Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_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: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:600787 original size:18 final size:18
Alignment explanation
Indices: 600756--600792 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
600746 GATACTAGGA
* *
600756 CCTTGGGTATCGATAATC
1 CCTTGAGTAGCGATAATC
600774 CCTTGAGTAGCGATAATC
1 CCTTGAGTAGCGATAATC
600792 C
1 C
600793 TTTAAGGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (18 bp):
CCTTGAGTAGCGATAATC
Found at i:603733 original size:21 final size:21
Alignment explanation
Indices: 603707--603759 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
603697 TCTTATAGGA
603707 GTATCGATACTGGTACCTTGG
1 GTATCGATACTGGTACCTTGG
603728 GTATCGATACTGGTACCTTGG
1 GTATCGATACTGGTACCTTGG
603749 GTATCGATACT
1 GTATCGATACT
603760 CCCTTGAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
GTATCGATACTGGTACCTTGG
Found at i:606879 original size:22 final size:22
Alignment explanation
Indices: 606841--606895 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
606831 ATATTAGAGA
*
606841 ATTTAAACTATTTGATAATAAAT
1 ATTTAAA-TATTGGATAATAAAT
* *
606864 GTTTAAATATTGGATAATGAAT
1 ATTTAAATATTGGATAATAAAT
606886 ATTTAAATAT
1 ATTTAAATAT
606896 CATATAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (22 bp):
ATTTAAATATTGGATAATAAAT
Found at i:609801 original size:56 final size:56
Alignment explanation
Indices: 609734--609843 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
609724 CGAAATACCC
609734 ATAACAGGACCCAACCTGGAGCCCAAACCAAACCGACCTGGAGCCTACCCTAACTA
1 ATAACAGGACCCAACCTGGAGCCCAAACCAAACCGACCTGGAGCCTACCCTAACTA
609790 ATAACAGGACCCAACCTGGAGCCCAAACCAAACCGACCTGGAGCCTACCCTAAC
1 ATAACAGGACCCAACCTGGAGCCCAAACCAAACCGACCTGGAGCCTACCCTAAC
609844 CTAAACCTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.38, G:0.16, T:0.10
Consensus pattern (56 bp):
ATAACAGGACCCAACCTGGAGCCCAAACCAAACCGACCTGGAGCCTACCCTAACTA
Found at i:610888 original size:109 final size:109
Alignment explanation
Indices: 610726--610931 Score: 258
Period size: 109 Copynumber: 1.9 Consensus size: 109
610716 GGACCAAATA
* * ** *
610726 TGTTATTTTCCCTTTTCTTTGCATGTTATATAATTGTTTATATATTCACTGTTTAGTCCCTCTAA
1 TGTTATTTTCCATTTTCCTTGCATGTTATATAATTGGGTATATATTCACTGTTTAGTCCCTATAA
*
610791 CTTTAGTGTGTTTTTACA-TTATGGTCATATGTGATGAGTGAAAC
66 CTTTAGCGTGTTTTTACACTT-TGGTCATATGTGATGAGTGAAAC
* *
610835 TGTTATTTTCCATTTTCCTTGCATGTTATAATATTATTGGGT-TAT-TT-ATTGTTTAGTTCCTA
1 TGTTATTTTCCATTTTCCTTGCATGTTAT-ATA--ATTGGGTATATATTCACTGTTTAGTCCCTA
* *
610897 TAAGTTTAGCGTGTTTTTACACTTTGGTTATATGT
63 TAACTTTAGCGTGTTTTTACACTTTGGTCATATGT
610932 AGTGACTGAT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
109 68 0.82
110 7 0.08
111 3 0.04
112 5 0.06
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (109 bp):
TGTTATTTTCCATTTTCCTTGCATGTTATATAATTGGGTATATATTCACTGTTTAGTCCCTATAA
CTTTAGCGTGTTTTTACACTTTGGTCATATGTGATGAGTGAAAC
Found at i:619615 original size:140 final size:140
Alignment explanation
Indices: 619272--620279 Score: 1181
Period size: 140 Copynumber: 7.3 Consensus size: 140
619262 ATAAACCAAC
* * * *
619272 TAACAATTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAGAAGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * *
619337 ATGAGAAGAATTTGTTC-ACCTTTGCTTGATTCATCGCATATGGAATTGAATCAGCGACGCCTCA
66 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
*
619401 CTCGAGGG-T
131 CTTGAGGGAT
* *
619410 TAACATTTCCAATTGAAGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * * *
619475 AAGAGAAGAACTTGTTCAACCTTTGCTAGATTTATCGCATATGGAGTTGAATCAGTGACGCCTCA
66 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
619540 CTTGAGGGAT
131 CTTGAGGGAT
* * * * ** *
619550 TAATATTTCTAATAGAGGGTTCATAATAAGGGGATCTCATCCGATAGAGGGAGAAGAAGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * * * * *
619615 ATAAGAAGAACTTGTTCAACTTTTTCTCGATTCATCACATATGGAGTTGAATTAGCGACGCTTCA
66 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
*
619680 CTCGAGGGAT
131 CTTGAGGGAT
* ** * * *
619690 TAACATTTCCAGTGGATAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAATACGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * * * * *
619755 ATGAGAATAACTTGTTCAACCTTTGCTCGATGCATCCCATATAGAGTTGAATCAGTGAAGCCTCA
66 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
619820 CTTGAGGGAT
131 CTTGAGGGAT
* * * *
619830 TAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAGGGAGAAGAAGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * ** * *
619895 ATGAGAAGAAC---TT--ACCTTTTCTCGATGCATCGCATATGGAGTTGAATCAGAAATGGCTCA
66 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
619955 CTTGAGGGAT
131 CTTGAGGGAT
* * * * *
619965 TAACATTTCAAATGGAGGGTTCGTAATAAGAAGAACTCAACAGATA-AGGGAGAAGAAGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * * * * * * *
620029 ATGAGAAGAACTTGTTCAACTTTTGCTTGATTCATCGTATATGGAGATGAATCAACAATGTCTCA
66 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
*
620094 CTTGAGGAAT
131 CTTGAGGGAT
* * * ** * *
620104 TAACATTTCCAGTGGAGGGTTCGTAATGAGAATAACTCATTTGAT-GAGAGAGAATAAGTTCATA
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
* * * * *
620168 ATGAGATA-AACTTGTTCAACCTTAGCTCAATTCATCGCATTTGGTGTTGAATCAGCGATGCCTC
66 ATGAGA-AGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTC
* * *
620232 AATCGAGGTAT
130 ACTTGAGGGAT
* * * * *
620243 CAACATTTTCAGTAGAGAGTTCATAATGAGAAGAACT
1 TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACT
620280 TACAGCTTAA
Statistics
Matches: 742, Mismatches: 119, Indels: 17
0.85 0.14 0.02
Matches are distributed among these distances:
134 29 0.04
135 87 0.12
137 4 0.01
138 74 0.10
139 241 0.32
140 307 0.41
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (140 bp):
TAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
CTTGAGGGAT
Found at i:620593 original size:23 final size:23
Alignment explanation
Indices: 620557--620601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
620547 AAAATACCCA
*
620557 AAACAGAACCCGACCCAAAGCCC
1 AAACAAAACCCGACCCAAAGCCC
* *
620580 AAACAAAACTCGACCCGAAGCC
1 AAACAAAACCCGACCCAAAGCC
620602 TACTCTAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.40, G:0.13, T:0.02
Consensus pattern (23 bp):
AAACAAAACCCGACCCAAAGCCC
Found at i:624882 original size:22 final size:22
Alignment explanation
Indices: 624845--624898 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
624835 TTTTAGAGAC
*
624845 TTTAAACTATTTGATAATGAACA
1 TTTAAA-TATTGGATAATGAACA
*
624868 TTTAAATATTGGATAATGAATA
1 TTTAAATATTGGATAATGAACA
624890 TTTAAATAT
1 TTTAAATAT
624899 CATATAGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTAAATATTGGATAATGAACA
Found at i:627613 original size:60 final size:59
Alignment explanation
Indices: 627486--627618 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 59
627476 TTCATAGGGT
* * * *
627486 AAAG-TACACAAATGGTCCTTCGACTGTAGGATGTTGTTTTGTTGAGCCTTCAACTATTA
1 AAAGTTACA-AAATGGTCCTTCGACTATAAGATATTGATTTGTTGAGCCTTCAACTATTA
* * *
627545 AAAGTTACAAAATGGTTCTTTGACTATAAGATATTGATTTGTTGAGTC-TCACGACTATTA
1 AAAGTTACAAAATGGTCCTTCGACTATAAGATATTGATTTGTTGAGCCTTCA--ACTATTA
627605 AAAGTTACAAAATG
1 AAAGTTACAAAATG
627619 ATCACCGACT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.05
59 36 0.56
60 25 0.39
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCTTCGACTATAAGATATTGATTTGTTGAGCCTTCAACTATTA
Found at i:644037 original size:30 final size:30
Alignment explanation
Indices: 644001--644060 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
643991 ATTAACCATA
*
644001 ACTAGGTTGAATCATCTTCATAAAATTTAT
1 ACTAGGTTGAATAATCTTCATAAAATTTAT
644031 ACTAGGTTGAATAATCTTCATAAAATTTAT
1 ACTAGGTTGAATAATCTTCATAAAATTTAT
644061 GTACGTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
ACTAGGTTGAATAATCTTCATAAAATTTAT
Found at i:651208 original size:14 final size:15
Alignment explanation
Indices: 651181--651209 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
651171 ATTTGATTCA
651181 AAAATTTATTAAATT
1 AAAATTTATTAAATT
651196 AAAATTT-TTAAATT
1 AAAATTTATTAAATT
651210 GAATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTATTAAATT
Found at i:653134 original size:30 final size:31
Alignment explanation
Indices: 653100--653165 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
653090 GTTGAACAGT
*
653100 AAATACATAAAGTTAAAGGA-CAAAAATA-AA
1 AAATACATAAACTTAAAGGAGCAAAAA-ACAA
653130 AAATACATAAACTTAAAGGAGCAAAAAACAA
1 AAATACATAAACTTAAAGGAGCAAAAAACAA
653161 AAATA
1 AAATA
653166 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (31 bp):
AAATACATAAACTTAAAGGAGCAAAAAACAA
Found at i:653223 original size:30 final size:30
Alignment explanation
Indices: 653189--653253 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
653179 CCAAATAAGT
* * *
653189 AAAAACATACATTTAAGGGATTAAAATAGC
1 AAAAACATACATTTAAAGGACTAAAACAGC
* *
653219 AAAAACATATATTTAAAGGACTAAAACAGT
1 AAAAACATACATTTAAAGGACTAAAACAGC
653249 AAAAA
1 AAAAA
653254 AAGAATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (30 bp):
AAAAACATACATTTAAAGGACTAAAACAGC
Found at i:654675 original size:20 final size:20
Alignment explanation
Indices: 654650--654690 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
654640 ATATGATTTA
654650 AATAAAAATATA-ATAATAAT
1 AATAAAAATA-ACATAATAAT
*
654670 AATAAATATAACATAATAAT
1 AATAAAAATAACATAATAAT
654690 A
1 A
654691 TTTTTGGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAAATAACATAATAAT
Found at i:654999 original size:40 final size:40
Alignment explanation
Indices: 654947--655215 Score: 182
Period size: 40 Copynumber: 6.4 Consensus size: 40
654937 TTGATACAGC
654947 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGT
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGT
* * * ** *
654987 TCCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCT
1 TCCTACGTGATGAGGAGGTCTGG---TCGGGGGATGACACGG-T
* * * *
655031 T-CTACGTAATGAGGAGGTTTGGTCGAGGGATGACACGAT
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGT
* * ** * **
655070 TCCTACGTGATGAGGACGTCAGGCCATCTTTAGGAATGATAACATTGT
1 TCCTACGTGATGAGGAGGTCTGG---TC----GG-GGGATGACACGGT
* * * * *
655118 TCCTACGTGATGAGGATGACTGATTATCAGGGG-TGACACGGC
1 TCCTACGTGATGAGGAGGTCTG---GTCGGGGGATGACACGGT
*
655160 TCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACGGT
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGT
655200 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
655216 TGGCAGGCCA
Statistics
Matches: 170, Mismatches: 42, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
39 8 0.05
40 74 0.44
42 24 0.14
43 32 0.19
44 3 0.02
47 1 0.01
48 28 0.16
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGT
Found at i:655036 original size:43 final size:42
Alignment explanation
Indices: 654906--655045 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 42
654896 AACATGGTTC
* * * * *
654906 CTACGCGATGAGGATGGCTGGGTATCTAGGGTTGATACAGCTC
1 CTACGCGATGAGGACGACT-GGTATCTAGGGTTGACACGGCTT
* * * ** *
654949 CTACGTGATGAGGAGGTCTGG--TCGGGGGATGACACGG-TT
1 CTACGCGATGAGGACGACTGGTATCTAGGGTTGACACGGCTT
654988 CCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTT
1 -CTACGCGATGAGGACGACTGG-TATCTAGGGTTGACACGGCTT
**
655032 CTACGTAATGAGGA
1 CTACGCGATGAGGA
655046 GGTTTGGTCG
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
39 1 0.01
40 29 0.39
42 2 0.03
43 41 0.55
44 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (42 bp):
CTACGCGATGAGGACGACTGGTATCTAGGGTTGACACGGCTT
Found at i:655043 original size:83 final size:83
Alignment explanation
Indices: 654901--655087 Score: 275
Period size: 83 Copynumber: 2.3 Consensus size: 83
654891 GCGATAACAT
* * * *
654901 GGTTCCTACGCGATGAGGATGGCTGGGTATCTAGGGTTGATACAGCTCCTACGTGATGAGGAGGT
1 GGTTCCTACGCGATGAGGACGACTGGGTATCTAGGGTTGACACAGCTCCTACGTAATGAGGAGGT
*
654966 CTGGTCGGGGGATGACAC
66 CTGGTCGAGGGATGACAC
* * *
654984 GGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTTCTACGTAATGAGGAGGT
1 GGTTCCTACGCGATGAGGACGACTGGGTATCTAGGGTTGACACAGCTCCTACGTAATGAGGAGGT
*
655049 TTGGTCGAGGGATGACAC
66 CTGGTCGAGGGATGACAC
* *
655067 GATTCCTACGTGATGAGGACG
1 GGTTCCTACGCGATGAGGACG
655088 TCAGGCCATC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (83 bp):
GGTTCCTACGCGATGAGGACGACTGGGTATCTAGGGTTGACACAGCTCCTACGTAATGAGGAGGT
CTGGTCGAGGGATGACAC
Found at i:655191 original size:130 final size:129
Alignment explanation
Indices: 654980--655363 Score: 527
Period size: 130 Copynumber: 2.9 Consensus size: 129
654970 TCGGGGGATG
* * * *
654980 ACACGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTTCTACGTAATGAGG
1 ACAC-GTTCCTACGTGATGAGGACGACTGATTATC-AGGGGTGACACGGCTTCTACGTGATGAGG
* * * *
655045 AGGTTTGGTCGAGGGATGACACGATTCCTACGTGATGAGGACGTCAGGCCATCTTTAGGAATGAT
64 AGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGGAATGAT
655110 A
129 A
* * *
655111 ACATTGTTCCTACGTGATGAGGATGACTGATTATCAGGGGTGACACGGCTCCTACGTGATGAGGA
1 ACA-CGTTCCTACGTGATGAGGACGACTGATTATCAGGGGTGACACGGCTTCTACGTGATGAGGA
* * *
655176 GGTCTAGTCGGGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAAGAATGATA
65 GGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGGAATGATA
* * * *
655241 ACACGATTCCTACGTGATGAGGACGACT-AGTTATTAGGAGAGACACGGCTTTTACGTGATGAGG
1 ACACG-TTCCTACGTGATGAGGACGACTGA-TTATCAGGGGTGACACGGCTTCTACGTGATGAGG
* * *
655305 AGGTCTGGTCGAGGGATGACATGGTTCCTAAGTGATGAGGATGGCAGACCATCTTTAGG
64 AGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGG
655364 GATTATAGTT
Statistics
Matches: 223, Mismatches: 27, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
129 2 0.01
130 191 0.86
131 30 0.13
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (129 bp):
ACACGTTCCTACGTGATGAGGACGACTGATTATCAGGGGTGACACGGCTTCTACGTGATGAGGAG
GTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGGAATGATA
Found at i:655457 original size:35 final size:36
Alignment explanation
Indices: 655417--655492 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 36
655407 GAGAAATTGT
655417 CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACA-A
1 CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGA
* *****
655452 CTC-AAAGATAGGTGTTTTGTTTCAAGGGAAACAGA
1 CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGA
655487 CTCAAA
1 CTCAAA
655493 GATAGGTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 24 0.73
35 7 0.21
36 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGA
Found at i:655471 original size:34 final size:35
Alignment explanation
Indices: 655433--655504 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
655423 AGAGACAAAA
655433 TTTGTTTCAAGGGAAACA-ACTCAAAGATAGGTGT
1 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
655467 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
1 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
655502 TTT
1 TTT
655505 CAAAAGAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.49
35 19 0.51
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (35 bp):
TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
Found at i:655514 original size:31 final size:32
Alignment explanation
Indices: 655434--655514 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 32
655424 GAGACAAAAT
**
655434 TTGTTTCAAGGGAAACAACTCAAAGATAGGTG
1 TTGTTTCAAAAGAAACAACTCAAAGATAGGTG
**
655466 TTTTGTTTCAAGGGAAACAGACTCAAAGATAGGTG
1 --TTGTTTCAAAAGAAACA-ACTCAAAGATAGGTG
655501 -T-TTTCAAAAGAAAC
1 TTGTTTCAAAAGAAAC
655515 TATCTCGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 11 0.25
32 1 0.02
34 17 0.39
35 15 0.34
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (32 bp):
TTGTTTCAAAAGAAACAACTCAAAGATAGGTG
Found at i:655623 original size:67 final size:64
Alignment explanation
Indices: 655467--655686 Score: 261
Period size: 67 Copynumber: 3.4 Consensus size: 64
655457 AGATAGGTGT
* * *
655467 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGTTTTCAAAAGAAACTATCTCGAGAGACAAAA
1 TTTGTTTCAAGAGAAACAGACTCAAAGAT--TTTTTTTCAAAAGAAACTATCTCGAGAGACAAAA
*
655532 T
64 A
* *
655533 TTTGTTTCAA-ATGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTATCTCGAGAGAGACAA
1 TTTGTTTCAAGA-GAAACAGACTCAAAGATTTTTTT-TCAAAAGAAACTATCTC--GAGAGACAA
655597 AAA
62 AAA
* * *
655600 TTTGTTTCCAGAGAAAGAGACTCAAAGA-TTTTTTT-AAAAGAAACTGTCTCGAGAGAC-AAAA
1 TTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAACTATCTCGAGAGACAAAAA
*
655661 TTTGTTTCAAGAGAAATA-ACTCAAAG
1 TTTGTTTCAAGAGAAACAGACTCAAAG
655687 GATACTGATA
Statistics
Matches: 136, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
60 8 0.06
61 20 0.15
62 7 0.05
64 17 0.12
65 17 0.12
66 32 0.24
67 34 0.25
68 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (64 bp):
TTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAACTATCTCGAGAGACAAAAA
Found at i:655797 original size:32 final size:32
Alignment explanation
Indices: 655756--655825 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
655746 TTCGCATCAG
* *
655756 GATGTTGAATCCCCAAAGATGCTCCAATATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
*
655788 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
655820 GATGTT
1 GATGTT
655826 TCTTACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAACATTC
Found at i:656895 original size:11 final size:12
Alignment explanation
Indices: 656870--656911 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
656860 TCTTGTCTTC
*
656870 TTTTTC-TTTGA
1 TTTTTCTTTTGT
656881 TTTTTCTTTTGTT
1 TTTTTCTTTTG-T
656894 TTTTTCTCTTTGT
1 TTTTTCT-TTTGT
656907 TTTTT
1 TTTTT
656912 TCCTTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
12 4 0.15
13 13 0.48
14 4 0.15
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTGT
Found at i:656905 original size:14 final size:14
Alignment explanation
Indices: 656881--656918 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
656871 TTTTCTTTGA
656881 TTTTTCT-TTTGTT
1 TTTTTCTCTTTGTT
656894 TTTTTCTCTTTGTT
1 TTTTTCTCTTTGTT
656908 TTTTTC-CTTTG
1 TTTTTCTCTTTG
656919 CTCTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTTCTCTTTGTT
Found at i:656910 original size:15 final size:13
Alignment explanation
Indices: 656881--656918 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
656871 TTTTCTTTGA
656881 TTTTTCTTTTGTT
1 TTTTTCTTTTGTT
656894 TTTTTCTCTTTGTT
1 TTTTTCT-TTTGTT
*
656908 TTTTTCCTTTG
1 TTTTTCTTTTG
656919 CTCTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTGTT
Found at i:656936 original size:21 final size:21
Alignment explanation
Indices: 656887--656937 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
656877 TTGATTTTTC
*
656887 TTTTGTTT--TTTTCTCTTTG
1 TTTTGTTTCCTTTGCTCTTTG
*
656906 TTTTT-TTCCTTTGCTCTTTG
1 TTTTGTTTCCTTTGCTCTTTG
656926 TTTTGTTTCCTT
1 TTTTGTTTCCTT
656938 CTGTTTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 14 0.54
21 6 0.23
ACGTcount: A:0.00, C:0.16, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTGTTTCCTTTGCTCTTTG
Found at i:656947 original size:25 final size:24
Alignment explanation
Indices: 656896--656955 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 24
656886 CTTTTGTTTT
656896 TTTCTCTTTGTTTT-TTTCCTTTG
1 TTTCTCTTTGTTTTGTTTCCTTTG
656919 ---CTCTTTGTTTTGTTTCCTTCTG
1 TTTCTCTTTGTTTTGTTTCCTT-TG
*
656941 TTTCTCTTTGCTTTG
1 TTTCTCTTTGTTTTG
656956 ATTGGATCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 2 0.06
25 11 0.35
ACGTcount: A:0.00, C:0.20, G:0.12, T:0.68
Consensus pattern (24 bp):
TTTCTCTTTGTTTTGTTTCCTTTG
Found at i:660684 original size:30 final size:29
Alignment explanation
Indices: 660650--660734 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
660640 GTTGAACAAT
* *
660650 AAATACATAAAGTTAAAGGACCAAAATAAC
1 AAATACAGAAACTTAAAGGACCAAAA-AAC
*
660680 AAATATAGAAACTTAAAGGACCAAAAAAC
1 AAATACAGAAACTTAAAGGACCAAAAAAC
* * * * *
660709 AAAAATAGAAATTTACAGGTCCAAAA
1 AAATACAGAAACTTAAAGGACCAAAA
660735 TAGTAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 25 0.52
30 23 0.48
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (29 bp):
AAATACAGAAACTTAAAGGACCAAAAAAC
Found at i:660719 original size:29 final size:30
Alignment explanation
Indices: 660662--660736 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
660652 ATACATAAAG
*
660662 TTAAAGGACCAAAATAACAAATATAGAAAC
1 TTAAAGGACCAAAATAACAAAAATAGAAAC
*
660692 TTAAAGGACCAAAA-AACAAAAATAGAAAT
1 TTAAAGGACCAAAATAACAAAAATAGAAAC
* *
660721 TTACAGGTCCAAAATA
1 TTAAAGGACCAAAATA
660737 GTAAAACCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.17
Consensus pattern (30 bp):
TTAAAGGACCAAAATAACAAAAATAGAAAC
Found at i:660765 original size:30 final size:30
Alignment explanation
Indices: 660731--660805 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
660721 TTACAGGTCC
* * *
660731 AAAATAGTAAAACCATACATTTAAGGGATT
1 AAAATAGTAAAAACATACATTTAAAGGACT
* *
660761 AAAATAGAAAAAACATATATTTAAAGGACT
1 AAAATAGTAAAAACATACATTTAAAGGACT
*
660791 AAAACAGTAAAAACA
1 AAAATAGTAAAAACA
660806 AAATCTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (30 bp):
AAAATAGTAAAAACATACATTTAAAGGACT
Found at i:661977 original size:20 final size:20
Alignment explanation
Indices: 661952--661990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
661942 GGTGCAGGTG
*
661952 GGACAGTCAGCGGCAGCAGT
1 GGACAGGCAGCGGCAGCAGT
*
661972 GGACAGGCGGCGGCAGCAG
1 GGACAGGCAGCGGCAGCAG
661991 CATGATATCC
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:0.23, C:0.26, G:0.46, T:0.05
Consensus pattern (20 bp):
GGACAGGCAGCGGCAGCAGT
Found at i:662247 original size:3 final size:3
Alignment explanation
Indices: 662234--662285 Score: 77
Period size: 3 Copynumber: 16.3 Consensus size: 3
662224 GATTTAAATA
662234 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT
662282 AAT A
1 AAT A
662286 TTTTTGGTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 37 0.80
4 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:667427 original size:2 final size:2
Alignment explanation
Indices: 667422--667461 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
667412 TGTCTGTGTG
667422 TA TA TA TA 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 TA TA TA TA
667462 AGTTATTGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:667627 original size:15 final size:15
Alignment explanation
Indices: 667594--667628 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
667584 TTAAATAATC
* *
667594 AATATAGAATATTAG
1 AATATAGAATATCAA
667609 AATATAGAATATCAA
1 AATATAGAATATCAA
667624 AATAT
1 AATAT
667629 CAAAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (15 bp):
AATATAGAATATCAA
Found at i:675169 original size:3 final size:3
Alignment explanation
Indices: 675161--675225 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
675151 TGCAAAAATT
* **
675161 ATA ATA ATAA ATA ATA ATA A-A ATA ATA A-G ATA ACG ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
675205 ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
675226 CGAAAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 44 0.85
4 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:675217 original size:32 final size:32
Alignment explanation
Indices: 675164--675228 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
675154 AAAAATTATA
*
675164 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
675196 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
675228 A
1 A
675229 AAAAAAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:675488 original size:42 final size:42
Alignment explanation
Indices: 675429--675662 Score: 146
Period size: 40 Copynumber: 5.6 Consensus size: 42
675419 AAAGGTGATA
* * *
675429 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGGTG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGGTG
* * **
675471 ACACGGCTCATACGTGAT-ACAGAGATCTGG---TCGGAGAATG
1 ACACGGCTCATACGTGATGA-AGAGAGCTGGTTATC-TAGGGTG
** ** *
675511 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT--AGG-G-TG
* * * *
675557 ACGCGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGGTG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGGTG
* *
675599 ACACGGCTCATACGTGATGAAGAGATCTGG---TC-GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGG--TG
675639 ACACGGCTCATACGTGATGAAGAG
1 ACACGGCTCATACGTGATGAAGAG
675663 TTTTGGCCAT
Statistics
Matches: 151, Mismatches: 26, Indels: 32
0.72 0.12 0.15
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 57 0.38
41 4 0.03
42 46 0.30
43 3 0.02
44 5 0.03
46 28 0.19
47 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (42 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGGTG
Found at i:675540 original size:40 final size:41
Alignment explanation
Indices: 675469--675662 Score: 148
Period size: 40 Copynumber: 4.6 Consensus size: 41
675459 TTATCTAGGG
675469 TGACACGGCTCATACGTGAT-ACAGAGATCTGG-TCGGAGAA
1 TGACACGGCTCATACGTGATGA-AGAGATCTGGATCGGAGAA
* *
675509 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-A
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC----GGAGAA
* * * * * * * **
675555 TAACGCGGTTCCTACGTGATGAGGACG-GCTGGTTATC-TAGGG
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATCGGAGAA
*
675597 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCGGAGAA
675637 TGACACGGCTCATACGTGATGAAGAG
1 TGACACGGCTCATACGTGATGAAGAG
675663 TTTTGGCCAT
Statistics
Matches: 119, Mismatches: 23, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
39 2 0.02
40 56 0.47
41 3 0.03
42 24 0.20
43 2 0.02
46 28 0.24
47 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (41 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGATCGGAGAA
Found at i:675610 original size:128 final size:128
Alignment explanation
Indices: 675390--675720 Score: 610
Period size: 128 Copynumber: 2.6 Consensus size: 128
675380 ACGACACTGT
675390 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
675455 CTGGTTATCTAGGGTGACACGGCTCATACGTGAT-ACAGAGATCTGGTCGGAGAATGACACGGC
66 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGA-AGAGATCTGGTCGGAGAATGACACGGC
*
675518 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACGCGGTTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
*
675583 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGC
66 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGAGAATGACACGGC
* *
675646 TCATACGTGATGAAGAGTTTTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
675711 CTGGTTATCT
66 CTGGTTATCT
675721 CTAGGGATAA
Statistics
Matches: 197, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
128 196 0.99
129 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (128 bp):
TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGAGAATGACACGGC
Found at i:676079 original size:66 final size:63
Alignment explanation
Indices: 675907--676083 Score: 176
Period size: 66 Copynumber: 2.7 Consensus size: 63
675897 AAAGCAACTA
* * * * *
675907 TCTCGAAAGAGACAAGATTCGTTTCAAAGGAAAC-AACCCAAAGATGGCATTTAAAGGGAATTG
1 TCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGCATTTAAAGGGAATTG
* ** * * * * *
675970 TCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGGCGTTTCATGGGAAAT
1 TCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGCATTTAAAGGG-AAT
676035 TG
62 TG
676037 TCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
676084 TTTGTTTTGT
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
62 2 0.02
63 12 0.13
64 13 0.14
65 9 0.10
66 35 0.38
67 20 0.22
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (63 bp):
TCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGCATTTAAAGGGAATTG
Found at i:676914 original size:65 final size:65
Alignment explanation
Indices: 676845--676968 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 65
676835 AAACGGTCTC
* * *
676845 AAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTC-AAAGAAATTAT
1 AAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTC-AAGATTTTTGTTTCAAAAGAAATTAT
676907 CTT
63 CTT
*
676910 AAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAGATTTTTGTTTCAAAAGAAA
1 AAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAGATTTTTGTTTCAAAAGAAA
676969 CACTCTCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
64 1 0.02
65 31 0.61
66 17 0.33
67 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (65 bp):
AAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAGATTTTTGTTTCAAAAGAAATTATCTT
Found at i:676965 original size:29 final size:30
Alignment explanation
Indices: 676923--676985 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
676913 AGAGACAAAA
*
676923 TTTTGTTTCCAAAGAAACAAACTC-AAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
**
676952 TTTTGTTTCAAAAGAAACACTCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
676982 TTTT
1 TTTT
676986 TCACAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:676992 original size:29 final size:29
Alignment explanation
Indices: 676933--676993 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
676923 TTTTGTTTCC
**
676933 AAAGAAACAAACTCAAGATTTTTGTTTCA
1 AAAGAAACAAACTCAAGATTTTTGTCACA
**
676962 AAAGAAACACTCTCAAAGATTTTT-TCACA
1 AAAGAAACAAACTC-AAGATTTTTGTCACA
676991 AAA
1 AAA
676994 TTGTCTCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (29 bp):
AAAGAAACAAACTCAAGATTTTTGTCACA
Found at i:677047 original size:52 final size:53
Alignment explanation
Indices: 676973--677075 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
676963 AAGAAACACT
*
676973 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
677026 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
677076 AATAAATAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 40 0.83
53 8 0.17
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:677100 original size:26 final size:26
Alignment explanation
Indices: 677071--677179 Score: 76
Period size: 30 Copynumber: 3.9 Consensus size: 26
677061 CAAAACTTTG
* *
677071 TTTCAAATAAATAGACTCAAAGAT-TT
1 TTTCAAAGAAACA-ACTCAAAGATATT
677097 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTC-AAAGAAACAACTCAAAGATATT
* * *
677124 TATTCAAAAGGAACAAACTCCAAGATTTTT
1 T-TTC-AAAGAAAC-AACTCAAAGA-TATT
*
677154 TATTCAAAAGGAACAGACTCAAAGAT
1 T-TTC-AAAGAAACA-ACTCAAAGAT
677180 TTATCTCAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.20
27 10 0.14
28 11 0.15
29 11 0.15
30 25 0.35
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (26 bp):
TTTCAAAGAAACAACTCAAAGATATT
Found at i:677131 original size:28 final size:28
Alignment explanation
Indices: 677085--677195 Score: 113
Period size: 30 Copynumber: 4.0 Consensus size: 28
677075 AAATAAATAG
677085 ACTCAAAGAT-TTT-TTCAAAAGAAACA
1 ACTCAAAGATATTTATTCAAAAGAAACA
*
677111 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATATTTATTCAAAAGAAAC-A
* * *
677140 ACTCCAAGATTTTTTATTCAAAAGGAACA
1 ACTCAAAGA-TATTTATTCAAAAGAAACA
*
677169 GACTCAAAG--ATTTATCTCAAGAGAAAC
1 -ACTCAAAGATATTTAT-TCAAAAGAAAC
677196 TGTCTCCAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.14
27 8 0.11
28 20 0.28
29 10 0.14
30 24 0.33
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (28 bp):
ACTCAAAGATATTTATTCAAAAGAAACA
Found at i:677158 original size:30 final size:30
Alignment explanation
Indices: 677085--677181 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
677075 AAATAAATAG
*
677085 ACTCAAAGA--TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTATTCAAAAGGAACAA
*
677111 ACTCAAAGA-TATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTATTCAAAAGGAACAA
* *
677140 ACTCCAAGATTTTTTATTCAAAAGGAACAG
1 ACTCAAAGATTTTTTATTCAAAAGGAACAA
677170 ACTCAAAGATTT
1 ACTCAAAGATTT
677182 ATCTCAAGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 9 0.15
27 3 0.05
28 11 0.18
29 9 0.15
30 29 0.48
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (30 bp):
ACTCAAAGATTTTTTATTCAAAAGGAACAA
Found at i:677523 original size:34 final size:35
Alignment explanation
Indices: 677485--677611 Score: 102
Period size: 35 Copynumber: 3.6 Consensus size: 35
677475 TCTCAAAAAA
*
677485 TCTCAAGCGAGACGAAATTTG-CTTTA-AGATATAG
1 TCTCAAGCGAGAC-AAATTTGTCTTTAGAGAAATAG
** * *
677519 TCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTG
1 TCTCAAGCGAGAC-AAATTTGTCTTTAGAGAAATAG
677555 TCTCAAGCGAGACAAAGTTTGT-TTT-GAGAAA-ACG
1 TCTCAAGCGAGACAAA-TTTGTCTTTAGAGAAATA-G
* *
677589 ATCTCAAGTGAGATCAACTTTGT
1 -TCTCAAGCGAGA-CAAATTTGT
677612 TTAATGTAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
34 25 0.33
35 26 0.34
36 25 0.33
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (35 bp):
TCTCAAGCGAGACAAATTTGTCTTTAGAGAAATAG
Found at i:677567 original size:36 final size:35
Alignment explanation
Indices: 677485--677579 Score: 111
Period size: 36 Copynumber: 2.7 Consensus size: 35
677475 TCTCAAAAAA
* * *
677485 TCTCAAGCGAGACGAAATTTG-CTTTAAGATATAG
1 TCTCAAGCGAGACAAAATTTGTTTTTAAGAAATAG
** *
677519 TCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTTA-AGAAATAG
*
677555 TCTCAAGCGAGACAAAGTTTGTTTT
1 TCTCAAGCGAGACAAAATTTGTTTT
677580 GAGAAAACGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 18 0.36
35 4 0.08
36 28 0.56
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.34
Consensus pattern (35 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAAGAAATAG
Found at i:677740 original size:105 final size:101
Alignment explanation
Indices: 677554--677784 Score: 288
Period size: 105 Copynumber: 2.2 Consensus size: 101
677544 TAGAGAAATT
*
677554 GTCTCAAGCGAGAC-AAAGTTTGTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACGAAA-TTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
677618 TAAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 TAAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
677655 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * * *
677719 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTAAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
677760 GTCTCAAGCGAGACGAAGTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTT
677785 AAGAGAATTT
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
101 23 0.20
102 3 0.03
103 2 0.02
104 4 0.04
105 76 0.67
106 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
AAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:677798 original size:35 final size:34
Alignment explanation
Indices: 677759--677838 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 34
677749 AAAGGAAAAA
* *
677759 TGTCTCAAGCGAGACGAAGTTTG-TTTAAGAGAATT
1 TGTCTCAAGCGAGAC-AACTTTGTTTTAA-AGAAAT
* * *
677794 TGTCTTAAGTGATACAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAACTTTG-TTTTAAAGAAAT
677829 TGTCTCAAGC
1 TGTCTCAAGC
677839 AAAACAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
34 6 0.17
35 25 0.69
36 5 0.14
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAACTTTGTTTTAAAGAAAT
Found at i:677889 original size:271 final size:256
Alignment explanation
Indices: 677332--677908 Score: 646
Period size: 271 Copynumber: 2.2 Consensus size: 256
677322 TTTTGAAAAA
* * * * * * *
677332 CTCAAGTGATATTAATTTTGTTTCAA-GTACAACAAATT-TAAATTTGTATCTCAGAGAAATGTC
1 CTCAAGTGAGATCAACTTTGTTT-AATGTAAAACAAATTCGAAATTTGGATCTCAGAGAAAGGTC
*
677395 TCAAGCGAAACGAAATTTGTCGAAATAAACAACAATATCAAGTGAGATTTTGTTTTAAGTGGAAA
65 TCAAGCGAAACGAAATTTGTCGAAAGAAACAACAATATCAAGTGAGATTTTGTTTTAAGTGGAAA
*
677460 AATTCAAAATTAGTATCTCAAAAAATCTCAAGCGAGACGAAATTTGCTTTAAGATATAGTCTCAA
130 AATTCAAAATTAGTATCTCAAAAAATCTCAAGCGAGACGAAATTTGCTTTAAGAAATAGTCTCAA
* * * *
677525 ATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTGAGAAAACGA
195 ATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA---T-ATTTGAGAAAACGA
677590 T
256 T
*
677591 CTCAAGTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGG
1 CTCAAGTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAATTTGGATCTC--AGAG-AAAGG
* * *
677656 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTTT
63 TCTCAAGCGAAACGAAATTTG--TCGAAAGAAACAACAATATCAA-GTGAG----ATTTTGTTTT
* *
677720 AAGT-GAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAGTTTG-T
121 AAGTGGAA--AAATTCAAAATTAGTATCTC--A--AAAAA--TCTCAAGCGAGACGAAATTTGCT
* * * * *
677783 TTAAGAGAATTTGTCTTAAGTGATAC-AACTTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA
178 TTAAGA-AA-TAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA
677847 -ATTTGAGAAAACGAT
241 TATTTGAGAAAACGAT
* *
677862 CTCAAGTGAGATCAACTTTGTTTAATGTGAATCAAATTCGAAATTTG
1 CTCAAGTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAATTTG
677909 TAAAAATGTC
Statistics
Matches: 270, Mismatches: 26, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
258 2 0.01
259 31 0.11
260 12 0.04
262 3 0.01
263 24 0.09
264 2 0.01
265 21 0.08
268 3 0.01
269 14 0.05
270 19 0.07
271 59 0.22
272 1 0.00
274 5 0.02
275 7 0.03
276 55 0.20
277 12 0.04
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (256 bp):
CTCAAGTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAATTTGGATCTCAGAGAAAGGTCT
CAAGCGAAACGAAATTTGTCGAAAGAAACAACAATATCAAGTGAGATTTTGTTTTAAGTGGAAAA
ATTCAAAATTAGTATCTCAAAAAATCTCAAGCGAGACGAAATTTGCTTTAAGAAATAGTCTCAAA
TGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAATATTTGAGAAAACGAT
Found at i:677964 original size:35 final size:33
Alignment explanation
Indices: 677915--678048 Score: 135
Period size: 35 Copynumber: 3.8 Consensus size: 33
677905 TTTGTAAAAA
* * *
677915 TGTCTCCAGTGAGACGAATTTGTTTTTCAAGAAAT
1 TGTCTCAAGCGAGACAAATTTG-TTTT-AAGAAAT
* *
677950 TGTCTCAAACGAGACAAAATTTGTTTT-AGAAAGC
1 TGTCTCAAGCGAGAC-AAATTTGTTTTAAGAAA-T
*
677984 TGTCTCAAGCGAGACAAATTTGCTTTGAAAGAAAT
1 TGTCTCAAGCGAGACAAATTTG-TTT-TAAGAAAT
678019 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC--AAATTTGTTTTAA
678049 AATTCTCAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
33 12 0.14
34 17 0.20
35 33 0.40
36 14 0.17
37 7 0.08
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (33 bp):
TGTCTCAAGCGAGACAAATTTGTTTTAAGAAAT
Found at i:678016 original size:69 final size:70
Alignment explanation
Indices: 677915--678047 Score: 196
Period size: 69 Copynumber: 1.9 Consensus size: 70
677905 TTTGTAAAAA
* * * * **
677915 TGTCTCCAGTGAGACGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGAC-AAAATTTGTTTTAG
1 TGTCTCAAGCGAGACAAATTTGCTTTGAAAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTAG
677979 AAAGC
66 AAAGC
*
677984 TGTCTCAAGCGAGACAAATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATTTGTTTTA
1 TGTCTCAAGCGAGACAAATTTGCTTTGAAAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTA
678048 AAATTCTCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
69 43 0.77
70 13 0.23
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (70 bp):
TGTCTCAAGCGAGACAAATTTGCTTTGAAAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTAG
AAAGC
Found at i:679845 original size:13 final size:12
Alignment explanation
Indices: 679813--679846 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
679803 TGTTCTTTGC
679813 TTTTCTTTGATT
1 TTTTCTTTGATT
*
679825 TTTGCTTTGATT
1 TTTTCTTTGATT
679837 TTTCTCTTTG
1 TTT-TCTTTG
679847 CTCTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTCTTTGATT
Found at i:679858 original size:20 final size:20
Alignment explanation
Indices: 679829--679866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
679819 TTGATTTTTG
679829 CTTTGATTTTTCTCTTTGCT
1 CTTTGATTTTTCTCTTTGCT
* *
679849 CTTTGTTTTTTTTCTTTG
1 CTTTGATTTTTCTCTTTG
679867 GTTTGATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.16, G:0.11, T:0.71
Consensus pattern (20 bp):
CTTTGATTTTTCTCTTTGCT
Found at i:680478 original size:26 final size:23
Alignment explanation
Indices: 680447--680517 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 23
680437 TCAAGGTGGA
680447 AAGAATATTTCAAGGTCTCAAAG
1 AAGAATATTTCAAGGTCTCAAAG
* *
680470 AGAGGGAATGTTTCAAGG--TCGAA-
1 A-A--GAATATTTCAAGGTCTCAAAG
680493 AAGAATATTTCAAGGTCTCAAAG
1 AAGAATATTTCAAGGTCTCAAAG
680516 AA
1 AA
680518 ATAGAATGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 12 0.32
22 5 0.13
23 4 0.11
24 5 0.13
26 12 0.32
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (23 bp):
AAGAATATTTCAAGGTCTCAAAG
Found at i:680503 original size:20 final size:20
Alignment explanation
Indices: 680435--680509 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
680425 AAATACAGTG
*
680435 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
680454 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
680480 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
680500 TTTCAAGGTC
1 TTTCAAGGTC
680510 TCAAAGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:680523 original size:26 final size:25
Alignment explanation
Indices: 680446--680524 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 25
680436 TTCAAGGTGG
680446 AAAGAATATTTCAAGGTCTCAAAGA
1 AAAGAATATTTCAAGGTCTCAAAGA
** *
680471 GAGGGAATGTTTCAAGG--TC---GA
1 -AAAGAATATTTCAAGGTCTCAAAGA
680492 AAAGAATATTTCAAGGTCTCAAAGA
1 AAAGAATATTTCAAGGTCTCAAAGA
680517 AATAGAAT
1 AA-AGAAT
680525 GTCGAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 4 0.10
26 18 0.44
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAGAATATTTCAAGGTCTCAAAGA
Found at i:680525 original size:46 final size:45
Alignment explanation
Indices: 680414--680526 Score: 145
Period size: 46 Copynumber: 2.4 Consensus size: 45
680404 TGACTTTTGT
* * *
680414 GTCTCAAAAGTAAATACAGTGTTTCAAGGTGGAAAGAATATTTCAAG
1 GTCTC-AAAG-AAATAGAATGTTTCAAGGTGAAAAGAATATTTCAAG
* **
680461 GTCTCAAAGAGAGGGAATGTTTCAAGGTCGAAAAGAATATTTCAAG
1 GTCTCAAAGAAATAGAATGTTTCAAGGT-GAAAAGAATATTTCAAG
680507 GTCTCAAAGAAATAGAATGT
1 GTCTCAAAGAAATAGAATGT
680527 CGAAAATTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
45 14 0.25
46 37 0.66
47 5 0.09
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.26
Consensus pattern (45 bp):
GTCTCAAAGAAATAGAATGTTTCAAGGTGAAAAGAATATTTCAAG
Found at i:682659 original size:177 final size:174
Alignment explanation
Indices: 682311--682662 Score: 677
Period size: 177 Copynumber: 2.0 Consensus size: 174
682301 ATGTCTTCGC
682311 TTAGATGGTGAGCCTGGAATGGATCACTGCTTCATCTCGGATCTTCGTCCTCATAATGATGCCCC
1 TTAGATGGTGAGCCTGGAATGGATCACTGCTTCATCTCGGATCTTCGTCCTCATAATGATGCCCC
682376 TCAAGCGCTCTGTAAACAAACTCTTTTAAGCCCCGGCGATGCTGAAGTCAGTGCTCACTCTTCGA
66 TCAAGCGCTCTGTAAACAAACTCTTTTAAGCCCCGGCGATGCTGAAGTCAGTGCTCACTCTTCGA
682441 TGAATAACGTCGGAACGATCGTAAATAATCTACTGCTGGATTAA
131 TGAATAACGTCGGAACGATCGTAAATAATCTACTGCTGGATTAA
682485 TTAGATGGTGAGCCTGGAATGGATCACTGCTTCATCTCGGATCTTCGTCCTCAATAATGATGCCC
1 TTAGATGGTGAGCCTGGAATGGATCACTGCTTCATCTCGGATCTTCGTCCTC-ATAATGATGCCC
682550 CTCAAGCGCTCTGTAAACAAACTCTTTTAATGCCCCGGCGATGCTGAAGTCAGTGCATCACTCTT
65 CTCAAGCGCTCTGTAAACAAACTCTTTTAA-GCCCCGGCGATGCTGAAGTCAGTGC-TCACTCTT
682615 CGATGAATAACGTCGGAACGATCGTAAATAATCTACTGCTGGATTAA
128 CGATGAATAACGTCGGAACGATCGTAAATAATCTACTGCTGGATTAA
682662 T
1 T
682663 CCCCAGACTT
Statistics
Matches: 175, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
174 52 0.30
175 42 0.24
176 25 0.14
177 56 0.32
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (174 bp):
TTAGATGGTGAGCCTGGAATGGATCACTGCTTCATCTCGGATCTTCGTCCTCATAATGATGCCCC
TCAAGCGCTCTGTAAACAAACTCTTTTAAGCCCCGGCGATGCTGAAGTCAGTGCTCACTCTTCGA
TGAATAACGTCGGAACGATCGTAAATAATCTACTGCTGGATTAA
Found at i:684820 original size:24 final size:25
Alignment explanation
Indices: 684793--684840 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
684783 GACAATATTT
684793 AAATAAAAAAATG-GAAATAAATAG
1 AAATAAAAAAATGTGAAATAAATAG
* *
684817 AAATAGAAATATGTGAAATAAATA
1 AAATAAAAAAATGTGAAATAAATA
684841 TTTACAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (25 bp):
AAATAAAAAAATGTGAAATAAATAG
Found at i:685269 original size:20 final size:19
Alignment explanation
Indices: 685246--685285 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
685236 TCAAATAACA
685246 GTAAAGATAATAAAATGCAT
1 GTAAAGATAATAAAAT-CAT
685266 GTAAAGATAATAAAATCAT
1 GTAAAGATAATAAAATCAT
685285 G
1 G
685286 GGATCAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (19 bp):
GTAAAGATAATAAAATCAT
Found at i:691657 original size:24 final size:24
Alignment explanation
Indices: 691638--691690 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
691628 AAAAACATTC
691638 ACGAATATAAATAAACAAACATAA
1 ACGAATATAAATAAACAAACATAA
* *
691662 ACGAATATAAATGAACGAACATAA
1 ACGAATATAAATAAACAAACATAA
691686 ACGAA
1 ACGAA
691691 CAGATTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.15
Consensus pattern (24 bp):
ACGAATATAAATAAACAAACATAA
Found at i:692062 original size:16 final size:19
Alignment explanation
Indices: 692031--692069 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
692021 TTTTGTTTGG
692031 TTTTATCTTATAAAAT-AT
1 TTTTATCTTATAAAATAAT
692049 TTTTAT-TT-TAAAATAAT
1 TTTTATCTTATAAAATAAT
692066 TTTT
1 TTTT
692070 GAATTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATCTTATAAAATAAT
Found at i:698610 original size:18 final size:18
Alignment explanation
Indices: 698587--698643 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
698577 ACCGGTTACA
698587 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
698605 ACCCGACCTGACCAGTTG
1 ACCCGACCCGACCCGTTG
*
698623 ACCGGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
698641 ACC
1 ACC
698644 GGTGCTGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:698652 original size:36 final size:37
Alignment explanation
Indices: 698591--698663 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
698581 GTTACAACCC
698591 GACCCGACCCGTTGACCCGACCTGACC-AGTTGACCG
1 GACCCGACCCGTTGACCCGACCTGACCAAGTTGACCG
* **
698627 GACCCGACCCGTTGACCGGTGCTGACCAAAGTTGACC
1 GACCCGACCCGTTGACCCGACCTGACC-AAGTTGACC
698664 AAAACCTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 24 0.75
38 8 0.25
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (37 bp):
GACCCGACCCGTTGACCCGACCTGACCAAGTTGACCG
Found at i:699965 original size:17 final size:18
Alignment explanation
Indices: 699943--699976 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
699933 TTGAAAGGTC
*
699943 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
699960 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
699977 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:703017 original size:18 final size:18
Alignment explanation
Indices: 702994--703050 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
702984 ACCGGTTACA
702994 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
703012 ACCCGACCTGACCAGTTG
1 ACCCGACCCGACCCGTTG
*
703030 ACCGGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
703048 ACC
1 ACC
703051 GGTGTTGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:704362 original size:17 final size:18
Alignment explanation
Indices: 704340--704373 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
704330 TTAAAAGGTC
*
704340 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
704357 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
704374 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:707867 original size:18 final size:18
Alignment explanation
Indices: 707840--707888 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
707830 ACCAGTTACA
* * *
707840 ACCCGACCCGATCCGTTT
1 ACCCGGCCCGACCCATTT
707858 ACCCGGCCCGACCCATTT
1 ACCCGGCCCGACCCATTT
707876 ACCCGGCCCGACC
1 ACCCGGCCCGACC
707889 AGTTGACCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.16, C:0.51, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGGCCCGACCCATTT
Found at i:707902 original size:31 final size:31
Alignment explanation
Indices: 707867--707941 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
707857 TACCCGGCCC
* *
707867 GACCCATTTACCCGGCCCGACCAGTTGACCT
1 GACCCATTGACCCGACCCGACCAGTTGACCT
* * *
707898 GACCCGTTGACCTGACCCGACCCGTTGACCGTT
1 GACCCATTGACCCGACCCGACCAGTTGACC--T
707931 GA-CCATTGACC
1 GACCCATTGACC
707942 GATGTTGACC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 25 0.69
32 8 0.22
33 3 0.08
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.20
Consensus pattern (31 bp):
GACCCATTGACCCGACCCGACCAGTTGACCT
Found at i:707927 original size:13 final size:13
Alignment explanation
Indices: 707885--707916 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
707875 TACCCGGCCC
*
707885 GACCAGTTGACCT
1 GACCCGTTGACCT
707898 GACCCGTTGACCT
1 GACCCGTTGACCT
707911 GACCCG
1 GACCCG
707917 ACCCGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (13 bp):
GACCCGTTGACCT
Found at i:709263 original size:17 final size:18
Alignment explanation
Indices: 709241--709274 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
709231 TTGAAAGGTC
*
709241 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
709258 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
709275 ACAAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:712000 original size:22 final size:23
Alignment explanation
Indices: 711957--712000 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
711947 TTTAACTTGT
*
711957 ATTATTATATAATTGTAGAACTA
1 ATTATTATATAATTATAGAACTA
*
711980 ATTATTATA-ATTTATAGAACT
1 ATTATTATATAATTATAGAACT
712001 TCATATCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (23 bp):
ATTATTATATAATTATAGAACTA
Found at i:712798 original size:12 final size:12
Alignment explanation
Indices: 712778--712840 Score: 65
Period size: 12 Copynumber: 5.2 Consensus size: 12
712768 AGAACCGAAA
*
712778 AAACAAGCTTAT
1 AAACGAGCTTAT
*
712790 AAACGAGCTGAT
1 AAACGAGCTTAT
*
712802 AAATGAGCTTAT
1 AAACGAGCTTAT
* *
712814 AAATGA-ATTGAT
1 AAACGAGCTT-AT
712826 AAACGAGCTTAT
1 AAACGAGCTTAT
712838 AAA
1 AAA
712841 GGAGTCGATA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (12 bp):
AAACGAGCTTAT
Found at i:712815 original size:24 final size:23
Alignment explanation
Indices: 712783--712858 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 23
712773 CGAAAAAACA
712783 AGCTTATAAACGAGCTGATAAATG
1 AGCTTATAAACGAG-TGATAAATG
* * *
712807 AGCTTATAAATGAATTGATAAACG
1 AGCTTATAAACG-AGTGATAAATG
*
712831 AGCTTATAAAGGAGTCGATAAATG
1 AGCTTATAAACGAGT-GATAAATG
712855 AGCT
1 AGCT
712859 CATTCGTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.05
24 41 0.93
25 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (23 bp):
AGCTTATAAACGAGTGATAAATG
Found at i:713743 original size:45 final size:46
Alignment explanation
Indices: 713691--713786 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 46
713681 AAGTGCCACA
*
713691 TAGAAATGTCCCAAAGAACTACA-AG-ATATGTCCCGAAGGACCGCG
1 TAGAAATGTCCCAAAGAACCACATAGAAT-TGTCCCGAAGGACCGCG
** * * *
713736 TAGAAATGTCCTGAAGGACCACATAGAATTTTCCCGAATGACCGCG
1 TAGAAATGTCCCAAAGAACCACATAGAATTGTCCCGAAGGACCGCG
713782 TAGAA
1 TAGAA
713787 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
45 19 0.44
46 22 0.51
47 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (46 bp):
TAGAAATGTCCCAAAGAACCACATAGAATTGTCCCGAAGGACCGCG
Found at i:713751 original size:23 final size:23
Alignment explanation
Indices: 713718--713786 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
713708 ACTACAAGAT
713718 ATGTCCCGAAGGACCGCGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
* * *
713741 ATGTCCTGAAGGACCACATAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
* * *
713764 TTTTCCCGAATGACCGCGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
713787 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
ATGTCCCGAAGGACCGCGTAGAA
Found at i:713915 original size:44 final size:45
Alignment explanation
Indices: 713862--714048 Score: 252
Period size: 45 Copynumber: 4.2 Consensus size: 45
713852 TTTACGCATT
*** * * * *
713862 TCACATAGCTTATATCACATAGACAAATAATCACATAGATC-ATG
1 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
713906 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
1 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
*
713951 TCACATAGCTTATATCTCATTTTCATATAATCACGTAGTTCAATA
1 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
* * *
713996 TCACATAGCTTATATCTCATTTTCATATAATCATGTAGATC-ATA
1 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
*
714040 TCATATAGC
1 TCACATAGC
714049 ATGAAATATA
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
44 46 0.35
45 85 0.65
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (45 bp):
TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
Found at i:713953 original size:15 final size:15
Alignment explanation
Indices: 713873--714003 Score: 62
Period size: 16 Copynumber: 8.7 Consensus size: 15
713863 CACATAGCTT
*
713873 ATATCACATAG-ACAA
1 ATATCACATAGTTC-A
*
713888 ATAATCACATAGATC-
1 AT-ATCACATAGTTCA
*
713903 ATGTCACATAGCTT--
1 ATATCACATAG-TTCA
*
713917 ATATCACAT-TTTCA
1 ATATCACATAGTTCA
*
713931 TATAATCACGTAGTTCA
1 -AT-ATCACATAGTTCA
713948 ATATCACATAGCTT--
1 ATATCACATAG-TTCA
* *
713962 ATATCTCAT-TTTCA
1 ATATCACATAGTTCA
*
713976 TATAATCACGTAGTTCA
1 -AT-ATCACATAGTTCA
713993 ATATCACATAG
1 ATATCACATAG
714004 CTTATATCTC
Statistics
Matches: 88, Mismatches: 14, Indels: 28
0.68 0.11 0.22
Matches are distributed among these distances:
12 4 0.05
14 24 0.27
15 25 0.28
16 26 0.30
17 9 0.10
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (15 bp):
ATATCACATAGTTCA
Found at i:713981 original size:89 final size:89
Alignment explanation
Indices: 713862--714048 Score: 250
Period size: 89 Copynumber: 2.1 Consensus size: 89
713852 TTTACGCATT
*
713862 TCACATAGCTTATATCACATAGACAAATAATCACATAGATC-ATGTCACATAGCTTATATCACAT
1 TCACATAGCTTATATCACATAGACAAATAATCACATAGATCAATATCACATAGCTTATATCACAT
*
713926 TTTCATATAATCACGTAGTTCAATA
66 TTTCATATAATCACGTAGATC-ATA
* *** * * * *
713951 TCACATAGCTTATATCTCATTTTCATATAATCACGTAGTTCAATATCACATAGCTTATATCTCAT
1 TCACATAGCTTATATCACATAGACAAATAATCACATAGATCAATATCACATAGCTTATATCACAT
*
714016 TTTCATATAATCATGTAGATCATA
66 TTTCATATAATCACGTAGATCATA
*
714040 TCATATAGC
1 TCACATAGC
714049 ATGAAATATA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 45 0.53
90 40 0.47
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (89 bp):
TCACATAGCTTATATCACATAGACAAATAATCACATAGATCAATATCACATAGCTTATATCACAT
TTTCATATAATCACGTAGATCATA
Found at i:714075 original size:90 final size:89
Alignment explanation
Indices: 713906--714077 Score: 195
Period size: 90 Copynumber: 1.9 Consensus size: 89
713896 ATAGATCATG
* * * * *
713906 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATATCACATAGCTTATATCTCAT
1 TCACATAGCTTATATCACATTTTCATATAATCACGTAGATCAATATCACATAGCTGAAATATAAT
* *
713971 TTTCATATAATCACGTAGTTCAATA
66 ATGCATAT-ATCACGTAGTTCAATA
* * *
713996 TCACATAGCTTATATCTCATTTTCATATAATCATGTAGATC-ATATCATATAGCATGAAATATAA
1 TCACATAGCTTATATCACATTTTCATATAATCACGTAGATCAATATCACATAGC-TGAAATAT-A
*
714060 ATAATGCATGT-TCACGTA
64 AT-ATGCATATATCACGTA
714078 ATATCAGAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
89 11 0.16
90 50 0.74
91 2 0.03
92 5 0.07
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (89 bp):
TCACATAGCTTATATCACATTTTCATATAATCACGTAGATCAATATCACATAGCTGAAATATAAT
ATGCATATATCACGTAGTTCAATA
Found at i:717181 original size:2 final size:2
Alignment explanation
Indices: 717174--717198 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
717164 GTTTCAGTAA
717174 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
717199 CTGAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:717468 original size:8 final size:8
Alignment explanation
Indices: 717457--717503 Score: 58
Period size: 8 Copynumber: 5.4 Consensus size: 8
717447 AAAAAATCTT
717457 AAAAAATA
1 AAAAAATA
717465 AAAATATTATTA
1 AAAA-A--AT-A
717477 AAAAAATA
1 AAAAAATA
717485 AAAAAATA
1 AAAAAATA
717493 AAAAAATA
1 AAAAAATA
717501 AAA
1 AAA
717504 CCCGCGTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 24 0.69
9 3 0.09
11 3 0.09
12 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (8 bp):
AAAAAATA
Found at i:718925 original size:19 final size:19
Alignment explanation
Indices: 718854--718925 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
718844 ATACCCATAT
718854 ATATATTATTTTTTAGATTAA
1 ATATATTATTTTTTA-A-TAA
*
718875 ATTCCTATT-TTTTATTGAATAA
1 A-T-ATATTATTTT-TT-AATAA
* *
718897 AAATAATATTTTTTAATAA
1 ATATATTATTTTTTAATAA
718916 ATATATTATT
1 ATATATTATT
718926 GCGGTTCGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
19 13 0.32
20 5 0.12
21 5 0.12
22 9 0.22
23 7 0.17
24 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
ATATATTATTTTTTAATAA
Found at i:719689 original size:22 final size:21
Alignment explanation
Indices: 719664--719719 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
719654 AAAGTGGTTA
*
719664 GTCAGAGGAAAATATTTTTCCG
1 GTCA-AGGAAAATATTTTTCAG
*
719686 GTCAA-TAGAAATATTTTTCAG
1 GTCAAGGA-AAATATTTTTCAG
*
719707 GTTAAAGGAAAAT
1 G-TCAAGGAAAAT
719720 GACCTTGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
22 11 0.41
23 1 0.04
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (21 bp):
GTCAAGGAAAATATTTTTCAG
Found at i:723232 original size:27 final size:27
Alignment explanation
Indices: 723190--723387 Score: 297
Period size: 27 Copynumber: 7.3 Consensus size: 27
723180 AATGACTCTA
* *
723190 AATCATTCAGAATGTACTTCTGTACTG
1 AATCATTCATAATGTACTTCTGTGCTG
* * * * *
723217 AATTATTCAGAATGTACTTTTATGTTG
1 AATCATTCATAATGTACTTCTGTGCTG
723244 AATCATTCATAATGTACTTCTGTGCTG
1 AATCATTCATAATGTACTTCTGTGCTG
723271 AATCATTCATAATGTACTTCTGTGCTG
1 AATCATTCATAATGTACTTCTGTGCTG
*
723298 AATCATTCATAATGTACTTCTATGCTG
1 AATCATTCATAATGTACTTCTGTGCTG
* *
723325 AATCATTCATAATGTACTTTTGTGTTG
1 AATCATTCATAATGTACTTCTGTGCTG
*
723352 AATCATTCATAATGTACTTCTATGCTG
1 AATCATTCATAATGTACTTCTGTGCTG
723379 AATCATTCA
1 AATCATTCA
723388 ACACTATTTT
Statistics
Matches: 154, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 154 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (27 bp):
AATCATTCATAATGTACTTCTGTGCTG
Found at i:726008 original size:14 final size:15
Alignment explanation
Indices: 725989--726019 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
725979 AAAATAATAT
725989 AAAATATTTTTT-AA
1 AAAATATTTTTTGAA
726003 AAAATATTTTTTGAA
1 AAAATATTTTTTGAA
726018 AA
1 AA
726020 TGTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AAAATATTTTTTGAA
Found at i:727090 original size:60 final size:59
Alignment explanation
Indices: 726997--727110 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 59
726987 TAGGGAGATT
* * *
726997 TAAGAGTTATATAGGTACAAATTTGATGCAAATATCATTTTTTAACATTTGAAATCAATG
1 TAAGAATTATATAGATACAAATCTGATGCAAATATCATTTTTTAACA-TTGAAATCAATG
727057 TAAGAATTATATAGATACAAATCTGATGCAAATATCATTTTTTAACATTGAAAT
1 TAAGAATTATATAGATACAAATCTGATGCAAATATCATTTTTTAACATTGAAAT
727111 TCGTGAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 7 0.14
60 44 0.86
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (59 bp):
TAAGAATTATATAGATACAAATCTGATGCAAATATCATTTTTTAACATTGAAATCAATG
Found at i:727365 original size:28 final size:28
Alignment explanation
Indices: 727312--727369 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
727302 TGAAAACAAA
*
727312 ATAAAGCATATAGAATTTCGGTTTTGTG
1 ATAAAGCATATAGAATTTCAGTTTTGTG
727340 ATAAAGCATATAGAATTTCTAG-TTTGTG
1 ATAAAGCATATAGAATTTC-AGTTTTGTG
727368 AT
1 AT
727370 CTTTAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (28 bp):
ATAAAGCATATAGAATTTCAGTTTTGTG
Found at i:729698 original size:21 final size:21
Alignment explanation
Indices: 729672--729808 Score: 163
Period size: 21 Copynumber: 6.6 Consensus size: 21
729662 GTTTCCAGAT
*
729672 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
729693 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
729714 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
729735 TCGCAATACGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
729755 TCACAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
*
729776 TTGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
729797 TCGCAATGCGAA
1 TCGCAATGCGAA
729809 TATGTAAATC
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
20 14 0.14
21 83 0.86
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:729763 original size:62 final size:62
Alignment explanation
Indices: 729709--729832 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
729699 TGCGAACTTG
729709 GACTATCGCAATGCGAACTTGGACTATCGCAATACGAATATGTAAATCACAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATACGAATATGTAAATCACAATGCGATAGTC
* * *
729771 GACTATTGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATACGAATATGTAAATCACAATGCGATAGTC
729833 CAAGTTTCCG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (62 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATACGAATATGTAAATCACAATGCGATAGTC
Found at i:729848 original size:62 final size:60
Alignment explanation
Indices: 729720--730023 Score: 190
Period size: 62 Copynumber: 5.1 Consensus size: 60
729710 ACTATCGCAA
* * * * * **
729720 TGCGAACTTGGACTATCGCAATACGAATATGTAAATCACAATGCGATAGT-CGACTATTGCAA
1 TGCGAA-TTGGACTATCGCAATGCG-ATATGTAAATCGCAATGCGATAGTCCAAGT-TTCCGT
729782 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGT
1 TGCGAA-TTGGACTATCGCAATGCG-ATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGT
* * * * *
729844 TGCGATAGTCGACTATCGCATTGCGATA-GTCCAAGTTCGCATTGCGATAGTCCAAG-TTCGCGT
1 TGCGA-ATTGGACTATCGCAATGCGATATGT--AA-ATCGCAATGCGATAGTCCAAGTTTC-CGT
*
729907 TGC--ATT-TA-T-TC-C-A----ATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGT
1 TGCGAATTGGACTATCGCAATGCGATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGT
* * * * * *
729956 TGCGATAGTCGACTATCGCATTGCGATA-GTCCAAGTTCGCATTGCGATAGTCGAAG-TTCGCGT
1 TGCGA-ATTGGACTATCGCAATGCGATATGT--AA-ATCGCAATGCGATAGTCCAAGTTTC-CGT
730019 TGCGA
1 TGCGA
730024 TTTATTCTAA
Statistics
Matches: 195, Mismatches: 23, Indels: 47
0.74 0.09 0.18
Matches are distributed among these distances:
49 25 0.13
50 5 0.03
51 3 0.02
52 4 0.02
53 1 0.01
54 1 0.01
55 2 0.01
56 2 0.01
57 2 0.01
58 1 0.01
59 1 0.01
60 6 0.03
61 6 0.03
62 81 0.42
63 55 0.28
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (60 bp):
TGCGAATTGGACTATCGCAATGCGATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGT
Found at i:729849 original size:21 final size:22
Alignment explanation
Indices: 729817--730024 Score: 155
Period size: 21 Copynumber: 9.5 Consensus size: 22
729807 AATATGTAAA
*
729817 TCGCAATGCGATAGTCCAAGTT
1 TCGCATTGCGATAGTCCAAGTT
* * * *
729839 TC-CGTTGCGATAGT-CGACTA
1 TCGCATTGCGATAGTCCAAGTT
729859 TCGCATTGCGATAGTCCAAG-T
1 TCGCATTGCGATAGTCCAAGTT
729880 TCGCATTGCGATAGTCCAAG-T
1 TCGCATTGCGATAGTCCAAGTT
* * *
729901 TCGCGTTGC-ATTTATTCCAATATGTAAA
1 TCGCATTGCGA--TAGTCC-A-A-GT--T
*
729929 TCGCAATGCGATAGTCCAAGTT
1 TCGCATTGCGATAGTCCAAGTT
* * * *
729951 TC-CGTTGCGATAGT-CGACTA
1 TCGCATTGCGATAGTCCAAGTT
729971 TCGCATTGCGATAGTCCAAG-T
1 TCGCATTGCGATAGTCCAAGTT
*
729992 TCGCATTGCGATAGTCGAAG-T
1 TCGCATTGCGATAGTCCAAGTT
*
730013 TCGCGTTGCGAT
1 TCGCATTGCGAT
730025 TTATTCTAAA
Statistics
Matches: 146, Mismatches: 27, Indels: 27
0.73 0.14 0.14
Matches are distributed among these distances:
20 11 0.08
21 102 0.70
22 13 0.09
23 1 0.01
24 3 0.02
25 2 0.01
26 1 0.01
27 5 0.03
28 7 0.05
29 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.30
Consensus pattern (22 bp):
TCGCATTGCGATAGTCCAAGTT
Found at i:730004 original size:112 final size:113
Alignment explanation
Indices: 729807--730030 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 113
729797 TCGCAATGCG
729807 AATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGTTGCGATAGTCGACTATCGCATTGCGATA
1 AATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGTTGCGATAGTCGACTATCGCATTGCGATA
729872 GTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGC-ATTTATTCC
66 GTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
729919 AATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGTTGCGATAGTCGACTATCGCATTGCGATA
1 AATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGTTGCGATAGTCGACTATCGCATTGCGATA
*
729984 GTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTC
66 GTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTC
730031 TAAATTCGTT
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
112 102 0.93
113 8 0.07
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (113 bp):
AATATGTAAATCGCAATGCGATAGTCCAAGTTTCCGTTGCGATAGTCGACTATCGCATTGCGATA
GTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
Found at i:730153 original size:6 final size:6
Alignment explanation
Indices: 730142--730167 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
730132 GACACGTATT
730142 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
730168 TAGAGACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:730643 original size:6 final size:6
Alignment explanation
Indices: 730634--731079 Score: 531
Period size: 6 Copynumber: 75.0 Consensus size: 6
730624 CGCCGCCGTC
* *
730634 CGTCGT CGTC-T CGTGGT CGTCTT CGTCGT CGTCGT CGTCGT C-TCGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * * *
730680 GGTCGT CGTCGT CGTCTT CGTCGT C-TCGT GGTCGT CGTCGT GGTCGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * * * * *
730727 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT CGTCGT GGTCGT CG-CGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * * * *
730774 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT CGTCGT CGTCGT CGTCGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * *
730822 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTGGT CGTGGT CGTGGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* *
730870 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT GGTCGT CGTCGT GGTCGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * * *
730918 CGTCGT CGTCGT CGTCGT CGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * * * *
730966 GGTCGT CGTCGT GGTCGT CGTCGT CGTCGT GGTCGT GGTCGT GGTCGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
* * * * *
731014 GGTCGT CGTCGT CGTCGT CGTGGT CGTCGT CGTCGT GGTTGT CGTGGT
1 CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT CGTCGT
*
731062 CGTGGT CGTCGT CGTCGT
1 CGTCGT CGTCGT CGTCGT
731080 GGTTGTGGTC
Statistics
Matches: 401, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
5 16 0.04
6 385 0.96
ACGTcount: A:0.00, C:0.26, G:0.40, T:0.34
Consensus pattern (6 bp):
CGTCGT
Found at i:732677 original size:138 final size:138
Alignment explanation
Indices: 732429--732690 Score: 402
Period size: 138 Copynumber: 1.9 Consensus size: 138
732419 CCGAAGTACT
* * **
732429 GAAATGGAAATTCACAAACTTATTATGAATTCCATGGATGCACACATAGTGCTGAAAGTACACAC
1 GAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACAC
* *
732494 AATACTGATACGAAAATGCACTGTTATGCATTAAACAAAATCGATCGATAACTTTTATACATAAT
66 AATACTGATACGAAAATGCACTATTATGCATTAAACAAAATCGATCGATAACTATTATACATAAT
732559 TGTATAAC
131 TGTATAAC
** *
732567 GAAATGGTGATTCACAAACTCATTATGAATACCAT-GATTGCATATC-TAGTGCCAAAAGTACAC
1 GAAATGGAAATTCACAAACTCATTATGAATACCATGGA-TGCACA-CATAGTGCCAAAAGTACAC
*
732630 ACATTACTGATACGAAAATGCACTATTATGCATTAAACAAAATCGATCGATAACTATTATA
64 ACAATACTGATACGAAAATGCACTATTATGCATTAAACAAAATCGATCGATAACTATTATA
732691 TACAATTTAT
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
137 2 0.02
138 109 0.97
139 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (138 bp):
GAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACAC
AATACTGATACGAAAATGCACTATTATGCATTAAACAAAATCGATCGATAACTATTATACATAAT
TGTATAAC
Found at i:735614 original size:18 final size:21
Alignment explanation
Indices: 735555--735608 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
735545 GGGCTTAATA
735555 GTATCGATACTACTGTTCATG
1 GTATCGATACTACTGTTCATG
735576 GTATCGATACTACTGTTCATG
1 GTATCGATACTACTGTTCATG
*
735597 GTATCAATACTA
1 GTATCGATACTA
735609 TTCATGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (21 bp):
GTATCGATACTACTGTTCATG
Found at i:735724 original size:19 final size:20
Alignment explanation
Indices: 735690--735729 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
735680 TACTGCTCAC
735690 ACAATATCGGTACTATTCAT
1 ACAATATCGGTACTATTCAT
*
735710 ACAATAT-GTTACTATTCAT
1 ACAATATCGGTACTATTCAT
735729 A
1 A
735730 AAAAATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (20 bp):
ACAATATCGGTACTATTCAT
Found at i:737079 original size:19 final size:20
Alignment explanation
Indices: 737043--737090 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
737033 TCTAAATCCT
* *
737043 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
737063 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
737082 ATTTCAAAA
1 TTTTCAAAA
737091 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:739181 original size:13 final size:13
Alignment explanation
Indices: 739163--739187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
739153 TATTTACGTT
739163 AAGAAATGACGCA
1 AAGAAATGACGCA
739176 AAGAAATGACGC
1 AAGAAATGACGC
739188 GGCTGTAAAA
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:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (13 bp):
AAGAAATGACGCA
Found at i:744724 original size:15 final size:15
Alignment explanation
Indices: 744704--744749 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
744694 AAAAGTATAC
*
744704 TAAAGATCAATTCTT
1 TAAAGATCGATTCTT
744719 TAAAGATCGATTCTT
1 TAAAGATCGATTCTT
744734 TAAAGATCGATTCTT
1 TAAAGATCGATTCTT
744749 T
1 T
744750 CTCCCTCCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (15 bp):
TAAAGATCGATTCTT
Found at i:750671 original size:35 final size:34
Alignment explanation
Indices: 750632--750697 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
750622 AAGCAATGTA
*
750632 TATCTGTTTAATATTTTAAAT-TTAAAAGATATTAT
1 TATCTATTTAA-A-TTTAAATATTAAAAGATATTAT
*
750667 TATCTATTTAAATTTATATATTAAAAGATAT
1 TATCTATTTAAATTTAAATATTAAAAGATAT
750698 CTAGTTGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 12 0.43
35 10 0.36
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (34 bp):
TATCTATTTAAATTTAAATATTAAAAGATATTAT
Found at i:750785 original size:82 final size:82
Alignment explanation
Indices: 750638--750789 Score: 241
Period size: 82 Copynumber: 1.9 Consensus size: 82
750628 TGTATATCTG
* * *
750638 TTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTATATATTAAAAGATATCTAGT
1 TTTAATATTTTAAATTTAAAAGATATCATTATCTATTTAAATTTAGATATTAAAAGAGATCTAGT
750703 TGGAGTAAATTCTCAAA
66 TGGAGTAAATTCTCAAA
* * * *
750720 TTTAATATTTTAAATTTAAAAGATATCATTATTTGTTTAAATTTAGATATTAAAATAGATTTAGT
1 TTTAATATTTTAAATTTAAAAGATATCATTATCTATTTAAATTTAGATATTAAAAGAGATCTAGT
750785 TGGAG
66 TGGAG
750790 AAAAACTCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.46
Consensus pattern (82 bp):
TTTAATATTTTAAATTTAAAAGATATCATTATCTATTTAAATTTAGATATTAAAAGAGATCTAGT
TGGAGTAAATTCTCAAA
Found at i:754734 original size:16 final size:16
Alignment explanation
Indices: 754713--754746 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
754703 GTTTATGTTC
754713 ATGTTCATGTTCATTT
1 ATGTTCATGTTCATTT
* *
754729 ATGTTCGTGTTCGTTT
1 ATGTTCATGTTCATTT
754745 AT
1 AT
754747 TTATTAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.56
Consensus pattern (16 bp):
ATGTTCATGTTCATTT
Found at i:754939 original size:5 final size:5
Alignment explanation
Indices: 754931--754961 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
754921 CTTCCCTTCC
754931 CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT C
1 CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT C
754962 AATCTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCCT
Found at i:756308 original size:42 final size:42
Alignment explanation
Indices: 756260--756342 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
756250 AATATTTTTC
*
756260 AATATTAAAATTTTAAAATATGATAGATATAAATAAAATTTA
1 AATATTAAAATTTTAAAATATGATAGATACAAATAAAATTTA
756302 AATATTAAAATTTTAAAATATGATAGATACAAATAAAATTT
1 AATATTAAAATTTTAAAATATGATAGATACAAATAAAATTT
756343 TAGATAGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (42 bp):
AATATTAAAATTTTAAAATATGATAGATACAAATAAAATTTA
Found at i:759116 original size:20 final size:20
Alignment explanation
Indices: 759091--759132 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
759081 TTTATGACTT
*
759091 CTATAGGTAGAGTATCGATA
1 CTATAGGGAGAGTATCGATA
*
759111 CTATAGGGATAGTATCGATA
1 CTATAGGGAGAGTATCGATA
759131 CT
1 CT
759133 TGTTCTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (20 bp):
CTATAGGGAGAGTATCGATA
Found at i:760402 original size:3 final size:3
Alignment explanation
Indices: 760388--760422 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
760378 AGAGATATTA
*
760388 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
760423 ATGTACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:761029 original size:64 final size:64
Alignment explanation
Indices: 760960--761118 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
760950 TTGAAGGTGT
** ***
760960 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATG
761023 C
64 C
* * * *
761024 ATCGATGCATAAGTAGTGCATCAATGCATACCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
* * *
761088 ACCGATGCATCAGTAGTGCATCGATACATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
761119 TTTCATTGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 76 0.95
65 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
Found at i:761781 original size:31 final size:31
Alignment explanation
Indices: 761743--761900 Score: 273
Period size: 31 Copynumber: 5.1 Consensus size: 31
761733 AGGGTCGAGG
761743 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
761774 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
761805 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
761836 GTTTACCTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
761867 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
761898 GTT
1 GTT
761901 CCTTCGGGAC
Statistics
Matches: 121, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
31 121 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:762695 original size:118 final size:118
Alignment explanation
Indices: 762485--762721 Score: 438
Period size: 118 Copynumber: 2.0 Consensus size: 118
762475 ATAAGTTGAA
762485 TGTTATAAAAGTTTTTAAATTACTCAATATTTTATACGAATAAATGTTTGAAAAGTCAATGTGAC
1 TGTTATAAAAGTTTTTAAATTACTCAATATTTTATACGAATAAATGTTTGAAAAGTCAATGTGAC
* *
762550 ACTTCGGACTCATATCCGGGTCGGATACGGGTTGGGGGTGTTACATTTAATGG
66 ACTTCGGACTCATATCCGGGTCAGATACGGGTTGGGGGTGTTAAATTTAATGG
762603 TGTTATAAAAGTTTTTAAATTACTCAATATTTTATACGAATAAATGTTTGAAAAGTCAATGTGAC
1 TGTTATAAAAGTTTTTAAATTACTCAATATTTTATACGAATAAATGTTTGAAAAGTCAATGTGAC
* *
762668 ACTTCGGACTCGTATTCGGGTCAGATACGGGTTGGGGGTGTTAAATTTAATGG
66 ACTTCGGACTCATATCCGGGTCAGATACGGGTTGGGGGTGTTAAATTTAATGG
762721 T
1 T
762722 ATCAGAGATA
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 115 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (118 bp):
TGTTATAAAAGTTTTTAAATTACTCAATATTTTATACGAATAAATGTTTGAAAAGTCAATGTGAC
ACTTCGGACTCATATCCGGGTCAGATACGGGTTGGGGGTGTTAAATTTAATGG
Found at i:764980 original size:3 final size:3
Alignment explanation
Indices: 764966--765000 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
764956 AGATATATTC
*
764966 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
765001 ATGTACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:766390 original size:31 final size:31
Alignment explanation
Indices: 766351--766475 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
766341 AGGGTCGAGG
766351 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
766382 ATTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
766413 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
766444 GCTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
766475 G
1 G
766476 GTCCTTTGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:767667 original size:20 final size:20
Alignment explanation
Indices: 767644--767683 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
767634 ACAGTTGACA
*
767644 TTGACAGTTAACTTTGACCG
1 TTGACAGTAAACTTTGACCG
* *
767664 TTGACCGTAAACTTTTACCG
1 TTGACAGTAAACTTTGACCG
767684 GTAAGCCGTT
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:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGACAGTAAACTTTGACCG
Found at i:768599 original size:27 final size:28
Alignment explanation
Indices: 768560--768613 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
768550 TATATAATTA
768560 CCCCTGAAATGTAAAATGACC-AAAATG
1 CCCCTGAAATGTAAAATGACCTAAAATG
*
768587 CCCCT-AAAGTGTAAAATGGCCTAAAAT
1 CCCCTGAAA-TGTAAAATGACCTAAAAT
768614 ATCTCTAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 3 0.12
27 16 0.67
28 5 0.21
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (28 bp):
CCCCTGAAATGTAAAATGACCTAAAATG
Found at i:774569 original size:23 final size:24
Alignment explanation
Indices: 774530--774575 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
774520 TGTGTGTGTT
774530 AATGTGATATTATTTATAGTATAC
1 AATGTGATATTATTTATAGTATAC
*
774554 AATGT-ATATGTA-TTATATTATA
1 AATGTGATAT-TATTTATAGTATA
774576 AATACATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (24 bp):
AATGTGATATTATTTATAGTATAC
Done.