Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007037.1 Hibiscus syriacus cultivar Beakdansim tig00018240_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: 194960
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4824 original size:50 final size:51
Alignment explanation
Indices: 4747--4875 Score: 161
Period size: 52 Copynumber: 2.5 Consensus size: 51
4737 CCCTACGTGG
* * * * * **
4747 CGTATAGCGCGTTGCAGGGGCCACGCTATA-CCCACGTGGCGCTAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCACCAAATCAC
*
4797 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCCACGTGGCACCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCCACGTGGCACCAAATCAC
*
4849 CGTATAGCGCGGTGTAGGGGGCGCGCT
1 CGTATAGCGCGGTGCAGGGGGCGCGCT
4876 TTACTGCTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 27 0.40
52 41 0.60
ACGTcount: A:0.18, C:0.31, G:0.34, T:0.17
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCACCAAATCAC
Found at i:5185 original size:3 final size:3
Alignment explanation
Indices: 5177--5275 Score: 141
Period size: 3 Copynumber: 33.3 Consensus size: 3
5167 GTACATTTGT
5177 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
5223 ATA ATA ATA ATA ATA ATTA ATA ATA ATA ATA A-A CAAA ATA ATA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
*
5269 GTA ATA A
1 ATA ATA A
5276 ATTAAAATAG
Statistics
Matches: 88, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
2 5 0.06
3 79 0.90
4 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7494 original size:31 final size:33
Alignment explanation
Indices: 7453--7522 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
7443 AAAATAGTTG
*
7453 TTATATTTTATATTAATAT-A-ATTATATAAATA
1 TTAT-TTTTATATTAAAATAATATTATATAAATA
*
7485 TTATTTTTATATTAAAATAATATTATATAATTA
1 TTATTTTTATATTAAAATAATATTATATAAATA
7518 TTATT
1 TTATT
7523 AATTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 13 0.38
32 5 0.15
33 16 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTATTTTTATATTAAAATAATATTATATAAATA
Found at i:7699 original size:22 final size:22
Alignment explanation
Indices: 7662--7717 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
7652 TTTTTTATAA
* * *
7662 TTAATGTTAATATTTATTATTATT
1 TTAAT-TTAAT-TTTATCATGAAT
7686 TTAATTTAATTTTATCATGAAT
1 TTAATTTAATTTTATCATGAAT
7708 TTAA-TTAATT
1 TTAATTTAATT
7718 ATACATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 13 0.45
23 5 0.17
24 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
TTAATTTAATTTTATCATGAAT
Found at i:9964 original size:34 final size:34
Alignment explanation
Indices: 9916--9984 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
9906 ATGTTTTTAT
*
9916 AATACAAATTATAGTATTCAAAATTTAACATTAA
1 AATACAAATTATAGTATTCAAAAATTAACATTAA
*
9950 AATATAAATTATAGTATTCAAAAATTAACATTAA
1 AATACAAATTATAGTATTCAAAAATTAACATTAA
9984 A
1 A
9985 TTCAACTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (34 bp):
AATACAAATTATAGTATTCAAAAATTAACATTAA
Found at i:10618 original size:61 final size:61
Alignment explanation
Indices: 10537--10657 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
10527 TAGGTACTGA
** * * *
10537 CATGAATAGTACCCTGGGGGACATGAGTGACATAATATAGAAATGATAACATATTCTCTGT
1 CATGAATAGTACCCCCGGGGACATGACTCACATAATAGAGAAATGATAACATATTCTCTGT
* * *
10598 CATGAATAGTGCCCCCGGGGACATGACTCACATAATAGGGCAATGATAACATATTCTCTG
1 CATGAATAGTACCCCCGGGGACATGACTCACATAATAGAGAAATGATAACATATTCTCTG
10658 ACATAACAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (61 bp):
CATGAATAGTACCCCCGGGGACATGACTCACATAATAGAGAAATGATAACATATTCTCTGT
Found at i:10890 original size:143 final size:141
Alignment explanation
Indices: 10602--10957 Score: 523
Period size: 143 Copynumber: 2.5 Consensus size: 141
10592 CTCTGTCATG
* * * *
10602 AATAGTGCCCCCGGGGACATGACTCACATAATAGGGCAATGATAACATATTCTCTGACATAACAA
1 AATAGTGCCCCCGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
* * * * * * *
10667 TCGAAGGCGCCTCCCCCCCGGGAACGCGCTTTCACCACTTTGCTAAGTCTCCTCAAACATAATAA
66 TGGAAGGCCCCCCCCCCCCGAGAACGCGCTTTCACCACTTTACCAAGTCCCCTCAAACATAATAA
*
10732 GTACTGACATG
131 GTACTGACATC
*
10743 AATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATA
1 AATAGTGCCCCCG-GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATA
* *
10808 ATGGAAGGCCCCCCCCCCCCCGAGAATGTGCTTTCACCACTTTACCAAGTCCCCTCAAACATAAT
65 ATGGAAGG-CCCCCCCCCCCCGAGAACGCGCTTTCACCACTTTACCAAGTCCCCTCAAACATAAT
*
10873 AAGTATTGACATC
129 AAGTACTGACATC
* *
10886 AATAGTGCCACCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATA
1 AATAGTGCC-CCCGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATA
10951 ATGGAAG
65 ATGGAAG
10958 ACGCGCCCCC
Statistics
Matches: 193, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
141 13 0.07
142 53 0.27
143 124 0.64
144 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (141 bp):
AATAGTGCCCCCGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
TGGAAGGCCCCCCCCCCCCGAGAACGCGCTTTCACCACTTTACCAAGTCCCCTCAAACATAATAA
GTACTGACATC
Found at i:14538 original size:60 final size:60
Alignment explanation
Indices: 14446--14558 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
14436 AAAAATACTA
* * *
14446 GCGTGGCATCCGACTAAGCAAAACCCAGGTAAAGCGCGT-CCCGGGGATGCGCCTTATAC
1 GCGTGGCATCCCAATAAGCAAAACCCAGGTAAAGCGCATCCCCGGGGATGCGCCTTATAC
* *
14505 GCGTGGCATCCCAATCAGCTAATACCCAGGTAAAGCGCATCCCCGGGGATGCGC
1 GCGTGGCATCCCAATAAGC-AAAACCCAGGTAAAGCGCATCCCCGGGGATGCGC
14559 TTTTGTGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 16 0.34
60 18 0.38
61 13 0.28
ACGTcount: A:0.25, C:0.32, G:0.28, T:0.15
Consensus pattern (60 bp):
GCGTGGCATCCCAATAAGCAAAACCCAGGTAAAGCGCATCCCCGGGGATGCGCCTTATAC
Found at i:15377 original size:18 final size:19
Alignment explanation
Indices: 15354--15396 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
15344 CAGTAATCCT
15354 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
15372 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
15392 ATTCC
1 ATTCC
15397 GTGAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:15384 original size:20 final size:20
Alignment explanation
Indices: 15359--15396 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15349 ATCCTATTCC
15359 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
15379 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
15397 GTGAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:20055 original size:24 final size:23
Alignment explanation
Indices: 20018--20069 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
20008 TTCGGGACAT
*
20018 TTCTACGAGACACTTCGGTGCATA
1 TTCTACGAGACACTTCGGTG-AAA
* * *
20042 TTCTACGCGGCACTTTGGTGAAA
1 TTCTACGAGACACTTCGGTGAAA
20065 TTCTA
1 TTCTA
20070 TGTGGCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTACGAGACACTTCGGTGAAA
Found at i:22513 original size:21 final size:21
Alignment explanation
Indices: 22467--22515 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
22457 TACTGAAGTG
* *
22467 CCACATAATTGTCTCGGAGGA
1 CCACATAATTGTCCCGAAGGA
*
22488 CCACATAATTGTCCCGAATGA
1 CCACATAATTGTCCCGAAGGA
*
22509 TCACATA
1 CCACATA
22516 GACCCTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:28119 original size:21 final size:21
Alignment explanation
Indices: 28093--28140 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
28083 CACCAAAGTG
*
28093 CCACATAATTGTCCCGGAGGA
1 CCACATAATTGTCCCGAAGGA
28114 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
28135 TCACAT
1 CCACAT
28141 GGACCCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:28980 original size:55 final size:55
Alignment explanation
Indices: 28916--29048 Score: 155
Period size: 55 Copynumber: 2.4 Consensus size: 55
28906 GCATTCGAAA
*
28916 TTTTAAGGGTATCGATACACTCAT-AGGTGTACTGATACACA-A-GTAGTACTCGATG
1 TTTTAAGGGTATCGATACACTCATCA-GTGTACTGATACACATATG-A-CACTCGATG
* * * *
28971 TTTTGAGGGTATTGATACTCTCCTCAGTGTACTGATACACATATGACACTCGATG
1 TTTTAAGGGTATCGATACACTCATCAGTGTACTGATACACATATGACACTCGATG
*
29026 TTTTCAAGGGTATCAATACACTC
1 TTTT-AAGGGTATCGATACACTC
29049 TCAACAGGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 47 0.72
56 17 0.26
57 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (55 bp):
TTTTAAGGGTATCGATACACTCATCAGTGTACTGATACACATATGACACTCGATG
Found at i:30439 original size:54 final size:54
Alignment explanation
Indices: 30371--30867 Score: 584
Period size: 54 Copynumber: 9.2 Consensus size: 54
30361 TTGATTGGAC
* *
30371 CACTTAATGTCGATACGGTCGTTCATCAACATATGATGAATTTCATGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* * * *
30425 CACTTAATACCGATACGGTTGTTCATTAACATATGATGATTTTCGTGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* * *
30479 CACTTAATGTCGATATGGTCGTTCATCAACAAATGATGAATTTCGTGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* *
30533 CACTTAATGTCAATACGGTCGTTCATCAACATATGATGAA-TTCTGTGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGTTGCA
* * *
30587 CACTTAATGCCTATACGGTCGTTCATCAACATACGATGAATTACGTGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* **
30641 CACTTAGTGCTTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* * * *** * * *
30695 AACATAGTGCCGATACAACCATTCATCAACATATGATGAATTCCATGGGTTGCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* ** * * * * *
30749 CACTTAGTGCATATACGATCGTTCATCAACATATGACGAATTACTTGGGTTTCA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
* * ** * * *
30803 CACTTAGTGCCTATATAGTCGTTCATTAACATATGATGAA-TTCTGTGGTTTGTA
1 CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGTTGCA
*
30857 CACTTAGTGCC
1 CACTTAATGCC
30868 TATAGTACAC
Statistics
Matches: 384, Mismatches: 56, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
53 5 0.01
54 377 0.98
55 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
CACTTAATGCCGATACGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCA
Found at i:34981 original size:54 final size:54
Alignment explanation
Indices: 34916--35250 Score: 456
Period size: 54 Copynumber: 6.2 Consensus size: 54
34906 TATTTGAGAG
* * * * *
34916 GCACACATAGTGTCGATACAGTCGTTCATAAACATATTATGAATTCTGTGGGTT
1 GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
*
34970 GCACACTTAGTGTCGATACGGTCGTTCATCAACATATGATGAATT-TCGTGGGTT
1 GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGTT
** * * *
35024 GTTCACTTAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTTGTGGGTT
1 GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
* * *
35078 GCACACTTAATGCCGATACGGTCGTTCATCAACTTATGATGAATTCCGTGGGTT
1 GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
* ** * * * *
35132 ACACACTTAGTGTTGATATGGTCGTTCATCAACATATAATGAATTCCGTAGGTT
1 GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
*
35186 GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
1 GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
35240 GCACACTTAGT
1 GCACACTTAGT
35251 TCCTATAGTA
Statistics
Matches: 246, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 244 0.99
55 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (54 bp):
GCACACTTAGTGCCGATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTT
Found at i:35131 original size:162 final size:162
Alignment explanation
Indices: 34929--35248 Score: 505
Period size: 162 Copynumber: 2.0 Consensus size: 162
34919 CACATAGTGT
* * *
34929 CGATACAGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCG
1 CGATACAGTCGTTCATAAACATATGATGAATTCCGTGGGTTACACACTTAGTGTCGATACGGTCG
* * * ** *
34994 TTCATCAACATATGATGAATTTCGTGGGTTGTTCACTTAGTGCCTATATGGTCGTTCATCAACAT
66 TTCATCAACATATAATGAATTCCGTAGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACAT
*
35059 ATGATGAATTTTGTGGGTTGCACACTTAATGC
131 ATGATGAATTCTGTGGGTTGCACACTTAATGC
* * * * *
35091 CGATACGGTCGTTCATCAACTTATGATGAATTCCGTGGGTTACACACTTAGTGTTGATATGGTCG
1 CGATACAGTCGTTCATAAACATATGATGAATTCCGTGGGTTACACACTTAGTGTCGATACGGTCG
35156 TTCATCAACATATAATGAATTCCGTAGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACAT
66 TTCATCAACATATAATGAATTCCGTAGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACAT
35221 ATGATGAATTCTGTGGGTTGCACACTTA
131 ATGATGAATTCTGTGGGTTGCACACTTA
35249 GTTCCTATAG
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
162 143 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (162 bp):
CGATACAGTCGTTCATAAACATATGATGAATTCCGTGGGTTACACACTTAGTGTCGATACGGTCG
TTCATCAACATATAATGAATTCCGTAGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACAT
ATGATGAATTCTGTGGGTTGCACACTTAATGC
Found at i:41003 original size:15 final size:15
Alignment explanation
Indices: 40983--41012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40973 ACATTAATAT
40983 TAAACAGAAAACAAA
1 TAAACAGAAAACAAA
*
40998 TAAACAGGAAACAAA
1 TAAACAGAAAACAAA
41013 ACCTACGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.10, T:0.07
Consensus pattern (15 bp):
TAAACAGAAAACAAA
Found at i:43843 original size:41 final size:41
Alignment explanation
Indices: 43785--43871 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
43775 GTTTTCTTCA
* *
43785 ATTTTCTTTGTTTGATAG-TTGAAAAATATTTTCCA-AAAAT
1 ATTTTATTTGTTTGATAGCTAG-AAAATATTTTCCATAAAAT
43825 ATTTTATTGTGTTTGATAGCTAGAAAATATTTTCCATAAAAT
1 ATTTTATT-TGTTTGATAGCTAGAAAATATTTTCCATAAAAT
*
43867 GTTTT
1 ATTTT
43872 CTATTATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 7 0.17
41 23 0.56
42 11 0.27
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (41 bp):
ATTTTATTTGTTTGATAGCTAGAAAATATTTTCCATAAAAT
Found at i:44041 original size:19 final size:19
Alignment explanation
Indices: 44019--44055 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44009 ATTTTATTCA
*
44019 TTTAATATTAATATAATAT
1 TTTAATATAAATATAATAT
*
44038 TTTAATATAAATTTAATA
1 TTTAATATAAATATAATA
44056 AAAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAATATAAATATAATAT
Found at i:44839 original size:5 final size:5
Alignment explanation
Indices: 44829--44853 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44819 ATTATTATCG
44829 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
44854 GAAAACAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:45489 original size:47 final size:46
Alignment explanation
Indices: 45401--45489 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
45391 TGACATTAAA
* * *
45401 AATAAAAAATAAATGTTAGTAGTTAGCTGTTAGTAGCGTTAGAAAT
1 AATAAAAAATAAAAGTTAGGAGTTAGCTGTTAGTAACGTTAGAAAT
*
45447 AATAATAAAATAAAAGTTAGGAGTTAGC-GATTAGTAATGTTAG
1 AATAA-AAAATAAAAGTTAGGAGTTAGCTG-TTAGTAACGTTAG
45490 CGTCTTAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 6 0.16
47 31 0.84
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.31
Consensus pattern (46 bp):
AATAAAAAATAAAAGTTAGGAGTTAGCTGTTAGTAACGTTAGAAAT
Found at i:50632 original size:13 final size:13
Alignment explanation
Indices: 50616--50640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50606 ATGAAAACGT
50616 AAAGATAAAACAA
1 AAAGATAAAACAA
50629 AAAGATAAAACA
1 AAAGATAAAACA
50641 CAGATAAAAT
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:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAGATAAAACAA
Found at i:54182 original size:19 final size:19
Alignment explanation
Indices: 54158--54203 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
54148 GGATAGATAG
54158 AAATAAAAAT-AAGGAAATA
1 AAATAAAAATAAAGG-AATA
54177 AAAT-AAAATAAAGGAATA
1 AAATAAAAATAAAGGAATA
*
54195 AAGTAAAAA
1 AAATAAAAA
54204 AAATATTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (19 bp):
AAATAAAAATAAAGGAATA
Found at i:54186 original size:18 final size:18
Alignment explanation
Indices: 54158--54202 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
54148 GGATAGATAG
54158 AAATAAAA-ATAAGGAAATA
1 AAATAAAATA-AAGG-AATA
54177 AAATAAAATAAAGGAATA
1 AAATAAAATAAAGGAATA
*
54195 AAGTAAAA
1 AAATAAAA
54203 AAAATATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 12 0.50
20 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAATAAAATAAAGGAATA
Found at i:54328 original size:8 final size:9
Alignment explanation
Indices: 54314--54352 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
54304 ATTATAAAGG
54314 AAAAAAAAT
1 AAAAAAAAT
54323 AAAAAAAAT
1 AAAAAAAAT
54332 AAATATGAAAAT
1 AAA-A--AAAAT
54344 AAAAAAAAT
1 AAAAAAAAT
54353 TCATTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 17 0.63
10 1 0.04
11 1 0.04
12 8 0.30
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:60289 original size:13 final size:13
Alignment explanation
Indices: 60260--60288 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
60250 AAATCAAATG
60260 AAAACAGAAAGAT
1 AAAACAGAAAGAT
60273 AAAACA-AAAGAT
1 AAAACAGAAAGAT
60285 AAAA
1 AAAA
60289 AATGAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAACAGAAAGAT
Found at i:60684 original size:17 final size:17
Alignment explanation
Indices: 60662--60697 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
60652 TATCTAAAAC
60662 CCATTGTTTACGTCGAT
1 CCATTGTTTACGTCGAT
60679 CCATTGTTTACGTCGAT
1 CCATTGTTTACGTCGAT
60696 CC
1 CC
60698 TCCTTAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (17 bp):
CCATTGTTTACGTCGAT
Found at i:62475 original size:80 final size:79
Alignment explanation
Indices: 62372--62598 Score: 242
Period size: 80 Copynumber: 2.8 Consensus size: 79
62362 AAAAATATTG
* * * * ** * *
62372 ATCCACCTCCTTCTGTGATGGAATCGAGCAGAGGTTGCCCAAGTTCTTATTATTATGAACTTATT
1 ATCCAACTCCTTTTATGATGGAATCGAGCA-AGGATGAACAAGTTCTTCTCATTATGAACTTATT
*
62437 CTCTTGGAAATGTTA
65 CTCTTGGAAATGCTA
* * *
62452 ATCCAACTCCTTTTATGATGGAATCGAGCCAAGGCTGAACAAGATCTTCTCATTATGAACTTCTT
1 ATCCAACTCCTTTTATGATGGAATCGAG-CAAGGATGAACAAGTTCTTCTCATTATGAACTTATT
*
62517 CTCTTGGAAATGCTG
65 CTCTTGGAAATGCTA
* * * *
62532 AT-CTA-TCACTTTCTATGATGAAATCGGGCAAAGGATGAACATGTTCTTCTCATTATGAACTTA
1 ATCCAACTC-CTTT-TATGATGGAATCGAGC-AAGGATGAACAAGTTCTTCTCATTATGAACTTA
62595 TTCT
63 TTCT
62599 TCCTCATCGG
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
78 2 0.02
79 7 0.06
80 113 0.91
81 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (79 bp):
ATCCAACTCCTTTTATGATGGAATCGAGCAAGGATGAACAAGTTCTTCTCATTATGAACTTATTC
TCTTGGAAATGCTA
Found at i:62591 original size:20 final size:20
Alignment explanation
Indices: 62566--62630 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
62556 CGGGCAAAGG
62566 ATGAACATGTTCTTCTCATT
1 ATGAACATGTTCTTCTCATT
* *
62586 ATGAACTTATTCTTCCTCA-T
1 ATGAACATGTTCTT-CTCATT
** *
62606 CGGAAGA-GTTCTTCTCATT
1 ATGAACATGTTCTTCTCATT
62625 ATGAAC
1 ATGAAC
62631 CCTTACTAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
18 4 0.12
19 9 0.27
20 16 0.48
21 4 0.12
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGAACATGTTCTTCTCATT
Found at i:67840 original size:17 final size:18
Alignment explanation
Indices: 67818--67856 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
67808 TTTAACACCG
* *
67818 TAAAAATT-CATATATTT
1 TAAAAATTGAATAAATTT
67835 TAAAAATTGAATAAATTT
1 TAAAAATTGAATAAATTT
67853 TAAA
1 TAAA
67857 TCAGGGTCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAAAATTGAATAAATTT
Found at i:70822 original size:15 final size:15
Alignment explanation
Indices: 70802--70836 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
70792 ACTATATCAT
70802 ATTTCTTGCATACTA
1 ATTTCTTGCATACTA
70817 ATTTCTTGCATACTA
1 ATTTCTTGCATACTA
70832 ATTTC
1 ATTTC
70837 CTATATTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (15 bp):
ATTTCTTGCATACTA
Found at i:72416 original size:11 final size:11
Alignment explanation
Indices: 72401--72446 Score: 74
Period size: 11 Copynumber: 4.2 Consensus size: 11
72391 TCTCCAGATT
* *
72401 TTTCCTTCTCT
1 TTTCCTTCCCC
72412 TTTCCTTCCCC
1 TTTCCTTCCCC
72423 TTTCCTTCCCC
1 TTTCCTTCCCC
72434 TTTCCTTCCCC
1 TTTCCTTCCCC
72445 TT
1 TT
72447 CTCCACGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTCCTTCCCC
Found at i:75161 original size:16 final size:18
Alignment explanation
Indices: 75140--75178 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
75130 AGCCTCTCTC
*
75140 TTTTAC-TTTTT-TTTTT
1 TTTTACATTTTTCTTTCT
75156 TTTTACATTTTTCTTTCT
1 TTTTACATTTTTCTTTCT
75174 TTTTA
1 TTTTA
75179 AACAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTACATTTTTCTTTCT
Found at i:76017 original size:69 final size:69
Alignment explanation
Indices: 75837--76162 Score: 280
Period size: 69 Copynumber: 4.7 Consensus size: 69
75827 TACGAATCAT
* * * * * * * **
75837 TCTAATCCTTTAGGGCTCACATACGAGACACCTGACA-AGATTATGATTAGGTACTCTCCCATAT
1 TCTAATCCTTTGGGGCTCCCTTGCGAGACACCCGACATA-ATTATGATTAGGT--GCTCCCGTGC
*
75901 GAGTCAC
63 AAGTCAC
* * * * *
75908 TTTAATCCTTT-GGGCT-CTTGTGCGATACACCCGACATAATTATGATTATGTGCTCTCGTGCAA
1 TCTAATCCTTTGGGGCTCCCT-TGCGAGACACCCGACATAATTATGATTAGGTGCTCCCGTGCAA
75971 GTCAC
65 GTCAC
* ** * *
75976 TCTAATCCTTTGGGGCTCCCTTGTGAGACACCTTACATAATTATGATTAGGTGCTCCCATGCGAG
1 TCTAATCCTTTGGGGCTCCCTTGCGAGACACCCGACATAATTATGATTAGGTGCTCCCGTGCAAG
* *
76041 TTAT
66 TCAC
* * * ** **
76045 TATAATCCTTTGGGGCTCCCATGCAAGACACCTAACATAATTATGATTAGGTGCTCCCGTGTTAG
1 TCTAATCCTTTGGGGCTCCCTTGCGAGACACCCGACATAATTATGATTAGGTGCTCCCGTGCAAG
76110 TCAC
66 TCAC
* *** * *
76114 CCTAATCCTTCAAGGCTCCCGTGCGAGACACCCGACATAATTGTGATTA
1 TCTAATCCTTTGGGGCTCCCTTGCGAGACACCCGACATAATTATGATTA
76163 AGTCATAAGG
Statistics
Matches: 205, Mismatches: 46, Indels: 10
0.79 0.18 0.04
Matches are distributed among these distances:
68 21 0.10
69 141 0.69
70 32 0.16
71 11 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (69 bp):
TCTAATCCTTTGGGGCTCCCTTGCGAGACACCCGACATAATTATGATTAGGTGCTCCCGTGCAAG
TCAC
Found at i:77288 original size:10 final size:10
Alignment explanation
Indices: 77269--77320 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
77259 ATTGTTCTTC
77269 TCTT-CTTTT
1 TCTTCCTTTT
77278 TCTTCCTTTT
1 TCTTCCTTTT
77288 TCTTCC-TTT
1 TCTTCCTTTT
*
77297 T-TTCTCATTT
1 TCTTC-CTTTT
*
77307 TCTTCTTTTT
1 TCTTCCTTTT
77317 TCTT
1 TCTT
77321 TTGGAGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 3 0.08
9 9 0.24
10 22 0.59
11 3 0.08
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (10 bp):
TCTTCCTTTT
Found at i:77291 original size:19 final size:19
Alignment explanation
Indices: 77269--77317 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
77259 ATTGTTCTTC
*
77269 TCTTCTTTTTCTTC-CTTTT
1 TCTTCTTTTT-TTCTCATTT
*
77288 TCTTCCTTTTTTCTCATTT
1 TCTTCTTTTTTTCTCATTT
77307 TCTTCTTTTTT
1 TCTTCTTTTTT
77318 CTTTTGGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (19 bp):
TCTTCTTTTTTTCTCATTT
Found at i:82805 original size:59 final size:59
Alignment explanation
Indices: 82738--83359 Score: 603
Period size: 59 Copynumber: 10.5 Consensus size: 59
82728 CAAATGGCAG
* * *
82738 TATATGTGCTAAAATGATAAGGAAATCATATTGAATGTATGAATTTCCATATGGAGCAC
1 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
*
82797 TA-AGTGTGCTAAAATGATAAGGAAATCATATTGAGTGTATGGATTTCCATATGGAGCAC
1 TATA-TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
* *
82856 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGTATTTCCATATGGAGAAC
1 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
82915 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
1 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
* *
82974 TATATGTGCTAAAATGATAATGAAATCATACTGAGTGTATGGTTTTCCATATGGAGCAC
1 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
* * * * * * *
83033 TGAGT-T-TGCTAAAATGATAAGGAAATCATATTGAATATATGGATATCTAGATAGG-GCAT
1 T-A-TATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAGCAC
* * * *** *
83092 TATATGTGCTAAAATGATAAGGGAATCATACTGAGTGTATAGATTTCCAGAAAAATCAC
1 TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
* * * * * *** *
83151 TA-AGGGTGCTACAAGGATAAGGAAATTATACTAACAATATGGATTTTCATATAGG-GCAC
1 TATA-TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAGCAC
* * * *
83210 T-TCATGTGCTAAAAATGGTAAAGG-GATCATACT-AATGGTATGGATTCTCGA-ATAGG-GCAC
1 TAT-ATGTGCT-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATT-TCCATAT-GGAGCAC
* * *
83270 T-TCATGTGCTAAAAATGGTAAAGG-AATCATACT-AATGGTATGGATTCTCGA-ATAGG-GCAC
1 TAT-ATGTGCT-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATT-TCCATAT-GGAGCAC
*
83330 T-TAATGTGCTAAAATGAGAAGGAAATCATA
1 TAT-ATGTGCTAAAATGATAAGGAAATCATA
83360 TTAAGTATAT
Statistics
Matches: 485, Mismatches: 61, Indels: 34
0.84 0.11 0.06
Matches are distributed among these distances:
57 1 0.00
58 8 0.02
59 366 0.75
60 103 0.21
61 7 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (59 bp):
TATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCAC
Found at i:83252 original size:60 final size:60
Alignment explanation
Indices: 83188--83343 Score: 269
Period size: 60 Copynumber: 2.6 Consensus size: 60
83178 ATACTAACAA
* *
83188 TATGGATTTTC-ATATAGGGCACTTCATGTGCTAAAAATGGTAAAGGGATCATACTAATGG
1 TATGGATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
83248 TATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
1 TATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
*
83308 TATGGATTCTCGAATAGGGCACTTAATGTGCTAAAA
1 TATGGATTCTCGAATAGGGCACTTCATGTGCTAAAA
83344 TGAGAAGGAA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (60 bp):
TATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGG
Found at i:83559 original size:44 final size:44
Alignment explanation
Indices: 83496--83847 Score: 634
Period size: 44 Copynumber: 8.0 Consensus size: 44
83486 TCAGTAATGC
83496 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
83540 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
83584 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
83628 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G
*
83673 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G
*
83718 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGATCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
83762 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGATTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
83806 AAATTA-GGTAAATATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
83848 AGATTAAATG
Statistics
Matches: 299, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
43 33 0.11
44 180 0.60
45 86 0.29
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:84802 original size:74 final size:73
Alignment explanation
Indices: 84703--84865 Score: 220
Period size: 74 Copynumber: 2.2 Consensus size: 73
84693 TACCTAGACC
* ** *
84703 AGGGAGTATCATACTCGGGCTTTGAGTATCGATATTGTACTAATAAAAACTA-TCCGTGTTTCGA
1 AGGGAGTATCATACTCGGGCTTTGAGTATCGATACTACACTAATAAAAACTAGT-CATGTTTCGA
*
84767 TTGTTGGAT
65 TCGTTGGAT
* * *
84776 CGGGAGTATCAGTACTCGGGCTTTGAGTATCGATACTACACTAATAAAAACTAGTCATTTTTTGA
1 AGGGAGTATCA-TACTCGGGCTTTGAGTATCGATACTACACTAATAAAAACTAGTCATGTTTCGA
84841 TCGTTGGAT
65 TCGTTGGAT
84850 AGGGAGTATCGATACT
1 AGGGAGTATC-ATACT
84866 ACTATACAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
73 10 0.13
74 66 0.85
75 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (73 bp):
AGGGAGTATCATACTCGGGCTTTGAGTATCGATACTACACTAATAAAAACTAGTCATGTTTCGAT
CGTTGGAT
Found at i:86344 original size:29 final size:29
Alignment explanation
Indices: 86310--86425 Score: 130
Period size: 30 Copynumber: 4.0 Consensus size: 29
86300 TTTATAAAAT
* *
86310 ATAATTCATTTTACGCAAAATTA-TTTCA
1 ATAATTCATTTTACGTAAAATTATTTTTA
* *
86338 AGTAATTCATTCTACGTAAAATAATTTTTA
1 A-TAATTCATTTTACGTAAAATTATTTTTA
86368 TATAATTCATTTTACGTAAAA-TAGTTTTTA
1 -ATAATTCATTTTACGTAAAATTA-TTTTTA
*
86398 ATTAATCCATTTTACGT-AAATTATTTTT
1 A-TAATTCATTTTACGTAAAATTATTTTT
86426 CAAGAAACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
28 1 0.01
29 29 0.39
30 44 0.59
31 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (29 bp):
ATAATTCATTTTACGTAAAATTATTTTTA
Found at i:86424 original size:59 final size:59
Alignment explanation
Indices: 86308--86425 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 59
86298 TTTTTATAAA
*
86308 ATATAATTCATTTTACGCAAAATTATTTCAAGTAATTCATTCTACGTAAAATAATTTTT
1 ATATAATTCATTTTACGCAAAATTATTTCAAGTAATCCATTCTACGTAAAATAATTTTT
* * * * *
86367 ATATAATTCATTTTACGTAAAA-TAGTTTTTAATTAATCCATTTTACGT-AAATTATTTTT
1 ATATAATTCATTTTACGCAAAATTA--TTTCAAGTAATCCATTCTACGTAAAATAATTTTT
86426 CAAGAAACCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
58 2 0.04
59 31 0.61
60 18 0.35
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (59 bp):
ATATAATTCATTTTACGCAAAATTATTTCAAGTAATCCATTCTACGTAAAATAATTTTT
Found at i:86837 original size:48 final size:49
Alignment explanation
Indices: 86760--86864 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 49
86750 TCACACTCCG
* * * *
86760 GTTTTCCTTCTCATTGCGATTAGGAGGGTTGGTTAGAGTCGATTATCGA
1 GTTTGCCTTCTCATTGCGATTAAGAGGGTTGGTTAGAGCCGATTATCAA
86809 GTTTGCCTTCTCA-TGCGATTAAGAGGGTTGGTTAGAGCCGATTATCAA
1 GTTTGCCTTCTCATTGCGATTAAGAGGGTTGGTTAGAGCCGATTATCAA
86857 GTTTGCCT
1 GTTTGCCT
86865 AGTCAATTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 40 0.77
49 12 0.23
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (49 bp):
GTTTGCCTTCTCATTGCGATTAAGAGGGTTGGTTAGAGCCGATTATCAA
Found at i:92117 original size:18 final size:18
Alignment explanation
Indices: 92094--92128 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
92084 AAGCCTACAA
92094 AAATAATAGA-AATAAAAT
1 AAATAATA-ATAATAAAAT
92112 AAATAATAATAATAAAA
1 AAATAATAATAATAAAA
92129 ACCCAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAATAATAATAAAAT
Found at i:92245 original size:25 final size:26
Alignment explanation
Indices: 92190--92251 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
92180 ATTATTAAAA
*
92190 TATTTAAAATATATTTATCAATAATT
1 TATTTAAAATATATATATCAATAATT
*
92216 T-TTTAAAATATA-ATAT-AATATTTT
1 TATTTAAAATATATATATCAATA-ATT
92240 TATTTAATAATA
1 TATTTAA-AATA
92252 CAATTTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 4 0.13
24 6 0.19
25 16 0.52
26 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTAAAATATATATATCAATAATT
Found at i:97337 original size:131 final size:129
Alignment explanation
Indices: 97157--97499 Score: 400
Period size: 131 Copynumber: 2.6 Consensus size: 129
97147 AAAATAATTT
* * * *
97157 TAATATTTCCAATCGAGAATAAATGATCTTTCATGCATTGAAACGGTCATTTATTACCCCAATTG
1 TAATATTTCCAATCGAGAATAAATGATCTCTCATGCCTT-AAACAGTCATTTATTACTCCAATTG
* * * * * * *
97222 AAAT-AAAGAGATATTACTATTTCGTCTTAAAATTCAATATCGATTCAAGTGAAAACGATAATAT
65 AAATGAAA-AGATATTACTATTCCATCTCAAAAATCAATATCAATTCAAGAGAAAACGAAAATAT
97286 C
129 C
** * * * *
97287 TAATGATTTCCAATCGAGAATAAATGGCCTCTCATACCTTAAAGCAGTCATTTAATACTCTAATC
1 TAAT-ATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAA-CAGTCATTTATTACTCCAATT
* * * * *
97352 GAAATGAAAAGATATCAATATTCCATCTCAAAAATCGATATTAATTCGAGAGAAAACGAAAATAT
64 GAAATGAAAAGATATTACTATTCCATCTCAAAAATCAATATCAATTCAAGAGAAAACGAAAATAT
97417 C
129 C
* * * *
97418 AAATTATTTCCAATTGAAAATAAATGATCTCTCATGCCTTAGACAGTCATTTATTACTCCAATTG
1 TAA-TATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAACAGTCATTTATTACTCCAATTG
97483 AAATGAAAAGATATTAC
65 AAATGAAAAGATATTAC
97500 CGTTCTCGTT
Statistics
Matches: 175, Mismatches: 34, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
130 41 0.23
131 130 0.74
132 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (129 bp):
TAATATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAACAGTCATTTATTACTCCAATTGA
AATGAAAAGATATTACTATTCCATCTCAAAAATCAATATCAATTCAAGAGAAAACGAAAATATC
Found at i:99558 original size:25 final size:25
Alignment explanation
Indices: 99529--99581 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
99519 GCATGTAGAA
*
99529 AATAAAATAAAAAATATTAATTAAT
1 AATAAAATAAAAAATATTAATAAAT
* * *
99554 AATAATATTAATAATATTAATAAAT
1 AATAAAATAAAAAATATTAATAAAT
99579 AAT
1 AAT
99582 TCAACGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAAAATAAAAAATATTAATAAAT
Found at i:99946 original size:134 final size:134
Alignment explanation
Indices: 99717--100103 Score: 553
Period size: 134 Copynumber: 2.9 Consensus size: 134
99707 ATCGGTTCCG
* * ** * *
99717 CTTCTTCTTGAGGGAAAATCAAATTTGGAAATGTTGACTCATTCCACTGTCACTCAGGGAAGATT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
* * *
99782 GGATCGAGGCAGACTTGTTC-CACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTG
66 GAATCGAGGCAGACTTGTTCTGA-TGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATG
99846 ATCCA
130 ATCCA
* * *
99851 CTTCTTCTTGAGGGAAAATTAGATCTGGGGACGTTGATTCATTCCATTGTCACT-ATGGGAAGAT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCA-GGGAAGAT
* * *
99915 TGAATCGAGGCATACTTGTTCTGGTGCTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATG
65 TGAATCGAGGCAGACTTGTTCTGATGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATG
* *
99980 TTTCA
130 ATCCA
* *
99985 CTTCTTCTTGAGTGAAAATCAGATATGGGGACTTTGATTCATTCCACTGTCACTCAGGGAAGATT
1 CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
* *
100050 GAATCAAGGTAGACTTGTTCTGATGTTACTCAGGGAATATCAAATCTTGAAAGA
66 GAATCGAGGCAGACTTGTTCTGATGTTACTCAGGGAATATCAAATCTTGAAAGA
100104 TAGGTGTAAC
Statistics
Matches: 224, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
133 1 0.00
134 222 0.99
135 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (134 bp):
CTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
GAATCGAGGCAGACTTGTTCTGATGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGA
TCCA
Found at i:100862 original size:49 final size:49
Alignment explanation
Indices: 100758--100863 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 49
100748 ACCATGAGTT
* * * * * *
100758 GCACCTTTTATGTCGAAATGTACTGTTATGCATTTAACTTTTATTTGTG
1 GCACCTTTTATGGCGAAATGCACCGTTATGCATTTAACTTTCATTAGAG
100807 GCACCTTTTATGGCGAAATGCACCGTTATGCATTTAACTTTCATTAGAAG
1 GCACCTTTTATGGCGAAATGCACCGTTATGCATTTAACTTTCATTAG-AG
100857 G-ACCTTT
1 GCACCTTT
100864 AATTCTCAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 48 0.96
50 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (49 bp):
GCACCTTTTATGGCGAAATGCACCGTTATGCATTTAACTTTCATTAGAG
Found at i:106997 original size:49 final size:49
Alignment explanation
Indices: 106914--107029 Score: 144
Period size: 49 Copynumber: 2.4 Consensus size: 49
106904 CGAAATGCGC
* * * *
106914 CGTTATGCATTTAACATTCATTTGTAGCATCTTTTATGCCGAAATGAAGT
1 CGTTATGCATTTAACTTTCATTTGTAGCACCTTTTATGACAAAATGAA-T
* * *
106964 -GTTATGCATTTAACTTTCATTTGTGGTACCTTTTATGACAAAATGTAT
1 CGTTATGCATTTAACTTTCATTTGTAGCACCTTTTATGACAAAATGAAT
*
107012 CATTATGCATTTAACTTT
1 CGTTATGCATTTAACTTT
107030 TATTAGCGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 56 0.98
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (49 bp):
CGTTATGCATTTAACTTTCATTTGTAGCACCTTTTATGACAAAATGAAT
Found at i:108731 original size:134 final size:133
Alignment explanation
Indices: 108482--108919 Score: 529
Period size: 134 Copynumber: 3.3 Consensus size: 133
108472 ATTACAATAA
* * * * * * * *
108482 GGATCTGTTTCGCTTCTTCTCGAGGGAAAATTAGATATGGGGATGTTGATTCATTCCACTATCAC
1 GGATATGTTTCACTTCTTCTTGA-GGAAAATCAGTTCTAGGGAAGTTGATTCATTCCACTATCAC
* * * *
108547 TCAGGTAAGATTGAATCGGGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAG
65 TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAG
*
108612 AGTG
130 AGAG
* * * *
108616 GGATATGTTTCTCTTTTTCTTAAGGAAAAATCAGTTCTAGGGAAGTTGATTCATTCCACTGTCAC
1 GGATATGTTTCACTTCTTCTTGAGG-AAAATCAGTTCTAGGGAAGTTGATTCATTCCACTATCAC
* * * * *
108681 TCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGAGAATATTAAATCTTAAAAT
65 TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAG
108746 AGAG
130 AGAG
* * * *
108750 GGATTTG-TTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACA-TTGATTCATTCCACTATCA
1 GGATATGTTTCACTTCTTCTTGA-GGAAAATCAGTTCTAGGGA-AGTTGATTCATTCCACTATCA
* * * * *
108813 TTTAGGGAAAATTGAATCAAGGTAGACTTGTTCCGCTGTTACTCAGGGAATATAAAATCTTAAAA
64 CTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAA
108878 GAGAG
129 GAGAG
* *
108883 GGATATGTTCCACTTCTTCTTGAGGGAAATCAGTTCT
1 GGATATGTTTCACTTCTTCTTGAGGAAAATCAGTTCT
108920 GAGGAAATTG
Statistics
Matches: 258, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
133 125 0.48
134 133 0.52
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (133 bp):
GGATATGTTTCACTTCTTCTTGAGGAAAATCAGTTCTAGGGAAGTTGATTCATTCCACTATCACT
CAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAGA
GAG
Found at i:108842 original size:133 final size:132
Alignment explanation
Indices: 108490--108930 Score: 551
Period size: 133 Copynumber: 3.3 Consensus size: 132
108480 AAGGATCTGT
* * * * *
108490 TTCGCTTCTTCTCGAGGGAAAATTAGATATGGGGATGTTGATTCATTCCACTATCACTCAGGTAA
1 TTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGA-ATTGATTCATTCCACTATCACTCAGGGAA
* * * *
108555 GATTGAATCGGGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGTGGGAT
65 GATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAGAGAGGGAT
108620 ATG
130 ATG
* * * * * * *
108623 TTTCTCTTTTTCTTAAGGAAAAATCAGTTCTAGGGAAGTTGATTCATTCCACTGTCACTCAGGGA
1 -TTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGAA-TTGATTCATTCCACTATCACTCAGGGA
* * * * *
108688 AGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGAGAATATTAAATCTTAAAATAGAGGGA
64 AGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAGAGAGGGA
*
108753 TTTG
129 TATG
* *
108757 TTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACATTGATTCATTCCACTATCATTTAGGGAA
1 TTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGA-ATTGATTCATTCCACTATCACTCAGGGAA
* * *
108822 AATTGAATCAAGGTAGACTTGTTCCGCTGTTACTCAGGGAATATAAAATCTTAAAAGAGAGGGAT
65 GATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAGAGAGGGAT
108887 ATG
130 ATG
* * *
108890 TTCCACTTCTTCTTGAGGG-AAATCAGTTCTGAGGAAATTGA
1 TT-CGCTTCTTCTTGAGGGAAAATCAGATCTG-GGGAATTGA
108931 ATCGAGGCAG
Statistics
Matches: 261, Mismatches: 42, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
133 131 0.50
134 130 0.50
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (132 bp):
TTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGAATTGATTCATTCCACTATCACTCAGGGAAG
ATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATAAAATCTTAAAAGAGAGGGATA
TG
Found at i:109001 original size:103 final size:103
Alignment explanation
Indices: 108821--109028 Score: 294
Period size: 103 Copynumber: 2.0 Consensus size: 103
108811 CATTTAGGGA
* *
108821 AAATTGAATCAAGGTAGACTTGTTCCGCTGTTACTCAGGGAATATAAAATCTTAAAAGAGAGGGA
1 AAATTGAATCAAGGCAGACTTGTTCCGCTGTTACTCAGAGAATATAAAATCTTAAAAGAGAGGGA
* *
108886 TATGTTCCACTTCTTCTTGAGGG-AAATCAGTTCTGAGG
66 TATGTTCCACTTCTTATTGAGGGAAAATCAGATCTG-GG
* * * *
108924 AAATTGAATCGAGGCAGACTTGTTCCAG-TGTTACTCATAGAATATCAAATCTTGAAAGAGAGGG
1 AAATTGAATCAAGGCAGACTTGTTCC-GCTGTTACTCAGAGAATATAAAATCTTAAAAGAGAGGG
* *
108988 ATTTGTTCTACTTCTTATTGAGGGAAAATCAGATCTGGG
65 ATATGTTCCACTTCTTATTGAGGGAAAATCAGATCTGGG
109027 AA
1 AA
109029 CGTTGATTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
103 81 0.87
104 12 0.13
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (103 bp):
AAATTGAATCAAGGCAGACTTGTTCCGCTGTTACTCAGAGAATATAAAATCTTAAAAGAGAGGGA
TATGTTCCACTTCTTATTGAGGGAAAATCAGATCTGGG
Found at i:113014 original size:16 final size:16
Alignment explanation
Indices: 112995--113033 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
112985 ATGCAATATA
112995 GATGCAATGTAAATAC
1 GATGCAATGTAAATAC
113011 GATGCAATGTAAATAC
1 GATGCAATGTAAATAC
*
113027 AATGCAA
1 GATGCAA
113034 GTTTTGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (16 bp):
GATGCAATGTAAATAC
Found at i:116951 original size:131 final size:132
Alignment explanation
Indices: 116717--117074 Score: 402
Period size: 131 Copynumber: 2.7 Consensus size: 132
116707 ATTTTAAGCG
* * * * * *
116717 TGAAAACCATAATATCTAATTATTTCCAATCGTGAATAAATGACCTTTCGTGCATTGAAA-CATT
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTT-AAAGCAGT
* * * * * * *
116781 CATTTATTACCCCAATTGAAAT-AAAGATATATTACTATTTCATCTTAAAATTCAATATCGATTC
65 CATTTATTACTCCAATCGAAATGAAA-AGATATCACTATTTCATCTAAAAAATCAATATCAATTC
116845 -AAA
129 GAAA
* * * *
116848 TGAAAACGATAATATCTAATGATTTCCAATCAAGAATAAATGACATCTCATACCTTAAAGCAGTC
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * * *
116913 ATTTATTGCTCCAATCGAAATGAAAAGATATCATTATTTCATCTAAAAAATCGATATTAATTCGA
66 ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTAAAAAATCAATATCAATTCGA
*
116978 GA
131 AA
* * * * * *
116980 -GAAAATGACAATATCAAATTATTTACAATCGAGAATAAATGACCTCTCACGCCTTAGAGCAGTC
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
117044 ATTTATTACTCCAA-CTGAAATGAAAAGATAT
66 ATTTATTACTCCAATC-GAAATGAAAAGATAT
117075 TACCATTCTC
Statistics
Matches: 190, Mismatches: 33, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
130 4 0.02
131 181 0.95
132 5 0.03
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (132 bp):
TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTAAAAAATCAATATCAATTCGA
AA
Found at i:119196 original size:3 final size:3
Alignment explanation
Indices: 119188--119221 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
119178 ATTAATTAAT
*
119188 TAA TAA TAA TAA TAA TAA TAA TAAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
119222 ATAACCAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:120081 original size:19 final size:20
Alignment explanation
Indices: 120046--120094 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
120036 TTAGTTATCG
120046 AATT-ATATT-TAATTATAT
1 AATTAATATTATAATTATAT
**
120064 TCTTAATATTATAA-TATAT
1 AATTAATATTATAATTATAT
120083 AATTAATATTAT
1 AATTAATATTAT
120095 TTATTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 20 0.80
20 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTAATATTATAATTATAT
Found at i:120271 original size:42 final size:42
Alignment explanation
Indices: 120207--120295 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
120197 ATCTTAATAA
* *
120207 TATTATTATTTTAATAAGTAATTAATATAGTTAATAATATAT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
* *
120249 TATTCTTATTTTAATAAATAATTAATATAATTTATAATA-AT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
120290 T-TTATT
1 TATTATT
120296 TTCATAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 4 0.10
41 3 0.07
42 35 0.83
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (42 bp):
TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
Found at i:120286 original size:23 final size:22
Alignment explanation
Indices: 120214--120288 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
120204 TAATATTATT
*
120214 ATTTTAATAAGTAATTAATAT-
1 ATTTTAATAAATAATTAATATA
* * * *
120235 A-GTTAAT-AATATATTATTCTT
1 ATTTTAATAAATA-ATTAATATA
120256 ATTTTAATAAATAATTAATATA
1 ATTTTAATAAATAATTAATATA
120278 ATTTATAATAA
1 ATTT-TAATAA
120289 TTTTATTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 11 0.27
21 2 0.05
22 15 0.37
23 10 0.24
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (22 bp):
ATTTTAATAAATAATTAATATA
Found at i:120303 original size:37 final size:39
Alignment explanation
Indices: 120201--120319 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 39
120191 TTTAATATCT
* *
120201 TAATAATATTATTATTTTAATAAGTAATTAATATAGTTAA
1 TAATAATATTATTATTTTAATAAATAATTAATATAATT-A
*
120241 TAATATATTATTCTTATTTTAATAAATAATTAATATAATT-
1 TAATA-A-TATTATTATTTTAATAAATAATTAATATAATTA
*
120281 T-ATAATAATT-TTATTTTCATAAAATATATTAATCATAAT
1 TAATAAT-ATTATTATTTTAAT-AAATA-ATTAAT-ATAAT
120320 ATTTTTATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
37 10 0.14
38 9 0.13
39 9 0.13
40 11 0.16
41 1 0.01
42 29 0.42
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (39 bp):
TAATAATATTATTATTTTAATAAATAATTAATATAATTA
Found at i:120435 original size:27 final size:28
Alignment explanation
Indices: 120368--120435 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
120358 TAATATTGAC
*
120368 ATAAATAATATTA-AATTATTTTAATAT
1 ATAAATAATATTATTATTATTTTAATAT
* * *
120395 TTAAA-AAAATTATTATTATTTTAGTA-
1 ATAAATAATATTATTATTATTTTAATAT
120421 ATAAATAATATTATT
1 ATAAATAATATTATT
120436 TACTGTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATAAATAATATTATTATTATTTTAATAT
Found at i:122512 original size:40 final size:40
Alignment explanation
Indices: 122468--122843 Score: 179
Period size: 40 Copynumber: 9.1 Consensus size: 40
122458 ATAACACTGC
* * *
122468 TCCTTCGTATTTAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
* * * * * *
122508 TCCTTCGTTTTAAGGA-AGTCTGGTTGTCTGAGGATGACACTGC
1 TCCTTCGTGTTGAGGAGA-TCT-G--GTCGGTGGATGACATTGT
* * * *
122551 ACCTTTGCGTTGAGGAGATCTGGTTGGTGGATGACATTGT
1 TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
* * * * * ** **
122591 TCCTTTGCGTGGAGGA-AGTCTGGTTGTCTGAGGATGACGCTAC
1 TCCTTCGTGTTGAGGAGA-TCT-G--GTCGGTGGATGACATTGT
* * *
122634 TCCTACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
* * * * * * *
122674 TCCTTCCTGCTT-AGGAAGTATGGTTGTCTGAGGATGACACTGC
1 TCCTTCGTG-TTGAGG-AG-AT-CTGGTCGGTGGATGACATTGT
*
122717 TCCTTCGCGTT-ATGGAGATCTGGTCGGTGGATGACATTGT
1 TCCTTCGTGTTGA-GGAGATCTGGTCGGTGGATGACATTGT
** * * *
122757 TCCTTCGTGTTGAGGA-AGTCTGGTTATATGAGGACGACATTGC
1 TCCTTCGTGTTGAGGAGA-TCTGG---TCGGTGGATGACATTGT
* * *
122800 TCGTACGCT-TTGAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTTCG-TGTTGAGGAGATCTGGTCGGTGGATGACATTGT
122840 TCCT
1 TCCT
122844 ACATGATGAA
Statistics
Matches: 247, Mismatches: 67, Indels: 44
0.69 0.19 0.12
Matches are distributed among these distances:
39 3 0.01
40 116 0.47
41 9 0.04
42 9 0.04
43 106 0.43
44 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.33
Consensus pattern (40 bp):
TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
Found at i:122542 original size:83 final size:83
Alignment explanation
Indices: 122433--122843 Score: 529
Period size: 83 Copynumber: 5.0 Consensus size: 83
122423 GTTCCTTTTC
* * * * ** *
122433 GTTGAAGAAGTCTGATTGTCTAAGGATAACACTGCTCCTTCGTATTTAGGAGATCTGGTCGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
122498 ACGACATTGTTCCTTCGT
66 ACGACATTGTTCCTTCGT
* * * * *
122516 TTTAAGGAAGTCTGGTTGTCTGAGGATGACACTGCACCTTTGCGTTGAGGAGATCTGGTTGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
* * *
122581 ATGACATTGTTCCTTTGC
66 ACGACATTGTTCCTTCGT
* * * *
122599 GTGGAGGAAGTCTGGTTGTCTGAGGATGACGCTACTCCTACGCGTTGAGGAGATCTGGTCGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
*
122664 ACGACATTGTTCCTTCCT
66 ACGACATTGTTCCTTCGT
*
122682 GCTT-AGGAAGTATGGTTGTCTGAGGATGACACTGCTCCTTCGCGTT-ATGGAGATCTGGTCGGT
1 G-TTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGA-GGAGATCTGGTCGGT
*
122745 GGATGACATTGTTCCTTCGT
64 GGACGACATTGTTCCTTCGT
* * * * * * *
122765 GTTGAGGAAGTCTGGTTATATGAGGACGACATTGCTCGTACGCTTTGAGGAGATCTGGTCGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
122830 ACGACATTGTTCCT
66 ACGACATTGTTCCT
122844 ACATGATGAA
Statistics
Matches: 280, Mismatches: 44, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
82 3 0.01
83 275 0.98
84 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (83 bp):
GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
ACGACATTGTTCCTTCGT
Found at i:122649 original size:43 final size:43
Alignment explanation
Indices: 122526--122823 Score: 167
Period size: 43 Copynumber: 7.1 Consensus size: 43
122516 TTTAAGGAAG
*
122526 TCTGGTTGTCTGAGGATGACACTGCACCTTTGCGTTGAGGAGA
1 TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * * *
122569 TCTGGTTG---GTGGATGACATTGTTCCTTTGCGTGGAGGA-A
1 TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * **
122608 GTCTGGTTGTCTGAGGATGACGCTACTCCTACGCGTTGAGGAGA
1 -TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * * * *
122652 TCT-G--GTCGGTGGACGACATTGTTCCTTCCTGC-TT-AGGA-A
1 TCTGGTTGTCTGAGGATGACACTGCTCCTT--TGCGTTGAGGAGA
* *
122691 GTATGGTTGTCTGAGGATGACACTGCTCCTTCGCGTT-ATGGAGA
1 -TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGA-GGAGA
* * * * * *
122735 TCT-G--GTCGGTGGATGACATTGTTCCTTCGTGTTGAGGA-A
1 TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * * * * ** *
122774 GTCTGGTTATATGAGGACGACATTGCTCGTACGCTTTGAGGAGA
1 -TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
122818 TCTGGT
1 TCTGGT
122824 CGGTGGACGA
Statistics
Matches: 190, Mismatches: 45, Indels: 40
0.69 0.16 0.15
Matches are distributed among these distances:
39 3 0.02
40 84 0.44
41 7 0.04
42 7 0.04
43 86 0.45
44 3 0.02
ACGTcount: A:0.17, C:0.18, G:0.33, T:0.32
Consensus pattern (43 bp):
TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
Found at i:123229 original size:139 final size:139
Alignment explanation
Indices: 122755--123234 Score: 599
Period size: 139 Copynumber: 3.5 Consensus size: 139
122745 GGATGACATT
* * * * ** * * *
122755 GTTCCTTCGTGTTGAGGAAGTCTGGTTATATGAGGACGAC-ATTGCTCGTACGCTTTGAGGAGAT
1 GTTCCTACGTGATGAGGAAGTTTGATTGCATGAGGATGACGA-TGCTCCTACGCGTTGAGGAGAT
* * *
122819 CTGGTCGGTGGACGACATTGTTCCTACATGATGAAGACGTATATCCATCTTTAGGGATAATTTGG
65 CTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACTTATATCCATCTTTAGGGATAATTTGG
* *
122884 AGATAACATG
130 AGACAACACG
* * * * * * *
122894 GTTCCTACGTGATGAGGAAGCTTGATTGCCA-GAGGATGATGTTGCTCTTACGTGTTAAGGATAT
1 GTTCCTACGTGATGAGGAAGTTTGATTG-CATGAGGATGACGATGCTCCTACGCGTTGAGGAGAT
122958 CTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGA-TGTATATCCATCTTTAGGGATAATTTG
65 CTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACT-TATATCCATCTTTAGGGATAATTTG
123022 GAGACAACACG
129 GAGACAACACG
* * * **
123033 GTTCCTAAGTGATGAGGAAGTTTGATTTCCTGAGGATGACGATGCTCCTACATGTTGAGGAGATC
1 GTTCCTACGTGATGAGGAAGTTTGATTGCATGAGGATGACGATGCTCCTACGCGTTGAGGAGATC
** * *
123098 TGGTTAGTGGACGACATTGTTCCTACGTGATGAGGACTTCTA-GCAGTCTTTAGGGATAATTTGG
66 TGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACTTATATCCA-TCTTTAGGGATAATTTGG
123162 AGACAACACG
130 AGACAACACG
* * *
123172 GTTCCTACGTGATGAGGAAGTTTGATTGCATGAGAATGACGCTACTCCTACGCGTTGAGGAGA
1 GTTCCTACGTGATGAGGAAGTTTGATTGCATGAGGATGACGATGCTCCTACGCGTTGAGGAGA
123235 GCTAGTCATA
Statistics
Matches: 293, Mismatches: 42, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
138 3 0.01
139 288 0.98
140 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (139 bp):
GTTCCTACGTGATGAGGAAGTTTGATTGCATGAGGATGACGATGCTCCTACGCGTTGAGGAGATC
TGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACTTATATCCATCTTTAGGGATAATTTGGA
GACAACACG
Found at i:126518 original size:18 final size:18
Alignment explanation
Indices: 126479--126532 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
126469 TCTTGTATAC
*
126479 TTTTTCTCTCTTTCTTCT-T
1 TTTTTCT-TTTTTCTT-TGT
126498 TTTTTCTTTTTTCTTTGT
1 TTTTTCTTTTTTCTTTGT
* *
126516 TTTTTCTCTTTGCTTTG
1 TTTTTCTTTTTTCTTTG
126533 ATTTGATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.03
18 23 0.74
19 7 0.23
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTTGT
Found at i:132140 original size:74 final size:75
Alignment explanation
Indices: 131998--132162 Score: 278
Period size: 74 Copynumber: 2.2 Consensus size: 75
131988 AATAAAATAA
* * *
131998 AATGTTAGCAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGTATGTTAATATGAACAATACAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGAATGTTAATATGAACAATAAAA
132063 TAAAAGTTAG
66 TAAAAGTTAG
* *
132073 AATGTTTGTAAGTTAGTAAGAACAATAAAAATAA-AAAGTTAGAATGTTAGTATGAACAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGAATGTTAATATGAACAATAAAA
132137 TAAAAGTTAG
66 TAAAAGTTAG
132147 AATGTTAGTAAGTTAG
1 AATGTTAGTAAGTTAG
132163 AAAAGTTAGA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 52 0.62
75 32 0.38
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (75 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGAATGTTAATATGAACAATAAAA
TAAAAGTTAG
Found at i:132154 original size:32 final size:32
Alignment explanation
Indices: 131987--132156 Score: 162
Period size: 32 Copynumber: 4.9 Consensus size: 32
131977 TTAGTTTGTG
*
131987 CAATAAAATAAAATGTTAGCAA-GTTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTATGAA
* *
132020 CAATAAAAATAATAAAGTTAGTATGTTAATATGAA
1 CAAT-AAAAT-A-AAAGTTAGAATGTTAGTATGAA
*
132055 CAATACAATAAAAGTTAGAATGTTTGTAAGTTAGTAAGAA
1 CAATAAAATAAAAGTTAGAATG--T-T-AG-TA-T--GAA
132095 CAATAAAAATAAAAAGTTAGAATGTTAGTATGAA
1 CAAT-AAAAT-AAAAGTTAGAATGTTAGTATGAA
132129 CAATAAAATAAAAGTTAGAATGTTAGTA
1 CAATAAAATAAAAGTTAGAATGTTAGTA
132157 AGTTAGAAAA
Statistics
Matches: 116, Mismatches: 7, Indels: 29
0.76 0.05 0.19
Matches are distributed among these distances:
32 30 0.26
33 10 0.09
34 18 0.16
35 20 0.17
36 5 0.04
37 4 0.03
38 3 0.03
39 1 0.01
40 8 0.07
41 4 0.03
42 13 0.11
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTATGAA
Found at i:132162 original size:40 final size:36
Alignment explanation
Indices: 131991--132162 Score: 145
Period size: 40 Copynumber: 4.6 Consensus size: 36
131981 TTTGTGCAAT
*
131991 AAAATAAAATGTTAGCAAGTTAGTAAGAACAATAAAA
1 AAAAT-AAATGTTAGTAAGTTAGTAAGAACAATAAAA
* * * *
132028 ATAATAAA-GTTAGTATGTTAATATGAACAATACAATA
1 AAAATAAATGTTAGTAAGTTAGTAAGAACAATA-AA-A
* *
132065 AAAGTTAGAATGTTTGTAAGTTAGTAAGAACAATAAAA
1 AAA-ATA-AATGTTAGTAAGTTAGTAAGAACAATAAAA
* *
132103 ATAA-AAA-GTTAG-AATGTTAGTATGAACAATAAAA
1 AAAATAAATGTTAGTAA-GTTAGTAAGAACAATAAAA
132137 TAAAAGTTAGAATGTTAGTAAGTTAG
1 -AAAA--TA-AATGTTAGTAAGTTAG
132163 AAAAGTTAGA
Statistics
Matches: 106, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
33 2 0.02
34 22 0.21
35 25 0.24
36 6 0.06
37 7 0.07
38 6 0.06
39 6 0.06
40 30 0.28
41 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.28
Consensus pattern (36 bp):
AAAATAAATGTTAGTAAGTTAGTAAGAACAATAAAA
Found at i:132389 original size:121 final size:125
Alignment explanation
Indices: 132175--132503 Score: 418
Period size: 121 Copynumber: 2.6 Consensus size: 125
132165 AAGTTAGAGA
* * * *
132175 TTAGTGGTTAGCAAGGTTCGAACCATAATAATGTGGATTATA-TCCCGAATCAGGTCACCACAAA
1 TTAGTGGTTAGCAA-GTTCGAACCATAATAATGTGGATCATACT-CCGGATCTGGTCACCACAAG
132239 GTCGAATCGAATAATTCAAACAAATATAT-A-AAAAT-A-AAATAAAATAAAATAAAAAA-G
64 GTCGAATCGAATAATTCAAACAAATATATAATAAAATAATAAATAAAATAAAATAAAAAAGG
* * * *
132296 TTAGTGGTTAGTAGAGTTTGAACCATAATAATATGGATCACACTCCGGATCTGGTCACCACAAGG
1 TTAGTGGTTAGCA-AGTTCGAACCATAATAATGTGGATCATACTCCGGATCTGGTCACCACAAGG
*
132361 CCGAATCGAATAATTCAAACAAATATATAAAAATAAAATGAAATAAATAAAATAAAATAAAAAAG
65 TCGAATCGAATAATTCAAACAAATATAT---AATAAAAT--AATAAATAAAATAAAATAAAAAAG
132426 G
125 G
* * * *
132427 TTAATGGTTAGGAAAGTTCGAACCATAATAATGTGGATCATACCCCAGATCTGGTCACCACAAGG
1 TTAGTGGTTA-GCAAGTTCGAACCATAATAATGTGGATCATACTCCGGATCTGGTCACCACAAGG
132492 TCGAATCGAATA
65 TCGAATCGAATA
132504 TTAGAAACAA
Statistics
Matches: 178, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
121 80 0.45
122 2 0.01
125 1 0.01
126 5 0.03
129 1 0.01
130 20 0.11
131 67 0.38
132 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (125 bp):
TTAGTGGTTAGCAAGTTCGAACCATAATAATGTGGATCATACTCCGGATCTGGTCACCACAAGGT
CGAATCGAATAATTCAAACAAATATATAATAAAATAATAAATAAAATAAAATAAAAAAGG
Found at i:132404 original size:5 final size:5
Alignment explanation
Indices: 132390--132422 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
132380 CAAATATATA
*
132390 AAAAT AAAAT GAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
132423 AAGGTTAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:132410 original size:14 final size:14
Alignment explanation
Indices: 132391--132421 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
132381 AAATATATAA
*
132391 AAATAAAATGAAAT
1 AAATAAAATAAAAT
132405 AAATAAAATAAAAT
1 AAATAAAATAAAAT
132419 AAA
1 AAA
132422 AAAGGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:132512 original size:131 final size:130
Alignment explanation
Indices: 132270--132521 Score: 364
Period size: 131 Copynumber: 1.9 Consensus size: 130
132260 AAATATATAA
* * * *
132270 AAATAAAATAAAATAAAATAAAAAAGTTAGTGGTTAGTAGAGTTTGAACCATAATAATATGGATC
1 AAATAAAATAAAATAAAATAAAAAAGTTAATGGTTAGGAAAGTTCGAACCATAATAATATGGATC
* * *
132335 ACACTCCGGATCTGGTCACCACAAGGCCGAATCGAATAATTCAAACAAATATATAAAAATAAAAT
66 ACACCCCAGATCTGGTCACCACAAGGCCGAATCGAATAATTCAAAC-AATAAATAAAAATAAAAT
132400 G
130 G
*
132401 AAAT-AAATAAAATAAAATAAAAAAGGTTAATGGTTAGGAAAGTTCGAACCATAATAATGTGGAT
1 AAATAAAATAAAATAAAATAAAAAA-GTTAATGGTTAGGAAAGTTCGAACCATAATAATATGGAT
* * *
132465 CATACCCCAGATCTGGTCACCACAAGGTCGAATCGAAT-ATTAGAAACAATAAATAAA
65 CACACCCCAGATCTGGTCACCACAAGGCCGAATCGAATAATT-CAAACAATAAATAAA
132522 TAAATAACAA
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
130 32 0.30
131 76 0.70
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (130 bp):
AAATAAAATAAAATAAAATAAAAAAGTTAATGGTTAGGAAAGTTCGAACCATAATAATATGGATC
ACACCCCAGATCTGGTCACCACAAGGCCGAATCGAATAATTCAAACAATAAATAAAAATAAAATG
Found at i:134427 original size:15 final size:15
Alignment explanation
Indices: 134407--134455 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
134397 TTTATAATAA
*
134407 TAAATTGATTTGTTT
1 TAAATTGATATGTTT
134422 TAAATTGATATGTTT
1 TAAATTGATATGTTT
* *
134437 TAAATTAATATATTT
1 TAAATTGATATGTTT
134452 TAAA
1 TAAA
134456 CTTTATAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (15 bp):
TAAATTGATATGTTT
Found at i:140647 original size:43 final size:44
Alignment explanation
Indices: 140588--140939 Score: 220
Period size: 43 Copynumber: 8.2 Consensus size: 44
140578 TTTTTTTAGA
* *
140588 AAACGCCGCAACAAGTCG-GATTTATAGCGGCGTTTTTCGGAAC
1 AAACGCCGCAATAAGTCGAGATCTATAGCGGCGTTTTTCGGAAC
* * * *
140631 AAATGCCGCAATAAGTCGAGCTCTATAACGGCG--TTTCCG-A-
1 AAACGCCGCAATAAGTCGAGATCTATAGCGGCGTTTTTCGGAAC
*
140671 AAACGCCGCAA-AAGGTC-AGATCTATAGCGGCGTTTTTTGGAAC
1 AAACGCCGCAATAA-GTCGAGATCTATAGCGGCGTTTTTCGGAAC
* * * *** *
140714 ACACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTTTTTTATAGA
1 AAACGCCGCAATAAGTCGAGATCTATAGCGGC-GTTTTTCGGA-A-C
* *
140761 AAACGCCACAA-AATGTCG-GATCTATAGCGGCG-TTTTGGGAGA-
1 AAACGCCGCAATAA-GTCGAGATCTATAGCGGCGTTTTTCGGA-AC
* * *
140803 AAACACTGCAA-AAGGTC-AGATTTATAGCGGCGTTTTT-GGAAC
1 AAACGCCGCAATAA-GTCGAGATCTATAGCGGCGTTTTTCGGAAC
* * * * * *
140845 AAACGCTGCAGA-AGGTCAAGATATATAGCGACGTTTTT-GGAAT
1 AAACGCCGCA-ATAAGTCGAGATCTATAGCGGCGTTTTTCGGAAC
* * * *
140888 AAACACCGTAA-AATTTC-AGATCTATAGCGGCGTTTTT-GGATGC
1 AAACGCCGCAATAA-GTCGAGATCTATAGCGGCGTTTTTCGGA-AC
140931 AAACGCCGC
1 AAACGCCGC
140940 TAATTATCGT
Statistics
Matches: 244, Mismatches: 46, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
39 15 0.06
40 13 0.05
41 6 0.02
42 70 0.29
43 73 0.30
44 32 0.13
45 7 0.03
46 15 0.06
47 13 0.05
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
AAACGCCGCAATAAGTCGAGATCTATAGCGGCGTTTTTCGGAAC
Found at i:140705 original size:83 final size:83
Alignment explanation
Indices: 140586--140745 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 83
140576 CGTTTTTTTA
* * *
140586 GAAAACGCCGCAACAAGTCGGATTTATAGCGGCGTTTTTCGGAACAAATGCCGCAATAAGTCGAG
1 GAAAACGCCGCAACAAGTCAGATCTATAGCGGCGTTTTTCGGAACAAACGCCGCAATAAGTCGAG
*
140651 CTCTATAACGGCGTTTCC
66 ATCTATAACGGCGTTTCC
* * *
140669 GAAAACGCCGCAA-AAGGTCAGATCTATAGCGGCGTTTTTTGGAACACACGCCGCAATAGGTCGA
1 GAAAACGCCGCAACAA-GTCAGATCTATAGCGGCGTTTTTCGGAACAAACGCCGCAATAAGTCGA
*
140733 GATCTATAGCGGC
65 GATCTATAACGGC
140746 TTTTTTTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 2 0.03
83 66 0.97
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (83 bp):
GAAAACGCCGCAACAAGTCAGATCTATAGCGGCGTTTTTCGGAACAAACGCCGCAATAAGTCGAG
ATCTATAACGGCGTTTCC
Found at i:140751 original size:44 final size:42
Alignment explanation
Indices: 140552--140924 Score: 217
Period size: 42 Copynumber: 8.7 Consensus size: 42
140542 AAAAAATGAT
* * * *
140552 GCAATAGGTCTAAATCTATAACGGCGTTTTTTTAGAAAACGCC
1 GCAATAGGTCGAGATCTATAGCGGCG-TTTTTTGGAAAACGCC
* * * * *
140595 GCAACAAGTCG-GATTTATAGCGGCGTTTTTCGGAACAAATGCC
1 GCAATAGGTCGAGATCTATAGCGGCGTTTTTTGG-A-AAACGCC
* * * **
140638 GCAATAAGTCGAGCTCTATAACGGCG--TTTCCGAAAACGCC
1 GCAATAGGTCGAGATCTATAGCGGCGTTTTTTGGAAAACGCC
*
140678 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTTGGAACACACGCC
1 GCAATAGGTCGAGATCTATAGCGGCGTTTTTTGGAA-A-ACGCC
* *
140721 GCAATAGGTCGAGATCTATAGCGGCTTTTTTTTTTATAGAAAACGCC
1 GCAATAGGTCGAGATCTATAGCGGC----GTTTTT-TGGAAAACGCC
* * * ** * *
140768 ACAAAATGTCG-GATCTATAGCGGCGTTTTGGGAGAAAACACT
1 GCAATAGGTCGAGATCTATAGCGGCGTTTTTTG-GAAAACGCC
* * *
140810 GCAAAAGGTC-AGATTTATAGCGGCG-TTTTTGGAACAAACGCT
1 GCAATAGGTCGAGATCTATAGCGGCGTTTTTTGG-A-AAACGCC
* * * *
140852 GCAGA-AGGTCAAGATATATAGCGACG-TTTTTGGAATAAACACC
1 GCA-ATAGGTCGAGATCTATAGCGGCGTTTTTTGG-A-AAACGCC
* * **
140895 GTAAAATTTC-AGATCTATAGCGGCGTTTTT
1 GCAATAGGTCGAGATCTATAGCGGCGTTTTT
140925 GGATGCAAAC
Statistics
Matches: 260, Mismatches: 49, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
39 13 0.05
40 15 0.06
41 18 0.07
42 78 0.30
43 75 0.29
44 25 0.10
46 13 0.05
47 13 0.05
48 6 0.02
49 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (42 bp):
GCAATAGGTCGAGATCTATAGCGGCGTTTTTTGGAAAACGCC
Found at i:144990 original size:41 final size:41
Alignment explanation
Indices: 144634--145023 Score: 258
Period size: 41 Copynumber: 9.5 Consensus size: 41
144624 TTGTAAACAC
* * *
144634 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTATAA
* * * * * * *
144675 AAATGCCGCTAAAGAACGTA-TTTATAGCGGTGTTTGAATAA
1 AAACGCCACTAAAGTAC-TACTCTATTGCGGCGTTTGTATAA
* * * *
144716 AAACGCCACTAAAGTACGT-GTCTATAGCGACTTTTGTATAA
1 AAACGCCACTAAAGTAC-TACTCTATTGCGGCGTTTGTATAA
* * *
144757 AAACGCCGCTAAAGTACTACTCTTTTGCGGTGTTTGTATAAA
1 AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTAT-AA
* * * * *
144799 AAACGCCGCTAAAGTACCACTCTGTTGCGACGTTTGT-TGA
1 AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTATAA
* * * * *
144839 AAATGCCA-TAATA-TA-TGAACCCTATTACGGCATTTTTATAA
1 AAACGCCACTAA-AGTACT--ACTCTATTGCGGCGTTTGTATAA
* * * ** * *
144880 AAATGCCACTAAAGTACTACTATGTCACGTCGTTTGTTTAAA
1 AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTAT-AA
* * *
144922 AAACGCCACT-ATGGA-TGAAC-CTATTGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACT--ACTCTATTGCGGCGTTTGTATAA
* *
144962 AAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGCATAA
1 AAACGCCACTAAAGTACTACTCTATTGCGGCG-TTTGTATAA
*
145004 AAACGCCGCTAAAGTTACTA
1 AAACGCCACTAAAG-TACTA
145024 TTTTGTGGCG
Statistics
Matches: 270, Mismatches: 60, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
39 5 0.02
40 37 0.14
41 146 0.54
42 76 0.28
43 6 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTATAA
Found at i:148192 original size:20 final size:22
Alignment explanation
Indices: 148144--148196 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
148134 TACCGAAAGA
148144 GGTATCGATACCATAATATAGT
1 GGTATCGATACCATAATATAGT
* **
148166 AGTATCGATACCATGGTA-AG-
1 GGTATCGATACCATAATATAGT
148186 GGTATCGATAC
1 GGTATCGATAC
148197 TAGGAAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 2 0.07
22 15 0.56
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCATAATATAGT
Found at i:148275 original size:95 final size:94
Alignment explanation
Indices: 148074--148293 Score: 314
Period size: 95 Copynumber: 2.3 Consensus size: 94
148064 AACAAGGTAA
* **
148074 TATCGATACCATGGTAAGGGTATCGATACCAAGTCACATCAAATAAAAAATGGGTATCGATACCG
1 TATCGATACCATGGTAAGGGTATCGATACTAAGAAACATCAAATAAAAAATGGGTATCGATACCG
148139 AAAGAGGTATCGATACCATAATATAGTAG
66 AAAGAGGTATCGATACCATAATATAGTAG
* * * *
148168 TATCGATACCATGGTAAGGGTATCGATACTAGGAAACATCGAATAAAAAATTTGGTATCGATACT
1 TATCGATACCATGGTAAGGGTATCGATACTAAGAAACATCAAATAAAAAA-TGGGTATCGATACC
* * *
148233 GAAGGGGGTATCGATACCATAGTATAGTAG
65 GAAAGAGGTATCGATACCATAATATAGTAG
* * *
148263 TATTGATTCCATGGTAGGGGTATCGATACTA
1 TATCGATACCATGGTAAGGGTATCGATACTA
148294 TAAAGTCAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 45 0.40
95 67 0.60
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (94 bp):
TATCGATACCATGGTAAGGGTATCGATACTAAGAAACATCAAATAAAAAATGGGTATCGATACCG
AAAGAGGTATCGATACCATAATATAGTAG
Found at i:148533 original size:16 final size:16
Alignment explanation
Indices: 148514--148545 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
148504 GTTTTGGATA
148514 CATAACAAGGAAAGTC
1 CATAACAAGGAAAGTC
148530 CATAACAAGGAAAGTC
1 CATAACAAGGAAAGTC
148546 AGGTGAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
CATAACAAGGAAAGTC
Found at i:148713 original size:55 final size:56
Alignment explanation
Indices: 148633--148744 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 56
148623 TACCAAATGA
*
148633 CACTATGTGTGTAAAAATTTAAGAAATTCATACTAAGTGTATGAATTTATGTATGGG
1 CACTATGTGTGCAAAAA-TTAAGAAATTCATACTAAGTGTATGAATTTATGTATGGG
* *
148690 CACTTTGTGTGCAAAAA-TAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGG
1 CACTATGTGTGCAAAAATTAAGAAATTCATACTAAGTGTATGAATTTATGTATGGG
148745 AAATAGATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 37 0.71
57 15 0.29
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (56 bp):
CACTATGTGTGCAAAAATTAAGAAATTCATACTAAGTGTATGAATTTATGTATGGG
Found at i:149066 original size:68 final size:68
Alignment explanation
Indices: 148954--149481 Score: 858
Period size: 68 Copynumber: 7.8 Consensus size: 68
148944 AAAGGATTAT
* * * *
148954 AGGCCTAACTATGCAAATGACTGAAAGGCGTCATTTATGACAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149019 TTA
66 TTA
* * *
149022 AGGCCTAACTGTGCACATGACAGAAATGTGTCATTTATGCCAGTTAAATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149087 TTA
66 TTA
* * * *
149090 AGGCCTAAGTGTGCAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGTTAGGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149155 TTA
66 TTA
* *
149158 AGGCCTAAGTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149223 TTA
66 TTA
*
149226 AGGCCTAACTGTGCAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149291 TTA
66 TTA
* * *
149294 AGGCCTAACTGTGCAAATGAAAGAAAGGTGTCATGTATGCCAGTTAGATGAAAGGTTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149359 TTA
66 TTA
*
149362 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
149427 TTA
66 TTA
* * * *
149430 AGGCCTAACTGTGCAATTGACATAAAGGTGTCAATTATGCCAGTTGGATGAA
1 AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
149482 CGGTTAAACA
Statistics
Matches: 428, Mismatches: 32, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 428 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (68 bp):
AGGCCTAACTGTGCAAATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTA
Found at i:149706 original size:20 final size:20
Alignment explanation
Indices: 149681--149727 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
149671 CGTAATTAGT
*
149681 ATGAAAGGATTCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* *
149701 ATGAAATGATGCATTAAGGG
1 ATGAAAGGATGCATTAAGGC
149721 ATGAAAG
1 ATGAAAG
149728 AATTTAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.28, T:0.23
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:157132 original size:30 final size:30
Alignment explanation
Indices: 157098--157159 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
157088 TTTTCACTAA
157098 ATTTATTCTTTATTTAAGGCTTTTTACTCC
1 ATTTATTCTTTATTTAAGGCTTTTTACTCC
157128 ATTTATTCTTTATTTAAGGCTTTTTACTCC
1 ATTTATTCTTTATTTAAGGCTTTTTACTCC
157158 AT
1 AT
157160 CTCTTTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.06, T:0.56
Consensus pattern (30 bp):
ATTTATTCTTTATTTAAGGCTTTTTACTCC
Found at i:170416 original size:19 final size:19
Alignment explanation
Indices: 170392--170444 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
170382 AAGTCAACTC
* *
170392 TGGTCAAAGTTAATGGTCT
1 TGGTCAAAGTCAATGATCT
* *
170411 TGGTCAAGGTCAACGATCT
1 TGGTCAAAGTCAATGATCT
170430 TGGTCAAAGTCAATG
1 TGGTCAAAGTCAATG
170445 CTTGAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (19 bp):
TGGTCAAAGTCAATGATCT
Found at i:174112 original size:3 final size:3
Alignment explanation
Indices: 174104--174155 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
174094 TTTTTTGCTA
174104 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
174152 ATT A
1 ATT A
174156 AGTGAAAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:187287 original size:16 final size:16
Alignment explanation
Indices: 187262--187295 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
187252 AACATTTATC
187262 ATTCAATGAATATTAA
1 ATTCAATGAATATTAA
* *
187278 ATTCATTGAATCTTAA
1 ATTCAATGAATATTAA
187294 AT
1 AT
187296 ATAAGGTAAA
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:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTCAATGAATATTAA
Done.