Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008554.1 Hibiscus syriacus cultivar Beakdansim tig00111458_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3217407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:995352 original size:17 final size:17
Alignment explanation
Indices: 995316--995353 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
995306 AGTCCATAAG
* *
995316 AAAATTATGGTTCAAGT
1 AAAATTATGGTTAAAAT
995333 AAAATTATGGTTAAAAT
1 AAAATTATGGTTAAAAT
995350 AAAA
1 AAAA
995354 CGAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (17 bp):
AAAATTATGGTTAAAAT
Found at i:995944 original size:31 final size:28
Alignment explanation
Indices: 995894--995967 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 28
995884 ATTTTGATAT
* * *
995894 AAAATGCTTTAGGTATTTATTTTGATCAA
1 AAAATACTTTAAGTATTTATTTAGA-CAA
*
995923 AAAGATAATTTTAAGTATTTATTTAGACAA
1 AAA-AT-ACTTTAAGTATTTATTTAGACAA
995953 AAAATACTTTAAGTA
1 AAAATACTTTAAGTA
995968 CTTAAATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 9 0.24
29 5 0.13
30 8 0.21
31 16 0.42
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (28 bp):
AAAATACTTTAAGTATTTATTTAGACAA
Found at i:996423 original size:33 final size:33
Alignment explanation
Indices: 996386--996455 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
996376 CTTTACAAAC
996386 TCCCTAGT-TTTTCACGGGATAAACTAGAACATT
1 TCCCTA-TCTTTTCACGGGATAAACTAGAACATT
* *
996419 TCCCTATCTTTTCACGGGATCAGCTAGAACATT
1 TCCCTATCTTTTCACGGGATAAACTAGAACATT
996452 TCCC
1 TCCC
996456 CTTTACAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (33 bp):
TCCCTATCTTTTCACGGGATAAACTAGAACATT
Found at i:996919 original size:20 final size:20
Alignment explanation
Indices: 996894--996933 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
996884 TGAGCAGTCA
*
996894 TAGGGGTATTGATACCCAGG
1 TAGGGGTATCGATACCCAGG
*
996914 TAGGGGTATCGGTACCCAGG
1 TAGGGGTATCGATACCCAGG
996934 GTATGGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (20 bp):
TAGGGGTATCGATACCCAGG
Found at i:997207 original size:21 final size:20
Alignment explanation
Indices: 997179--997234 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 20
997169 TGTTTAATGA
*
997179 AAAAGATATCAATTGTTTAT
1 AAAAGATACCAATTGTTTAT
997199 AAAAGGATACCAATTG-TTA-
1 AAAA-GATACCAATTGTTTAT
997218 AAAAGATACCAATTGTT
1 AAAAGATACCAATTGTT
997235 GGAAAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 7 0.21
21 10 0.30
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (20 bp):
AAAAGATACCAATTGTTTAT
Found at i:998376 original size:23 final size:23
Alignment explanation
Indices: 998317--998376 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
998307 CTCGTATAAA
***
998317 TGCACCGAAGTGCAATGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
998340 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
998363 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
998377 ATATAAGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:1001825 original size:61 final size:61
Alignment explanation
Indices: 1001692--1001825 Score: 232
Period size: 61 Copynumber: 2.2 Consensus size: 61
1001682 GATCTCTAAT
*
1001692 TCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCATTTTGCGTTGCGATAGTTGAAAA
1 TCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAA
**
1001753 TCGCAACGCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAA
*
1001814 TCGCGTTGCGAT
1 TCGCATTGCGAT
1001826 TTTCCATTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (61 bp):
TCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAA
Found at i:1001843 original size:20 final size:20
Alignment explanation
Indices: 1001814--1001906 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
1001804 TAGTTGAAAA
1001814 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
1001834 TCGTGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * * ** **
1001854 TCGTGTTGCAATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
1001875 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1001895 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1001907 AGTCTACAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1001854 original size:61 final size:61
Alignment explanation
Indices: 1001789--1001906 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
1001779 ATTCGCGTTG
* *
1001789 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGTGTTGCGATTTTC
1 CATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
*
1001850 CATTTCGTGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 CATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1001907 AGTCTACAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (61 bp):
CATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:1001926 original size:22 final size:22
Alignment explanation
Indices: 1001898--1001950 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1001888 TTCCATTTCG
1001898 CGTTGCGATAGTCTACAATTGT
1 CGTTGCGATAGTCTACAATTGT
*
1001920 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
*
1001942 TGTTGCGAT
1 CGTTGCGAT
1001951 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAATTGT
Found at i:1002060 original size:6 final size:6
Alignment explanation
Indices: 1002049--1002093 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1002039 AACACGTATT
1002049 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1002094 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1002594 original size:5 final size:5
Alignment explanation
Indices: 1002584--1002624 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
1002574 GCCGTCTGTC
1002584 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
1002625 TGATCGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:1002613 original size:6 final size:6
Alignment explanation
Indices: 1002587--1002646 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
1002577 GTCTGTCTCG
*
1002587 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GATCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1002632 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
1002647 AATACGTGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 15 0.29
6 37 0.71
ACGTcount: A:0.02, C:0.17, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1002742 original size:19 final size:19
Alignment explanation
Indices: 1002718--1002783 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1002708 TTAACTATCA
1002718 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
1002737 CAACGACAACTGTAGATTATCG
1 CAACG--AA-TTTGGAAAATCG
1002759 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
1002778 CAACGA
1 CAACGA
1002784 CTATCGCAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:1014897 original size:18 final size:19
Alignment explanation
Indices: 1014871--1014907 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1014861 GGTATGGACA
*
1014871 AAAATAAAA-TAAAATGTG
1 AAAACAAAATTAAAATGTG
1014889 AAAACAAAATTAAAATGTG
1 AAAACAAAATTAAAATGTG
1014908 TGGAAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (19 bp):
AAAACAAAATTAAAATGTG
Found at i:1015962 original size:12 final size:12
Alignment explanation
Indices: 1015945--1015973 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1015935 TTATTTAATA
1015945 ATAATAATATAT
1 ATAATAATATAT
1015957 ATAATAATATAT
1 ATAATAATATAT
1015969 ATAAT
1 ATAAT
1015974 TATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:1015963 original size:18 final size:19
Alignment explanation
Indices: 1015930--1015965 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1015920 TGGACGTTTG
*
1015930 TAATATTATTTAATAATAA
1 TAATATTATATAATAATAA
1015949 TAATA-TATATAATAATA
1 TAATATTATATAATAATA
1015966 TATATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTATATAATAATAA
Found at i:1016360 original size:42 final size:42
Alignment explanation
Indices: 1016300--1016381 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
1016290 AAGGACTTAT
* *
1016300 CATCTTGCTCAAAAGACTAACAAATGACCCGAGGGATTTAAG
1 CATCATGCTCAAAAGACTAACAAATGACCCGAAGGATTTAAG
* *
1016342 CATCATGCTCAAAAGACTAACAGATGACCTGAAGGATTTA
1 CATCATGCTCAAAAGACTAACAAATGACCCGAAGGATTTA
1016382 CAAATTTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (42 bp):
CATCATGCTCAAAAGACTAACAAATGACCCGAAGGATTTAAG
Found at i:1023111 original size:45 final size:45
Alignment explanation
Indices: 1023026--1023112 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
1023016 TCATATATAT
* * * *
1023026 CCTAACCTCATGCTTTCTAGTTCCATTCTTTGTTTGGAAAATAAA
1 CCTAACCACATGATTTCTAGTTCCATGCTTTGATTGGAAAATAAA
*
1023071 CCTAACCACATGATTTCTAGTTCGCATGCATTT-ATTGAAAAA
1 CCTAACCACATGATTTCTAGTTC-CATGC-TTTGATTGGAAAA
1023113 AATAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
45 21 0.60
46 11 0.31
47 3 0.09
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (45 bp):
CCTAACCACATGATTTCTAGTTCCATGCTTTGATTGGAAAATAAA
Found at i:1024365 original size:16 final size:18
Alignment explanation
Indices: 1024331--1024366 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
1024321 AAATATAAAT
1024331 AAAATAATAATAGTATTA
1 AAAATAATAATAGTATTA
1024349 AAAATAA-AATA-TATTA
1 AAAATAATAATAGTATTA
1024365 AA
1 AA
1024367 TTTTGAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATAATAATAGTATTA
Found at i:1024527 original size:2 final size:2
Alignment explanation
Indices: 1024520--1024551 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1024510 AATTTTACCC
1024520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1024552 GGTATGGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1025738 original size:12 final size:12
Alignment explanation
Indices: 1025721--1025749 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1025711 TCATTTAATA
1025721 ATAATAATATAT
1 ATAATAATATAT
1025733 ATAATAATATAT
1 ATAATAATATAT
1025745 ATAAT
1 ATAAT
1025750 TATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:1025739 original size:18 final size:19
Alignment explanation
Indices: 1025706--1025741 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1025696 TGGGCTTTTG
*
1025706 TAATATCATTTAATAATAA
1 TAATATCATATAATAATAA
1025725 TAATAT-ATATAATAATA
1 TAATATCATATAATAATA
1025742 TATATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATCATATAATAATAA
Found at i:1026262 original size:24 final size:24
Alignment explanation
Indices: 1026200--1026279 Score: 99
Period size: 24 Copynumber: 3.4 Consensus size: 24
1026190 GAGTTGAGGG
* *
1026200 TTCTACATGGTCCTTCGAGAC-AT
1 TTCTACATGGTCCTTCGGGACAAA
*
1026223 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACATGGTCCTTCGGGACAAA
* * *
1026247 TTCCACATGGTCCTTCAGGACAAG
1 TTCTACATGGTCCTTCGGGACAAA
1026271 TTCTACATG
1 TTCTACATG
1026280 ACACTTCAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 19 0.40
24 29 0.60
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (24 bp):
TTCTACATGGTCCTTCGGGACAAA
Found at i:1030876 original size:18 final size:18
Alignment explanation
Indices: 1030853--1030889 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1030843 TTTCAATTGT
1030853 TGGTTTATTTGTTTGACA
1 TGGTTTATTTGTTTGACA
1030871 TGGTTTATTTGTTTGACA
1 TGGTTTATTTGTTTGACA
1030889 T
1 T
1030890 TTTTTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (18 bp):
TGGTTTATTTGTTTGACA
Found at i:1031715 original size:23 final size:24
Alignment explanation
Indices: 1031689--1031740 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1031679 TCTACACGGA
* *
1031689 CCTTCGAGAC-ATTTCTACGTGGT
1 CCTTCGAGACAAATTCCACGTGGT
*
1031712 CCTTCGGGACAAATTCCACGTGGT
1 CCTTCGAGACAAATTCCACGTGGT
1031736 CCTTC
1 CCTTC
1031741 AGGACAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (24 bp):
CCTTCGAGACAAATTCCACGTGGT
Found at i:1033562 original size:22 final size:22
Alignment explanation
Indices: 1033531--1033582 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1033521 TGGATGAAAG
*
1033531 CATGACATACAAAATTGTTCTA
1 CATGAAATACAAAATTGTTCTA
*
1033553 CATGAAATACAAAATTGTTTTA
1 CATGAAATACAAAATTGTTCTA
1033575 CATGAAAT
1 CATGAAAT
1033583 TCTCTATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (22 bp):
CATGAAATACAAAATTGTTCTA
Found at i:1034146 original size:13 final size:13
Alignment explanation
Indices: 1034099--1034140 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
1034089 GAAGTTTATG
1034099 TGTAATGTTTAAA
1 TGTAATGTTTAAA
1034112 TGTAATGTTTAAA
1 TGTAATGTTTAAA
1034125 TGTAATGTTTAAA
1 TGTAATGTTTAAA
1034138 TGT
1 TGT
1034141 GTTGTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.48
Consensus pattern (13 bp):
TGTAATGTTTAAA
Found at i:1036414 original size:18 final size:18
Alignment explanation
Indices: 1036391--1036427 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1036381 TTTCAATTGT
1036391 TGGTTTATTTGTTTGACA
1 TGGTTTATTTGTTTGACA
1036409 TGGTTTATTTGTTTGACA
1 TGGTTTATTTGTTTGACA
1036427 T
1 T
1036428 TTTTTTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (18 bp):
TGGTTTATTTGTTTGACA
Found at i:1036835 original size:11 final size:11
Alignment explanation
Indices: 1036821--1036852 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
1036811 GATATTAAGT
1036821 ATTTATTTTAA
1 ATTTATTTTAA
1036832 ATTTA-TTTAA
1 ATTTATTTTAA
1036842 ATTTATTTTAA
1 ATTTATTTTAA
1036853 TAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTATTTTAA
Found at i:1038377 original size:290 final size:291
Alignment explanation
Indices: 1037825--1038969 Score: 1903
Period size: 290 Copynumber: 4.0 Consensus size: 291
1037815 GCAAAGTAAG
* *
1037825 AAAATAGTTCAAAAGACAAAGAAGGCTTACATATGCTAGCCTTAAAACAAACTTAAATAAGATAG
1 AAAATAGTTCAAAAGACAAAGAAGGCTTACAGATGCTAGCCTTAAAACAAACTTAAATAAGAGAG
1037890 AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
66 AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
* * * *
1037955 AAATCCAAAAAAAACAAAGACGACGATGACTACTTACGTTCCCACACAACATCGAAAGAGGAAGA
131 AAATCCCAAAAAAACAAAGATGACGATGACTCCTTAAGTTCCCACACAACATCGAAAGAGGAAGA
1038020 ATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGAAA
196 ATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGAAA
1038085 CTCAAAAAGCGATTCAAGGAGGCTCGAGCAT
261 CTCAAAAAGCGATTCAAGGAGGCTCGAGCAT
1038116 AAAATAGTTCAAAAGACAAAGAAGGCTTA-AGATGCTAGCCTTAAAACAAACTTAAATAAGAGAG
1 AAAATAGTTCAAAAGACAAAGAAGGCTTACAGATGCTAGCCTTAAAACAAACTTAAATAAGAGAG
*
1038180 ATAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
66 AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
* *
1038245 AAATCCCCAAAAAACAAAGATGACGATGACTCCTTAAGCTCCCACACAACATCGAAAGAGGAAGA
131 AAATCCCAAAAAAACAAAGATGACGATGACTCCTTAAGTTCCCACACAACATCGAAAGAGGAAGA
1038310 ATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGAAA
196 ATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGAAA
*
1038375 CTCAAAAAGTGATTCAAGGAGGCTCGAGCAT
261 CTCAAAAAGCGATTCAAGGAGGCTCGAGCAT
* * *
1038406 AAAATAGTTCAAAAGACAAAGAAGGTTTACAGATGCTAGGCTTAAAACAAATTTAAATAAGAGAG
1 AAAATAGTTCAAAAGACAAAGAAGGCTTACAGATGCTAGCCTTAAAACAAACTTAAATAAGAGAG
* *
1038471 AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTTGAGAAAAAAACTAAAGACCACTGGTGAGA
66 AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
*
1038536 AAATCCCCAAAAAACAAAGATGAC---G--------AG-----ACACAACATCGAAAGAGGAAGA
131 AAATCCCAAAAAAACAAAGATGACGATGACTCCTTAAGTTCCCACACAACATCGAAAGAGGAAGA
* *
1038585 ATTGAGCAAGAGGAGAGGAAAAATAGGGGACCAACAAAGAAAACAAGATTCCTTATACAAAGAAA
196 ATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGAAA
1038650 CTCAAAAAGCGATTCAAGGAGGCTCGAGCAT
261 CTCAAAAAGCGATTCAAGGAGGCTCGAGCAT
* *
1038681 AAAATAGTTCAAAAGACAAAGAAGACTTACAGATGCTAGCCTTAAAATAAACTTAAATAAGAGAG
1 AAAATAGTTCAAAAGACAAAGAAGGCTTACAGATGCTAGCCTTAAAACAAACTTAAATAAGAGAG
* ** *
1038746 AGAAAAGAAAATCTAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCGTTGGTGAGG
66 AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
*
1038811 AAATCCCTAAAAAAAACAAAGATGACAATGACTCCTTAAGTTCCCACACAACATCGAAAGAGGAA
131 AAATCCC--AAAAAAACAAAGATGACGATGACTCCTTAAGTTCCCACACAACATCGAAAGAGGAA
*
1038876 GAATTGAGCAAGA-GAGAGGAAAAACAGGGGATCAACAAAGAAAACAAGATTCCCTATACAAAGA
194 GAATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGA
*
1038940 AACTCAAAAAGCGATTCAAGGAGGCCCGAG
259 AACTCAAAAAGCGATTCAAGGAGGCTCGAG
1038970 ATTCCGACGG
Statistics
Matches: 800, Mismatches: 35, Indels: 37
0.92 0.04 0.04
Matches are distributed among these distances:
275 241 0.30
277 16 0.02
280 3 0.00
288 3 0.00
290 279 0.35
291 148 0.19
292 77 0.10
293 33 0.04
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (291 bp):
AAAATAGTTCAAAAGACAAAGAAGGCTTACAGATGCTAGCCTTAAAACAAACTTAAATAAGAGAG
AGAAAAGAAAATCCAAAAAAGCGCTCAAATAAACTCGAGCAAAAAACTAAAGACCACTGGTGAGA
AAATCCCAAAAAAACAAAGATGACGATGACTCCTTAAGTTCCCACACAACATCGAAAGAGGAAGA
ATTGAGCAAGAGGAGAGGAAAAACAGGGGACCAACAAAGAAAACAAGATTCCCTATACAAAGAAA
CTCAAAAAGCGATTCAAGGAGGCTCGAGCAT
Found at i:1040404 original size:43 final size:43
Alignment explanation
Indices: 1040356--1040442 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
1040346 AAGGTGGCAG
1040356 TCGAAAAATAGTTTGCTCGAAAAACTCGTGCTACGAGGGAACC
1 TCGAAAAATAGTTTGCTCGAAAAACTCGTGCTACGAGGGAACC
1040399 TCGAAAAATAGTTTGCTCGAAAAACTCGTGCTACGAGGGAACC
1 TCGAAAAATAGTTTGCTCGAAAAACTCGTGCTACGAGGGAACC
1040442 T
1 T
1040443 AGATTGTGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (43 bp):
TCGAAAAATAGTTTGCTCGAAAAACTCGTGCTACGAGGGAACC
Found at i:1044420 original size:32 final size:32
Alignment explanation
Indices: 1044397--1044506 Score: 148
Period size: 32 Copynumber: 3.4 Consensus size: 32
1044387 AACGCTTCTG
1044397 TGCATTATCTGAATTCAACACTAACCCTATCA
1 TGCATTATCTGAATTCAACACTAACCCTATCA
*
1044429 TGCATTATCTGAATTTAACACTAACCCTATCA
1 TGCATTATCTGAATTCAACACTAACCCTATCA
* * * * * **
1044461 TGCATTATCTGAATACAATATTAATCATATTG
1 TGCATTATCTGAATTCAACACTAACCCTATCA
1044493 TGCATTATCTGAAT
1 TGCATTATCTGAAT
1044507 GCTATGCTGA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (32 bp):
TGCATTATCTGAATTCAACACTAACCCTATCA
Found at i:1045080 original size:21 final size:22
Alignment explanation
Indices: 1045039--1045080 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1045029 ATATCGTAGA
**
1045039 TGTTATTGTTTCTAGTTGTTAC
1 TGTTATTGTTTCTAGCAGTTAC
1045061 TGTT-TTGTTTCTAGCAGTTA
1 TGTTATTGTTTCTAGCAGTTA
1045081 TATCACTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.14, C:0.10, G:0.19, T:0.57
Consensus pattern (22 bp):
TGTTATTGTTTCTAGCAGTTAC
Found at i:1047406 original size:32 final size:32
Alignment explanation
Indices: 1047383--1047492 Score: 125
Period size: 32 Copynumber: 3.4 Consensus size: 32
1047373 AACGCTCCTG
*
1047383 TGCATTATCTGAATTCAACACTAACCTTATCA
1 TGCATTATCTGAATTCAACACTAACCTCATCA
1047415 TGCATTATCTGAATTCAACACTAACC-CTATCA
1 TGCATTATCTGAATTCAACACTAACCTC-ATCA
* * * * **
1047447 TGCATTATCTAAATACAATATTAACCAT-ATTG
1 TGCATTATCTGAATTCAACACTAACC-TCATCA
1047479 TGCATTATCTGAAT
1 TGCATTATCTGAAT
1047493 GCTATGTTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (32 bp):
TGCATTATCTGAATTCAACACTAACCTCATCA
Found at i:1047535 original size:32 final size:32
Alignment explanation
Indices: 1047499--1047573 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
1047489 GAATGCTATG
*
1047499 TTGACTATACTATGCAATATCTAAATACCAAA
1 TTGACTATACTATGCAATATCTAAATACAAAA
* * *
1047531 TTGACTATGA-TGTGCATTATCTGAATACAAAA
1 TTGACTAT-ACTATGCAATATCTAAATACAAAA
* *
1047563 ATGACTCTACT
1 TTGACTATACT
1047574 GTACATTATC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 1 0.03
32 33 0.94
33 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (32 bp):
TTGACTATACTATGCAATATCTAAATACAAAA
Found at i:1047568 original size:64 final size:64
Alignment explanation
Indices: 1047446--1047573 Score: 143
Period size: 64 Copynumber: 2.0 Consensus size: 64
1047436 TAACCCTATC
* * * ***
1047446 ATGCATTATCTAAATACAATATTAACCATATTGTGCATTATCTGAATGCTATGTTGACTATACT
1 ATGCAATATCTAAATACAATATTAACCATATTGTGCATTATCTGAATACAAAAATGACTATACT
* * *
1047510 ATGCAATATCTAAATACCAA-ATTGACTATGA-TGTGCATTATCTGAATACAAAAATGACTCTAC
1 ATGCAATATCTAAATA-CAATATTAACCAT-ATTGTGCATTATCTGAATACAAAAATGACTATAC
1047573 T
64 T
1047574 GTACATTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
64 49 0.92
65 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (64 bp):
ATGCAATATCTAAATACAATATTAACCATATTGTGCATTATCTGAATACAAAAATGACTATACT
Found at i:1052187 original size:32 final size:32
Alignment explanation
Indices: 1052054--1052187 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 32
1052044 ACTAATATTA
* * *
1052054 TTGTGCATTATCTAAATGCCATGA-TAACTATG
1 TTGTGCATTATCTAAATGCAAT-ACTGACTCTG
* * * *
1052086 CTATGCATTATCTAAATCCCATACTGACTCTG
1 TTGTGCATTATCTAAATGCAATACTGACTCTG
* * * * *
1052118 TTGGGCATTATCTGAATGTAATACTGATTCTA
1 TTGTGCATTATCTAAATGCAATACTGACTCTG
* * *
1052150 CTGTGCATTATCTGAATGCAATATTGACTCTG
1 TTGTGCATTATCTAAATGCAATACTGACTCTG
1052182 TTGTGC
1 TTGTGC
1052188 CTCATACTCT
Statistics
Matches: 80, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
31 1 0.01
32 79 0.99
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (32 bp):
TTGTGCATTATCTAAATGCAATACTGACTCTG
Found at i:1057533 original size:23 final size:23
Alignment explanation
Indices: 1057489--1057538 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1057479 AAAGAGTGTG
*
1057489 ATCAAAATGAGGGAAGACAAATC
1 ATCAAAATGAGGGAAGACAAATA
1057512 ATCAAAATGAGGGAAGGA-AAATA
1 ATCAAAATGAGGGAA-GACAAATA
1057535 ATCA
1 ATCA
1057539 TTCTTTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.54, C:0.10, G:0.22, T:0.14
Consensus pattern (23 bp):
ATCAAAATGAGGGAAGACAAATA
Found at i:1068310 original size:18 final size:18
Alignment explanation
Indices: 1068287--1068321 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1068277 CCAGCACTCA
1068287 AAAAG-AAGAAAAGAAAAG
1 AAAAGAAAG-AAAGAAAAG
1068305 AAAAGAAAGAAAGAAAA
1 AAAAGAAAGAAAGAAAA
1068322 TTTGAAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAGAAAGAAAGAAAAG
Found at i:1071525 original size:21 final size:19
Alignment explanation
Indices: 1071474--1071525 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
1071464 CGGCCAAGAA
* *
1071474 CATGTATCTTCATTAAAGT
1 CATGTATTTTCATTAAAAT
* *
1071493 CTTGTTTTTTCATTAACAAAT
1 CATGTATTTTCATT-A-AAAT
1071514 CATGTATTTTCA
1 CATGTATTTTCA
1071526 AAGGGATTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 11 0.44
20 1 0.04
21 13 0.52
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:1074123 original size:49 final size:49
Alignment explanation
Indices: 1074060--1074184 Score: 205
Period size: 49 Copynumber: 2.6 Consensus size: 49
1074050 AATACCATGA
* **
1074060 GTGGCACCTTTTATGCTAAAATGCACCGTTATGCATTTAACTTTCATTT
1 GTGGCAACTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
*
1074109 GTGGTAACTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
1 GTGGCAACTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
*
1074158 GTGGCACCTTTTATGCCGAAATGCACC
1 GTGGCAACTTTTATGCCGAAATGCACC
1074185 TATGACTCTC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (49 bp):
GTGGCAACTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTT
Found at i:1076115 original size:15 final size:15
Alignment explanation
Indices: 1076095--1076136 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1076085 GCAAGAGTAG
1076095 TATTGGTACTCACAA
1 TATTGGTACTCACAA
*
1076110 TATTGGTACACACAA
1 TATTGGTACTCACAA
*
1076125 TATCGGTACTCA
1 TATTGGTACTCA
1076137 AAGTCTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (15 bp):
TATTGGTACTCACAA
Found at i:1077937 original size:17 final size:17
Alignment explanation
Indices: 1077908--1077948 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1077898 AGCTACATAC
1077908 CTAAGCTACCTAGCTAG
1 CTAAGCTACCTAGCTAG
1077925 CTAA-CTACACTAGCTAG
1 CTAAGCTAC-CTAGCTAG
1077942 CT-AGCTA
1 CTAAGCTA
1077949 TGACTCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (17 bp):
CTAAGCTACCTAGCTAG
Found at i:1085533 original size:25 final size:25
Alignment explanation
Indices: 1085505--1085559 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
1085495 ATTTCCTGAA
1085505 AAGTTGTCAAATTTGCAGTCAACAG
1 AAGTTGTCAAATTTGCAGTCAACAG
1085530 AAGTTGTCAAATTTGCAGTCAACAG
1 AAGTTGTCAAATTTGCAGTCAACAG
1085555 AAGTT
1 AAGTT
1085560 CCCTCTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (25 bp):
AAGTTGTCAAATTTGCAGTCAACAG
Found at i:1095777 original size:19 final size:20
Alignment explanation
Indices: 1095749--1095788 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1095739 GGATAATAAT
1095749 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
1095769 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
1095788 A
1 A
1095789 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:1100041 original size:13 final size:12
Alignment explanation
Indices: 1100017--1100075 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
1100007 CTTTTTGAAT
1100017 TTTTC-TTTTTC
1 TTTTCTTTTTTC
1100028 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
1100041 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
1100055 TCTTCTTTTATC
1 TTTTCTTTTTTC
1100067 TTTTTCTTT
1 -TTTTCTTT
1100076 CTTTTTTGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:1100041 original size:19 final size:19
Alignment explanation
Indices: 1100019--1100075 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
1100009 TTTTGAATTT
1100019 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
1100038 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
1100057 TTCTTTTATCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
1100076 CTTTTTTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:1100374 original size:19 final size:20
Alignment explanation
Indices: 1100346--1100385 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1100336 GGATAATAAT
1100346 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
1100366 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
1100385 A
1 A
1100386 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:1103504 original size:17 final size:17
Alignment explanation
Indices: 1103482--1103525 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
1103472 GAAGATCATT
1103482 TTGACCCAAACCCTATG
1 TTGACCCAAACCCTATG
1103499 TTGACCCAAACCCTATG
1 TTGACCCAAACCCTATG
1103516 TTGACCCAAA
1 TTGACCCAAA
1103526 GGACTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.23
Consensus pattern (17 bp):
TTGACCCAAACCCTATG
Found at i:1109313 original size:26 final size:27
Alignment explanation
Indices: 1109262--1109315 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1109252 AAGTTGTTTG
* **
1109262 AATG-TTTAATTATTTAATTCATTTTT
1 AATGTTTTAAGTATTTAAGACATTTTT
1109288 AATGTTTTAAGTATTTAAGACATTTTT
1 AATGTTTTAAGTATTTAAGACATTTTT
1109315 A
1 A
1109316 TATTTTACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (27 bp):
AATGTTTTAAGTATTTAAGACATTTTT
Found at i:1124621 original size:29 final size:28
Alignment explanation
Indices: 1124576--1124630 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1124566 TTACAAAAAA
1124576 TTATAAATTAAAATAAAATACAAAACTTT
1 TTATAAATTAAAAT-AAATACAAAACTTT
* *
1124605 TTATAAATTACACTAAATACAAAACT
1 TTATAAATTAAAATAAATACAAAACT
1124631 ATTTGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
TTATAAATTAAAATAAATACAAAACTTT
Found at i:1124640 original size:28 final size:27
Alignment explanation
Indices: 1124591--1124685 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 27
1124581 AATTAAAATA
*
1124591 AAATACAAAACT-TTTTATAAATTACACT
1 AAATACAAAACTATTTGA-AAA-TACACT
*
1124619 AAATACAAAACTATTTGAAAATACAACA
1 AAATACAAAACTATTTGAAAATAC-ACT
* * *
1124647 AAATAAAAAACTAATTGTAAAATACAAT
1 AAATACAAAACTATTTG-AAAATACACT
1124675 AAAGTACAAAA
1 AAA-TACAAAA
1124686 TTTCTTCTGC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.05
28 36 0.64
29 17 0.30
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (27 bp):
AAATACAAAACTATTTGAAAATACACT
Found at i:1124685 original size:29 final size:29
Alignment explanation
Indices: 1124560--1124685 Score: 109
Period size: 29 Copynumber: 4.5 Consensus size: 29
1124550 CAAAACTTTT
* * *
1124560 AATAAATTACAAAA--AATTATAAATTAA
1 AATAAAATACAAAACTAATTATAAAATAC
** *
1124587 AATAAAATACAAAACTTTTTATAAATTAC
1 AATAAAATACAAAACTAATTATAAAATAC
*
1124616 ACT-AAATACAAAACT-ATT-TGAAAATAC
1 AATAAAATACAAAACTAATTAT-AAAATAC
* * *
1124643 AACAAAATAAAAAACTAATTGTAAAATAC
1 AATAAAATACAAAACTAATTATAAAATAC
*
1124672 AATAAAGTACAAAA
1 AATAAAATACAAAA
1124686 TTTCTTCTGC
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
26 1 0.01
27 22 0.28
28 23 0.29
29 33 0.41
30 1 0.01
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (29 bp):
AATAAAATACAAAACTAATTATAAAATAC
Found at i:1128180 original size:127 final size:127
Alignment explanation
Indices: 1127954--1128202 Score: 428
Period size: 127 Copynumber: 2.0 Consensus size: 127
1127944 GCATGTTTAG
*
1127954 AAAAATGCTGTGATTCTTGAGTTGAGATGGTCCATGAAGATGTTAGATGTTAAATATGGCAAAAC
1 AAAAATGCTGTGATTCTTGAGTTGAGATGGTCCATGAAGATGTTAGATGTTAAAGATGGCAAAAC
* *
1128019 GAAGTAAAGTTAGTTGGGTTAAGTAAATAGGAGTTAGATAGTATTGTTGGAGGTAAAAGTAT
66 GAAGTAAAGTTAGCTGGGTTAAGTAAATAGGAGTTAGATAGTATTGTTGGAGATAAAAGTAT
* *
1128081 AAAAATGGTGT-ATTTCTTGAGTTGAGATGGTCCATGAAGATGTTAGATGTTAAAGATGGCAAAC
1 AAAAATGCTGTGA-TTCTTGAGTTGAGATGGTCCATGAAGATGTTAGATGTTAAAGATGGCAAAA
*
1128145 CGAAGTAAAGTTAGCTGGGTTAAGTAATTAGGAGTTAGATAGTATTGTTGGAGATAAA
65 CGAAGTAAAGTTAGCTGGGTTAAGTAAATAGGAGTTAGATAGTATTGTTGGAGATAAA
1128203 TGAATGAGAT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 1 0.01
127 114 0.99
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (127 bp):
AAAAATGCTGTGATTCTTGAGTTGAGATGGTCCATGAAGATGTTAGATGTTAAAGATGGCAAAAC
GAAGTAAAGTTAGCTGGGTTAAGTAAATAGGAGTTAGATAGTATTGTTGGAGATAAAAGTAT
Found at i:1129018 original size:46 final size:46
Alignment explanation
Indices: 1128945--1129661 Score: 639
Period size: 46 Copynumber: 15.5 Consensus size: 46
1128935 CTAAACAGAA
*
1128945 GCCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
1128991 ACCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
1129037 GCCATAATTAAAATGCATTAATGGATGCATTACGACATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
1129083 GCCATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * * *
1129129 GTCATAACTAAAATGCATAAAAGGATGCCATAACTAAAATGCATGAAAAGAT
1 GCCATAATTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGAT
* ***
1129181 G-C---ATT--AAGGCATGAAAGGATGCCATAATTAAAATATATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAAGGAT
*
1129227 G---T-ATT-AAA-GCATGAAAGGATGCCATAATTAAAATGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAAGGAT
** *
1129273 G-C---ATT--ACGGCATGAAAGGATGCCATAATTGAAATGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAAGGAT
* * * *
1129319 GCCATAATTGAAATACATGAAATGATGCATTAAGGTATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
1129365 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * *
1129411 TCCATAATTAAAATTCATGAATA-GATGCATTAAGGCATGAAATGAT
1 GCCATAATTAAAATGCATGAA-AGGATGCATTAAGGCATGAAAGGAT
* * * * * *
1129457 GCCATAATTGAAATGCATTAAAAGATGTATTAAGGCAGGAAATGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
1129503 GTCATAATTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
1129549 GACATAATTGAAATGCATGTAAGGATGCATTAAGGAATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
1129595 ACCGTAACT-AAATGCATGAAATGATGCATT-AGCGCATGAAAGGAT
1 GCCATAATTAAAATGCATGAAAGGATGCATTAAG-GCATGAAAGGAT
* *
1129640 GCCATGATTAAAATGTATGAAA
1 GCCATAATTAAAATGCATGAAA
1129662 AAAGACATAT
Statistics
Matches: 574, Mismatches: 74, Indels: 46
0.83 0.11 0.07
Matches are distributed among these distances:
44 2 0.00
45 37 0.06
46 489 0.85
47 7 0.01
48 5 0.01
49 2 0.00
50 4 0.01
51 2 0.00
52 26 0.05
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (46 bp):
GCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
Found at i:1129167 original size:118 final size:117
Alignment explanation
Indices: 1129025--1129392 Score: 460
Period size: 118 Copynumber: 3.1 Consensus size: 117
1129015 ATGCATTAAG
* * *
1129025 GCATGAAAGGATGCCATAATTAAAATGCATTAATGGATGCATTACGACATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAA-TAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAA
* *
1129090 TTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAT
65 TTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * *
1129143 GCATAAAAGGATGCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAA-TAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAA
* * * * *
1129208 TTAAAATATATGAAAGGATGTATTAAAGCATGAAAGGATGCCATAATTAAAAT
65 TTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
**
1129261 GCATGAAAGGATG-CAT--T--ACGGCATGAAAGGATGCCA-TAATTGAAATGCATGAAAGGATG
1 GCATGAAAGGATGCCATAATAAAATGCATGAAAGGATG-CATTAA--G--A--CATGAAAGGATG
* *
1129320 CCATAATTGAAATACATGAAATGATGCATTAAGGTATGAAAGGATGCCATAACTAAAAT
59 CCATAATTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1129379 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1129393 ATTAAGGCAT
Statistics
Matches: 216, Mismatches: 26, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
112 16 0.07
113 2 0.01
114 2 0.01
117 3 0.01
118 193 0.89
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (117 bp):
GCATGAAAGGATGCCATAATAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAAT
TGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
Found at i:1129255 original size:164 final size:164
Alignment explanation
Indices: 1128979--1129480 Score: 738
Period size: 164 Copynumber: 3.1 Consensus size: 164
1128969 ATGCATTAAG
* * *
1128979 GCATGAAAGGATACCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATAAAAGGATGCCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
* * * *
1129044 TTAAAATGCATTAATGGATGCATT-ACGACATGAAAGGATGCCATAATTGAAATGCATGAAAGGA
66 TTAAAATGCATGAAAGGATGCATTAAAG-CATGAAAGGATGCCATAATTAAAATGCATGAAAGGA
* * *
1129108 TGCATTAAGGCATGAAAGGATGTCATAACTAAAAT
130 TGCATTAAGGCATGAAAGGATGCCATAATTGAAAT
*
1129143 GCATAAAAGGATGCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATAAAAGGATGCCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
** *
1129208 TTAAAATATATGAAAGGATGTATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGAT
66 TTAAAATGCATGAAAGGATGCATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGAT
*
1129273 GCATTACGGCATGAAAGGATGCCATAATTGAAAT
131 GCATTAAGGCATGAAAGGATGCCATAATTGAAAT
* * * * *
1129307 GCATGAAAGGATGCCATAATTGAAATACATGAAATGATGCATTAAGGTATGAAAGGATGCCATAA
1 GCATAAAAGGATGCCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
* * * *
1129372 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAATTAAAATTCATGAATA-GA
66 TTAAAATGCATGAAAGGATGCATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAA-AGGA
*
1129436 TGCATTAAGGCATGAAATGATGCCATAATTGAAAT
130 TGCATTAAGGCATGAAAGGATGCCATAATTGAAAT
1129471 GCATTAAAAG
1 GCA-TAAAAG
1129481 ATGTATTAAG
Statistics
Matches: 304, Mismatches: 31, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
164 296 0.97
165 8 0.03
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (164 bp):
GCATAAAAGGATGCCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAA
TTAAAATGCATGAAAGGATGCATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGAT
GCATTAAGGCATGAAAGGATGCCATAATTGAAAT
Found at i:1129307 original size:210 final size:206
Alignment explanation
Indices: 1128945--1129576 Score: 849
Period size: 210 Copynumber: 3.0 Consensus size: 206
1128935 CTAAACAGAA
* *
1128945 GCCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATACCATAATTAAAATGCATG
1 GCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATACCATAATTAAAAT-TATG
* *
1129010 AAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATTAATGGATGCATTACGACAT
65 AAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATTAAAGGATGCATTACGGCAT
1129075 GAAAGGATGCCATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAA
130 GAAAGGATGCCATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-CATAA-T-A
*
1129140 AATGCATAAAAGGAT
192 AATGCATGAAAGGAT
*
1129155 GCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATATATG
1 GCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATACCATAATTAAAAT-TATG
* * *
1129220 AAAGGATGTATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTACGGCAT
65 AAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATTAAAGGATGCATTACGGCAT
** *
1129285 GAAAGGATGCCATAATTGAAATGCATGAAAGGATGCCATAATTGAAATACATGAAATGATGCAT-
130 GAAAGGATGCCATAATTGAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAAGGATGCATA
* *
1129349 -T-AAGGTATGAAAGGAT
189 ATAAATGCATGAAAGGAT
* *
1129365 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAATTAAAATTCATG
1 GCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATACCATAATTAAAATT-ATG
* * * * *
1129430 AATA-GATGCATTAAGGCATGAAATGATGCCATAATTGAAATGCATTAAAAGATGTATTAAGGCA
65 AA-AGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATTAAAGGATGCATTACGGCA
* * * * *
1129494 GGAAATGATGTCATAATTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGACATAATTG
129 TGAAAGGATGCCATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-CATAA-T-
*
1129559 AAATGCATGTAAGGAT
191 AAATGCATGAAAGGAT
1129575 GC
1 GC
1129577 ATTAAGGAAT
Statistics
Matches: 372, Mismatches: 36, Indels: 28
0.85 0.08 0.06
Matches are distributed among these distances:
204 13 0.03
205 3 0.01
206 3 0.01
208 1 0.00
209 2 0.01
210 328 0.88
211 2 0.01
212 1 0.00
214 3 0.01
215 3 0.01
216 13 0.03
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (206 bp):
GCCATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATACCATAATTAAAATTATGA
AAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATTAAAGGATGCATTACGGCATG
AAAGGATGCCATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATAATAAATG
CATGAAAGGAT
Found at i:1129402 original size:118 final size:117
Alignment explanation
Indices: 1129072--1129431 Score: 469
Period size: 118 Copynumber: 3.1 Consensus size: 117
1129062 TGCATTACGA
* *
1129072 CATGAAAGGATGCCATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAC
1 CATGAAAGGATGCCATAATTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAC
* * * *
1129137 TAAAATGCATAAAAGGATGCCATAACTAAAATGCATGAAAAGATG-C---ATT-AAGG
66 TAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCCATAATTAAATG
* * * * *
1129190 CATGAAAGGATGCCATAATTAAAATATATGAAAGGATGTATTAAAGCATGAAAGGATGCCATAAT
1 CATGAAAGGATGCCATAATTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAC
*
1129255 TAAAATGCATGAAAGGATGCATTACGGCATGAAAGGATGCCATAATTGAAATG
66 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATT-AAATG
* *
1129308 CATGAAAGGATGCCATAATTGAAATACATGAAATGATGCATTAAGGTATGAAAGGATGCCATAAC
1 CATGAAAGGATGCCATAATTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAC
* *
1129373 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAATTAAAATT
66 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATT-AAATG
1129426 CATGAA
1 CATGAA
1129432 TAGATGCATT
Statistics
Matches: 213, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
112 13 0.06
113 1 0.00
114 1 0.00
116 3 0.01
117 3 0.01
118 192 0.90
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.23
Consensus pattern (117 bp):
CATGAAAGGATGCCATAATTGAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAC
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAATG
Found at i:1129566 original size:26 final size:25
Alignment explanation
Indices: 1128947--1129575 Score: 250
Period size: 26 Copynumber: 27.0 Consensus size: 25
1128937 AAACAGAAGC
*
1128947 CATAATTAAAATGCATGAAAAGATG-
1 CATAATT-AAATGCATGAAAGGATGA
*
1128972 C---ATT-AAGGCATGAAAGGAT-A
1 CATAATTAAATGCATGAAAGGATGA
1128992 CCATAATTAAAATGCATGAAAGGATG-
1 -CATAATT-AAATGCATGAAAGGATGA
* *
1129018 C---ATT-AAGGCATGAAAGGATGC
1 CATAATTAAATGCATGAAAGGATGA
* *
1129039 CATAATTAAAATGCATTAATGGATG-
1 CATAATT-AAATGCATGAAAGGATGA
* *
1129064 C---ATT--ACGACATGAAAGGATGC
1 CATAATTAAATG-CATGAAAGGATGA
1129085 CATAATTGAAATGCATGAAAGGATG-
1 CATAATT-AAATGCATGAAAGGATGA
* *
1129110 C---ATT-AAGGCATGAAAGGATGT
1 CATAATTAAATGCATGAAAGGATGA
* * *
1129131 CATAACTAAAATGCATAAAAGGATGC
1 CATAA-TTAAATGCATGAAAGGATGA
* *
1129157 CATAACTAAAATGCATGAAAAGATG-
1 CATAA-TTAAATGCATGAAAGGATGA
* *
1129182 C---ATT-AAGGCATGAAAGGATGC
1 CATAATTAAATGCATGAAAGGATGA
**
1129203 CATAATTAAAATATATGAAAGGATG-
1 CATAATT-AAATGCATGAAAGGATGA
*
1129228 --T-ATTAAA-GCATGAAAGGATGC
1 CATAATTAAATGCATGAAAGGATGA
1129249 CATAATTAAAATGCATGAAAGGATG-
1 CATAATT-AAATGCATGAAAGGATGA
** *
1129274 C---ATT-ACGGCATGAAAGGATGC
1 CATAATTAAATGCATGAAAGGATGA
*
1129295 CATAATTGAAATGCATGAAAGGATGC
1 CATAATT-AAATGCATGAAAGGATGA
* *
1129321 CATAATTGAAATACATGAAATGATG-
1 CATAATT-AAATGCATGAAAGGATGA
* * *
1129346 C---ATT-AAGGTATGAAAGGATGC
1 CATAATTAAATGCATGAAAGGATGA
*
1129367 CATAACTAAAATGCATGAAAGGATG-
1 CATAA-TTAAATGCATGAAAGGATGA
* **
1129392 C---ATT-AAGGCATGAAAGGATTC
1 CATAATTAAATGCATGAAAGGATGA
*
1129413 CATAATTAAAATTCATGAATA-GATG-
1 CATAATT-AAATGCATGAA-AGGATGA
* * *
1129438 C---ATT-AAGGCATGAAATGATGC
1 CATAATTAAATGCATGAAAGGATGA
* *
1129459 CATAATTGAAATGCATTAAAAGATG-
1 CATAATT-AAATGCATGAAAGGATGA
* * * *
1129484 --T-ATT-AAGGCAGGAAATGATGT
1 CATAATTAAATGCATGAAAGGATGA
1129505 CATAATTAAAATGCATGAAAGGAT-A
1 CATAATT-AAATGCATGAAAGGATGA
*
1129530 C---ATT-AAGGCATGAAAGGATGA
1 CATAATTAAATGCATGAAAGGATGA
*
1129551 CATAATTGAAATGCATGTAAGGATG
1 CATAATT-AAATGCATGAAAGGATG
1129576 CATTAAGGAA
Statistics
Matches: 465, Mismatches: 61, Indels: 155
0.68 0.09 0.23
Matches are distributed among these distances:
19 3 0.01
20 156 0.34
21 16 0.03
22 32 0.07
23 4 0.01
24 32 0.07
25 15 0.03
26 204 0.44
27 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.24
Consensus pattern (25 bp):
CATAATTAAATGCATGAAAGGATGA
Found at i:1135324 original size:3 final size:3
Alignment explanation
Indices: 1135316--1135370 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1135306 ATTAGGATAG
*
1135316 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1135363 TAT T-T TAT
1 TAT TAT TAT
1135371 GCTTTGATCA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1138938 original size:13 final size:14
Alignment explanation
Indices: 1138910--1138943 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1138900 AATAGTACTC
*
1138910 GTGAATATTGAACA
1 GTGAATAGTGAACA
1138924 GTGAATAGT-AACA
1 GTGAATAGTGAACA
1138937 GTGAATA
1 GTGAATA
1138944 ATACCCGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (14 bp):
GTGAATAGTGAACA
Found at i:1139406 original size:44 final size:44
Alignment explanation
Indices: 1139340--1139490 Score: 232
Period size: 44 Copynumber: 3.4 Consensus size: 44
1139330 GTGCAATATT
*
1139340 TTACCATTTAATACCATAAGCTTGTAAGCTTATTTTACCAATATAC
1 TTACCATTT-AT-CCATAAGCTTGTAAGCTTATTTTACCAATACAC
1139386 TTACCATTTATCCATAAGCTTGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTTGTAAGCTTATTTTACCAATACAC
* *
1139430 TTACCATTTATCCATAAGCTTATAAGCTTATTTTACCAATACAT
1 TTACCATTTATCCATAAGCTTGTAAGCTTATTTTACCAATACAC
*
1139474 TTGCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
1139491 CCATATACCA
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
43 3 0.03
44 86 0.86
45 2 0.02
46 9 0.09
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTTGTAAGCTTATTTTACCAATACAC
Found at i:1142619 original size:20 final size:20
Alignment explanation
Indices: 1142594--1142632 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1142584 ACTGAAAATG
1142594 AATATT-AAATGTTGATTTTT
1 AATATTGAAATGTTG-TTTTT
*
1142614 AATATTGGAATGTTGTTTT
1 AATATTGAAATGTTGTTTT
1142633 GCATCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (20 bp):
AATATTGAAATGTTGTTTTT
Found at i:1143785 original size:23 final size:26
Alignment explanation
Indices: 1143720--1143786 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
1143710 TATTTCAAAA
* *
1143720 TTATA-ATTTTTAGAAAAAAAATAAT
1 TTATATATATTTAGAAATAAAATAAT
*
1143745 TTATATATATTTATAAATAAAAT-AT
1 TTATATATATTTAGAAATAAAATAAT
1143770 TTAT-T-TATTTAGAAATA
1 TTATATATATTTAGAAATA
1143787 TCAGAAAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.30
24 1 0.03
25 11 0.30
26 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
TTATATATATTTAGAAATAAAATAAT
Found at i:1145317 original size:3 final size:3
Alignment explanation
Indices: 1145288--1145362 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
1145278 TTGGGTTTTG
* * *
1145288 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1145335 TAA TAA TAA TAA TAA TAA -AA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1145363 TAAATAACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 55 0.87
4 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1145378 original size:23 final size:23
Alignment explanation
Indices: 1145311--1145371 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
1145301 TAATATATAT
* *
1145311 TAATAATAATAATAATTATAATAA
1 TAATAATAATAACAA-TAAAATAA
*
1145335 TAATAATAATAATAATAAAATAA
1 TAATAATAATAACAATAAAATAA
1145358 TAAT-ATAAATAACA
1 TAATAAT-AATAACA
1145372 TTTAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 17 0.50
24 15 0.44
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TAATAATAATAACAATAAAATAA
Found at i:1145631 original size:17 final size:17
Alignment explanation
Indices: 1145609--1145658 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1145599 TTGAATAAGC
1145609 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
*
1145626 TCTTCTTCA-GATGAA-T
1 TCTTCTT-ATTATGAACT
* *
1145642 TCTTCTCATTGTGAACT
1 TCTTCTTATTATGAACT
1145659 CTTTCTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.04
16 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (17 bp):
TCTTCTTATTATGAACT
Found at i:1145936 original size:95 final size:92
Alignment explanation
Indices: 1145745--1145936 Score: 208
Period size: 92 Copynumber: 2.1 Consensus size: 92
1145735 TATGAACTTC
* * * ** * *
1145745 TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGAAAAGTTGATCTATTGAGTT
1 TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCACTGAAAAGCTGATCCATCAAATG
* * *
1145810 ATGAATTCGAGCGAAAAGTTGAACAAG
66 ATGAATTCAAACGAAAAGTTGAACAAA
** *
1145837 TTCTTCTCTT-TTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGGGATGCTGATCCATCA
1 TTCTTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTC--TCACT-GAAAAGCTGATCCATCA
1145901 AATGATGAATTCAAAC-AAAAGGTTGAACAAA
62 AATGATGAATTCAAACGAAAA-GTTGAACAAA
1145932 TTCTT
1 TTCTT
1145937 TTCATTATGA
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
92 36 0.44
93 2 0.02
94 8 0.10
95 36 0.44
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (92 bp):
TTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCACTGAAAAGCTGATCCATCAAATG
ATGAATTCAAACGAAAAGTTGAACAAA
Found at i:1146046 original size:113 final size:113
Alignment explanation
Indices: 1145837--1146440 Score: 971
Period size: 113 Copynumber: 5.3 Consensus size: 113
1145827 GTTGAACAAG
* ** * *
1145837 TTCTTCTCTT-TTCAGATGAGTTCTTCTCATTATGAACTCTTTCACTGGGGATGCTGATCCATCA
1 TTCTTC-CTTCTTCAGATGAGTTCTTCTCATTATGAA--CTTTCTCTGGCAAAGCTAATCCATCA
* * ** * * *
1145901 AATGATGAATTCAAACAAAAGGTTGAACAAATTCTTTTCATTATGAACTTC
63 AGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
* * *
1145952 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG-AGAAGCTGATCCATCAAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCA-AAGCTAATCCATCAAG
*
1146016 TGATGGATTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
65 TGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
1146065 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGT
*
1146130 GATGGACTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
1146178 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGT
1146243 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
*
1146291 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCCAATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGT
* *
1146356 GATGGATTTGAGCAAAA-GTTGACCAAATTCTTCTCATTATGAACTTC
66 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
1146403 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1146441 CTAACTGACA
Statistics
Matches: 468, Mismatches: 18, Indels: 9
0.95 0.04 0.02
Matches are distributed among these distances:
112 66 0.14
113 366 0.78
114 4 0.01
115 32 0.07
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGT
GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
Found at i:1146853 original size:52 final size:52
Alignment explanation
Indices: 1146775--1146880 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
1146765 CAACATGTTA
1146775 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1146827 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1146879 AT
1 AT
1146881 ATATCGATAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (52 bp):
ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
Found at i:1147555 original size:94 final size:94
Alignment explanation
Indices: 1147411--1148071 Score: 1083
Period size: 94 Copynumber: 7.0 Consensus size: 94
1147401 CTTATTTCTA
* * * * * * *
1147411 CTATGAGCAAATTCATTTTTCAATATCCAATGATTGGTTCTGT-GGTTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAA-ATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATC
1147475 AGATAACTCAAAGAACACTTCCAGAAGATG
65 AGATAACTCAAAGAACACTTCCAGAAGATG
* * * * *
1147505 CTATTAGCATATTCATCTTTCAAATTTAATGATTGGTTTTTTAGGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
1147570 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
* *
1147599 CTATGAGCACATTCATCTTCCAAATTTAATGATTGGTTTTTTGGGGTTCATACCAAACAAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
*
1147664 GATAACTCAAAGAACACTTCCAGAAGATT
66 GATAACTCAAAGAACACTTCCAGAAGATG
* *
1147693 CTATGAGCACATTCATCTTCCAAATTCAACGATTGGTTTTTTGGGGTTCATAACAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
* *
1147758 TATAACTCAAAGAACACTTCTAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1147787 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTT-ATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
*
1147851 TATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1147880 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCATATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
1147945 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
* *
1147974 TTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
1148039 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
1148068 CTAT
1 CTAT
1148072 TGGGTCTACG
Statistics
Matches: 533, Mismatches: 32, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
93 105 0.20
94 428 0.80
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (94 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1147915 original size:281 final size:283
Alignment explanation
Indices: 1147411--1148071 Score: 1087
Period size: 281 Copynumber: 2.3 Consensus size: 283
1147401 CTTATTTCTA
* * * * * * *
1147411 CTATGAGCAAATTCATTTTTCAATATCCAATGATTGGTTCTGT-GGTTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCCAA-ATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATC
* * * *
1147475 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCATATTCATCTTTCAAATTTAATGATTG
65 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTG
1147540 GTTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
130 GTTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
1147605 GCACATTCATCTTCCAAATTTAATGATTGGTTTTTTGGGGTTCATACCAAACAAGATCAGATAAC
195 GCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACAAGATCAGATAAC
1147670 TCAAAGAACACTTCCAGAAGAT-T
260 TCAAAGAACACTTCCAGAAGATGT
* *
1147693 CTATGAGCACATTCATCTTCCAAATTCAACGATTGGTTTTTTGGGGTTCATAACAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
* * *
1147758 TATAACTCAAAGAACACTTCTAGAAGATGCTATGAGTACATTCATCTTCCAAATTCAATGATTGG
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGG
* *
1147823 TTTTTTGGGGTT-ATACCAAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
131 TTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
* *
1147887 CACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCATATCAGATAACT
196 CACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACAAGATCAGATAACT
1147952 CAAAGAACACTTCCAGAAGATGT
261 CAAAGAACACTTCCAGAAGATGT
*
1147975 -TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
1148039 GATAACTCAAAGAACACTTCCAGAAGATGCTAT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTAT
1148072 TGGGTCTACG
Statistics
Matches: 351, Mismatches: 26, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
281 241 0.69
282 110 0.31
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (283 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGG
TTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
CACATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACAAGATCAGATAACT
CAAAGAACACTTCCAGAAGATGT
Found at i:1150215 original size:2 final size:2
Alignment explanation
Indices: 1150208--1150249 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1150198 ACAACAAAGG
1150208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1150250 GGATAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153241 original size:14 final size:14
Alignment explanation
Indices: 1153207--1153260 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1153197 TTGTGCAATA
* *
1153207 CAAATGCAAAGATG
1 CAAATGTAAATATG
1153221 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
1153236 CAAATGTAAAAATG
1 CAAATGTAAATATG
* *
1153250 TAAATTTAAAT
1 CAAATGTAAAT
1153261 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1155429 original size:23 final size:26
Alignment explanation
Indices: 1155386--1155435 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1155376 TTGAGAAAAA
*
1155386 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
1155412 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
1155435 A
1 A
1155436 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:1156676 original size:3 final size:3
Alignment explanation
Indices: 1156651--1156732 Score: 101
Period size: 3 Copynumber: 26.7 Consensus size: 3
1156641 TTGGGTTTTG
* * * *
1156651 TAA TAT TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1156698 TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1156733 TAAATAACAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
3 65 0.92
4 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1158229 original size:20 final size:20
Alignment explanation
Indices: 1158204--1158247 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1158194 ATTTTCCATT
1158204 AAAAGA-AAAAAAAATACCAA
1 AAAAGAGAAAAAAAA-ACCAA
*
1158224 AAAAGAGAGAAAAAAACCAA
1 AAAAGAGAAAAAAAAACCAA
1158244 AAAA
1 AAAA
1158248 AATTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (20 bp):
AAAAGAGAAAAAAAAACCAA
Found at i:1167413 original size:17 final size:17
Alignment explanation
Indices: 1167402--1167435 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1167392 AAATGAATTG
1167402 GTTTGATGAATGAACTA
1 GTTTGATGAATGAACTA
*
1167419 GTTTGATTAATGAACTA
1 GTTTGATGAATGAACTA
1167436 ACTTTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (17 bp):
GTTTGATGAATGAACTA
Found at i:1172057 original size:24 final size:24
Alignment explanation
Indices: 1172013--1172087 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 24
1172003 GTGGCCTCTA
*
1172013 TCACTTGCACTCGAGAA-TGCCATT
1 TCACTTGCACTTGA-AAGTGCCATT
*
1172037 TCACTTGCACTTTAAAGTGCCATTT
1 TCACTTGCACTTGAAAGTGCCA-TT
* *
1172062 ATCAATTGCACTTGAAGGTGCCATT
1 -TCACTTGCACTTGAAAGTGCCATT
1172087 T
1 T
1172088 ATACCAATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.05
24 18 0.42
25 4 0.09
26 19 0.44
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (24 bp):
TCACTTGCACTTGAAAGTGCCATT
Found at i:1173385 original size:19 final size:20
Alignment explanation
Indices: 1173368--1173406 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1173358 GCCCAATTTT
1173368 ACACTCTAACATCAATTTCA
1 ACACTCTAACATCAATTTCA
* *
1173388 ACATTCTAACATAAATTTC
1 ACACTCTAACATCAATTTC
1173407 CAGTATAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (20 bp):
ACACTCTAACATCAATTTCA
Found at i:1177807 original size:4 final size:4
Alignment explanation
Indices: 1177798--1177848 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
1177788 TGGTTTAATA
* * * * *
1177798 ATAT ATAT ATAT ATAT ATAT ACAT ACAT ACAT ATAT ACAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1177846 ATA
1 ATA
1177849 CTTCTACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:1178521 original size:117 final size:117
Alignment explanation
Indices: 1178353--1178563 Score: 334
Period size: 117 Copynumber: 1.8 Consensus size: 117
1178343 ATAGGTATAG
* * *
1178353 TGGTACGCAACAACATTATACTAACAATTACATAGTGGTAATTCACTAAGAATACCATCCTTGCA
1 TGGTACACAACAACACTATACTAACAATTACAAAGTGGTAATTCACTAAGAATACCATCCTTGCA
1178418 CACAAAGTGCACCAAATAAGCACCTAAGTTCCACAATGATATATAGGCACTA
66 CACAAAGTGCACCAAATAAGCACCTAAGTTCCACAATGATATATAGGCACTA
* *
1178470 TGGTACACATCAACACTATATTAACAATT-CTAAAGTGGTAATTCACTAAGAATACCATCCTTGC
1 TGGTACACAACAACACTATACTAACAATTAC-AAAGTGGTAATTCACTAAGAATACCATCCTTGC
* * *
1178534 ACACAAAGTGGAGCTAATAAGCACCTAAGT
65 ACACAAAGTGCACCAAATAAGCACCTAAGT
1178564 GCTATAGTAC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
116 1 0.01
117 84 0.99
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (117 bp):
TGGTACACAACAACACTATACTAACAATTACAAAGTGGTAATTCACTAAGAATACCATCCTTGCA
CACAAAGTGCACCAAATAAGCACCTAAGTTCCACAATGATATATAGGCACTA
Found at i:1178680 original size:26 final size:26
Alignment explanation
Indices: 1178606--1178719 Score: 133
Period size: 26 Copynumber: 4.5 Consensus size: 26
1178596 CTGCACACAT
* * *
1178606 AGTGCCCTTTATCACTTGCACTCGAA
1 AGTGCCATTTATGAATTGCACTCGAA
* * *
1178632 AATGCCATTT-CG-CTTGCACTCGAA
1 AGTGCCATTTATGAATTGCACTCGAA
1178656 AGTGCCATTTATGAATTGCACTCGAA
1 AGTGCCATTTATGAATTGCACTCGAA
*
1178682 AGTGCCAATTATGAATTGCACTCGAA
1 AGTGCCATTTATGAATTGCACTCGAA
* *
1178708 TGTGTCATTTAT
1 AGTGCCATTTAT
1178720 ATCAAAGACT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
24 21 0.28
25 1 0.01
26 53 0.71
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (26 bp):
AGTGCCATTTATGAATTGCACTCGAA
Found at i:1178718 original size:52 final size:50
Alignment explanation
Indices: 1178606--1178719 Score: 131
Period size: 50 Copynumber: 2.2 Consensus size: 50
1178596 CTGCACACAT
* * * *
1178606 AGTGCCCTTTATCACTTGCACTCGAAAATGCCATTTCGCTTGCACTCGAA
1 AGTGCCATTTATGAATTGCACTCGAAAATGCCATTTCGATTGCACTCGAA
*
1178656 AGTGCCATTTATGAATTGCACTCGAAAGTGCCAATTAT-GAATTGCACTCGAA
1 AGTGCCATTTATGAATTGCACTCGAAAATGCC-ATT-TCG-ATTGCACTCGAA
* *
1178708 TGTGTCATTTAT
1 AGTGCCATTTAT
1178720 ATCAAAGACT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 28 0.52
51 4 0.07
52 22 0.41
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (50 bp):
AGTGCCATTTATGAATTGCACTCGAAAATGCCATTTCGATTGCACTCGAA
Found at i:1182936 original size:21 final size:22
Alignment explanation
Indices: 1182905--1182945 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1182895 GCACACAAAG
1182905 TTCCATAGTACACAAAGTACTA
1 TTCCATAGTACACAAAGTACTA
1182927 TTCCA-AGTACACAAAGTAC
1 TTCCATAGTACACAAAGTAC
1182946 AGGTACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (22 bp):
TTCCATAGTACACAAAGTACTA
Found at i:1190976 original size:21 final size:22
Alignment explanation
Indices: 1190951--1190996 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1190941 AATCGCTTGG
1190951 TTTCATG-AAATTTATCCTTA-A
1 TTTCATGTAAATTTA-CCTTATA
*
1190972 TTTCATGTTAATTTACCTTATA
1 TTTCATGTAAATTTACCTTATA
1190994 TTT
1 TTT
1190997 AAGCTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCATGTAAATTTACCTTATA
Found at i:1196856 original size:14 final size:14
Alignment explanation
Indices: 1196837--1196864 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1196827 GAACAATTGC
1196837 CTTGATATGAATCT
1 CTTGATATGAATCT
1196851 CTTGATATGAATCT
1 CTTGATATGAATCT
1196865 AGTTGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
CTTGATATGAATCT
Found at i:1198507 original size:15 final size:15
Alignment explanation
Indices: 1198487--1198519 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1198477 GAAAACCTTT
1198487 AAAGAAAA-ATAAAAG
1 AAAGAAAAGA-AAAAG
1198502 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
1198517 AAA
1 AAA
1198520 AAGTAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1199532 original size:10 final size:10
Alignment explanation
Indices: 1199517--1199547 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1199507 TATTCACTCT
1199517 TTCTTTTTTC
1 TTCTTTTTTC
1199527 TTCTTTTTTCC
1 TTCTTTTTT-C
1199538 TTCTTTTTTC
1 TTCTTTTTTC
1199548 GAAACTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:1199534 original size:11 final size:11
Alignment explanation
Indices: 1199517--1199547 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1199507 TATTCACTCT
1199517 TTCTTTTTT-C
1 TTCTTTTTTCC
1199527 TTCTTTTTTCC
1 TTCTTTTTTCC
1199538 TTCTTTTTTC
1 TTCTTTTTTC
1199548 GAAACTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTTTTCC
Found at i:1204186 original size:28 final size:30
Alignment explanation
Indices: 1204136--1204192 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
1204126 ATTTAAGGCA
1204136 AAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAATGGTTTTTGGACTTGAATTGAATTTAC
1204166 AAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAATGGTTTTTGGACTTGAATTGAATTTA
1204193 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 11 0.41
29 12 0.44
30 4 0.15
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.46
Consensus pattern (30 bp):
AAATGGTTTTTGGACTTGAATTGAATTTAC
Found at i:1204300 original size:21 final size:21
Alignment explanation
Indices: 1204272--1204329 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1204262 AGGGTGTCAA
1204272 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
1204293 ATTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
1204314 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1204330 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1207700 original size:29 final size:30
Alignment explanation
Indices: 1207630--1207689 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1207620 CAATTTAAGG
1207630 CAAAATGGTTTTTGGACTCGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTCGAATTGAATTTA
*
1207661 CAAAATGTTTTTGGACT-TAATTGAATTTA
1 CAAAATGTTTTTGGACTCGAATTGAATTTA
1207690 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTCGAATTGAATTTA
Found at i:1207796 original size:21 final size:21
Alignment explanation
Indices: 1207770--1207827 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1207760 AGGGTGTCAA
1207770 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* ** *
1207791 AGTGCATCCATGCATCGTTGC
1 AGTGCATCCATGCACCCCTAC
1207812 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1207828 TACACTACTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:1207858 original size:42 final size:41
Alignment explanation
Indices: 1207769--1207868 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 41
1207759 AAGGGTGTCA
*
1207769 AAGTGCATCCATGCACCCCTACAGTGCATCCATGCATCGTTG
1 AAGTGCATCCATGCACCCCTACA-TGCATCCATGCATCGATG
* *
1207811 CAGTGCATCCATGCACCTACACTAC-TGCATCGATGCATC-ATG
1 AAGTGCATCCATGCACC--C-CTACATGCATCCATGCATCGATG
1207853 AAGTGCATCCATGCAC
1 AAGTGCATCCATGCAC
1207869 TCAAACACCG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
42 33 0.65
43 13 0.25
44 1 0.02
45 4 0.08
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (41 bp):
AAGTGCATCCATGCACCCCTACATGCATCCATGCATCGATG
Found at i:1208360 original size:34 final size:32
Alignment explanation
Indices: 1208321--1208390 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1208311 TTTTGTAAAG
* *
1208321 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1208355 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1208387 GGGA
1 GGGA
1208391 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1210380 original size:18 final size:19
Alignment explanation
Indices: 1210359--1210404 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1210349 ACAAGCTTTA
*
1210359 TTAAATGAA-ATAGCATAC
1 TTAAATGAAGATAACATAC
* *
1210377 TT-AATTAAGATAACATGC
1 TTAAATGAAGATAACATAC
1210395 TTAAATGAAG
1 TTAAATGAAG
1210405 TACATGCTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.23
18 11 0.50
19 6 0.27
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (19 bp):
TTAAATGAAGATAACATAC
Found at i:1210411 original size:17 final size:17
Alignment explanation
Indices: 1210389--1210479 Score: 74
Period size: 17 Copynumber: 5.3 Consensus size: 17
1210379 AATTAAGATA
1210389 ACATGCTTAAATGAAGT
1 ACATGCTTAAATGAAGT
** *
1210406 ACATGCTTGTATGAACT
1 ACATGCTTAAATGAAGT
* * * **
1210423 ACATGCTTTAGTTATCT
1 ACATGCTTAAATGAAGT
*
1210440 ATATGCTTAAATGAAGT
1 ACATGCTTAAATGAAGT
* *
1210457 ATATGCTTGAATGAAGT
1 ACATGCTTAAATGAAGT
1210474 AGCATG
1 A-CATG
1210480 TTTATTTATT
Statistics
Matches: 57, Mismatches: 16, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
17 54 0.95
18 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (17 bp):
ACATGCTTAAATGAAGT
Found at i:1210450 original size:51 final size:51
Alignment explanation
Indices: 1210391--1210488 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
1210381 TTAAGATAAC
*
1210391 ATGCTTAAATGAAGTACATGCTTGTATGAACTA-CATGCTTTAGTTATCTAT
1 ATGCTTAAATGAAGTACATGCTTGAATGAACTAGCATG-TTTAGTTATCTAT
* * *
1210442 ATGCTTAAATGAAGTATATGCTTGAATGAAGTAGCATGTTTATTTAT
1 ATGCTTAAATGAAGTACATGCTTGAATGAACTAGCATGTTTAGTTAT
1210489 TCATGTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 38 0.90
52 4 0.10
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (51 bp):
ATGCTTAAATGAAGTACATGCTTGAATGAACTAGCATGTTTAGTTATCTAT
Found at i:1217615 original size:2 final size:2
Alignment explanation
Indices: 1217603--1217642 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1217593 TTTCATACAC
*
1217603 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1217643 CCCTTCTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1218654 original size:3 final size:3
Alignment explanation
Indices: 1218646--1218718 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
1218636 CTATCAAAAA
1218646 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1218693 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1218719 ACAAAAATAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1219096 original size:22 final size:23
Alignment explanation
Indices: 1219055--1219108 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
1219045 AAGGAGAACA
1219055 TTTGGGGTGTTGAAAAAAAGCCT
1 TTTGGGGTGTTGAAAAAAAGCCT
1219078 TTTGGGGTGTTG-AAAAAAGCCT
1 TTTGGGGTGTTGAAAAAAAGCCT
*
1219100 TTCGGGGTG
1 TTTGGGGTG
1219109 AGAAGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.31
Consensus pattern (23 bp):
TTTGGGGTGTTGAAAAAAAGCCT
Found at i:1219117 original size:22 final size:22
Alignment explanation
Indices: 1219058--1219117 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1219048 GAGAACATTT
* *
1219058 GGGGTGTTGAAAAAAAGCCTTTT
1 GGGGTGTAG-AAAAAAGCCTTTC
*
1219081 GGGGTGTTGAAAAAAGCCTTTC
1 GGGGTGTAGAAAAAAGCCTTTC
1219103 GGGGTG-AGAAGAAAA
1 GGGGTGTAGAA-AAAA
1219118 AACCAGAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 22 0.65
23 9 0.26
ACGTcount: A:0.33, C:0.08, G:0.35, T:0.23
Consensus pattern (22 bp):
GGGGTGTAGAAAAAAGCCTTTC
Found at i:1220156 original size:30 final size:30
Alignment explanation
Indices: 1220122--1220305 Score: 106
Period size: 30 Copynumber: 6.2 Consensus size: 30
1220112 AGGTCCTCCT
* *
1220122 AGTTTTTATTAATATTATTTTAGTCCTTTA
1 AGTTTCTATTAATACTATTTTAGTCCTTTA
** *
1220152 AGTTTCTATTTTTGCTATTTTAGTCCTTTA
1 AGTTTCTATTAATACTATTTTAGTCCTTTA
* ** * * *
1220182 ACTTTCTATTTTTTCTA-TTTAGACCCTTA
1 AGTTTCTATTAATACTATTTTAGTCCTTTA
** * *
1220211 AGTTTCTATTTTTACTAGTATA-TCCCTTTA
1 AGTTTCTATTAATACTATTTTAGT-CCTTTA
** **
1220241 AGTTTCTATTTTTGTTATTTTAGTCCTTTA
1 AGTTTCTATTAATACTATTTTAGTCCTTTA
* * * *
1220271 AATTTTTGTT-TTAGCTATTTTAG-CCTTTCA
1 AGTTTCTATTAATA-CTATTTTAGTCCTTT-A
1220301 AGTTT
1 AGTTT
1220306 GGTTAAATTT
Statistics
Matches: 125, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
29 32 0.26
30 92 0.74
31 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (30 bp):
AGTTTCTATTAATACTATTTTAGTCCTTTA
Found at i:1220212 original size:59 final size:60
Alignment explanation
Indices: 1220136--1220298 Score: 190
Period size: 59 Copynumber: 2.8 Consensus size: 60
1220126 TTTATTAATA
1220136 TTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTT-
1 TTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTTG
* * * * * *
1220195 TCTA-TTTAGACCCTTAAGTTTCTATTTTTACTAGTATA-TCCCTTTAAGTTTCTATTTTTG
1 T-TATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT-CCTTTAACTTTCTATTTTTG
* * * *
1220255 TTATTTTAGTCCTTTAAATTTTTGTTTTAGCTATTTTAG-CCTTT
1 TTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTT
1220299 CAAGTTTGGT
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
58 1 0.01
59 55 0.65
60 28 0.33
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.59
Consensus pattern (60 bp):
TTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTTG
Found at i:1223959 original size:31 final size:32
Alignment explanation
Indices: 1223924--1224017 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 32
1223914 AAGATCAAAT
* * *
1223924 CAAAGCAGAGAGAAAAGAAA-AGAAAAAGAAA
1 CAAAGCAAAGAAAAAACAAAGAGAAAAAGAAA
1223955 CAAAGCAAAGAAAAAACAAAGAGAAAAAGCAAAGA
1 CAAAGCAAAGAAAAAACAAAGAGAAAAAG--AA-A
* *
1223990 GAAAAACAAAGAAAAAA-AAAGA-AAAAAG
1 -CAAAGCAAAGAAAAAACAAAGAGAAAAAG
1224018 TGAAGAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
31 17 0.32
32 8 0.15
34 8 0.15
35 6 0.11
36 14 0.26
ACGTcount: A:0.74, C:0.07, G:0.18, T:0.00
Consensus pattern (32 bp):
CAAAGCAAAGAAAAAACAAAGAGAAAAAGAAA
Found at i:1223964 original size:24 final size:23
Alignment explanation
Indices: 1223937--1224016 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 23
1223927 AGCAGAGAGA
1223937 AAAGAAAAGAA-AAAGAAACAAAGC
1 AAAGAAAA-AACAAAGAAA-AAAGC
1223961 AAAGAAAAAACAAAGAGAAAAAGC
1 AAAGAAAAAACAAAGA-AAAAAGC
1223985 AAAGAGAAAAACAAAGAAAAAA--
1 AAAGA-AAAAACAAAGAAAAAAGC
1224007 AAAGAAAAAA
1 AAAGAAAAAA
1224017 GTGAAGAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.09
22 5 0.09
23 2 0.04
24 28 0.53
25 13 0.25
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAACAAAGAAAAAAGC
Found at i:1223966 original size:13 final size:11
Alignment explanation
Indices: 1223937--1224016 Score: 92
Period size: 11 Copynumber: 6.9 Consensus size: 11
1223927 AGCAGAGAGA
1223937 AAAGAAAAGAA-
1 AAAGAAAA-AAC
1223948 AAAGAAACAAAGC
1 AAAGAAA-AAA-C
1223961 AAAGAAAAAAC
1 AAAGAAAAAAC
1223972 AAAGAGAAAAAGC
1 AAAGA-AAAAA-C
1223985 AAAGAGAAAAAC
1 AAAGA-AAAAAC
1223997 AAAGAAAAAA-
1 AAAGAAAAAAC
1224007 AAAGAAAAAA
1 AAAGAAAAAA
1224017 GTGAAGAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.16
11 20 0.31
12 15 0.23
13 19 0.30
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAC
Found at i:1224007 original size:25 final size:25
Alignment explanation
Indices: 1223939--1224007 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
1223929 CAGAGAGAAA
* *
1223939 AGAAAAGAAAAAGAAACAAAGCAAAG
1 AGAAAA-ACAAAGAAAAAAAGCAAAG
*
1223965 A-AAAAACAAAGAGAAAAAGCAAAG
1 AGAAAAACAAAGAAAAAAAGCAAAG
1223989 AGAAAAACAAAGAAAAAAA
1 AGAAAAACAAAGAAAAAAA
1224008 AAGAAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 17 0.45
25 20 0.53
26 1 0.03
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (25 bp):
AGAAAAACAAAGAAAAAAAGCAAAG
Found at i:1224016 original size:11 final size:11
Alignment explanation
Indices: 1223936--1224016 Score: 65
Period size: 12 Copynumber: 7.0 Consensus size: 11
1223926 AAGCAGAGAG
*
1223936 AAAAGAAAAGA
1 AAAAGAAAAAA
1223947 AAAAGAAACAAA
1 AAAAGAAA-AAA
*
1223959 GCAAAGAAAAAA
1 -AAAAGAAAAAA
*
1223971 CAAAGAGAAAAAG
1 -AAA-AGAAAAAA
*
1223984 CAAAGAGAAAAA
1 AAAAGA-AAAAA
*
1223996 CAAAG-AAAAA
1 AAAAGAAAAAA
1224006 AAAAGAAAAAA
1 AAAAGAAAAAA
1224017 GTGAAGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
10 9 0.16
11 16 0.28
12 18 0.32
13 14 0.25
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:1227416 original size:11 final size:11
Alignment explanation
Indices: 1227387--1227425 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1227377 AACTTCTTTC
1227387 TTCTTCTTTTT
1 TTCTTCTTTTT
*
1227398 ATTTTTCTTTTT
1 -TTCTTCTTTTT
1227410 TTCTTCTTTTT
1 TTCTTCTTTTT
1227421 TTCTT
1 TTCTT
1227426 TCGAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (11 bp):
TTCTTCTTTTT
Found at i:1237978 original size:2 final size:2
Alignment explanation
Indices: 1237971--1237999 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1237961 CCTGCCCCTT
1237971 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 T
1238000 GATGATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1239751 original size:15 final size:15
Alignment explanation
Indices: 1239731--1239784 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
1239721 GTCTACGAAA
1239731 ATATTTTATTATATT
1 ATATTTTATTATATT
1239746 ATA-TTTATT-TATT
1 ATATTTTATTATATT
**
1239759 AT-TAATATTATTATT
1 ATATTTTATTA-TATT
1239774 -TATTTTATTAT
1 ATATTTTATTAT
1239785 TTTTACAGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
13 10 0.32
14 8 0.26
15 13 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTTATTATATT
Found at i:1239785 original size:15 final size:14
Alignment explanation
Indices: 1239732--1239785 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
1239722 TCTACGAAAA
1239732 TATTTTATTA-TAT
1 TATTTTATTATTAT
1239745 TATATTTA-T-TTAT
1 TAT-TTTATTATTAT
*
1239758 TATTAATATTATTATT
1 TATT-TTATTATTA-T
1239774 TATTTTATTATT
1 TATTTTATTATT
1239786 TTTACAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
12 1 0.03
13 12 0.36
14 5 0.15
15 10 0.30
16 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTTATTATTAT
Found at i:1239785 original size:24 final size:21
Alignment explanation
Indices: 1239736--1239785 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 21
1239726 CGAAAATATT
1239736 TTATTATATTATATTTATTTA
1 TTATTATATTATATTTATTTA
1239757 TTATTAATATTATTATTTATTTTA
1 TTATT-ATATTA-TATTTA-TTTA
1239781 TTATT
1 TTATT
1239786 TTTACAGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.19
22 6 0.23
23 6 0.23
24 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATATTATATTTATTTA
Found at i:1239786 original size:12 final size:12
Alignment explanation
Indices: 1239747--1239786 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1239737 TATTATATTA
1239747 TATTTA-TTTAT
1 TATTTATTTTAT
* *
1239758 TATTAATATTAT
1 TATTTATTTTAT
1239770 TATTTATTTTAT
1 TATTTATTTTAT
1239782 TATTT
1 TATTT
1239787 TTACAGGCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTATTTTAT
Found at i:1239867 original size:33 final size:33
Alignment explanation
Indices: 1239830--1239933 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
1239820 TGAGATTCAG
*
1239830 AAACCAACATATTTGAATCCTATTGAAACACTA
1 AAACCAACATATTTGAATCTTATTGAAACACTA
* *
1239863 AAACCAACGTATTT-AAGTCTTATTGAAATACTA
1 AAACCAACATATTTGAA-TCTTATTGAAACACTA
*
1239896 AAACCAACATATTTGAGTCTTATTGAAACACTA
1 AAACCAACATATTTGAATCTTATTGAAACACTA
1239929 AAACC
1 AAACC
1239934 GAAGCATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.95
34 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (33 bp):
AAACCAACATATTTGAATCTTATTGAAACACTA
Found at i:1240349 original size:14 final size:14
Alignment explanation
Indices: 1240326--1240364 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1240316 TCATTTTTTC
1240326 ATTTT-TTATTAAT
1 ATTTTATTATTAAT
1240339 ATTATTA-TATTAAT
1 ATT-TTATTATTAAT
1240353 ATTTTATTATTA
1 ATTTTATTATTA
1240365 TTCTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTATTATTAAT
Done.