Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007981.1 Hibiscus syriacus cultivar Beakdansim tig00110422_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: 1405786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:970971 original size:14 final size:14
Alignment explanation
Indices: 970952--971041 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 14
970942 TGCGAAATGC
*
970952 AAATCGCAACGACA
1 AAATCGCAACGAAA
970966 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG-AA--A
*
970985 AAATCGCAATGAAA
1 AAATCGCAACGAAA
*
970999 AAATCGCAATGTGAAA
1 AAATCGCAA--CGAAA
*
971015 TGAAATCGCAACGACA
1 --AAATCGCAACGAAA
971031 AAATCGCAACG
1 AAATCGCAACG
971042 CGAAACACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 30 0.48
16 12 0.19
17 2 0.03
18 9 0.14
19 10 0.16
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (14 bp):
AAATCGCAACGAAA
Found at i:970977 original size:33 final size:33
Alignment explanation
Indices: 970935--971055 Score: 172
Period size: 33 Copynumber: 3.7 Consensus size: 33
970925 GGAAATGACT
970935 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* * *
970968 ATCGCAATGCGAAATGAAAATCGCAATGAAAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
971001 ATCGCAATGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* **
971033 ATCGCAACGCGAAACACAAATCG
1 ATCGCAATGCGAAATGCAAATCG
971056 TATTGCGACT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:971079 original size:19 final size:18
Alignment explanation
Indices: 971057--971149 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
971047 CACAAATCGT
971057 ATTGCGACTTTCATTTCGC
1 ATTGCGA-TTTCATTTCGC
*
971076 ATTGCGATTT--TGTCG-
1 ATTGCGATTTCATTTCGC
971091 -TTGCGATTTTCATTTCGC
1 ATTGCGA-TTTCATTTCGC
*
971109 ATTGCGATTT--TGTCG-
1 ATTGCGATTTCATTTCGC
*
971124 -TTGCGATTTTCATTTCAC
1 ATTGCGA-TTTCATTTCGC
971142 ATTGCGAT
1 ATTGCGAT
971150 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
14 12 0.20
15 6 0.10
16 8 0.14
17 7 0.12
18 7 0.12
19 19 0.32
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.46
Consensus pattern (18 bp):
ATTGCGATTTCATTTCGC
Found at i:971096 original size:14 final size:14
Alignment explanation
Indices: 971077--971133 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
971067 TCATTTCGCA
971077 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
971091 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
971108 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
971124 TTGCGATTTT
1 TTGCGATTTT
971134 CATTTCACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:971102 original size:33 final size:33
Alignment explanation
Indices: 971058--971149 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
971048 ACAAATCGTA
*
971058 TTGCGACTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
971091 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
971124 TTGCGATTTTCATTTCACATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
971150 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:971156 original size:19 final size:20
Alignment explanation
Indices: 971134--971177 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
971124 TTGCGATTTT
971134 CATTT-CACATTGCGATAGC
1 CATTTCCACATTGCGATAGC
* * *
971153 CATTTCCGCGTTGCGATAGT
1 CATTTCCACATTGCGATAGC
971173 CATTT
1 CATTT
971178 TTATGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCACATTGCGATAGC
Found at i:971691 original size:18 final size:18
Alignment explanation
Indices: 971665--971709 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
971655 GTCGATCAGA
*
971665 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
971683 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
971701 TGATGGCTC
1 TGATGGCTC
971710 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:973063 original size:20 final size:20
Alignment explanation
Indices: 973040--973085 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
973030 AAATGAAAAA
973040 CGCAACACGAAAATGACTAT
1 CGCAACACGAAAATGACTAT
* **
973060 CGCAACGCGAATTTGACTAT
1 CGCAACACGAAAATGACTAT
973080 CGCAAC
1 CGCAAC
973086 GAGAGAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (20 bp):
CGCAACACGAAAATGACTAT
Found at i:973606 original size:20 final size:20
Alignment explanation
Indices: 973581--973632 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
973571 ATTATGTATT
973581 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
973601 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
973621 ATCTCGTTGCGA
1 ATCGCGTTGCGA
973633 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:973669 original size:20 final size:20
Alignment explanation
Indices: 973641--973694 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
973631 GATTTTGTAT
973641 TATCACATTGCGATAGTAAG
1 TATCACATTGCGATAGTAAG
* *
973661 TATCTCATTGCGATAGTCAG
1 TATCACATTGCGATAGTAAG
*
973681 TATCGCATTGCGAT
1 TATCACATTGCGAT
973695 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
TATCACATTGCGATAGTAAG
Found at i:973672 original size:61 final size:61
Alignment explanation
Indices: 973560--973697 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
973550 CGCGTTGAAA
* * * * *
973560 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
973621 ATCTCGTTGCGATTTTGTATTATCACATTGCGATAGTAAGTATCTCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
973682 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
973698 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:973727 original size:20 final size:21
Alignment explanation
Indices: 973683--973734 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
973673 ATAGTCAGTA
*
973683 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
973704 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
973724 TCGCATTGCGA
1 TCGCATTGCGA
973735 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:974172 original size:50 final size:50
Alignment explanation
Indices: 974113--974229 Score: 146
Period size: 50 Copynumber: 2.3 Consensus size: 50
974103 AAAGCGCTCC
* * *
974113 CTGAACCGCGCTATACGCTGATTTGACACCACGTGGGTATAGCGCGCCC-
1 CTGACCCGCGCTATACGCTGATCTAACACCACGTGGGTATAGCGCGCCCT
* * * *
974162 CTTGCCCCGCGATATACGGTGATCTAACGCCACGTGGGTATAGCGCGCCCT
1 C-TGACCCGCGCTATACGCTGATCTAACACCACGTGGGTATAGCGCGCCCT
*
974213 CTGATCCGCGCTATACG
1 CTGACCCGCGCTATACG
974230 TGGGTATCTA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
49 1 0.02
50 54 0.96
51 1 0.02
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.21
Consensus pattern (50 bp):
CTGACCCGCGCTATACGCTGATCTAACACCACGTGGGTATAGCGCGCCCT
Found at i:974250 original size:50 final size:48
Alignment explanation
Indices: 974140--974258 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 48
974130 CTGATTTGAC
* *
974140 ACCACGTGGGTATAGCGCGCCCCTTGCCCCGCGATATACGGTGATCTA
1 ACCACGTGGGTATAGCGCGCCCCTTGACCCGCGATATACGGGGATCTA
* *
974188 ACGCCACGTGGGTATAGCGCG-CCCTCTGATCCGCGCTATACGTGGGTATCTA
1 A--CCACGTGGGTATAGCGCGCCCCT-TGACCCGCGATATACG-GGG-ATCTA
974240 A-CACGTTGGGTATAGCGCG
1 ACCACG-TGGGTATAGCGCG
974259 GTGCAGGGGC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
48 1 0.02
49 8 0.13
50 44 0.72
51 2 0.03
52 6 0.10
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.22
Consensus pattern (48 bp):
ACCACGTGGGTATAGCGCGCCCCTTGACCCGCGATATACGGGGATCTA
Found at i:974382 original size:20 final size:19
Alignment explanation
Indices: 974351--974390 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
974341 TTATAACACC
*
974351 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAATACTCT
974370 AAATTTCTCTCAAATACTCT
1 AAATTT-TCTCAAATACTCT
974390 A
1 A
974391 TCTTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTTCTCAAATACTCT
Found at i:974654 original size:112 final size:111
Alignment explanation
Indices: 974515--974737 Score: 401
Period size: 112 Copynumber: 2.0 Consensus size: 111
974505 ATGGAATCAT
* *
974515 ATATCTCTACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
974580 TATTTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TA-ATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
974627 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
974692 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
974738 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
111 42 0.39
112 65 0.61
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
Found at i:976271 original size:18 final size:18
Alignment explanation
Indices: 976244--976287 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
976234 TCAATAGCCA
*
976244 CCGCAACCATATATGATG
1 CCGCATCCATATATGATG
976262 CCGCATCCATATATGATG
1 CCGCATCCATATATGATG
976280 CCGTCATC
1 CCG-CATC
976288 GCCTTTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (18 bp):
CCGCATCCATATATGATG
Found at i:980196 original size:80 final size:80
Alignment explanation
Indices: 980020--980184 Score: 294
Period size: 80 Copynumber: 2.1 Consensus size: 80
980010 TTATACATAA
*
980020 ATCAACGGAGTATTATCATTTGAAACTCCGAAAAAATGATTGTTCATCAGTATTTAAGTGTTAAC
1 ATCAACGGAGTATTATCATTTGAAACTCCGAAAAAATGATTGTTCATCAGAATTTAAGTGTTAAC
980085 AGACCCTGTCAGGTG
66 AGACCCTGTCAGGTG
* *
980100 ATCAACGGAGTATTATCATTTGGAACTCCGAAAAAATGATTGTTCATCAGAATTTTAGTGTTAAC
1 ATCAACGGAGTATTATCATTTGAAACTCCGAAAAAATGATTGTTCATCAGAATTTAAGTGTTAAC
980165 AGACCCTGTCAGGTG
66 AGACCCTGTCAGGTG
*
980180 GTCAA
1 ATCAA
980185 AATTGATTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (80 bp):
ATCAACGGAGTATTATCATTTGAAACTCCGAAAAAATGATTGTTCATCAGAATTTAAGTGTTAAC
AGACCCTGTCAGGTG
Found at i:987902 original size:8 final size:8
Alignment explanation
Indices: 987889--987922 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
987879 TAAAATATTT
987889 AAAAATAA
1 AAAAATAA
987897 AAAAATATA
1 AAAAATA-A
987906 AACAAATAA
1 AA-AAATAA
987915 AAAAATAA
1 AAAAATAA
987923 TTAAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 13 0.54
9 6 0.25
10 5 0.21
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAATAA
Found at i:987903 original size:18 final size:17
Alignment explanation
Indices: 987880--987930 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
987870 GACACCATAT
987880 AAAATATTTAAAAATAAA
1 AAAATA-TTAAAAATAAA
*
987898 AAAATATAAACAAATAAA
1 AAAATATTAA-AAATAAA
987916 AAAATAATTAAAAAT
1 AAAAT-ATTAAAAAT
987931 TTGAAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 22 0.76
19 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATATTAAAAATAAA
Found at i:989040 original size:15 final size:16
Alignment explanation
Indices: 989023--989053 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
989013 TTTTTTGGAA
989023 TTTATAATTTTTTTAT
1 TTTATAATTTTTTTAT
*
989039 TTTGTAATTTTTTTA
1 TTTATAATTTTTTTA
989054 AAATAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATAATTTTTTTAT
Found at i:989652 original size:23 final size:24
Alignment explanation
Indices: 989622--989672 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
989612 TTAAAAACAT
*
989622 TTTTTGAAAATGTATAATATAT-G
1 TTTTTGAAAACGTATAATATATAG
989645 TTTTTGAAAACGTATAATATATAG
1 TTTTTGAAAACGTATAATATATAG
989669 TTTT
1 TTTT
989673 AAAAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (24 bp):
TTTTTGAAAACGTATAATATATAG
Found at i:989655 original size:36 final size:35
Alignment explanation
Indices: 989530--989655 Score: 123
Period size: 35 Copynumber: 3.6 Consensus size: 35
989520 TTTAAAATAA
**
989530 ATAATATATAGTTTTTGGAAA-A-TTTTGAAAACGT
1 ATAATATAT-GTTTTTAAAAACATTTTTGAAAACGT
* * * *
989564 ATAATATATGGTTCTAAAAACATTATTGAAAACAT
1 ATAATATATGTTTTTAAAAACATTTTTGAAAACGT
* *
989599 ATAATTTAT-TATTTTAAAAACATTTTTTGAAAATGT
1 ATAATATATGT-TTTTAAAAACA-TTTTTGAAAACGT
*
989635 ATAATATATGTTTTTGAAAAC
1 ATAATATATGTTTTTAAAAAC
989656 GTATAATATA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
33 7 0.10
34 10 0.14
35 28 0.38
36 27 0.37
37 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (35 bp):
ATAATATATGTTTTTAAAAACATTTTTGAAAACGT
Found at i:989661 original size:59 final size:61
Alignment explanation
Indices: 989589--989719 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 61
989579 AAAAACATTA
* *
989589 TTGAAAACATATAATTTATTA-TTTT-AAAAACATTTTT-TGAAA-ATGTATAATATATGTTT
1 TTGAAAACATATAATATA-TAGTTTTAAAAAACATTTTTGTGAAACATATATAATATA-GTTT
* *
989648 TTGAAAACGTATAATATATAGTTTTAAAAAACATTTTTGTTAAACATATATAATATAG-TT
1 TTGAAAACATATAATATATAGTTTTAAAAAACATTTTTGTGAAACATATATAATATAGTTT
*
989708 TTAAAAACATAT
1 TTGAAAACATAT
989720 TTTGAAAACG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 2 0.03
59 20 0.32
60 24 0.39
61 5 0.08
62 11 0.18
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (61 bp):
TTGAAAACATATAATATATAGTTTTAAAAAACATTTTTGTGAAACATATATAATATAGTTT
Found at i:989685 original size:36 final size:35
Alignment explanation
Indices: 989645--989735 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 35
989635 ATAATATATG
989645 TTTTTGAAAACGTATA-ATATATAGTTTTAAAAAACA
1 TTTTTGAAAACGTATATA-ATATAGTTTT-AAAAACA
* *
989681 TTTTTGTTAAACATATATAATATAGTTTTAAAAACA
1 TTTTTG-AAAACGTATATAATATAGTTTTAAAAACA
*
989717 TATTTTGAAAACGTGTATA
1 T-TTTTGAAAACGTATATA
989736 TAGTTTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
36 23 0.49
37 23 0.49
38 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (35 bp):
TTTTTGAAAACGTATATAATATAGTTTTAAAAACA
Found at i:989723 original size:96 final size:92
Alignment explanation
Indices: 989552--989743 Score: 244
Period size: 94 Copynumber: 2.0 Consensus size: 92
989542 TTTTGGAAAA
* *
989552 TTTTGAAAACGTATAATATATGGTTCTAAAAACATTATTGAAAACATATAATTTATTATTTTAAA
1 TTTTGAAAACGTATAATATATAGTTCTAAAAACATTATTGAAAACATATAATATATTATTTTAAA
* *
989617 AACATTTTTTGAAAATGTATAATATATGT
66 AACATATTTTGAAAACGTAT-ATATA-GT
* * *
989646 TTTTGAAAACGTATAATATATAGTTTTAAAAAACATTTTTGTTAAACATAT-ATA-ATATAGTTT
1 TTTTGAAAACGTATAATATATAGTTCT-AAAAACATTATTG-AAAACATATAATATAT-TA-TTT
*
989709 TAAAAACATATTTTGAAAACGTGTATATAGT
62 TAAAAACATATTTTGAAAACGTATATATAGT
989740 TTTT
1 TTTT
989744 AAATATTCTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
94 33 0.38
95 21 0.24
96 32 0.37
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (92 bp):
TTTTGAAAACGTATAATATATAGTTCTAAAAACATTATTGAAAACATATAATATATTATTTTAAA
AACATATTTTGAAAACGTATATATAGT
Found at i:989794 original size:17 final size:17
Alignment explanation
Indices: 989769--989801 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
989759 AATATATATT
989769 ATATAATTTTTGAAAAC
1 ATATAATTTTTGAAAAC
*
989786 ATATTATTTTTGAAAA
1 ATATAATTTTTGAAAA
989802 TATAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (17 bp):
ATATAATTTTTGAAAAC
Found at i:996203 original size:23 final size:24
Alignment explanation
Indices: 996159--996204 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
996149 TTAGATAATG
996159 CAAAAGAACAATAAAAAGAAAAAA
1 CAAAAGAACAATAAAAAGAAAAAA
996183 CAAAAGAAC-AT-AAAAGAAAAAA
1 CAAAAGAACAATAAAAAGAAAAAA
996205 GAGAACCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
24 9 0.41
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (24 bp):
CAAAAGAACAATAAAAAGAAAAAA
Found at i:996720 original size:1 final size:1
Alignment explanation
Indices: 996714--996756 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
996704 AAATTTTGAC
* * * *
996714 TTTTTTTATTTTTTATTTTTTTTATTTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
996757 AAATAGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:996725 original size:7 final size:7
Alignment explanation
Indices: 996715--996754 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
996705 AATTTTGACT
996715 TTTTTTA
1 TTTTTTA
996722 TTTTTTA
1 TTTTTTA
996729 TTTTTT-
1 TTTTTTA
996735 TTATTTT-
1 TT-TTTTA
996742 TTTTTTA
1 TTTTTTA
996749 TTTTTT
1 TTTTTT
996755 TTAAATAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTTA
Found at i:996726 original size:9 final size:9
Alignment explanation
Indices: 996714--996757 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
996704 AAATTTTGAC
996714 TTTTTTTA-
1 TTTTTTTAT
996722 -TTTTTTAT
1 TTTTTTTAT
996730 TTTTTTTATTT
1 TTTTTTTA--T
996741 TTTTTTTAT
1 TTTTTTTAT
996750 TTTTTTTA
1 TTTTTTTA
996758 AATAGAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.22
9 16 0.50
11 9 0.28
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:996726 original size:16 final size:16
Alignment explanation
Indices: 996707--996742 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
996697 TGTTTTGAAA
996707 TTTTGACTTTTTTTAT
1 TTTTGACTTTTTTTAT
* *
996723 TTTTTATTTTTTTTAT
1 TTTTGACTTTTTTTAT
996739 TTTT
1 TTTT
996743 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTGACTTTTTTTAT
Found at i:996743 original size:16 final size:15
Alignment explanation
Indices: 996714--996756 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
996704 AAATTTTGAC
996714 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTT-T
996730 TTTTTTTATTTTTTT
1 TTTTTTTATTTTTTT
996745 TTTATTTT-TTTT
1 TTT-TTTTATTTT
996757 AAATAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTTTATTTTTTT
Found at i:996747 original size:20 final size:21
Alignment explanation
Indices: 996717--996757 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
996707 TTTTGACTTT
996717 TTTTATTTTTTATTTTTTTTA
1 TTTTATTTTTTATTTTTTTTA
996738 TTTT-TTTTTTATTTTTTTTA
1 TTTTATTTTTTATTTTTTTTA
996758 AATAGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (21 bp):
TTTTATTTTTTATTTTTTTTA
Found at i:998676 original size:18 final size:16
Alignment explanation
Indices: 998653--998713 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
998643 CATTTAAACC
998653 CTTTTAATTTAAAGTTTT
1 CTTTTAATTTAAA--TTT
* *
998671 CTTTTACTTTATATTT
1 CTTTTAATTTAAATTT
*
998687 -TTTTAATTTAATTTT
1 CTTTTAATTTAAATTT
* *
998702 GTTTTACTTTAA
1 CTTTTAATTTAA
998714 TAACTAAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 12 0.33
16 13 0.36
18 11 0.31
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.66
Consensus pattern (16 bp):
CTTTTAATTTAAATTT
Found at i:998712 original size:16 final size:15
Alignment explanation
Indices: 998667--998714 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
998657 TAATTTAAAG
998667 TTTTCTTTTACTTT-A
1 TTTT-TTTTACTTTAA
*
998682 TATTTTTTTAATTTAA
1 T-TTTTTTTACTTTAA
998698 TTTTGTTTTACTTTAA
1 TTTT-TTTTACTTTAA
998714 T
1 T
998715 AACTAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTTTTACTTTAA
Found at i:1000874 original size:20 final size:20
Alignment explanation
Indices: 1000849--1000902 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1000839 AATAAGATTT
1000849 ATGCATCGATGCATGGTGTA
1 ATGCATCGATGCATGGTGTA
1000869 ATGCATCGATGCATGGTGTA
1 ATGCATCGATGCATGGTGTA
1000889 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1000903 ACCTCCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
ATGCATCGATGCATGGTGTA
Found at i:1001515 original size:103 final size:103
Alignment explanation
Indices: 1001336--1001663 Score: 620
Period size: 103 Copynumber: 3.2 Consensus size: 103
1001326 GTAGAGGGTC
*
1001336 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1001401 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
1001439 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1001504 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1001542 TATATGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGAAACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1001607 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1001645 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
1001664 ACTTTATATT
Statistics
Matches: 220, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 220 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1001706 original size:23 final size:23
Alignment explanation
Indices: 1001674--1001740 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
1001664 ACTTTATATT
*
1001674 GCACTTCGGTGCATTTCTATGCG
1 GCACTTCGGTGCATTTCTACGCG
* * *
1001697 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCG
*
1001720 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
1001741 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Found at i:1002656 original size:23 final size:23
Alignment explanation
Indices: 1002611--1002658 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1002601 TAACATATTT
* **
1002611 GGTAGCGTTTATATAATGTAATA
1 GGTAGCGCTTATATAATAAAATA
1002634 GGTAGCGCTTATATAATAAAATA
1 GGTAGCGCTTATATAATAAAATA
1002657 GG
1 GG
1002659 CATTTAACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (23 bp):
GGTAGCGCTTATATAATAAAATA
Found at i:1002713 original size:23 final size:23
Alignment explanation
Indices: 1002687--1002745 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
1002677 ATCAAGTGCA
1002687 ATAACAT-ATCAGATAGCGCTTAT
1 ATAACATAAT-AGATAGCGCTTAT
** *
1002710 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
* *
1002733 ATAATAAAATAGA
1 ATAACATAATAGA
1002746 CATTTAACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:1002718 original size:87 final size:87
Alignment explanation
Indices: 1002572--1002821 Score: 437
Period size: 87 Copynumber: 2.9 Consensus size: 87
1002562 TATGTTATAT
* *
1002572 CATTTAACCGGAAATATTATCAAGTACAATAACATATTTGGTAGCGTTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
1002637 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGA
* * *
1002659 CATTTAACCGGAAATATTATCAAGTGCAATAACATATCAGATAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1002724 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
*
1002746 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGCAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1002811 AGCGCTTATAT
66 AGCGCTTATAT
1002822 TGACCTATTT
Statistics
Matches: 153, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 153 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGA
Found at i:1003272 original size:200 final size:198
Alignment explanation
Indices: 1002845--1003337 Score: 624
Period size: 200 Copynumber: 2.5 Consensus size: 198
1002835 AACTAAACTG
* *
1002845 GTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * *
1002910 TGAGATCGATTCAATTT--TAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTC
66 TGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATACATGCACCTCGTTGGGCATTCATTC
*
1002973 TGGAAAAAAGTATCGACACAATCTTAAAATGTGTCGATACATTATGTAGACTTATTTTCACATAA
130 TGGAAAAAAGTATCGACACAATCTTAAAATGTGTCGATACATTATGTAGACTTATTCTCACATAA
1003038 AACA
195 AACA
* * * * * *
1003042 TGTATATTTCTACCGGGTACATTCTAAATTTACATATTACATTGTAATTATCGGTTTCGTTGTTT
1 -GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
1003107 TTGGGATTGATACTTTTAATAAATGTATCGACACTTTATACGTGCACCTCGTTTGGCATTCATTC
65 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATACATGCACCTCGTTGGGCATTCATTC
* * * *
1003172 TGGACAAAATA-TATCGACAC-TTTTTAAATTTGTGTCGATACATTATGTTGA-TCTATTCT-AT
130 TGGA-AAAA-AGTATCGACACAATCTTAAA-ATGTGTCGATACATTATGTAGACT-TATTCTCA-
1003233 CATAAAATC-
190 CATAAAA-CA
* * *
1003242 GATATATTTATACCGATTATATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
1 G-TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
*
1003307 TTGGGGTCGATACTTTTAGA-AAATGTATCGA
65 TTGGGATCGATACTTTTA-ATAAATGTATCGA
1003338 TACATATGTT
Statistics
Matches: 254, Mismatches: 31, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
197 3 0.01
198 66 0.26
199 56 0.22
200 126 0.50
201 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (198 bp):
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTAATAAATGTATCGACACTTTATACATGCACCTCGTTGGGCATTCATTCT
GGAAAAAAGTATCGACACAATCTTAAAATGTGTCGATACATTATGTAGACTTATTCTCACATAAA
ACA
Found at i:1003818 original size:124 final size:124
Alignment explanation
Indices: 1003671--1004019 Score: 545
Period size: 125 Copynumber: 2.8 Consensus size: 124
1003661 ACCGATAAAA
* * *
1003671 AATAACAAAACCGGTAGTGCTTTTACCGGTTTTATTAAAAACCCGATAAAATGCCAAAATAATAA
1 AATAACAAAACCGGTAGCGCTTTTACCGGTTTTGTTAAAAACCCGGTAAAATGCCAAAATAATAA
* * * * *
1003736 CAAAACCGGTAGAAATAATGATATTTTCGGTAATTTTTATCGGTTTTGTTATGTACAAC
66 CAAAACCGGTAGAAATAATGATGTTTTCGATAATTTTTACCAGTTTTGTTATGCACAAC
*
1003795 AATAACAAAACCGGTAGCGCTTTTACCGGTTTTGTTAAGAAACCCGGTAAAATGTCAAAATAATA
1 AATAACAAAACCGGTAGCGCTTTTACCGGTTTTGTTAA-AAACCCGGTAAAATGCCAAAATAATA
1003860 ACAAAACCGGTAGAAATAATGATGTTTTCGATAATTTTTACCAGTTTTGTTATGCACAAC
65 ACAAAACCGGTAGAAATAATGATGTTTTCGATAATTTTTACCAGTTTTGTTATGCACAAC
** * *
1003920 AATAACAAAACCAATAGCTCTTTTACCGATTTTGTTAGAAAACCCGGTAAAATGCCAAAATAATA
1 AATAACAAAACCGGTAGCGCTTTTACCGGTTTTGTTA-AAAACCCGGTAAAATGCCAAAATAATA
* *
1003985 ACAAAACCGATAAAAATAATGATGTTTTCGATAAT
65 ACAAAACCGGTAGAAATAATGATGTTTTCGATAAT
1004020 AATAGAACCG
Statistics
Matches: 207, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
124 36 0.17
125 170 0.82
126 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (124 bp):
AATAACAAAACCGGTAGCGCTTTTACCGGTTTTGTTAAAAACCCGGTAAAATGCCAAAATAATAA
CAAAACCGGTAGAAATAATGATGTTTTCGATAATTTTTACCAGTTTTGTTATGCACAAC
Found at i:1004048 original size:97 final size:98
Alignment explanation
Indices: 1003939--1004117 Score: 290
Period size: 98 Copynumber: 1.8 Consensus size: 98
1003929 ACCAATAGCT
*
1003939 CTTTTACCGATTTTGTTAGAAAA-CCCGGTAAAATGCCAAAATAATAACAAAACC-GATAAAAAT
1 CTTTTACCGATTTTGTTAAAAAACCCCGGTAAAATGCCAAAATAATAACAAAACCTG-TAAAAAT
*
1004002 AATGATGTTTTCGATAATAATAGAACCGGTAATA
65 AATGATATTTTCGATAATAATAGAACCGGTAATA
** *
1004036 CTTTTACCGATTTTGTTAAAAAACCCCGGTAAAATGTTAAAATAATAACAAAACCTGTAGAAATA
1 CTTTTACCGATTTTGTTAAAAAACCCCGGTAAAATGCCAAAATAATAACAAAACCTGTAAAAATA
1004101 ATGATATTTTCGATAAT
66 ATGATATTTTCGATAAT
1004118 TTTTATCGGT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
97 22 0.29
98 52 0.69
99 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (98 bp):
CTTTTACCGATTTTGTTAAAAAACCCCGGTAAAATGCCAAAATAATAACAAAACCTGTAAAAATA
ATGATATTTTCGATAATAATAGAACCGGTAATA
Found at i:1004753 original size:23 final size:24
Alignment explanation
Indices: 1004716--1004761 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1004706 TTCGATATTG
1004716 AAAAAATATTAAAATAATTTATTTT
1 AAAAAATATTAAAATAA-TTATTTT
*
1004741 AAAAAATA-T-AAATTATTATTT
1 AAAAAATATTAAAATAATTATTT
1004762 ATCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 1 0.05
25 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAATATTAAAATAATTATTTT
Found at i:1006231 original size:3 final size:3
Alignment explanation
Indices: 1006223--1006293 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
1006213 AATATATATT
* *
1006223 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1006271 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1006294 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1006745 original size:113 final size:112
Alignment explanation
Indices: 1006609--1007271 Score: 1132
Period size: 113 Copynumber: 5.9 Consensus size: 112
1006599 TGATAGTATC
* * *
1006609 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *** * * *
1006673 TCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC
66 TCATTATGAA-CTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
1006721 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1006786 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGACTTT
66 TCATTATGAA-CTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
1006834 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1006899 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAA-CTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
1006947 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1007012 TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
1007059 AAAC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1007123 TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
1007170 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1007235 TCATTATGAACTTATCTGGCAATGAATGATCCATCAA
66 TCATTATGAACTTATCTGGCAATG-TTGATCCATCAA
1007272 GTGGATTTGA
Statistics
Matches: 533, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
111 111 0.21
112 128 0.24
113 294 0.55
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (112 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGAATTT
Found at i:1008067 original size:83 final size:83
Alignment explanation
Indices: 1007928--1008729 Score: 1406
Period size: 83 Copynumber: 9.7 Consensus size: 83
1007918 CTTACTAAAA
* *
1007928 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
* *
1007993 TGATTGATTCTATCCAAC
66 TGATTGGTTCTGTCCAAC
*
1008011 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
* *
1008076 TGATTGATTCTATCCAAC
66 TGATTGGTTCTGTCCAAC
*
1008094 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
1008159 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
*
1008177 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
1008242 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
1008260 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
*
1008325 TGATTGGTTCTGTCCGAC
66 TGATTGGTTCTGTCCAAC
*
1008343 CAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
*
1008408 TGATTGGTTCTGTCCGAC
66 TGATTGGTTCTGTCCAAC
*
1008426 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
**
1008491 TGATTGGTTCTGTTAAAC
66 TGATTGGTTCTGTCCAAC
* * *
1008509 CAGGTCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
**
1008574 TGATTGGTTCTGTTAAAC
66 TGATTGGTTCTGTCCAAC
* *
1008592 CAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
1008657 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
1008675 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTT
1008730 TCAGTTAATG
Statistics
Matches: 699, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 699 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAA
TGATTGGTTCTGTCCAAC
Found at i:1009434 original size:20 final size:20
Alignment explanation
Indices: 1009387--1009426 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1009377 AATTCAATAG
*
1009387 AAAAGAATAAATTGAATTTCC
1 AAAA-AATAAATTGAATCTCC
1009408 AAAAAATAAATTGAATCTC
1 AAAAAATAAATTGAATCTC
1009427 AAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAAATAAATTGAATCTCC
Found at i:1009781 original size:5 final size:5
Alignment explanation
Indices: 1009766--1009842 Score: 67
Period size: 5 Copynumber: 15.8 Consensus size: 5
1009756 CTTAATCCTT
*
1009766 TTTTC TTTT- TTCTTT TTTTC -TTT- TTTTC TTTT- TTTTC TTTTC TTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
1009813 TCCCTTT- TTTTC TTTTC TTTTC TTTT- TTTT
1 T---TTTC TTTTC TTTTC TTTTC TTTTC TTTT
1009843 TTCAAGCATA
Statistics
Matches: 62, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
4 19 0.31
5 37 0.60
6 2 0.03
7 1 0.02
8 3 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:1009782 original size:8 final size:8
Alignment explanation
Indices: 1009764--1009841 Score: 81
Period size: 8 Copynumber: 9.8 Consensus size: 8
1009754 ACCTTAATCC
1009764 TTTTTTC-
1 TTTTTTCT
1009771 TTTTTTCT
1 TTTTTTCT
1009779 TTTTTTCT
1 TTTTTTCT
1009787 TTTTTTC-
1 TTTTTTCT
1009794 TTTTTT-T
1 TTTTTTCT
*
1009801 TCTTTTCT
1 TTTTTTCT
**
1009809 TTTCTCCCT
1 TTT-TTTCT
1009818 TTTTTTCTT
1 TTTTTTC-T
1009827 TTCTTTTCT
1 TT-TTTTCT
1009836 TTTTTT
1 TTTTTT
1009842 TTTCAAGCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
7 18 0.31
8 24 0.41
9 12 0.20
10 5 0.08
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1009788 original size:22 final size:22
Alignment explanation
Indices: 1009763--1009844 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 22
1009753 CACCTTAATC
1009763 CTTTTTTCTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTCTTTTTTT
*
1009785 CTTTTTTTCTTTTTT-TTCTTTT
1 C-TTTTTTCTTTTTTCTTTTTTT
*
1009807 CTTTTCTCCCTTTTTTTCTTTTCTTTT
1 CTTTT-T-TC-TTTTTTC-TTT-TTTT
1009834 CTTTTTT-TTTT
1 CTTTTTTCTTTT
1009845 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
21 4 0.08
22 9 0.18
23 18 0.37
24 6 0.12
26 3 0.06
27 9 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
CTTTTTTCTTTTTTCTTTTTTT
Found at i:1021160 original size:23 final size:24
Alignment explanation
Indices: 1021124--1021168 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
1021114 TTCGATATTG
1021124 AAAAATATTAAAATAATTTATTTTA
1 AAAAATATTAAAATAA-TTATTTTA
*
1021149 AAAAATA-T-AAATTATTATTT
1 AAAAATATTAAAATAATTATTT
1021169 CATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 1 0.05
25 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAAATATTAAAATAATTATTTTA
Found at i:1022616 original size:15 final size:17
Alignment explanation
Indices: 1022604--1022681 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 17
1022594 ATTATTTATT
1022604 TAATATATATTTAATAA
1 TAATATATATTTAATAA
1022621 TAATATATA--TAATAA
1 TAATATATATTTAATAA
*
1022636 T-ATA-ATA-ATAATAA
1 TAATATATATTTAATAA
*
1022650 TAATA-ATA-CTAATAA
1 TAATATATATTTAATAA
*
1022665 TAATA-ATA-ATAATAA
1 TAATATATATTTAATAA
1022680 TA
1 TA
1022682 TGGATAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
13 3 0.05
14 10 0.18
15 35 0.61
17 9 0.16
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATATATTTAATAA
Found at i:1022623 original size:3 final size:3
Alignment explanation
Indices: 1022615--1022681 Score: 102
Period size: 3 Copynumber: 22.7 Consensus size: 3
1022605 AATATATATT
*
1022615 TAA TAA TAA T-A TATA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAC
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1022659 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1022682 TGGATAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1022959 original size:26 final size:26
Alignment explanation
Indices: 1022923--1022972 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1022913 AATTACCCTG
*
1022923 TTTCTTAACACCCAAAGTTCTGATTC
1 TTTCTTAACACCCAAAATTCTGATTC
1022949 TTTCTTAACACCCAAAATTCTGAT
1 TTTCTTAACACCCAAAATTCTGAT
1022973 CCTTCCCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (26 bp):
TTTCTTAACACCCAAAATTCTGATTC
Found at i:1026223 original size:35 final size:36
Alignment explanation
Indices: 1026148--1026241 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 36
1026138 TATTTACAGT
* **
1026148 TATCAGATGATTT-TCAGTTATCAGATGATTTACAGT
1 TATCAGATGATTTAT-AGTTATCAGATGAATTACAAA
*
1026184 TATCAGATGATTTATAGTTATCGGAT-AATTACAAA
1 TATCAGATGATTTATAGTTATCAGATGAATTACAAA
* *
1026219 TATCATAT-ATTTTACAGTTATCA
1 TATCAGATGA-TTTATAGTTATCA
1026242 TATACAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
34 1 0.02
35 24 0.49
36 23 0.47
37 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (36 bp):
TATCAGATGATTTATAGTTATCAGATGAATTACAAA
Found at i:1026245 original size:18 final size:18
Alignment explanation
Indices: 1026139--1026241 Score: 120
Period size: 18 Copynumber: 5.8 Consensus size: 18
1026129 AATTCTAAAT
1026139 ATTTACAGTTATCAGATG
1 ATTTACAGTTATCAGATG
*
1026157 ATTTTCAGTTATCAGATG
1 ATTTACAGTTATCAGATG
1026175 ATTTACAGTTATCAGATG
1 ATTTACAGTTATCAGATG
* *
1026193 ATTTATAGTTATCGGAT-
1 ATTTACAGTTATCAGATG
* ** *
1026210 AATTACAAATATCATAT-
1 ATTTACAGTTATCAGATG
1026227 ATTTTACAGTTATCA
1 A-TTTACAGTTATCA
1026242 TATACAAATT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
17 12 0.17
18 59 0.83
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (18 bp):
ATTTACAGTTATCAGATG
Found at i:1028501 original size:200 final size:199
Alignment explanation
Indices: 1028143--1028721 Score: 601
Period size: 200 Copynumber: 2.9 Consensus size: 199
1028133 CAACGAAAAC
* * * * * *
1028143 TTTCGAGTTTGATTCCATTCAGCTCGAGATTGCACCAACCACATGGTAGCAGCGAGAAACTACCT
1 TTTCGAGTTTGATTCCACTCAGCTCAAGAATGCATCGACTACATGGTAGCAGCGAG-AACTACCT
* * * * *
1028208 TTTGATCAAAATTTAAACCGATGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTACGATTTGGC
65 TATGATCAAAATTCAAACTGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTGCGATTTGGC
* ** *
1028273 AATAAGGAACCACTTTCCAGTCAAATTTTGACATAGCTTAAGGTGAGAAGAGTTATCTATCAACC
130 AACAAGGAACCACTTTCCAGTCAAATTTTGACATAGCTTAAGACGAGAAGAGCTATCTATCAACC
1028338 AAAGT
195 AAAGT
* * * *
1028343 TTTCAAGTTTGATTCCACTCAGCTCAAGAGTGCATCGACTGCATGGTAGCAGCGATGAACTATCT
1 TTTCGAGTTTGATTCCACTCAGCTCAAGAATGCATCGACTACATGGTAGCAGCGA-GAACTACCT
* * *
1028408 TATGGTCAAAAGTCAAACTGAGGTCTTTAAGCCAAGAAGAAGACCTAAGTTGACTGCGATTTGGC
65 TATGATCAAAATTCAAACTGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTGCGATTTGGC
* * * * *
1028473 AACAAGGAATCAC-TTCGCTA-TTAAATTTTGACATAGCTTAAGACGAGAATAGCTATCTGTCGA
130 AACAAGGAACCACTTTC-C-AGTCAAATTTTGACATAGCTTAAGACGAGAAGAGCTATCTATCAA
1028536 CCAAAGT
193 CCAAAGT
* * * * * * * * *
1028543 TTTTGAGTTCGATTCCACTCAACTCAA-AATCGCATTGACTATATAGTTA-TATCAAGGAACTAC
1 TTTCGAGTTTGATTCCACTCAGCTCAAGAAT-GCATCGACTACAT-GGTAGCAGCGA-GAACTAC
*** * * * * *
1028606 CTTCCAATCAAATTTCAAAATAAGGTCTTTAAACCAAGAAGAAGACATAGGTTGACTGCGATTTG
63 CTTATGATCAAAATTCAAACTGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTGCGATTTG
* ** * * *
1028671 GCAACAAGGAACCA-TCTCCTAACCAGATTTCGACATAGCTTAAGTCGAGAA
128 GCAACAAGGAACCACTTTCC-AGTCAAATTTTGACATAGCTTAAGACGAGAA
1028722 TCTATCGAGT
Statistics
Matches: 314, Mismatches: 58, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
199 8 0.03
200 301 0.96
201 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (199 bp):
TTTCGAGTTTGATTCCACTCAGCTCAAGAATGCATCGACTACATGGTAGCAGCGAGAACTACCTT
ATGATCAAAATTCAAACTGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTGCGATTTGGCA
ACAAGGAACCACTTTCCAGTCAAATTTTGACATAGCTTAAGACGAGAAGAGCTATCTATCAACCA
AAGT
Found at i:1029524 original size:42 final size:42
Alignment explanation
Indices: 1029466--1029555 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
1029456 TGGTTTATTT
*
1029466 TTAC-AGGTTCAATTTACAAGAACGATCCAGGAGAGTCCACA
1 TTACAAGGTTCAATTTACAAGAACAATCCAGGAGAGTCCACA
* *
1029507 TTACAAGGTTCAATTTACAAGACCAATCTAGGAGAGTCCACA
1 TTACAAGGTTCAATTTACAAGAACAATCCAGGAGAGTCCACA
1029549 TTACAAG
1 TTACAAG
1029556 CCCGATAGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (42 bp):
TTACAAGGTTCAATTTACAAGAACAATCCAGGAGAGTCCACA
Found at i:1030731 original size:16 final size:17
Alignment explanation
Indices: 1030700--1030732 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1030690 TTGAACCCCA
1030700 AATTTATTTTTATTTGT
1 AATTTATTTTTATTTGT
*
1030717 AATTTGTTTTT-TTTGT
1 AATTTATTTTTATTTGT
1030733 GTTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (17 bp):
AATTTATTTTTATTTGT
Found at i:1030968 original size:13 final size:13
Alignment explanation
Indices: 1030950--1030977 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1030940 CCTAACATGA
1030950 TTTTTATTTAAAT
1 TTTTTATTTAAAT
1030963 TTTTTATTTAAAT
1 TTTTTATTTAAAT
1030976 TT
1 TT
1030978 CTAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATTTAAAT
Found at i:1036180 original size:4 final size:4
Alignment explanation
Indices: 1036171--1036315 Score: 103
Period size: 4 Copynumber: 35.0 Consensus size: 4
1036161 ATTTTGAATA
* * * * *
1036171 ATTT ATTT ATTT CTTT AATA ATTT ATTT GTTT ATTT GTTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* ** * *
1036219 ATTT CAAATTT ATTT GTTT ATTT ATTT ATTT ATTT -TGA ATTT AGTT AGTT
1 ATTT ---ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * *
1036269 AGTT AGTT AGTT AGTT ATTT CGAATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ---ATTT ATTT ATTT ATTT ATTT ATTT
1036316 GAAGAGATAT
Statistics
Matches: 116, Mismatches: 18, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
3 1 0.01
4 107 0.92
7 8 0.07
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:1038444 original size:29 final size:29
Alignment explanation
Indices: 1038411--1038469 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1038401 AAAAAAAAAA
* *
1038411 TAGTTAGTCGAACTGCATTTTCCTTTTTT
1 TAGTTAATCGAACTCCATTTTCCTTTTTT
* * *
1038440 TAGTTAATCTAACTCCGTTTTCTTTTTTT
1 TAGTTAATCGAACTCCATTTTCCTTTTTT
1038469 T
1 T
1038470 TAATTAGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (29 bp):
TAGTTAATCGAACTCCATTTTCCTTTTTT
Found at i:1040586 original size:23 final size:23
Alignment explanation
Indices: 1040553--1040613 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1040543 CTCGTATAAA
1040553 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* * *
1040576 TGTACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
1040599 TGCACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
1040614 TATAAGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:1041322 original size:63 final size:66
Alignment explanation
Indices: 1041255--1041415 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 66
1041245 TCCCTTGACG
* *
1041255 GGTGCATCGATGCACTATC-TATGCATCGATACA-TAAAT-CCTATTCGATGTTTATA-TTT-AA
1 GGTGCATCGATGCACTATCATGTGCATCGATACACT-AATGAC-ATTCGATGTTTATATTTTAAA
1041315 GGA
64 GGA
* * **
1041318 GGTGCATCGATGCACTA-CTTGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAATT
1 GGTGCATCGATGCACTATCATGTGCATCGATACACTAATGACATTCGATGTTTATATTTTAAAGG
1041382 A
66 A
1041383 -GTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGTGCATCGATGCACTATCATGTGCATCGATACAC
1041416 CTTGAACAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
62 1 0.01
63 46 0.53
64 36 0.42
65 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (66 bp):
GGTGCATCGATGCACTATCATGTGCATCGATACACTAATGACATTCGATGTTTATATTTTAAAGG
A
Found at i:1041948 original size:13 final size:13
Alignment explanation
Indices: 1041930--1041955 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1041920 CTTCACGGTG
1041930 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
1041943 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
1041956 GAAATCTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:1047535 original size:23 final size:23
Alignment explanation
Indices: 1047517--1047577 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1047507 TTCGTATAAA
1047517 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1047540 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1047563 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1047578 TATAAGATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1052413 original size:49 final size:49
Alignment explanation
Indices: 1052336--1052518 Score: 213
Period size: 49 Copynumber: 3.7 Consensus size: 49
1052326 GTTGTCATAA
* * * * *
1052336 TAAATGTATAATGGTGCATTTCGACATAAAATGTACCATTAATGACAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCATTAATGAAAGT
** *
1052385 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGTCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCATTAATGAAAGT
* * * *
1052434 TAAAATGCATAACGGTGTATTTCGGCACAAAAGGTTCCATTAATGATAGT
1 T-AAATGCATAACGGTGCATTTCGGCATAAAAGGTACCATTAATGAAAGT
** *
1052484 TAAATGCATAACGGTATATTTTCGGCATGAAAGGT
1 TAAATGCATAACGGTGCA-TTTCGGCATAAAAGGT
1052519 GCCACTTATG
Statistics
Matches: 115, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
49 58 0.50
50 57 0.50
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCATTAATGAAAGT
Found at i:1052456 original size:50 final size:49
Alignment explanation
Indices: 1052336--1052524 Score: 216
Period size: 50 Copynumber: 3.8 Consensus size: 49
1052326 GTTGTCATAA
* * * * * * *
1052336 TAAATGTATAATGGTGCATTTCGACATAAAATGTACCATTAATGACAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
*
1052385 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGTCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
* * * * *
1052434 TAAAATGCATAACGGTGTATTTCGGCACAAAAGGTTCCATTAATGATAGT
1 T-AAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
** *
1052484 TAAATGCATAACGGTATATTTTCGGCATGAAAGGTGCCACT
1 TAAATGCATAACGGTGCA-TTTCGGCATAAAAGGTGCCACT
1052525 TATGGTATTC
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
49 58 0.49
50 61 0.51
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
Found at i:1059139 original size:62 final size:62
Alignment explanation
Indices: 1059042--1059161 Score: 206
Period size: 62 Copynumber: 1.9 Consensus size: 62
1059032 GGTGTATTTT
*
1059042 GGCATAAAAGGTGACATTAATGATAGTTAAATGCATAACGGTGCATTTC-AGCATAAAAGGTC
1 GGCATAAAAGGTGACATTAATGAAAGTTAAATGCATAACGGTGCATTTCGA-CATAAAAGGTC
*
1059104 GGCATAAAAGGTGCCATTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
1 GGCATAAAAGGTGACATTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
1059162 TGTGACATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
62 54 0.98
63 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (62 bp):
GGCATAAAAGGTGACATTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTC
Found at i:1059171 original size:49 final size:50
Alignment explanation
Indices: 1059106--1059215 Score: 168
Period size: 49 Copynumber: 2.2 Consensus size: 50
1059096 AAAAGGTCGG
* *
1059106 CATAAAAGGTGCCATTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGA
1 CATAAAAGGTGACATTAATGAAAGTTAAATGAATAACGGTGCATTTTCGA
* * *
1059155 CATAAAATGTGACATTAATGATAGTTAAATGAATAACGGTGCATTTTCGG
1 CATAAAAGGTGACATTAATGAAAGTTAAATGAATAACGGTGCATTTTCGA
1059205 CATAAAAGGTG
1 CATAAAAGGTG
1059216 CCACTCGTGG
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
49 39 0.72
50 15 0.28
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (50 bp):
CATAAAAGGTGACATTAATGAAAGTTAAATGAATAACGGTGCATTTTCGA
Found at i:1062663 original size:64 final size:65
Alignment explanation
Indices: 1062567--1062728 Score: 186
Period size: 65 Copynumber: 2.5 Consensus size: 65
1062557 GGTGCACTAA
* *
1062567 AAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCATAGTGCATCGATGCATGG
1 AAGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA-AGCCATAGTGCATCGATGCATGG
1062630 CT
65 -T
* * * * * *
1062632 -GGTGCATCGATGTATCAAATGTATTCAATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGT
1 AAGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAAGCCATAGTGCATCGATGCATGGT
* * *
1062696 AAGTGCATCGATGCATGAAATACATTCGATGTT
1 AAGTGCATCGATGCATCAAATGCATTCAATGTT
1062729 CAATTTAATT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
64 26 0.32
65 51 0.64
66 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
AAGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAAGCCATAGTGCATCGATGCATGGT
Found at i:1065419 original size:23 final size:22
Alignment explanation
Indices: 1065390--1065490 Score: 86
Period size: 23 Copynumber: 4.6 Consensus size: 22
1065380 ACATAACCCC
1065390 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1065412 CGTGCATCGATGCATCA-TC-ATG
1 -GTGCATCGATGCA-CATTCAAGG
* **
1065434 ATAAATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
1065457 GATGCATCGATGCACTATT-AA--
1 G-TGCATCGATGCAC-ATTCAAGG
1065478 GTGCATCGATGCA
1 GTGCATCGATGCA
1065491 TGAAGCACAG
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.22
21 13 0.20
22 2 0.03
23 19 0.30
24 13 0.20
25 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1065486 original size:44 final size:43
Alignment explanation
Indices: 1065390--1065490 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 43
1065380 ACATAACCCC
*
1065390 GTGCATCGATGCACATTCAAGGCGTGCATCGATGCATCATCAT
1 GTGCATCGATGCACATTCAAGGCGTGCATCGATGCATCATCAA
** *
1065433 GATAAATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTATTAA
1 G-TGCATCGATGCACATTC-AAGGCG-TGCATCGATGCATC-ATCAA
1065478 GTGCATCGATGCA
1 GTGCATCGATGCA
1065491 TGAAGCACAG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.02
44 27 0.56
45 20 0.42
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
GTGCATCGATGCACATTCAAGGCGTGCATCGATGCATCATCAA
Found at i:1071353 original size:65 final size:65
Alignment explanation
Indices: 1071219--1071379 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
1071209 GTGCACTAAG
* *
1071219 AGTGCACCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
* * ** * *
1071283 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGCATTGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAGAGTGCATCGATGCATGGC
1071346 T
65 T
*
1071347 AAGTGCATCGATGCATGAAATGCATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
1071380 CAATTTAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.33
65 53 0.63
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
Found at i:1079009 original size:43 final size:42
Alignment explanation
Indices: 1078957--1079156 Score: 220
Period size: 43 Copynumber: 4.7 Consensus size: 42
1078947 TGTGACCAAA
* *
1078957 AAACGCCGCAATAGGTCAAGATCTATCGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGAAC
* * ***
1079000 AAATGCCGCAAAAGGTCGATATCTATAGCGGCATTTTCAAAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGAAC
* *
1079043 AAACGCCGCAAAAGGTCGAGATCTATAGTGGCTTTTTTGGAGAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGA-AC
* * * * *
1079087 AAACGCCACAAAAAGTCAGATCTATAGCTGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGAAC
* *
1079129 AAACGCCGTAAAAAGTCAGATCTATAGC
1 AAACGCCGCAAAAGGTCAGATCTATAGC
1079157 TACGTTTTTT
Statistics
Matches: 133, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
42 28 0.21
43 88 0.66
44 17 0.13
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGAAC
Found at i:1079143 original size:42 final size:43
Alignment explanation
Indices: 1078957--1079179 Score: 213
Period size: 43 Copynumber: 5.2 Consensus size: 43
1078947 TGTGACCAAA
* * * * * *
1078957 AAACGCCGCAATAGGTCAAGATCTATCGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCTGCGTTTTTTGAAC
* * * * ***
1079000 AAATGCCGCAAAAGGTCGATATCTATAGCGGCATTTTCAAAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCTGCGTTTTTTGAAC
1079043 AAACGCCGCAAAAGGTCGAGATCTATAG-TG-GCTTTTTTGGAGAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCTGCG-TTTTTT-GA-AC
* *
1079087 AAACGCCACAAAAAGTC-AGATCTATAGCTGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCTGCGTTTTTTGAAC
* * *
1079129 AAACGCCGTAAAAAGTC-AGATCTATAGCTACGTTTTTT-ATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCTGCGTTTTTTGA-AC
1079171 AAACGCCGC
1 AAACGCCGC
1079180 GAATTAAAAC
Statistics
Matches: 153, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 52 0.34
43 74 0.48
44 25 0.16
45 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCTGCGTTTTTTGAAC
Found at i:1083071 original size:42 final size:42
Alignment explanation
Indices: 1083002--1083225 Score: 227
Period size: 42 Copynumber: 5.4 Consensus size: 42
1082992 TATCACACTA
* * * * *
1083002 CTTTAGCGGCATTTTTA-TACAAACGCCGCTAAATACTTGTT
1 CTTTAGCGGCGTTTTAAGAACAAACGCCGCTAAATACTCGTG
*
1083043 CTTTAGCGGCGTTTTAAGAACAAACGCCGCTAAATACTCCTG
1 CTTTAGCGGCGTTTTAAGAACAAACGCCGCTAAATACTCGTG
* * *
1083085 CTTTAGCAGCGTTTTAAGAACAAACACCGTTAAATACTCGTG
1 CTTTAGCGGCGTTTTAAGAACAAACGCCGCTAAATACTCGTG
* * * * *
1083127 CTTTAGCGGCGTGTTAA-ACACAAACACCGCTAAAGACTCTTA
1 CTTTAGCGGCGTTTTAAGA-ACAAACGCCGCTAAATACTCGTG
* * ** * *
1083169 CTTTAGTGGCGTTTTAAGCACAAACGTTGCTAAATACTCATA
1 CTTTAGCGGCGTTTTAAGAACAAACGCCGCTAAATACTCGTG
* *
1083211 CTTTTGTGGCGTTTT
1 CTTTAGCGGCGTTTT
1083226 TATATAATCA
Statistics
Matches: 155, Mismatches: 25, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
41 16 0.10
42 139 0.90
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTAAGAACAAACGCCGCTAAATACTCGTG
Found at i:1085491 original size:25 final size:24
Alignment explanation
Indices: 1085463--1085510 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1085453 AATTTATACT
* *
1085463 AACAGATGAGCTTATAATATTTTAG
1 AACA-ATGAACTTATAAAATTTTAG
*
1085488 AACAATGAATTTATAAAATTTTA
1 AACAATGAACTTATAAAATTTTA
1085511 TGAGACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (24 bp):
AACAATGAACTTATAAAATTTTAG
Found at i:1092749 original size:25 final size:25
Alignment explanation
Indices: 1092685--1092750 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
1092675 TTGCCCCGTC
*
1092685 CCCGAACCCGACCCAAAATATTATA
1 CCCGAACCCGACCCGAAATATTATA
1092710 CCCGAACCCGACCCGAAATATTATA
1 CCCGAACCCGACCCGAAATATTATA
1092735 CCCGAACCCGACCCGA
1 CCCGAACCCGACCCGA
1092751 TCCCGAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.35, C:0.41, G:0.12, T:0.12
Consensus pattern (25 bp):
CCCGAACCCGACCCGAAATATTATA
Found at i:1094235 original size:18 final size:18
Alignment explanation
Indices: 1094212--1094258 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1094202 TGTTTATGAG
*
1094212 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
*
1094230 GGAATTGGAATATGTCAA
1 GGAATTGGAATCTGTCAA
1094248 -GAATTGGAATC
1 GGAATTGGAATC
1094259 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:1094902 original size:190 final size:194
Alignment explanation
Indices: 1094650--1094997 Score: 528
Period size: 192 Copynumber: 1.8 Consensus size: 194
1094640 ATTTTTATTC
1094650 AATATATGAATTAGAAACCCAACCCGACACGACACAAAATAATAAAAAATATTTTTATTCAATAA
1 AATATATGAATTAGAAACCCAACCCGACAC-ACACAAAATAATAAAAAATATTTTTATTCAATAA
* * *
1094715 AAACATTGATTTAATTGAA-A-AAATATATAGAGAGGGGTATTATTGTAATTATTTCTAAATATA
65 AAACATTGACTTAATTGAATATAAATATATAGAGAGGGATATTATTGTAATTATTCCTAAATATA
* *
1094778 TAAGGTAAAATTATATATTTTTTTCGGGTTGGTCCGGTTTTTTCACCCTGAACCCGACCCAACCC
130 TAAAGTAAAATTATATA-TATTTTCGGGTTGGTCCGGTTTTTTCACCCTGAACCCGACCCAACCC
1094843 G
194 G
* * *
1094844 AATATATGAATTAGAAATCCGACCC-A-AC-C-CGAAATAATAAAAAAATATTTTTATTCAATAA
1 AATATATGAATTAGAAACCCAACCCGACACACACAAAATAAT-AAAAAATATTTTTATTCAATAA
* * *
1094905 AAACATTGACTTAATTGAATATATATATATATATAGGGATATTATTGTAATTATTCCTAAATATA
65 AAACATTGACTTAATTGAATATAAATATATAGAGAGGGATATTATTGTAATTATTCCTAAATATA
1094970 TAAAGTAAAATTATATATATTTTCGGGT
130 TAAAGTAAAATTATATATATTTTCGGGT
1094998 CGGGTATTTT
Statistics
Matches: 140, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
189 8 0.06
190 41 0.29
191 11 0.08
192 56 0.40
193 1 0.01
194 23 0.16
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (194 bp):
AATATATGAATTAGAAACCCAACCCGACACACACAAAATAATAAAAAATATTTTTATTCAATAAA
AACATTGACTTAATTGAATATAAATATATAGAGAGGGATATTATTGTAATTATTCCTAAATATAT
AAAGTAAAATTATATATATTTTCGGGTTGGTCCGGTTTTTTCACCCTGAACCCGACCCAACCCG
Found at i:1099948 original size:20 final size:21
Alignment explanation
Indices: 1099923--1099974 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1099913 TTTTCCCAAT
*
1099923 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1099943 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1099964 TCGCAATGCGA
1 TCGCAATGCGA
1099975 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1099988 original size:20 final size:20
Alignment explanation
Indices: 1099963--1100016 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1099953 AATTGGGAAA
1099963 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1099983 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
1100003 ATCGCAATGCGATA
1 ATCGCAATGCGATA
1100017 ATACAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1100621 original size:18 final size:19
Alignment explanation
Indices: 1100575--1100640 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
1100565 TTCGAGAATG
*
1100575 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAACA
**
1100595 ACTATCGCAACGCGAAA-A
1 AAAATCGCAACGCGAAACA
*
1100613 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACA
1100632 AAAATCGCA
1 AAAATCGCA
1100641 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
18 16 0.40
19 13 0.32
20 11 0.28
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:1100704 original size:29 final size:29
Alignment explanation
Indices: 1100643--1100724 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
1100633 AAATCGCATT
* *
1100643 GCGATTTTCATTTCGCGTTGCGATGCGTT
1 GCGATTGTCATTTCGCGTTGCGATGCGTC
*
1100672 GCGATTGTCGATTTCGCGTTGCGCTG-GTC
1 GCGATTGTC-ATTTCGCGTTGCGATGCGTC
*
1100701 GCGATAGTCATTTCGCGTTGCGAT
1 GCGATTGTCATTTCGCGTTGCGAT
1100725 TCTCTCGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
28 14 0.30
29 18 0.38
30 15 0.32
ACGTcount: A:0.11, C:0.22, G:0.30, T:0.37
Consensus pattern (29 bp):
GCGATTGTCATTTCGCGTTGCGATGCGTC
Found at i:1100722 original size:28 final size:29
Alignment explanation
Indices: 1100650--1100724 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
1100640 ATTGCGATTT
* *
1100650 TCATTTCGCGTTGCGATGCGTTGCGATTG
1 TCATTTCGCGTTGCGATGCGTCGCGATAG
*
1100679 TCGATTTCGCGTTGCGCTG-GTCGCGATAG
1 TC-ATTTCGCGTTGCGATGCGTCGCGATAG
1100708 TCATTTCGCGTTGCGAT
1 TCATTTCGCGTTGCGAT
1100725 TCTCTCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 14 0.34
29 12 0.29
30 15 0.37
ACGTcount: A:0.11, C:0.23, G:0.31, T:0.36
Consensus pattern (29 bp):
TCATTTCGCGTTGCGATGCGTCGCGATAG
Found at i:1100764 original size:20 final size:19
Alignment explanation
Indices: 1100727--1100787 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
1100717 GTTGCGATTC
**
1100727 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
1100746 TC-CGCATTGCGATTCTCATT
1 TCTCG--TTGCGATTCTCATT
*
1100766 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
1100786 TC
1 TC
1100788 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 2 0.06
22 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:1102849 original size:42 final size:42
Alignment explanation
Indices: 1102789--1102911 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
1102779 GCCCGACTCG
* * *
1102789 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
1102831 CCTATCATTCTTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1102873 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1102912 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1102869 original size:21 final size:21
Alignment explanation
Indices: 1102845--1102911 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1102835 TCATTCTTCG
1102845 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1102866 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1102887 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1102908 AGAG
1 AGAG
1102912 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1104288 original size:14 final size:14
Alignment explanation
Indices: 1104269--1104304 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1104259 ATTGTTTAAT
1104269 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1104283 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1104297 TGATTTGT
1 TGATTTGT
1104305 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1104505 original size:19 final size:19
Alignment explanation
Indices: 1104483--1104633 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1104473 CGAAATTAAA
1104483 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1104502 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1104517 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1104535 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
1104549 TTAGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1104568 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1104583 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
1104601 TTCGCATTGCGATTGTAAT
1 TTCGCGTTGCGATTTTCAT
1104620 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1104634 GGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 45 0.48
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1104529 original size:33 final size:32
Alignment explanation
Indices: 1104487--1104614 Score: 186
Period size: 33 Copynumber: 3.9 Consensus size: 32
1104477 ATTAAATTCG
1104487 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1104520 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1104553 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1104586 CGTTGCGATTTTCATTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
1104615 GTAATTTCCG
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1104576 original size:66 final size:66
Alignment explanation
Indices: 1104480--1104612 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1104470 ACGCGAAATT
* *
1104480 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1104545 G
66 G
*
1104546 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1104611 G
66 G
1104612 A
1 A
1104613 TTGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1106923 original size:12 final size:12
Alignment explanation
Indices: 1106906--1106930 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1106896 TCTTCGGGGA
1106906 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1106918 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1106930 C
1 C
1106931 AAGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1107138 original size:24 final size:24
Alignment explanation
Indices: 1107104--1107157 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1107094 CTGAAACATC
* * *
1107104 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTAACCAAG
*
1107128 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGGGTATTAACCAAG
1107152 ATCAAA
1 ATCAAA
1107158 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTAACCAAG
Found at i:1108126 original size:20 final size:20
Alignment explanation
Indices: 1108101--1108158 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1108091 AATCATTTGA
1108101 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1108121 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1108141 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1108159 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1108201 original size:33 final size:33
Alignment explanation
Indices: 1108164--1108234 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1108154 AAAATCGCAA
*
1108164 TGCGAAATGAAAATCGCATTGTGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1108197 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1108230 TGCGA
1 TGCGA
1108235 TAGCCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1108205 original size:14 final size:14
Alignment explanation
Indices: 1108186--1108235 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
1108176 ATCGCATTGT
1108186 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
1108200 GATTTTCATTTCGCATTGC
1 GATTTTC---TCG--TTGC
1108219 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
1108233 GAT
1 GAT
1108236 AGCCATTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.45
16 3 0.10
17 3 0.10
19 11 0.35
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
GATTTTCTCGTTGC
Found at i:1108235 original size:33 final size:33
Alignment explanation
Indices: 1108177--1108254 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
1108167 GAAATGAAAA
* ***
1108177 TCGCATTGTGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1108210 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
1108243 TCGCGTTGCGAT
1 TCGCATTGCGAT
1108255 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:1108361 original size:14 final size:14
Alignment explanation
Indices: 1108342--1108378 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1108332 CATCAATTAA
1108342 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1108356 ACAAATCATCTTTT
1 ACAAATCAACATTT
1108370 ACAAATCAA
1 ACAAATCAA
1108379 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1109191 original size:20 final size:20
Alignment explanation
Indices: 1109166--1109203 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1109156 AATAGTTTTT
1109166 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1109186 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1109204 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1109475 original size:22 final size:22
Alignment explanation
Indices: 1109448--1109491 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1109438 GATGGAGATA
1109448 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1109470 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1109492 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1109750 original size:21 final size:21
Alignment explanation
Indices: 1109717--1109836 Score: 63
Period size: 20 Copynumber: 5.9 Consensus size: 21
1109707 TGCGAAAGTA
* * *
1109717 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1109738 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
1109758 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
1109780 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
*
1109801 A-T-TCGCATTGCGATTTTCC
1 AGTATCGCATTGCGATTTTTC
* *
1109820 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
1109837 ACTTATTCGC
Statistics
Matches: 77, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 44 0.57
21 27 0.35
22 3 0.04
23 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1109765 original size:20 final size:20
Alignment explanation
Indices: 1109659--1109773 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
1109649 CGCTTTGAAA
*
1109659 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1109680 ATCGCGTTACGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1109700 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1109720 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1109741 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1109761 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1109774 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1109792 original size:41 final size:40
Alignment explanation
Indices: 1109701--1109834 Score: 135
Period size: 41 Copynumber: 3.3 Consensus size: 40
1109691 AAAGTCAGTA
* * * ** *
1109701 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
* *
1109741 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
* **
1109783 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCAAT
1109823 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1109835 TTACTTATTC
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 20 0.26
41 56 0.72
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:1109806 original size:20 final size:20
Alignment explanation
Indices: 1109781--1109846 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1109771 GATTTTCCCA
1109781 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
1109801 ATTCGCATTGCGATTTTCCA
1 ATTCGCGTTGCGATTTACTT
1109821 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
1109841 ATTCGC
1 ATTCGC
1109847 ATTGTGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:1109833 original size:40 final size:41
Alignment explanation
Indices: 1109762--1109850 Score: 171
Period size: 40 Copynumber: 2.2 Consensus size: 41
1109752 ATAGTCAGTA
1109762 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1109803 TCGCATTGCGATTTT-CCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1109843 TCGCATTG
1 TCGCATTG
1109851 TGAATTGGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 33 0.69
41 15 0.31
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1112329 original size:7 final size:7
Alignment explanation
Indices: 1112317--1112344 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1112307 CAAGAGGCTG
1112317 TAAATAT
1 TAAATAT
1112324 TAAATAT
1 TAAATAT
1112331 TAAATAT
1 TAAATAT
1112338 TAAATAT
1 TAAATAT
1112345 CAAAGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAAATAT
Found at i:1112918 original size:18 final size:18
Alignment explanation
Indices: 1112895--1112930 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1112885 GATAGACTCG
1112895 TCCATGACTTGGAATTCA
1 TCCATGACTTGGAATTCA
1112913 TCCATGACTTGGAATTCA
1 TCCATGACTTGGAATTCA
1112931 GACTCCAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
TCCATGACTTGGAATTCA
Found at i:1118284 original size:13 final size:14
Alignment explanation
Indices: 1118257--1118288 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1118247 TTTATGAAAT
1118257 ATAAA-GTAAATAA
1 ATAAATGTAAATAA
1118270 ATAAATGTAAA-AA
1 ATAAATGTAAATAA
1118283 ATAAAT
1 ATAAAT
1118289 TTTTACATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
ATAAATGTAAATAA
Found at i:1119414 original size:17 final size:18
Alignment explanation
Indices: 1119392--1119430 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1119382 GACGTCATCT
1119392 AAAATATT-TAAAAATAA
1 AAAATATTATAAAAATAA
1119409 AAAATATTATAAAAATAA
1 AAAATATTATAAAAATAA
1119427 AAAA
1 AAAA
1119431 GAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATTATAAAAATAA
Found at i:1119437 original size:17 final size:18
Alignment explanation
Indices: 1119400--1119439 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1119390 CTAAAATATT
* *
1119400 TAAAAATAAAAAATATTA
1 TAAAAATAAAAAAGATAA
1119418 TAAAAATAAAAAAGA-AA
1 TAAAAATAAAAAAGATAA
1119435 TAAAA
1 TAAAA
1119440 TTTTGAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAATAAAAAAGATAA
Found at i:1127028 original size:31 final size:31
Alignment explanation
Indices: 1126967--1127049 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
1126957 CCATAATTAT
* *
1126967 AAAATAGTCAATATATTTTATCCAACTGTTAC
1 AAAATAGTCAATA-AATTTATCAAACTGTTAC
* * *
1126999 AAAATAGTCATTAAATTTATCAAAGTGTTAT
1 AAAATAGTCAATAAATTTATCAAACTGTTAC
* *
1127030 GAAATAGTCACTAAATTTAT
1 AAAATAGTCAATAAATTTAT
1127050 TAATATTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 32 0.73
32 12 0.27
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
AAAATAGTCAATAAATTTATCAAACTGTTAC
Found at i:1127655 original size:16 final size:16
Alignment explanation
Indices: 1127634--1127690 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
1127624 ATTTTATATT
1127634 AAAAATATAAATATAA
1 AAAAATATAAATATAA
* * *
1127650 AAAAATTTAAAGATAT
1 AAAAATATAAATATAA
*
1127666 AAAAATAAATAAT-TAA
1 AAAAATATA-AATATAA
1127682 TAAAAATAT
1 -AAAAATAT
1127691 GTAAAAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
16 22 0.71
17 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAATATAAATATAA
Found at i:1128326 original size:164 final size:163
Alignment explanation
Indices: 1128055--1128357 Score: 432
Period size: 164 Copynumber: 1.9 Consensus size: 163
1128045 AATAATATAA
**
1128055 TTTAGTGGTGTTTTTATACAAACGACGCTAAAGGTCATACTTTAGTGGCGTTTTAAGCACAAACG
1 TTTAGTGGTGTTTTTATACAAACGACGCTAAAGGTCATACTTTAGTGGCGTTGCAAGCACAAACG
* * *
1128120 CCACTAATTAGACGCTCTTTAGTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACTCTAGT
66 CCACTAATTACACGCTCTTTAGTGGCATTTTACGCACAAACGCCGCT-ATTACACGTACTCTAGT
*
1128185 TGCATTTTTATATAAACGTCGAGAAATACTGTAC
130 GGCATTTTTATATAAACGTCGAGAAATACTGTAC
*
1128219 TTTAGTGGTGTTTTTATACAAACG-CTGCTAACGGTCATACTTTAGTGGC-TTGGCAAGCACAAA
1 TTTAGTGGTGTTTTTATACAAACGAC-GCTAAAGGTCATACTTTAGTGGCGTT-GCAAGCACAAA
* * * ** *
1128282 CGCCGCTAATTACACG-TATTTTTGTGTTATTTTACGCACAAACGCCGCTATTACACGTACTTTA
64 CGCCACTAATTACACGCT-CTTTAGTGGCATTTTACGCACAAACGCCGCTATTACACGTACTCTA
1128346 GTGGCATTTTTA
128 GTGGCATTTTTA
1128358 AAAAACGCCG
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
163 29 0.24
164 94 0.76
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (163 bp):
TTTAGTGGTGTTTTTATACAAACGACGCTAAAGGTCATACTTTAGTGGCGTTGCAAGCACAAACG
CCACTAATTACACGCTCTTTAGTGGCATTTTACGCACAAACGCCGCTATTACACGTACTCTAGTG
GCATTTTTATATAAACGTCGAGAAATACTGTAC
Found at i:1128357 original size:42 final size:41
Alignment explanation
Indices: 1128092--1128371 Score: 168
Period size: 42 Copynumber: 6.8 Consensus size: 41
1128082 CTAAAGGTCA
* * *
1128092 TACTTTAGTGGCGTTTTAAGCACAAACGCCACTAATTAGACG
1 TACTTTAGTGGC-TTTTTAGCACAAACGCCGCTAATTACACG
*
1128134 CT-CTTTAGTGGCGTTTTATGCACAAACGCCGCTAATTACACG
1 -TACTTTAGTGGCTTTTTA-GCACAAACGCCGCTAATTACACG
* * * * * ** * *
1128176 TACTCTAGTTGCATTTTTA-TATAAACGTCGAGAAATAC-TG
1 TACTTTAGTGGC-TTTTTAGCACAAACGCCGCTAATTACACG
* * * *
1128216 TACTTTAGTGGTGTTTTTA-TACAAACGCTGCTAACGGT-CA--
1 TACTTTAGTGG-CTTTTTAGCACAAACGCCGCTAA--TTACACG
***
1128256 TACTTTAGTGGCTTGGCAAGCACAAACGCCGCTAATTACACG
1 TACTTTAGTGGCTT-TTTAGCACAAACGCCGCTAATTACACG
* * *
1128298 TATTTTTGT-GTTATTTTACGCACAAACGCCGCT-ATTACACG
1 TACTTTAGTGGCT-TTTTA-GCACAAACGCCGCTAATTACACG
*
1128339 TACTTTAGTGGCATTTTTA--AAAAACGCCGCTAA
1 TACTTTAGTGGC-TTTTTAGCACAAACGCCGCTAA
1128372 AGGTCATCTT
Statistics
Matches: 180, Mismatches: 40, Indels: 37
0.70 0.16 0.14
Matches are distributed among these distances:
39 14 0.08
40 41 0.23
41 50 0.28
42 68 0.38
43 7 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
TACTTTAGTGGCTTTTTAGCACAAACGCCGCTAATTACACG
Found at i:1138086 original size:43 final size:42
Alignment explanation
Indices: 1137914--1138109 Score: 137
Period size: 43 Copynumber: 4.6 Consensus size: 42
1137904 ATACAAACAC
* * * *
1137914 CGCTAAATCTGAAAACCTAGTGCGACGTTTGTGGGAAAA-AT
1 CGCTAAATCTCAACACCTACTGCGACGTTTGTGGGAAAACGT
* * ** * *
1137955 ACCGCTAAA-CATCATCACATTTTGCGACGTTTGTGGGAAAAATGC
1 --CGCTAAATC-TCAACACCTACTGCGACGTTTGTGGG-AAAACGT
* * * * * * * *
1138000 CGCAAAATATCAAAACCTTCTACGGCGTTTGTAAGTAAAACGT
1 CGCTAAATCTCAACACCTACTGCGACGTTTGT-GGGAAAACGT
1138043 CGCTAAATCTCAACACCTACTGCGACGTTTGTAGGGAAAACGT
1 CGCTAAATCTCAACACCTACTGCGACGTTTGT-GGGAAAACGT
*
1138086 CGCTAAA-CATCAACACCTATTGCG
1 CGCTAAATC-TCAACACCTACTGCG
1138110 GCATTTTTTT
Statistics
Matches: 118, Mismatches: 29, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
42 2 0.02
43 111 0.94
44 5 0.04
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (42 bp):
CGCTAAATCTCAACACCTACTGCGACGTTTGTGGGAAAACGT
Done.