACAA
1010388 TGTATCGATACAA
1 TGTATCGATACAA
1010401 AACTACACTG
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:1016415 original size:21 final size:21
Alignment explanation
Indices: 1016391--1016449 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1016381 ACAAAAGATC
1016391 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
1016412 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
*
1016433 ATTGTATCGATACATTT
1 AATGTATCGATACATTT
1016450 CCTTGGCAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (21 bp):
AATGTATCGATACATTTGAGT
Found at i:1016502 original size:19 final size:17
Alignment explanation
Indices: 1016477--1016651 Score: 75
Period size: 13 Copynumber: 10.9 Consensus size: 17
1016467 TAGCGATACA
1016477 TTGTATCGATACAAAACT
1 TTGTATCGATAC-AAACT
1016495 TATGTATCGATAC--A--
1 T-TGTATCGATACAAACT
1016509 TTGTATCGATACAACACTT
1 TTGTATCGATACAA-AC-T
*
1016528 TTGCATCGATAC--A--
1 TTGTATCGATACAAACT
1016541 TTGTATCGATACAACACT
1 TTGTATCGATACAA-ACT
*
1016559 TATGCATCGATAC--A--
1 T-TGTATCGATACAAACT
1016573 TTGTATCGATACAACACT
1 TTGTATCGATACAA-ACT
*
1016591 TATGCATCGATAC--A--
1 T-TGTATCGATACAAACT
1016605 TTGTATCGATACAACACT
1 TTGTATCGATACAA-ACT
* *
1016623 TATGCATTGATAC--A--
1 T-TGTATCGATACAAACT
1016637 TTGTATCGATACAAA
1 TTGTATCGATACAAA
1016652 TTGTTGAAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 57
0.64 0.05 0.30
Matches are distributed among these distances:
13 51 0.43
14 4 0.03
15 1 0.01
16 9 0.08
18 4 0.03
19 51 0.43
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (17 bp):
TTGTATCGATACAAACT
Found at i:1016511 original size:32 final size:32
Alignment explanation
Indices: 1016470--1016650 Score: 326
Period size: 32 Copynumber: 5.7 Consensus size: 32
1016460 AGCTTCGTAG
* *
1016470 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGCAT
*
1016502 CGATACATTGTATCGATACAACACTTTTGCAT
1 CGATACATTGTATCGATACAACACTTATGCAT
1016534 CGATACATTGTATCGATACAACACTTATGCAT
1 CGATACATTGTATCGATACAACACTTATGCAT
1016566 CGATACATTGTATCGATACAACACTTATGCAT
1 CGATACATTGTATCGATACAACACTTATGCAT
1016598 CGATACATTGTATCGATACAACACTTATGCAT
1 CGATACATTGTATCGATACAACACTTATGCAT
*
1016630 TGATACATTGTATCGATACAA
1 CGATACATTGTATCGATACAA
1016651 ATTGTTGAAA
Statistics
Matches: 144, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 144 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGCAT
Found at i:1018640 original size:21 final size:20
Alignment explanation
Indices: 1018614--1018666 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1018604 AACTCACTCA
*
1018614 GTATCGATACATACTTGAATT
1 GTATCGATACATA-ATGAATT
* *
1018635 GTATCGATAGATAATGCATT
1 GTATCGATACATAATGAATT
1018655 GTATCGATACAT
1 GTATCGATACAT
1018667 TGAGTCAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (20 bp):
GTATCGATACATAATGAATT
Found at i:1025326 original size:52 final size:51
Alignment explanation
Indices: 1025246--1025364 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
1025236 AAAAGTTGCT
*
1025246 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
1025298 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
1025349 TGCATGTATCGATACA
1 TGCATGTATCGATACA
1025365 AAGCTCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:1025377 original size:51 final size:52
Alignment explanation
Indices: 1025246--1025384 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 52
1025236 AAAAGTTGCT
** *
1025246 TGCATGTATCGATAC-ATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACAAGCT-ACAGTGTATCGATACATCTGGGCAAATTTACC
*** * * *
1025298 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-TTGCC
1 TGCATGTATCGATACAAGCTACAGTGTATCGATACATCTGGGCAAATTTACC
1025349 TGCATGTATCGATACAAAGCT-CAGTGTATCGATACA
1 TGCATGTATCGATAC-AAGCTACAGTGTATCGATACA
1025385 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
51 32 0.42
52 42 0.55
53 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
TGCATGTATCGATACAAGCTACAGTGTATCGATACATCTGGGCAAATTTACC
Found at i:1025391 original size:13 final size:13
Alignment explanation
Indices: 1025373--1025397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1025363 CAAAGCTCAG
1025373 TGTATCGATACAA
1 TGTATCGATACAA
1025386 TGTATCGATACA
1 TGTATCGATACA
1025398 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1025475 original size:33 final size:33
Alignment explanation
Indices: 1025438--1025504 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1025428 AGTAGCTTAA
1025438 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1025471 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1025504 A
1 A
1025505 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1025478 original size:13 final size:13
Alignment explanation
Indices: 1025460--1025484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1025450 CAAAAAAATA
1025460 TGTATCGATACAT
1 TGTATCGATACAT
1025473 TGTATCGATACA
1 TGTATCGATACA
1025485 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1026396 original size:52 final size:52
Alignment explanation
Indices: 1026264--1026475 Score: 199
Period size: 52 Copynumber: 4.2 Consensus size: 52
1026254 GAAAAGTGAT
* * * * * * * *
1026264 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
1026318 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
1026371 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
1026414 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1026466 AAAGGTGCCA
1 AAAGGTGCCA
1026476 CCGATTTGTG
Statistics
Matches: 129, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 37 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.33
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:1026432 original size:43 final size:43
Alignment explanation
Indices: 1026371--1026460 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1026361 TAAAGATGGA
*
1026371 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
1026414 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1026457 AAAG
1 AAAG
1026461 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1026563 original size:28 final size:29
Alignment explanation
Indices: 1026495--1026634 Score: 187
Period size: 30 Copynumber: 4.9 Consensus size: 29
1026485 GGTCTTCGGA
* *
1026495 AAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1026523 -AAGGTTGCCACTGACTTGTGGGCTTTT-
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1026550 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
**
1026579 AAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTG
* *
1026609 AAAAGGGTGCCACTAACTTGTGGGCT
1 -AAAGGTTGCCACTGACTTGTGGGCT
1026635 AAAAAGAGTG
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.21
28 30 0.30
29 4 0.04
30 41 0.41
31 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTG
Found at i:1026570 original size:85 final size:86
Alignment explanation
Indices: 1026466--1026634 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 86
1026456 TAAAGATGGA
* * * * * *
1026466 AAAGGTGCCACCGATTTGTGGTCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 AAAGGTGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
1026529 GCCACTGACTTGTGGGCTTTT
66 GCCACTAACTTGTGGGCTTTT
* ** *
1026550 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTG-AAAGG
1026615 GTGCCACTAACTTGTGGGCT
64 GTGCCACTAACTTGTGGGCT
1026635 AAAAAGAGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 5 0.07
85 39 0.56
86 4 0.06
88 22 0.31
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (86 bp):
AAAGGTGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAGGGT
GCCACTAACTTGTGGGCTTTT
Found at i:1026592 original size:30 final size:29
Alignment explanation
Indices: 1026464--1026634 Score: 177
Period size: 30 Copynumber: 5.9 Consensus size: 29
1026454 CTTAAAGATG
* * * * **
1026464 GAAAAGGTGCCACCGATTTGTGGTCTTCG
1 GAAAAGTTGCCACTGACTTGTGGGCTTTT
* *
1026493 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAA-GTTGCCACTGACTTGTGGGCTTTT
*
1026522 G-AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGTTGCCACTGACTTGTGGGCTTTT
*
1026550 -AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGTTGCCACTGACTTGTGGGCTTTT
*
1026578 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGT-TGCCACTGACTTGTGGGCTTTT
* *
1026608 GAAAAGGGTGCCACTAACTTGTGGGCT
1 GAAAA-GTTGCCACTGACTTGTGGGCT
1026635 AAAAAGAGTG
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
27 18 0.15
28 32 0.26
29 11 0.09
30 63 0.51
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (29 bp):
GAAAAGTTGCCACTGACTTGTGGGCTTTT
Found at i:1026706 original size:30 final size:30
Alignment explanation
Indices: 1026671--1026758 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
1026661 TTACAAAAGA
* * *
1026671 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTGG
*
1026701 AAAAGA-TGCCACCGACTTGTGGGCTTCGG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTGG
* * *
1026730 AAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTG
1026759 AAGGTTGATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (30 bp):
AAAAGAGTGCCACCGACTTGTGGGCTTTGG
Found at i:1028205 original size:1 final size:1
Alignment explanation
Indices: 1028201--1028295 Score: 64
Period size: 1 Copynumber: 95.0 Consensus size: 1
1028191 CCGGACCCCC
* * * * * ** * **
1028201 TTTTTTTGTTTTTTTATTGTTTTTGTTTTTTTGTTTTTTTTTTTTCCTTTTGTTTTTTTTTTTGG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** **
1028266 TTTTTCATTTTTTTCGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1028296 GGAGGACGCC
Statistics
Matches: 72, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:1028223 original size:17 final size:15
Alignment explanation
Indices: 1028201--1028296 Score: 86
Period size: 17 Copynumber: 6.0 Consensus size: 15
1028191 CCGGACCCCC
*
1028201 TTTTTTTGTTTTTTTA
1 TTTTTTT-TTTTTTTG
1028217 TTGTTTTTGTTTTTTTG
1 TT-TTTTT-TTTTTTTG
1028234 TTTTTTTTTTTTCCTT-
1 TTTTTTTTTTTT--TTG
*
1028250 TTGTTTTTTTTTTTGG
1 TT-TTTTTTTTTTTTG
* *
1028266 TTTTTCATTTTTTTCG
1 TTTTT-TTTTTTTTTG
1028282 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
1028297 GAGGACGCCG
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
15 17 0.25
16 24 0.35
17 27 0.40
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:1028261 original size:47 final size:48
Alignment explanation
Indices: 1028199--1028293 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 48
1028189 ATCCGGACCC
* *
1028199 CCTTTTTTTGTTTTTTTATTGTTTTT-GTTTTTTT-GTTTTTTTTTTTT
1 CCTTTTTTTGTTTTTTT-TGGTTTTTCATTTTTTTCGTTTTTTTTTTTT
1028246 CCTTTTGTTT-TTTTTTTTGGTTTTTCATTTTTTTCGTTTTTTTTTTTT
1 CCTTTT-TTTGTTTTTTTTGGTTTTTCATTTTTTTCGTTTTTTTTTTTT
1028294 TTGGAGGACG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
46 7 0.16
47 20 0.47
48 16 0.37
ACGTcount: A:0.02, C:0.06, G:0.08, T:0.83
Consensus pattern (48 bp):
CCTTTTTTTGTTTTTTTTGGTTTTTCATTTTTTTCGTTTTTTTTTTTT
Found at i:1028297 original size:32 final size:31
Alignment explanation
Indices: 1028220--1028297 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
1028210 TTTTTTATTG
* *
1028220 TTTTTGTTTTTTT-GTTTTTTTTTTTTCCTT
1 TTTTTTTTTTTTTGGTTTTTTTTTTTTCCGT
1028250 TTGTTTTTTTTTTTGGTTTTTCATTTTTTT-CGT
1 TT-TTTTTTTTTTTGGTTTTT--TTTTTTTCCGT
1028283 TTTTTTTTTTTTTGG
1 TTTTTTTTTTTTTGG
1028298 AGGACGCCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 2 0.05
31 10 0.24
32 19 0.45
33 4 0.10
34 7 0.17
ACGTcount: A:0.01, C:0.05, G:0.10, T:0.83
Consensus pattern (31 bp):
TTTTTTTTTTTTTGGTTTTTTTTTTTTCCGT
Found at i:1042250 original size:52 final size:51
Alignment explanation
Indices: 1042170--1042288 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
1042160 AAAAGTTGCT
*
1042170 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
1042222 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
1042273 TGCATGTATCGATACA
1 TGCATGTATCGATACA
1042289 AAGCTCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:1042301 original size:51 final size:52
Alignment explanation
Indices: 1042170--1042308 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 52
1042160 AAAAGTTGCT
** *
1042170 TGCATGTATCGATAC-ATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACAAGCT-ACAGTGTATCGATACATCTGGGCAAATTTACC
*** * * *
1042222 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-TTGCC
1 TGCATGTATCGATACAAGCTACAGTGTATCGATACATCTGGGCAAATTTACC
1042273 TGCATGTATCGATACAAAGCT-CAGTGTATCGATACA
1 TGCATGTATCGATAC-AAGCTACAGTGTATCGATACA
1042309 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
51 32 0.42
52 42 0.55
53 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
TGCATGTATCGATACAAGCTACAGTGTATCGATACATCTGGGCAAATTTACC
Found at i:1042315 original size:13 final size:13
Alignment explanation
Indices: 1042297--1042321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1042287 CAAAGCTCAG
1042297 TGTATCGATACAA
1 TGTATCGATACAA
1042310 TGTATCGATACA
1 TGTATCGATACA
1042322 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1042399 original size:33 final size:33
Alignment explanation
Indices: 1042362--1042428 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1042352 AGTAGCTTAA
1042362 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1042395 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1042428 A
1 A
1042429 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1042402 original size:13 final size:13
Alignment explanation
Indices: 1042384--1042408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1042374 CAAAAAAATA
1042384 TGTATCGATACAT
1 TGTATCGATACAT
1042397 TGTATCGATACA
1 TGTATCGATACA
1042409 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1043984 original size:52 final size:52
Alignment explanation
Indices: 1043901--1044031 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
1043891 CCCGAAATAT
*
1043901 GAAAATTTGCCTGCATGAATCGATACATTTCATAGTGCATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGCATCGATACATCTGG
* * * *
1043953 GAAAATTTGCCTGTATGTATCGATACTTTTCATAGTGTATCGATATATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGCATCGATACATCTGG
*
1044005 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
1044032 ATGTATCGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGCATCGATACATCTGG
Found at i:1044037 original size:13 final size:13
Alignment explanation
Indices: 1044019--1044044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1044009 ATTTGCCTGC
1044019 ATGTATCGATACA
1 ATGTATCGATACA
1044032 ATGTATCGATACA
1 ATGTATCGATACA
1044045 TTCGAGCAAT
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:1044107 original size:13 final size:13
Alignment explanation
Indices: 1044089--1044172 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1044079 AGCTTCGTAG
1044089 CGATACATTGTAT
1 CGATACATTGTAT
1044102 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1044121 CGATACATTGTAT
1 CGATACATTGTAT
1044134 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1044153 CGATACATTGTAT
1 CGATACATTGTAT
1044166 CGATACA
1 CGATACA
1044173 AATCGTTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1044121 original size:19 final size:18
Alignment explanation
Indices: 1044097--1044159 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1044087 AGCGATACAT
1044097 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1044116 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1044129 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1044148 TGTATCGATACA
1 TGTATCGATACA
1044160 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1044130 original size:32 final size:32
Alignment explanation
Indices: 1044089--1044174 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
1044079 AGCTTCGTAG
1044089 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1044121 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1044153 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
1044175 TCGTTAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1050638 original size:12 final size:12
Alignment explanation
Indices: 1050621--1050650 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1050611 TCTAGTGATT
1050621 ATTAGTCATAGG
1 ATTAGTCATAGG
1050633 ATTAGTCATAGG
1 ATTAGTCATAGG
*
1050645 AGTAGT
1 ATTAGT
1050651 TGTATGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (12 bp):
ATTAGTCATAGG
Found at i:1051761 original size:21 final size:21
Alignment explanation
Indices: 1051735--1051811 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
1051725 GGATCGATAC
1051735 ATTGTATCGATACATACTTGA
1 ATTGTATCGATACATACTTGA
1051756 ATTGTATCGATACATACTTGA
1 ATTGTATCGATACATACTTGA
* *
1051777 ATTGTATCGATACATA-GTGC
1 ATTGTATCGATACATACTTGA
*
1051797 ATTATATCGATACAT
1 ATTGTATCGATACAT
1051812 TGAGCCCAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 16 0.30
21 37 0.70
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (21 bp):
ATTGTATCGATACATACTTGA
Found at i:1053675 original size:94 final size:94
Alignment explanation
Indices: 1053572--1054108 Score: 437
Period size: 94 Copynumber: 5.7 Consensus size: 94
1053562 TTTTTGGTCG
** * * * *
1053572 AACTCTTTCCATTCTTGTTTGATTGTATTGGCATTAGGACTTGGTCAAACTCTTCTCATCCTCGT
1 AACTCTTTCCACCCTCGTTTGATTATATTGGCATTAGGACCTGGTCAAACTCTTCTCATCCTCAT
* * *
1053637 TTAACTGTATTGGCGTTAGGACCTAGTTA
66 TTGACTGTATTGGCATTAGGACCTAGTCA
* * * * * * *
1053666 AACTCTTTCCACTCTCGTTTGACTATATTAGCGTTAGGACCTAGTCAAACTCTT-TCCATTCTCG
1 AACTCTTTCCACCCTCGTTTGATTATATTGGCATTAGGACCTGGTCAAACTCTTCT-CATCCTCA
*
1053730 TTTGACTGTATTAGCATTAGGACCTAGTCA
65 TTTGACTGTATTGGCATTAGGACCTAGTCA
* * * * *
1053760 AACTC-TTCTCATCCTCGTTTGATTGTATTGGCCTTAGGACCTGGTCAAACTC-TCTCTTCCTTT
1 AACTCTTTC-CACCCTCGTTTGATTATATTGGCATTAGGACCTGGTCAAACTCTTCTCATCC-TC
* * *
1053823 ATTTTGA-TGTATTGGCATTA-GCCCTGGCCA
64 A-TTTGACTGTATTGGCATTAGGACCTAGTCA
* ** * * ** *
1053853 AACCCTTTTTACCCAT-ATTTGACTATATTGGCATTAAAACCTGGTCAAACTCAAATC-CA-CTC
1 AACTCTTTCCACCC-TCGTTTGATTATATTGGCATTAGGACCTGGTCAAACTC--TTCTCATC-C
* *
1053915 TCATTTGACTATATTGGCATTAGGACCTAGTTA
62 TCATTTGACTGTATTGGCATTAGGACCTAGTCA
* * * * * **
1053948 AACTCTTTCCACTCTCGTTTGATTAAATTGGCATTAGTACCTAGTCAAACGTTTTC-CAAACTCA
1 AACTCTTTCCACCCTCGTTTGATTATATTGGCATTAGGACCTGGTCAAAC-TCTTCTCATCCTCA
* *
1054012 TTTGATTGTATTGGCATTAGAACCTAGTCA
65 TTTGACTGTATTGGCATTAGGACCTAGTCA
* * * * * * * *
1054042 AACTCTTTCCTACCCTTGTTTAATTGTATTAGCATTA-GCCCTCGATCAAATTCTTTTCATCCTC
1 AACTCTTTCC-ACCCTCGTTTGATTATATTGGCATTAGGACCT-GGTCAAACTCTTCTCATCCTC
1054106 ATT
64 ATT
1054109 CGACATGATG
Statistics
Matches: 347, Mismatches: 77, Indels: 37
0.75 0.17 0.08
Matches are distributed among these distances:
93 57 0.16
94 203 0.59
95 84 0.24
96 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (94 bp):
AACTCTTTCCACCCTCGTTTGATTATATTGGCATTAGGACCTGGTCAAACTCTTCTCATCCTCAT
TTGACTGTATTGGCATTAGGACCTAGTCA
Found at i:1054051 original size:47 final size:47
Alignment explanation
Indices: 1053572--1054079 Score: 389
Period size: 47 Copynumber: 10.8 Consensus size: 47
1053562 TTTTTGGTCG
** * * * *
1053572 AACTCTTTCCATTCTTGTTTGATTGTATTGGCATTAGGACTTGGTCA
1 AACTCTTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* * * *
1053619 AACTC-TTCTCATCCTCGTTTAACTGTATTGGCGTTAGGACCTAGTTA
1 AACTCTTTC-CACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* * * *
1053666 AACTCTTTCCACTCTCGTTTGACTATATTAGCGTTAGGACCTAGTCA
1 AACTCTTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
** *
1053713 AACTCTTTCCATTCTCGTTTGACTGTATTAGCATTAGGACCTAGTCA
1 AACTCTTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* * * *
1053760 AACTC-TTCTCATCCTCGTTTGATTGTATTGGCCTTAGGACCTGGTCA
1 AACTCTTTC-CACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* ** * ** * * *
1053807 AACTCTCTCTTCCTTTATTTTGA-TGTATTGGCATTA-GCCCTGGCCA
1 AACTCTTTCCACC-CTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* ** * * ** *
1053853 AACCCTTTTTACCCAT-ATTTGACTATATTGGCATTAAAACCTGGTCA
1 AACTCTTTCCACCC-TCGTTTGACTGTATTGGCATTAGGACCTAGTCA
** * * * *
1053900 AACTCAAATCCACTCTCATTTGACTATATTGGCATTAGGACCTAGTTA
1 AACTC-TTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* * ** *
1053948 AACTCTTTCCACTCTCGTTTGATTAAATTGGCATTAGTACCTAGTCA
1 AACTCTTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
** * * *
1053995 AACGT-TTTCCAAACTCATTTGATTGTATTGGCATTAGAACCTAGTCA
1 AAC-TCTTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
* * * *
1054042 AACTCTTTCCTACCCTTGTTTAATTGTATTAGCATTAG
1 AACTCTTTCC-ACCCTCGTTTGACTGTATTGGCATTAG
1054080 CCCTCGATCA
Statistics
Matches: 377, Mismatches: 71, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
45 5 0.01
46 37 0.10
47 266 0.71
48 69 0.18
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (47 bp):
AACTCTTTCCACCCTCGTTTGACTGTATTGGCATTAGGACCTAGTCA
Found at i:1054328 original size:85 final size:85
Alignment explanation
Indices: 1054169--1054445 Score: 346
Period size: 85 Copynumber: 3.3 Consensus size: 85
1054159 GGTATCGTTT
* * * * *
1054169 TTCATC-CCTTGTTTACCTGTCAGCTTAGTCCTCGATAAACCCATTACCACCTATGGTGACCTGT
1 TTCATCTCATTGTTTACCTGTCAGCTCAGTTCTCGGTAAACCCATTACC-CCTATGGTGACCTAT
*
1054233 CAGCTCAGTCTTCGGTCAACC
65 CAGCTTAGTCTTCGGTCAACC
* *
1054254 TTCATCTCATTGTTTACTTGTCAGCTCAGTTCTCGGTAAACCCACTACCCCTATGGTGACCTATC
1 TTCATCTCATTGTTTACCTGTCAGCTCAGTTCTCGGTAAACCCATTACCCCTATGGTGACCTATC
* *
1054319 AACTTAGTCTTCGATCAACC
66 AGCTTAGTCTTCGGTCAACC
* * *
1054339 TTTATCTCTTTGTTTA-CTGGTCAGCTCAG-TCCCTGGTAAACCCATTACCCCTATGGTGACCTA
1 TTCATCTCATTGTTTACCT-GTCAGCTCAGTTCTC-GGTAAACCCATTACCCCTATGGTGACCTA
* *
1054402 TCAGCTTAGTC-TCTAGTAAACC
64 TCAGCTTAGTCTTC-GGTCAACC
*
1054424 TCCATCTCATTGTTTACCTGTC
1 TTCATCTCATTGTTTACCTGTC
1054446 GGCCTAGTCC
Statistics
Matches: 165, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
84 6 0.04
85 121 0.73
86 38 0.23
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.35
Consensus pattern (85 bp):
TTCATCTCATTGTTTACCTGTCAGCTCAGTTCTCGGTAAACCCATTACCCCTATGGTGACCTATC
AGCTTAGTCTTCGGTCAACC
Found at i:1054421 original size:43 final size:43
Alignment explanation
Indices: 1054289--1054423 Score: 105
Period size: 43 Copynumber: 3.2 Consensus size: 43
1054279 TCAGTTCTCG
* * *
1054289 GTAAACCCACTACCCCTATGGTGACCTATCAACTTAGTCT-TC
1 GTAAACCCATTACCCCTATGGTGACCTATCAGCTTAGTCTCTA
* * * * * * * * * * *
1054331 GATCAA-CCTTTATCTCTTTGTTTA-CTGGTCAGCTCAGTCCCTG
1 G-TAAACCCATTACCCCTATGGTGACCT-ATCAGCTTAGTCTCTA
1054374 GTAAACCCATTACCCCTATGGTGACCTATCAGCTTAGTCTCTA
1 GTAAACCCATTACCCCTATGGTGACCTATCAGCTTAGTCTCTA
1054417 GTAAACC
1 GTAAACC
1054424 TCCATCTCAT
Statistics
Matches: 64, Mismatches: 24, Indels: 9
0.66 0.25 0.09
Matches are distributed among these distances:
41 2 0.03
42 24 0.38
43 36 0.56
44 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (43 bp):
GTAAACCCATTACCCCTATGGTGACCTATCAGCTTAGTCTCTA
Found at i:1055763 original size:164 final size:164
Alignment explanation
Indices: 1055334--1056368 Score: 1055
Period size: 164 Copynumber: 6.3 Consensus size: 164
1055324 TTCAAACATC
* * * * * * *
1055334 AAAATTCTTCAAATATTATTATTTAATTCCTATAAAATCA-ATTTTAAAAATTC-TT-TTTATTT
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATT-TTC
* * ** * * *
1055396 ATTAGGTTATTG-ATTTTCTT-TTGGAATTCTTTCAATTTTCAAATTACAGG-GTTTTCTTCCCC
65 ATGA-GTT-TTGAATTTT-TTCTT-GAAAT-TTTCTTTTTTCAAAATAC-GGAGTTTTCTACTCC
* * * * **
1055458 GTAAATTTTTTTTGGAGGATTTTCATAGGTTTAAAATTTTT
124 ATAAATTTTTTTAGGGGGATTTTCATTGGTTTTTAATTTTT
* ** * *
1055499 AAAAATCAAAAAATATTATTATTTAATTCATATTAAATAAG-TTTTAAAAAATCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
* * * * * *
1055563 TGTGTTTTTTAATTTGTT-TTGAAATTTCCCTATTTTCAAAATACGGATTTTTCTACTCCAT-AA
66 TGAG-TTTTGAATTTTTTCTTGAAATTT-TCTTTTTTCAAAATACGGAGTTTTCTACTCCATAAA
1055626 TTTTTTTAGGGGGATTTTTC-TTGGTTTTTAATTTTT
129 TTTTTTTAGGGGGA-TTTTCATTGGTTTTTAATTTTT
* * * *
1055662 AAAATTCATCAAATATTATTATTTAATTTATAATAAATTATTTTTTAAAAATTTATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
*
1055727 TGAGTTTTGATTTTTTTCTTGAAATTTTCTTATTTTCAAAATACGGAGTTTTCTACTCCATAAAT
66 TGAGTTTTGAATTTTTTCTTGAAATTTTCTT-TTTTCAAAATACGGAGTTTTCTACTCCATAAAT
* * *
1055792 TCTTTCAGGGGGATTTTTATTGGTTTTTAATTTTT
130 TTTTTTAGGGGGATTTTCATTGGTTTTTAATTTTT
* *
1055827 AAAA-TCATCAAATATTATTATTTAATTCATATTAAATTATTTTTTAAAAATTCATTCATTTTTA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
* * * * * *
1055891 TGAGTTTTTGAATTTTTTCTTGAAATTCTCTTGTTTCCAAAATACGAAGTTTTCTACTTCGTAAT
66 TGAG-TTTTGAATTTTTTCTTGAAATTTTCTT-TTTTCAAAATACGGAGTTTTCTACTCCATAAA
*
1055956 TTTTTTTA-GGGGATTTTCTTTGGTTTTTAACTTTTT
129 TTTTTTTAGGGGGATTTTCATTGGTTTTTAA-TTTTT
* *
1055992 -AAATTCATAAAATATTATTATTTAATTCATATTAAATT-GGTTTTAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
* * * * * * * * *
1056055 TAGATTTTTAAATTTTTTCTTGAAACTCTCCTTTTTTCGAAATATGAAGTTTTCTTCTCTATAAA
66 T-GAGTTTTGAATTTTTTCTTGAAA-TTTTCTTTTTTCAAAATACGGAGTTTTCTACTCCATAAA
* **
1056120 TTTTTTCAGAAGGATTTTCATTGGTTTTTAATTTTT
129 TTTTTTTAGGGGGATTTTCATTGGTTTTTAATTTTT
* *
1056156 AAAATTCATCAAATATCATTATTTAATTCTTATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
* * * * * *
1056221 TTCATTTTTGAATTTTTTCTTAAAATTTTCTTTTTTGAAAA-ACTGAGTTTTCTTCTCCATAAAT
66 -TGAGTTTTGAATTTTTTCTTGAAATTTTCTTTTTTCAAAATACGGAGTTTTCTACTCCATAAAT
* **
1056285 TTTTTCTA-GGGGATTTTC-TCT-ATTTAAAATTTTT
130 TTTTT-TAGGGGGATTTTCAT-TGGTTTTTAATTTTT
* * * * *
1056319 AGAATTCAT-ATAATATTGTCATTAAATTCATATTAAATCAGTTTTTAAAA
1 AAAATTCATCA-AATATTATTATTTAATTCATATTAAATTAGTTTTTAAAA
1056369 TTTTAAATTA
Statistics
Matches: 734, Mismatches: 111, Indels: 52
0.82 0.12 0.06
Matches are distributed among these distances:
162 1 0.00
163 129 0.18
164 291 0.40
165 254 0.35
166 56 0.08
167 3 0.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (164 bp):
AAAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTTTTAAAAATTCATTCATTTTCA
TGAGTTTTGAATTTTTTCTTGAAATTTTCTTTTTTCAAAATACGGAGTTTTCTACTCCATAAATT
TTTTTAGGGGGATTTTCATTGGTTTTTAATTTTT
Found at i:1056014 original size:329 final size:327
Alignment explanation
Indices: 1055430--1056373 Score: 1102
Period size: 329 Copynumber: 2.9 Consensus size: 327
1055420 AATTCTTTCA
* * * ** * **
1055430 ATTTTCAAATTACAGG-GTTTTCTTCCCCGTAAATTTTTTTTGGAGGATTTTCATAGGTTTAAAA
1 ATTTTCAAAATAC-GGAGTTTTCTTCTCCATAAATTTTTTCAGGAGGATTTTCATTGGTTTTTAA
** * *
1055494 TTTTTAAAAATCAAAAAATATTATTATTTAATTCATATTAAA-TAAGTTTTAAAAAATCATTCAT
65 TTTTT-AAAATCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTCATTCAT
* * * * *
1055558 TTTCATGTGTTTTTTAATTTGTT-TTGAAATTTCCCTATTTTCAAAATACGGATTTTTCTACTCC
129 TTTCATGAGTTTTTGAATTTTTTCTTGAAA-TTCTCT-TTTTCAAAATAC-GAGTTTTCTACTCC
*
1055622 ATAA-TTTTTTTAGGGGGATTTT-TCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
191 ATAATTTTTTTTA-GGGGATTTTCT-TTGGTTTTTAATTTTT-AAATTCATAAAATATTATTATT
* * * * *
1055685 TAATTTATAATAAATTATTTTTTAAAAATTTATTCATTTTCAT-GAGTTTTGATTTTTTTCTTGA
253 TAATTCATATTAAATTAGTTTTTAAAAATTTATTCATTTTCATAGAGTTTTAAATTTTTTCTTGA
* *
1055749 AA-TTTTCTT
318 AACTCTCCTT
* * * *
1055758 ATTTTCAAAATACGGAGTTTTCTACTCCATAAATTCTTTCAGGGGGATTTTTATTGGTTTTTAAT
1 ATTTTCAAAATACGGAGTTTTCTTCTCCATAAATTTTTTCAGGAGGATTTTCATTGGTTTTTAAT
*
1055823 TTTTAAAATCATCAAATATTATTATTTAATTCATATTAAATTATTTTTTAAAAATTCATTCATTT
66 TTTTAAAATCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTCATTCATTT
* * *
1055888 TTATGAGTTTTTGAATTTTTTCTTGAAATTCTCTTGTTTCCAAAATACGAAGTTTTCTACTTCGT
131 TCATGAGTTTTTGAATTTTTTCTTGAAATTCTCTT-TTT-CAAAATACG-AGTTTTCTACTCCAT
1055953 AATTTTTTTTAGGGGATTTTCTTTGGTTTTTAACTTTTTAAATTCATAAAATATTATTATTTAAT
193 AATTTTTTTTAGGGGATTTTCTTTGGTTTTTAA-TTTTTAAATTCATAAAATATTATTATTTAAT
* * *
1056018 TCATATTAAATT-GGTTTTAAAAATTCATTCATTTTCATAGATTTTTAAATTTTTTCTTGAAACT
257 TCATATTAAATTAGTTTTTAAAAATTTATTCATTTTCATAGAGTTTTAAATTTTTTCTTGAAACT
1056082 CTCCTT
322 CTCCTT
* * * * *
1056088 -TTTTCGAAATATGAAGTTTTCTTCTCTATAAATTTTTTCAGAAGGATTTTCATTGGTTTTTAAT
1 ATTTTCAAAATACGGAGTTTTCTTCTCCATAAATTTTTTCAGGAGGATTTTCATTGGTTTTTAAT
* * *
1056152 TTTTAAAATTCATCAAATATCATTATTTAATTCTTATTAAATTAGTTTTTAAAAATTCATTCATT
66 TTTTAAAA-TCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTCATTCATT
* * * * *
1056217 TTCATTCA-TTTTTGAATTTTTTCTTAAAATTTTCTTTTTTGAAAA-ACTGAGTTTTCTTCTCCA
130 TTCA-TGAGTTTTTGAATTTTTTCTTGAAATTCTC-TTTTTCAAAATAC-GAGTTTTCTACTCCA
* * * ** * * * *
1056280 TAAATTTTTTCTAGGGGATTTTCTCT-ATTTAAAATTTTTAGAATTCATATAATATTGTCATTAA
192 T-AATTTTTTTTAGGGGATTTTCTTTGGTTTTTAATTTTTA-AATTCATAAAATATTATTATTTA
* *
1056344 ATTCATATTAAATCAGTTTTTAAAATTTTA
255 ATTCATATTAAATTAGTTTTTAAAAATTTA
1056374 AATTATTTCA
Statistics
Matches: 529, Mismatches: 69, Indels: 35
0.84 0.11 0.06
Matches are distributed among these distances:
327 43 0.08
328 175 0.33
329 205 0.39
330 102 0.19
331 4 0.01
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (327 bp):
ATTTTCAAAATACGGAGTTTTCTTCTCCATAAATTTTTTCAGGAGGATTTTCATTGGTTTTTAAT
TTTTAAAATCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTCATTCATTT
TCATGAGTTTTTGAATTTTTTCTTGAAATTCTCTTTTTCAAAATACGAGTTTTCTACTCCATAAT
TTTTTTTAGGGGATTTTCTTTGGTTTTTAATTTTTAAATTCATAAAATATTATTATTTAATTCAT
ATTAAATTAGTTTTTAAAAATTTATTCATTTTCATAGAGTTTTAAATTTTTTCTTGAAACTCTCC
TT
Found at i:1058136 original size:19 final size:18
Alignment explanation
Indices: 1058108--1058165 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
1058098 CTGTATCGAT
*
1058108 ACATTATATCGATACATG
1 ACATTGTATCGATACATG
1058126 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
1058146 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1058165 A
1 A
1058166 AACTGGCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 17 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:1058154 original size:20 final size:20
Alignment explanation
Indices: 1058109--1058164 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1058099 TGTATCGATA
*
1058109 CATTATATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
1058128 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
1058147 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1058165 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:1058227 original size:13 final size:13
Alignment explanation
Indices: 1058209--1058261 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1058199 CGATACATGG
1058209 TACATTGTATCGA
1 TACATTGTATCGA
*
1058222 TACATTGTATCAA
1 TACATTGTATCGA
1058235 TACA-TG-AT-G-
1 TACATTGTATCGA
1058244 -A-ATTGTATCGA
1 TACATTGTATCGA
1058255 TACATTG
1 TACATTG
1058262 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 1 0.03
11 2 0.06
12 3 0.09
13 20 0.62
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1058238 original size:33 final size:33
Alignment explanation
Indices: 1058193--1058261 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1058183 CTACCACTAT
* *
1058193 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCAATACATGATGA-ATTGTATCGATACA
1058226 TTGTATCAATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAATTGTATCGATACA
1058259 TTG
1 TTG
1058262 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCAATACATGATGAATTGTATCGATACA
Found at i:1058719 original size:23 final size:23
Alignment explanation
Indices: 1058688--1058732 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1058678 TCTTAGAAAC
1058688 TTGGGGTATAGTTCTTAAAGAGT
1 TTGGGGTATAGTTCTTAAAGAGT
* *
1058711 TTGGTGTATAGTTCTTGAAGAG
1 TTGGGGTATAGTTCTTAAAGAG
1058733 ATTGAGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.40
Consensus pattern (23 bp):
TTGGGGTATAGTTCTTAAAGAGT
Found at i:1059904 original size:12 final size:12
Alignment explanation
Indices: 1059869--1059904 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1059859 GTCAACCATC
*
1059869 AATGATGATGAA
1 AATGATGATGAT
*
1059881 AATGATAATGAT
1 AATGATGATGAT
1059893 AATGATGATGAT
1 AATGATGATGAT
1059905 GATGGTGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (12 bp):
AATGATGATGAT
Found at i:1064467 original size:205 final size:205
Alignment explanation
Indices: 1064115--1064524 Score: 802
Period size: 205 Copynumber: 2.0 Consensus size: 205
1064105 TTTCAGATCA
1064115 ATGTATCGATACATTATGAATTGTATCGATACATGGCTACGGGAATGCATTAAAACAAGCACCAA
1 ATGTATCGATACATTATGAATTGTATCGATACATGGCTACGGGAATGCATTAAAACAAGCACCAA
1064180 ACAAGCTTACAATGGCTAGAAACACAATCATTCAACCTCCAACGTATATGTCAGCATTCAAGCCT
66 ACAAGCTTACAATGGCTAGAAACACAATCATTCAACCTCCAACGTATATGTCAGCATTCAAGCCT
1064245 ATAAATTTGAGTTTCCAATAGCTGAAATGCAAAAGAAGAAAACCAAGAAATGCCAAGAGATCAAG
131 ATAAATTTGAGTTTCCAATAGCTGAAATGCAAAAGAAGAAAACCAAGAAATGCCAAGAGATCAAG
1064310 TATTCAAAGT
196 TATTCAAAGT
*
1064320 ATGTATCGATACATTGTGAATTGTATCGATACATGGCTACGGGAATGCATTAAAACAAGCACCAA
1 ATGTATCGATACATTATGAATTGTATCGATACATGGCTACGGGAATGCATTAAAACAAGCACCAA
1064385 ACAAGCTTACAATGGCTAGAAACACAATCATTCAACCTCCAACGTATATGTCAGCATTCAAGCCT
66 ACAAGCTTACAATGGCTAGAAACACAATCATTCAACCTCCAACGTATATGTCAGCATTCAAGCCT
*
1064450 ATAAATTTGAGTTTCCAATAGCTGAAATGCAAGAGAAGAAAACCAAGAAATGCCAAGAGATCAAG
131 ATAAATTTGAGTTTCCAATAGCTGAAATGCAAAAGAAGAAAACCAAGAAATGCCAAGAGATCAAG
1064515 TATTCAAAGT
196 TATTCAAAGT
1064525 TTGATTAGTT
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
205 203 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (205 bp):
ATGTATCGATACATTATGAATTGTATCGATACATGGCTACGGGAATGCATTAAAACAAGCACCAA
ACAAGCTTACAATGGCTAGAAACACAATCATTCAACCTCCAACGTATATGTCAGCATTCAAGCCT
ATAAATTTGAGTTTCCAATAGCTGAAATGCAAAAGAAGAAAACCAAGAAATGCCAAGAGATCAAG
TATTCAAAGT
Found at i:1068445 original size:13 final size:13
Alignment explanation
Indices: 1068427--1068452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1068417 CAATTTTTTG
1068427 TGTATCGATACAT
1 TGTATCGATACAT
1068440 TGTATCGATACAT
1 TGTATCGATACAT
1068453 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1069201 original size:21 final size:21
Alignment explanation
Indices: 1069160--1069203 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1069150 CTCCCCTTTA
* *
1069160 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1069181 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1069202 TC
1 TC
1069204 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1073098 original size:15 final size:15
Alignment explanation
Indices: 1073078--1073108 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1073068 ATTTCGTTTG
*
1073078 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1073093 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1073108 G
1 G
1073109 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1074941 original size:21 final size:21
Alignment explanation
Indices: 1074912--1074956 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1074902 AAGTTTTCAT
*
1074912 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1074932 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1074954 TTT
1 TTT
1074957 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1077190 original size:13 final size:13
Alignment explanation
Indices: 1077172--1077197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1077162 CAATTTTTTG
1077172 TGTATCGATACAT
1 TGTATCGATACAT
1077185 TGTATCGATACAT
1 TGTATCGATACAT
1077198 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1079628 original size:20 final size:20
Alignment explanation
Indices: 1079599--1079669 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
1079589 AGGCACTCAT
1079599 CTCC-AGGTCGCGATCGGCA
1 CTCCTAGGTCGCGATCGGCA
* *
1079618 CTCTTAGGTCGCGATTGGCA
1 CTCCTAGGTCGCGATCGGCA
*
1079638 CTCCTAGGTCGCGATCGGTA
1 CTCCTAGGTCGCGATCGGCA
1079658 CTCCTAGGTCGC
1 CTCCTAGGTCGC
1079670 AACTGGGTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 3 0.07
20 43 0.93
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.24
Consensus pattern (20 bp):
CTCCTAGGTCGCGATCGGCA
Found at i:1081102 original size:22 final size:22
Alignment explanation
Indices: 1081077--1081118 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1081067 TTTTTTAAGA
1081077 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
1081099 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
1081119 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:1081774 original size:20 final size:19
Alignment explanation
Indices: 1081728--1081786 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 19
1081718 TTGTATTGAT
* *
1081728 ACATTGTATCGATACATGT
1 ACATTGTATCAATACATGA
*
1081747 TCATTGTATCAATACATGA
1 ACATTGTATCAATACATGA
1081766 ACAATTGTATCAATACATGA
1 AC-ATTGTATCAATACATGA
1081786 A
1 A
1081787 ACTGGTAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
ACATTGTATCAATACATGA
Found at i:1081850 original size:13 final size:13
Alignment explanation
Indices: 1081829--1081859 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1081819 CGATACATGG
*
1081829 TACAATGTATTGA
1 TACATTGTATTGA
1081842 TACATTGTATTGA
1 TACATTGTATTGA
1081855 TACAT
1 TACAT
1081860 GATGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATTGA
Found at i:1082940 original size:24 final size:24
Alignment explanation
Indices: 1082864--1082941 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
1082854 TGATATAACA
*
1082864 AAAAGGGGGAGAAATATTGCTTTTG
1 AAAATGGGGAGAAATATTG-TTTTG
*** * * *
1082889 AAAAT-AAAATAAATTTTGCTTTG
1 AAAATGGGGAGAAATATTGTTTTG
1082912 AAAAATGGGGAGAAATATTGTTTTG
1 -AAAATGGGGAGAAATATTGTTTTG
1082937 AAAAT
1 AAAAT
1082942 AAATTTTTAT
Statistics
Matches: 38, Mismatches: 13, Indels: 5
0.68 0.23 0.09
Matches are distributed among these distances:
23 4 0.11
24 18 0.47
25 16 0.42
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (24 bp):
AAAATGGGGAGAAATATTGTTTTG
Found at i:1083599 original size:13 final size:13
Alignment explanation
Indices: 1083581--1083607 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1083571 ACATTATGCT
1083581 TTGTATCGATACA
1 TTGTATCGATACA
1083594 TTGTATCGATACA
1 TTGTATCGATACA
1083607 T
1 T
1083608 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1083604 original size:33 final size:32
Alignment explanation
Indices: 1083562--1083626 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1083552 CACACCCAGA
* *
1083562 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCGATACAT
1083595 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTGTATCGATACAT
1083627 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACAT
Found at i:1083616 original size:19 final size:18
Alignment explanation
Indices: 1083591--1083648 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
1083581 TTGTATCGAT
1083591 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
1083609 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
1083629 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1083648 A
1 A
1083649 AACTGGCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:1083637 original size:20 final size:20
Alignment explanation
Indices: 1083592--1083647 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1083582 TGTATCGATA
1083592 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
1083611 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
1083630 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1083648 AAACTGGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:1083701 original size:20 final size:20
Alignment explanation
Indices: 1083676--1083729 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1083666 TTACCACTGT
* *
1083676 TTGTATCAATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
1083696 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
1083716 TTGTATCGATACAT
1 TTGTATCGATACAT
1083730 TGCCTGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:1089632 original size:28 final size:28
Alignment explanation
Indices: 1089563--1090712 Score: 901
Period size: 28 Copynumber: 40.8 Consensus size: 28
1089553 CACCAACTTG
* * *
1089563 TGTGGGCTTTAGAGAAAGTTGCCACCGACT
1 TGTGGGCTTTA-A-AAGGATGCCACTGACT
* *
1089593 TGTGTGGACTTTAAAAGGATGCCGCTAACT
1 TGTG-GG-CTTTAAAAGGATGCCACTGACT
* **
1089623 TGTGGGCTTTAAGAATG-TGCCTTTGACT
1 TGTGGGCTTTAA-AAGGATGCCACTGACT
** * *
1089651 TGTGGGCTTTGTGAATG-TGCCACTGATT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
1089679 TGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* *
1089707 TGTGGGCTATAAAAAGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
1089735 TGTGGGCTTTGAAAA-AAGTGCCACTGACT
1 TGTGGGCTTT-AAAAGGA-TGCCACTGACT
* *
1089764 TGTGGGCTGTGAAAAGG-TGCCACTGATT
1 TGTGGGCT-TTAAAAGGATGCCACTGACT
* * * *
1089792 TGTGAGCTTTGAAAA-GTTGTCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* ** *
1089820 TATGGGCATGGAAAA-AATGCCACTGACT
1 TGTGGGC-TTTAAAAGGATGCCACTGACT
*
1089848 TGTAGGCTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* ** *
1089876 TATAAGCTTTGAAAA-GAAGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1089904 TATGGGCTTTGAAAA-AATGCCATTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
**
1089932 TGTTTGCTTTTAAAAGGATGCCACTGAC-
1 TGTGGGC-TTTAAAAGGATGCCACTGACT
* **
1089960 TATGGGCTTTGAAAAGGATGCCACAAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
1089989 TGTGGACTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
1090017 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
1090045 TGTAGGCTTGGAAAA-GATGCCATTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
*
1090073 TGTGGGCTTTGAAAA-GATGCCACCGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1090101 TATGGGCTTTGAAAA-GATGCTAGTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * * *
1090129 TATGGGCTTTAAAAAGACGCCATTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
** *
1090157 TGTTTGCTTTTGAAAGGATGCCACTGAC-
1 TGTGGGC-TTTAAAAGGATGCCACTGACT
* **
1090185 TATGGGCTTTGAAAAGGATGCCACAAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
1090214 TGTGGACTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
** *
1090242 TGTTAGCTTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTTAAAAGGATGCCACTGACT
* *
1090271 TGTGGGCTTGGAAAA-GATGCCACTAACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
1090299 TGTGGGCTTTGAAAA-GATGCCA-TCGACT
1 TGTGGGCTTT-AAAAGGATGCCACT-GACT
*
1090327 TGTGGGCTTTGAAAA-GATGCCACCGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1090355 TGTTGGCTTTCGAAAGGATGCCATTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
1090384 TGTGGGCTTTGAAAAGGATACCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1090413 TGTGGACTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
1090441 TGTGGGCTTTGAAAAGG-TCCCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
1090469 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1090497 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * * *
1090525 TGTGGACTTTGAAAAAGACGCCACGGAGT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1090554 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
1090581 TGTGGACTTTAAAAGGATGCCACAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
1090609 TGTGGACTTTAAAAGGATACCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
1090637 TGTTGAC-TTAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * *
1090664 TGTGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
1090692 TGTGGAC-TTAAAAGGTTGCCA
1 TGTGGGCTTTAAAAGGATGCCA
1090713 TGAAGCTATG
Statistics
Matches: 928, Mismatches: 156, Indels: 75
0.80 0.13 0.06
Matches are distributed among these distances:
27 83 0.09
28 640 0.69
29 177 0.19
30 20 0.02
31 3 0.00
32 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:1089785 original size:113 final size:113
Alignment explanation
Indices: 1089563--1090631 Score: 902
Period size: 113 Copynumber: 9.5 Consensus size: 113
1089553 CACCAACTTG
* * * *
1089563 TGTGGGCTTTAGAGAAAGTTGCCACCGACTTGTGTGGACTTTAAAAGGATGCCGCTAACTTGTGG
1 TGTGGGCTTT-GA-AAAGGTGCCACTGACTTGTG-GG-CTTTAAAAGGATGCCACTGACTTGTGG
* * ** ** * *
1089628 GCTTT-AAGAATGTGCCTTTGACTTGTGGGCTTTGTGAATGTGCCACTGATT
62 GCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
1089679 TGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGCTATAAAAAGATGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT
* *
1089744 TGAAAAAAGTGCCACTGACTTGTGGGCTGTGAAAAGGTGCCACTGATT
66 TGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * * * ** * *
1089792 TGTGAGCTTTGAAAAGTTGTCACTAACTTATGGGCATGGAAAA-AATGCCACTGACTTGTAGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC-TTTAAAAGGATGCCACTGACTTGTGGGCT
* * ** **
1089856 TTGAAAAGA-TGCCACTGACTTATAAGCTTTGAAAAGAAGCCACTGACT
65 TTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* ** * ** *
1089904 TATGGGCTTTGAAAAAATGCCATTGACTTGTTTGCTTTTAAAAGGATGCCACTGAC-TATGGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC-TTTAAAAGGATGCCACTGACTTGTGGGCT
* ** *
1089968 TTG-AAAAGGATGCCACAAACTTGTGGACTTT-AAAAGGATGCCACTGACT
65 TTGAAAAAAG-TGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * * *
1090017 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTAGGCTTGGAAAA-GATGCCATTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT-TAAAAGGATGCCACTGACTTGTGGGCT
* * * * * *
1090081 TTGAAAAGA-TGCCACCGACTTATGGGCTTTGAAAAGATGCTAGTGACT
65 TTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * ** * ** * *
1090129 TATGGGCTTTAAAAAGACGCCATTGACTTGTTTGCTTTTGAAAGGATGCCACTGAC-TATGGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC-TTTAAAAGGATGCCACTGACTTGTGGGCT
* ** *
1090193 TTG-AAAAGGATGCCACAAACTTGTGGACTTT-AAAAGGATGCCACTGACT
65 TTGAAAAAAG-TGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
** * *
1090242 TGTTAGCTTTTG-AAAGGATGCCACTGACTTGTGGGCTTGGAAAA-GATGCCACTAACTTGTGGG
1 TGTGGGC-TTTGAAAAGG-TGCCACTGACTTGTGGGCTT-TAAAAGGATGCCACTGACTTGTGGG
* * *
1090305 CTTTGAAAAGA-TGCCA-TCGACTTGTGGGCTTTGAAAAGATGCCACCGACT
63 CTTTGAAAAAAGTGCCACT-GACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * *
1090355 TGTTGGCTTTCG-AAAGGATGCCATTGACTTGTGGGCTTTGAAAAGGATACCACTGACTTGTGGA
1 TGTGGGCTTT-GAAAAGG-TGCCACTGACTTGTGGGCTTT-AAAAGGATGCCACTGACTTGTGGG
** * * *
1090419 CTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGGTCCCACTAACT
63 CTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * * *
1090469 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGACTT
1 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT
* * * * * *
1090534 TG-AAAAAGACGCCACGGAGTTGTGGAC-TT-AAAAGGATGCCACGGAGT
66 TGAAAAAAG-TGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * * *
1090581 TGTGGACTTT-AAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGATACCAC
1 TGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTAAAAGGATGCCAC
1090632 GGAGTTGTTG
Statistics
Matches: 763, Mismatches: 159, Indels: 66
0.77 0.16 0.07
Matches are distributed among these distances:
111 21 0.03
112 260 0.34
113 334 0.44
114 132 0.17
115 6 0.01
116 10 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (113 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTT
TGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:1090574 original size:27 final size:27
Alignment explanation
Indices: 1090196--1091110 Score: 702
Period size: 27 Copynumber: 33.1 Consensus size: 27
1090186 ATGGGCTTTG
** *
1090196 AAAAGGATGCCACAAACTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
* * *
1090224 AAAAGGATGCCACTGACTTGT-TAGCTTTT
1 AAAAGGATGCCACGGAGTTGTGGA-C--TT
* * * *
1090253 GAAAGGATGCCACTGACTTGTGGGCTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
** * *
1090280 GGAAAA-GATGCCACTAACTTGTGGGCTTT
1 --AAAAGGATGCCACGGAGTTGTGGAC-TT
* *
1090309 GAAAA-GATGCCATC-GACTTGTGGGCTTT
1 -AAAAGGATGCCA-CGGAGTTGTGGAC-TT
* *
1090337 GAAAA-GATGCCACCGACTTGTTGG-CTTT
1 -AAAAGGATGCCACGGAGTTG-TGGAC-TT
* ** * *
1090365 CGAAAGGATGCCATTGACTTGTGGGCTTT
1 -AAAAGGATGCCACGGAGTTGTGGAC-TT
* * *
1090394 GAAAAGGATACCACTGACTTGTGGACTTT
1 -AAAAGGATGCCACGGAGTTGTGGAC-TT
* ** * *
1090423 GAAAGGATGCCACTAACTTGTGGGCTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
* ** * *
1090451 GAAAAGG-TCCCACTAACTTGTGGGCTTT
1 -AAAAGGATGCCACGGAGTTGTGGAC-TT
** * *
1090479 GAAAAGG-TGCCACTAACTTGTGGGCTTT
1 -AAAAGGATGCCACGGAGTTGTGGAC-TT
* * * *
1090507 GAAAGGGTGCCACTGATTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
* *
1090535 GAAAAAGACGCCACGGAGTTGTGGACTT
1 -AAAAGGATGCCACGGAGTTGTGGACTT
1090563 AAAAGGATGCCACGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
*
1090591 AAAAGGATGCCACAGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
* *
1090619 AAAAGGATACCACGGAGTTGTTGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
1090646 AAAAGGATGCCATGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
1090674 AAAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* * * * *
1090701 AAAAGGTTGCCATGAAGCTATGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* *
1090728 AAAAGGTTGCCACGGAGTTGTAGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* * *
1090755 AAAAGGTTGCCACGGAGCTGTTGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* * *
1090782 AAAAGGTTGTCACGGAGCTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* *
1090809 AAAAGGTTGCCACAGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* * * **
1090836 AAAGGGTTGCCACGGAGCTGTGGAGAT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* *
1090863 AAAA-GATTGCCACGGAGTTATGAACTT
1 AAAAGGA-TGCCACGGAGTTGTGGACTT
* *
1090890 AAAAGGTTGCCACGGAGCTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
1090917 AAAAGTG-TGCCACGGAGTTGTGGACTT
1 AAAAG-GATGCCACGGAGTTGTGGACTT
*
1090944 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
1090971 AAAAGGTTGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* ** *
1090998 AAAAATG-TGCCAAAGAGTTATGGACTT
1 -AAAAGGATGCCACGGAGTTGTGGACTT
* *
1091025 AAAAGGTTGCCACGGAGTTATGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
*
1091053 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
1091080 AAAAGTG-TGCCACGGAGTTGTAGACTT
1 AAAAG-GATGCCACGGAGTTGTGGACTT
1091107 AAAA
1 AAAA
1091111 AAAAAGGTTG
Statistics
Matches: 773, Mismatches: 90, Indels: 49
0.85 0.10 0.05
Matches are distributed among these distances:
26 7 0.01
27 375 0.49
28 293 0.38
29 98 0.13
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (27 bp):
AAAAGGATGCCACGGAGTTGTGGACTT
Found at i:1090574 original size:84 final size:85
Alignment explanation
Indices: 1089563--1091075 Score: 901
Period size: 84 Copynumber: 18.1 Consensus size: 85
1089553 CACCAACTTG
* * * * *
1089563 TGTGGGCTTTAGAGAAAGTTGCCACCGACTTGTGTGGACTTT-AAAAGGATGCCGCTAACTTGTG
1 TGTGGGCTTT-GA-AAGGATGCCACTGAC-T-TGTGGACTTTGAAAAGGATGCCACTGACTTGTG
* * **
1089627 GGCTTTAAGAATG-TGCCTTTGACT
62 GACTTTAA-AAGGATGCCACTGACT
* * * * * *
1089651 TGTGGGCTTTGTGAATG-TGCCACTGATTTGTGGGCTTTGAAAAGG-TACCACTGACTTGTGGGC
1 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGAC
* *
1089714 TATAAAAAGATGCCACTGACT
65 TTTAAAAGGATGCCACTGACT
** * * *
1089735 TGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTGTGAAAAGG-TGCCACTGATTTGT-GAG
1 TGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGA-
* * *
1089798 CTTTGAAAA-GTTGTCACTAACT
64 CTTT-AAAAGGATGCCACTGACT
* * * ** * *
1089820 TATGGGCATGGAAAAAATGCCACTGACTTGTAGG-CTTTGAAAA-GATGCCACTGACTTAT-AAG
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGT-GGACTTTGAAAAGGATGCCACTGACTTGTGGA-
*
1089882 CTTTGAAAA-GAAGCCACTGACT
64 CTTT-AAAAGGATGCCACTGACT
* ** * * *
1089904 TATGGGCTTTGAAAAAATGCCATTGACTTGTTTG-CTTTTAAAAGGATGCCACTGACTATG-GG-
1 TGTGGGCTTTGAAAGGATGCCACTGACTTG-TGGACTTTGAAAAGGATGCCACTGACT-TGTGGA
**
1089966 CTTTGAAAAGGATGCCACAAACT
64 CTTT-AAAAGGATGCCACTGACT
* * * * *
1089989 TGTGGACTTTAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTAGG-C
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGT-GGAC
* *
1090052 TTGGAAAA-GATGCCATTGACT
65 TT-TAAAAGGATGCCACTGACT
* * * * * * * *
1090073 TGTGGGCTTTGAAAAGATGCCACCGACTTATGGGCTTTGAAAA-GATGCTAGTGACTTATGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGACT
* * *
1090137 TTAAAAAGACGCCATTGACT
66 TTAAAAGGATGCCACTGACT
** **
1090157 TGTTTGCTTTTGAAAGGATGCCACTGACTATG-GG-CTTTGAAAAGGATGCCACAAACTTGTGGA
1 TGTGGGC-TTTGAAAGGATGCCACTGACT-TGTGGACTTTGAAAAGGATGCCACTGACTTGTGGA
1090220 CTTTAAAAGGATGCCACTGACT
64 CTTTAAAAGGATGCCACTGACT
** * * * *
1090242 TGTTAGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTGGAAAA-GATGCCACTAACTTGTGGGC
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGAC
1090306 TTTGAAAA-GATGCCA-TCGACT
65 TTT-AAAAGGATGCCACT-GACT
* * * *
1090327 TGTGGGCTTTGAAAAGATGCCACCGACTTGTTGG-CTTTCG-AAAGGATGCCATTGACTTGTGGG
1 TGTGGGCTTTGAAAGGATGCCACTGACTTG-TGGACTTT-GAAAAGGATGCCACTGACTTGTGGA
*
1090390 CTTTGAAAAGGATACCACTGACT
64 CTTT-AAAAGGATGCCACTGACT
* * * * * *
1090413 TGTGGACTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGG-TCCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGACT
*
1090477 TTGAAAAGG-TGCCACTAACT
66 TT-AAAAGGATGCCACTGACT
* * * * * *
1090497 TGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGACTTTGAAAAAGACGCCACGGAGTTGTGGAC-
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGACT
* *
1090561 TTAAAAGGATGCCACGGAGT
66 TTAAAAGGATGCCACTGACT
* * * * * * * *
1090581 TGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTT-AAAAGGATACCACGGAGTTGTTGAC-
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGACT
*
1090644 TTAAAAGGATGCCA-TGGAGT
66 TTAAAAGGATGCCACT-GACT
* * * * * *
1090664 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGTTGCCA-TGAAGC-TATGGA
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTG-A-CTTGTGGA
* * *
1090725 C-TTAAAAGGTTGCCACGGAGT
64 CTTTAAAAGGATGCCACTGACT
* * * * * * * * *
1090746 TGTAGAC-TTAAAAGGTTGCCACGGAGC-TGTTGAC-TT-AAAAGGTTGTCACGGAGC-TGTGGA
1 TGTGGGCTTTGAAAGGATGCCACTGA-CTTGTGGACTTTGAAAAGGATGCCACTGA-CTTGTGGA
* * *
1090806 C-TTAAAAGGTTGCCACAGAGT
64 CTTTAAAAGGATGCCACTGACT
* * * ** * * * *
1090827 TGTGGAC-TT-AAAGGGTTGCCACGGAGC-TGTGGA-GAT-AAAA-GATTGCCACGGAGTTATGA
1 TGTGGGCTTTGAAA-GGATGCCACTGA-CTTGTGGACTTTGAAAAGGA-TGCCACTGACTTGTGG
* *
1090886 AC-TTAAAAGGTTGCCACGGAGC-
63 ACTTTAAAAGGATGCCACTGA-CT
* * * * * * *
1090908 TGTGGAC-TTAAAAGTG-TGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGAC
1 TGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGAC
* * *
1090969 -TTAAAAGGTTGCCACGGAGT
65 TTTAAAAGGATGCCACTGACT
* ** * ** * * * * * *
1090989 TGTGGACTTAAAAATG-TGCCAAAGAGTTATGGAC-TT-AAAAGGTTGCCACGGAGTTATGGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGACT
* * *
1091051 TTAAAAGGGTGCCACGGAGT
66 TTAAAAGGATGCCACTGACT
1091071 TGTGG
1 TGTGG
1091076 ACTTAAAAGT
Statistics
Matches: 1197, Mismatches: 172, Indels: 118
0.80 0.12 0.08
Matches are distributed among these distances:
80 4 0.00
81 239 0.20
82 76 0.06
83 93 0.08
84 370 0.31
85 329 0.27
86 71 0.06
87 5 0.00
88 10 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGGATGCCACTGACTTGTGGACT
TTAAAAGGATGCCACTGACT
Found at i:1092503 original size:37 final size:37
Alignment explanation
Indices: 1092462--1092532 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1092452 TATTTTTTAA
1092462 TTTTTGTTATTCCCTTTTC-TTATTT-TACTTTTGCACC
1 TTTTTGTT-TT-CCTTTTCATTATTTGTACTTTTGCACC
* *
1092499 TTTTTGTTTTTCTTTTCATTTTTTGTACTTTTGC
1 TTTTTGTTTTCCTTTTCATTATTTGTACTTTTGC
1092533 TTTTAACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 6 0.20
36 7 0.23
37 17 0.57
ACGTcount: A:0.08, C:0.17, G:0.07, T:0.68
Consensus pattern (37 bp):
TTTTTGTTTTCCTTTTCATTATTTGTACTTTTGCACC
Found at i:1096675 original size:154 final size:154
Alignment explanation
Indices: 1096416--1096698 Score: 494
Period size: 154 Copynumber: 1.8 Consensus size: 154
1096406 AGAATGTGTA
1096416 CTCGACCCTGACAATAAGGATAAAAAACCCGCGCCCGACTTAATATCCCTTATGATTGGGGATTT
1 CTCGACCCTGACAATAAGGATAAAAAACCCGCGCCCGACTTAATATCCCTTATGATTGGGGATTT
*
1096481 TTATGGCATGGTAAGAGATATGTGTTGAAATGGGAAAGATCGGTAGATGAATCACCCATCTAACC
66 TTATGGCATGGTAAGAGATATGTGTTGAAAAGGGAAAGATCGGTAGATGAATCACCCATCTAACC
1096546 GAGGCCAAGCTATAGCAACGTGCG
131 GAGGCCAAGCTATAGCAACGTGCG
* ** **
1096570 CTCGACCCTGACAATAGGGATAAATGAGGCGCGCCCGACTTAATATCCCTTATGATTGGGGATTT
1 CTCGACCCTGACAATAAGGATAAAAAACCCGCGCCCGACTTAATATCCCTTATGATTGGGGATTT
* *
1096635 TTATGGCATGGTAAGAGATATGTGTTGAAAAGGGGAAGATCGGTAGATGAATCGCCCATCTAAC
66 TTATGGCATGGTAAGAGATATGTGTTGAAAAGGGAAAGATCGGTAGATGAATCACCCATCTAAC
1096699 TGATCCTCGA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 121 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (154 bp):
CTCGACCCTGACAATAAGGATAAAAAACCCGCGCCCGACTTAATATCCCTTATGATTGGGGATTT
TTATGGCATGGTAAGAGATATGTGTTGAAAAGGGAAAGATCGGTAGATGAATCACCCATCTAACC
GAGGCCAAGCTATAGCAACGTGCG
Found at i:1098872 original size:23 final size:20
Alignment explanation
Indices: 1098823--1098939 Score: 126
Period size: 20 Copynumber: 5.7 Consensus size: 20
1098813 TTTTAACTAG
*
1098823 ATGTATCGATACATTGAACA
1 ATGTATCGATACATTGAAGA
*
1098843 ATGTATCGATACATCTGGGTAGA
1 ATGTATCGATACAT-T--GAAGA
1098866 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
* * ***
1098886 ATATATCGATACATTCATCC
1 ATGTATCGATACATTGAAGA
* *
1098906 ATGTACCGATACATTGAAAA
1 ATGTATCGATACATTGAAGA
1098926 ATGTATCGATACAT
1 ATGTATCGATACAT
1098940 CTGGGTAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
20 60 0.76
21 1 0.01
22 1 0.01
23 17 0.22
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:1099604 original size:20 final size:20
Alignment explanation
Indices: 1099570--1099623 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
1099560 CATTTTGGGC
1099570 ATGTATCGA-ATCATT-CACTT
1 ATGTATCGATA-CATTGC-CTT
1099590 ATGTATCGATACATTGCCTT
1 ATGTATCGATACATTGCCTT
*
1099610 ATTGTATTGATACA
1 A-TGTATCGATACA
1099624 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGCCTT
Done.