Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 94 of 150
Found at i:29505188 original size:18 final size:18
Alignment explanation
Indices: 29505148--29505190 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29505138 TTTCAAGGTG
29505148 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
29505166 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
29505184 TAATTAA
1 TAATTAA
29505191 AAAACTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:29509794 original size:14 final size:14
Alignment explanation
Indices: 29509775--29509809 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
29509765 TATATATATA
29509775 TATACATACTAGCC
1 TATACATACTAGCC
29509789 TATACATACTAGCC
1 TATACATACTAGCC
29509803 TATACAT
1 TATACAT
29509810 GTCATATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (14 bp):
TATACATACTAGCC
Found at i:29510682 original size:59 final size:62
Alignment explanation
Indices: 29510500--29510721 Score: 292
Period size: 63 Copynumber: 3.6 Consensus size: 62
29510490 CGTAGCAAAT
**
29510500 ATACATTCGGATAACATA-TATATAATTCATACAATTAAATTCAACTTATAGAACTCAAAAC
1 ATACATTCGGATAACATATTATATAATTCATACAATTAGTTTCAACTTATAGAACTCAAAAC
* * *
29510561 ATACATTCGGAAAACATATATATATAATTTATACAATTAGTTTCAACTCATAGAACTCAAAAC
1 ATACATTCGGATAACATAT-TATATAATTCATACAATTAGTTTCAACTTATAGAACTCAAAAC
* *
29510624 ATACATT-GGCTAAC-TATT-TATAATTCATACAATTAGTTTCAACTTATCA-AACTTAAAAC
1 ATACATTCGGATAACATATTATATAATTCATACAATTAGTTTCAACTTAT-AGAACTCAAAAC
* * *
29510683 ATACATTCAGCTAACATATTTATATAATTCATAAAATTA
1 ATACATTCGGATAACATA-TTATATAATTCATACAATTA
29510722 AATCCAGCTT
Statistics
Matches: 142, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
59 43 0.30
60 8 0.06
61 22 0.15
62 7 0.05
63 62 0.44
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (62 bp):
ATACATTCGGATAACATATTATATAATTCATACAATTAGTTTCAACTTATAGAACTCAAAAC
Found at i:29514648 original size:17 final size:18
Alignment explanation
Indices: 29514616--29514653 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29514606 ACAGTAATGA
*
29514616 GCTTGCGGCGGTGAT-AG
1 GCTTGCGGCGGCGATAAG
*
29514633 GCTTGCGGTGGCGATAAG
1 GCTTGCGGCGGCGATAAG
29514651 GCT
1 GCT
29514654 GCTCCAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.13, C:0.18, G:0.45, T:0.24
Consensus pattern (18 bp):
GCTTGCGGCGGCGATAAG
Found at i:29518170 original size:40 final size:40
Alignment explanation
Indices: 29518126--29518368 Score: 296
Period size: 40 Copynumber: 6.1 Consensus size: 40
29518116 AATTATTGTA
* *
29518126 TGAATGCACATATGTGCCTTTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCC
*
29518166 TGAATGCACATGCGTG-CCTCTGTTTGTACTT-GAGTACCCC
1 TGAATGCACATACGTGCCCT-TGTTTGTACTTCG-GTACCCC
* * *
29518206 TGAATGCACATACGTGCCCATG-TTGTACTTTGGTATCCC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCC
* * *
29518245 TGAATGCACATGCGTGCCCTTATTTGTACTTTGGTACCCC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCC
*
29518285 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCC
* * * * * *
29518325 TGAATGCACTTATGTG-CCTTGTTTATACTCCGGTAACTC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCC
29518364 TGAAT
1 TGAAT
29518369 TATGTAGTAT
Statistics
Matches: 177, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
39 59 0.33
40 116 0.66
41 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCC
Found at i:29518342 original size:119 final size:119
Alignment explanation
Indices: 29518126--29518342 Score: 321
Period size: 119 Copynumber: 1.8 Consensus size: 119
29518116 AATTATTGTA
* * * *
29518126 TGAATGCACATATGTGCCTTTGTTTGTACTTCGGTACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCTCTGTTT
29518191 GTACTTGAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
66 GTACTTGAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
* *
29518245 TGAATGCACATGCGTGCCCTTATTTGTACTTTGGTACCCCTGAATGCACATACGTGCC-CTTGTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCTC-TGTT
* * *
29518309 TGTACTTCG-GTACCCTTGAATGCACTTATGTGCC
65 TGTACTT-GAGTACCCCTGAATGCACATACGTGCC
29518343 TTGTTTATAC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
118 1 0.01
119 85 0.98
120 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (119 bp):
TGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCTCTGTTT
GTACTTGAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
Found at i:29518367 original size:119 final size:119
Alignment explanation
Indices: 29518126--29518368 Score: 303
Period size: 119 Copynumber: 2.0 Consensus size: 119
29518116 AATTATTGTA
* * * *
29518126 TGAATGCACATATGTGCCTTTGTTTGTACTTCGGTACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCTCTGTTT
* ** *
29518191 GTACTTGAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
66 GTACTTGAGTACCCCTGAATGCACATACGTGCCCATGTTATACTCCGGTAACCC
* *
29518245 TGAATGCACATGCGTGCCCTTATTTGTACTTTGGTACCCCTGAATGCACATACGTGCC-CTTGTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCTC-TGTT
* * * * *
29518309 TGTACTTCG-GTACCCTTGAATGCACTTATGTG-CCTTGTTTATACTCCGGTAACTC
65 TGTACTT-GAGTACCCCTGAATGCACATACGTGCCCATG-TTATACTCCGGTAACCC
29518364 TGAAT
1 TGAAT
29518369 TATGTAGTAT
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 5 0.05
119 100 0.94
120 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (119 bp):
TGAATGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCCTCTGTTT
GTACTTGAGTACCCCTGAATGCACATACGTGCCCATGTTATACTCCGGTAACCC
Found at i:29518368 original size:79 final size:77
Alignment explanation
Indices: 29518126--29518353 Score: 305
Period size: 79 Copynumber: 2.9 Consensus size: 77
29518116 AATTATTGTA
* *
29518126 TGAATGCACATATGTGCCTTTGTTTGTACTTCGGTACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTA-CCCTGAATGCACATGCGTGCCT-TGTTT
29518191 GTACTTGAGTACCCC
64 GTACTTG-GTACCCC
* * *
29518206 TGAATGCACATACGTGCCCATG-TTGTACTTTGGTATCCCTGAATGCACATGCGTGCCCTTATTT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTA-CCCTGAATGCACATGCGTG-CCTTGTTT
29518270 GTACTTTGGTACCCC
64 GTAC-TTGGTACCCC
* ** *
29518285 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCTTGAATGCACTTATGTGCCTTGTTTA
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCC-TGAATGCACATGCGTGCCTTGTTTG
29518350 TACT
65 TACT
29518354 CCGGTAACTC
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 80 0.61
80 50 0.38
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (77 bp):
TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCTGAATGCACATGCGTGCCTTGTTTGT
ACTTGGTACCCC
Found at i:29519514 original size:39 final size:40
Alignment explanation
Indices: 29519440--29519592 Score: 186
Period size: 39 Copynumber: 3.9 Consensus size: 40
29519430 TATTGTATGG
* * *
29519440 ATGCACATGCGTACCTCTGTTTGTACTTCGGTACCCCTAA
1 ATGCACATGCGTGCCCCTGCTTGTACTTCGGTACCCCTAA
* *
29519480 AGGCACATGCGTGCCCCTG-TTGTACTTCAGTACCCC-AGA
1 ATGCACATGCGTGCCCCTGCTTGTACTTCGGTACCCCTA-A
* *
29519519 ATGCACATACGTGCCCCTG-TTGTACTTCGGTACCCCTGA
1 ATGCACATGCGTGCCCCTGCTTGTACTTCGGTACCCCTAA
* * *
29519558 ATGCACATGCATGCCCTTGCTTCTACTTCGGTACC
1 ATGCACATGCGTGCCCCTGCTTGTACTTCGGTACC
29519593 TCTGACTACT
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 67 0.68
40 30 0.31
ACGTcount: A:0.19, C:0.33, G:0.20, T:0.29
Consensus pattern (40 bp):
ATGCACATGCGTGCCCCTGCTTGTACTTCGGTACCCCTAA
Found at i:29519573 original size:78 final size:80
Alignment explanation
Indices: 29519440--29519592 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 80
29519430 TATTGTATGG
* * * *
29519440 ATGCACATGCGTACCTCTGTTTGTACTTCGGTACCCCTAAAGGCACATGCGTGCCCCTG-TTGTA
1 ATGCACATACGTACCCCTGTTTGTACTTCGGTACCCCTAAAGGCACATGCATGCCCCTGCTTCTA
29519504 CTTCAGTACCCCAGA
66 CTTCAGTACCCCAGA
* * * *
29519519 ATGCACATACGTGCCCCTG-TTGTACTTCGGTACCCCTGAATGCACATGCATGCCCTTGCTTCTA
1 ATGCACATACGTACCCCTGTTTGTACTTCGGTACCCCTAAAGGCACATGCATGCCCCTGCTTCTA
*
29519583 CTTCGGTACC
66 CTTCAGTACC
29519593 TCTGACTACT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
78 35 0.55
79 29 0.45
ACGTcount: A:0.19, C:0.33, G:0.20, T:0.29
Consensus pattern (80 bp):
ATGCACATACGTACCCCTGTTTGTACTTCGGTACCCCTAAAGGCACATGCATGCCCCTGCTTCTA
CTTCAGTACCCCAGA
Found at i:29523848 original size:16 final size:16
Alignment explanation
Indices: 29523824--29523861 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29523814 TTTGGTTCAC
* *
29523824 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
29523840 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29523856 TGTAAT
1 TGTAAT
29523862 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29523945 original size:39 final size:43
Alignment explanation
Indices: 29523840--29523949 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
29523830 GGATTAGAGG
29523840 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
29523885 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
29523925 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
29523950 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:29524123 original size:14 final size:15
Alignment explanation
Indices: 29524084--29524125 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29524074 TTTAAACATG
*
29524084 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29524099 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29524113 A-TATAATTTAATA
1 ATTATAATTAAATA
29524126 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29541777 original size:26 final size:26
Alignment explanation
Indices: 29541714--29541767 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
29541704 TCCACAAAAT
29541714 ATCAATCTTTTAATATGGTATTTGAA
1 ATCAATCTTTTAATATGGTATTTGAA
29541740 ATCAATCTTTTAATATGGTATTTGAA
1 ATCAATCTTTTAATATGGTATTTGAA
29541766 AT
1 AT
29541768 TTTCTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (26 bp):
ATCAATCTTTTAATATGGTATTTGAA
Found at i:29546401 original size:31 final size:31
Alignment explanation
Indices: 29546357--29546425 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
29546347 GTTTGATTGA
*
29546357 TTATAA-TTATTTTTGCAATTTATATAATTTC
1 TTATAATTTATTTTTACAATTTATAT-ATTTC
* * * *
29546388 TTATAGTTTTTTTTTACAATTTTTATATTTT
1 TTATAATTTATTTTTACAATTTATATATTTC
29546419 TTATAAT
1 TTATAAT
29546426 GATTTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (31 bp):
TTATAATTTATTTTTACAATTTATATATTTC
Found at i:29548789 original size:14 final size:14
Alignment explanation
Indices: 29548770--29548800 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29548760 AAGAAAACCC
*
29548770 ATACCACAGTTTAT
1 ATACCACAATTTAT
29548784 ATACCACAATTTAT
1 ATACCACAATTTAT
29548798 ATA
1 ATA
29548801 ACTTAATGAC
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:0.42, C:0.19, G:0.03, T:0.35
Consensus pattern (14 bp):
ATACCACAATTTAT
Found at i:29551162 original size:14 final size:15
Alignment explanation
Indices: 29551128--29551171 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
29551118 ATATGATAAT
29551128 ATGCGAACCCTATAC
1 ATGCGAACCCTATAC
* *
29551143 ATGCGAACCC-CTAG
1 ATGCGAACCCTATAC
29551157 ATGCGAACCTCTATA
1 ATGCGAACC-CTATA
29551172 TATCTGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.46
15 11 0.46
16 2 0.08
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (15 bp):
ATGCGAACCCTATAC
Found at i:29561967 original size:31 final size:34
Alignment explanation
Indices: 29561929--29561996 Score: 106
Period size: 31 Copynumber: 2.1 Consensus size: 34
29561919 ATTCCTCTTA
29561929 AAAAAAGCTTTAA-TTT-TTTTT-AATTATTTTT
1 AAAAAAGCTTTAATTTTATTTTTAAATTATTTTT
*
29561960 AAAAAAGCTTTAATTTTATTTTTAAATTTTTTTT
1 AAAAAAGCTTTAATTTTATTTTTAAATTATTTTT
29561994 AAA
1 AAA
29561997 TCATAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 13 0.39
32 3 0.09
33 5 0.15
34 12 0.36
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (34 bp):
AAAAAAGCTTTAATTTTATTTTTAAATTATTTTT
Found at i:29564202 original size:18 final size:18
Alignment explanation
Indices: 29564179--29564221 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29564169 TGCCAGGTGC
* *
29564179 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
29564197 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
29564215 GTTTCCT
1 GTATCCT
29564222 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:29564459 original size:21 final size:21
Alignment explanation
Indices: 29564417--29564459 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29564407 AGATCCCCTA
* * *
29564417 CCGGAGAAACCAGAATCTCCG
1 CCGGAGAAACCACAACCCCCG
*
29564438 CCGGAGCAACCACAACCCCCG
1 CCGGAGAAACCACAACCCCCG
29564459 C
1 C
29564460 TAGAAGGTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.44, G:0.21, T:0.05
Consensus pattern (21 bp):
CCGGAGAAACCACAACCCCCG
Found at i:29568024 original size:126 final size:126
Alignment explanation
Indices: 29567799--29568087 Score: 479
Period size: 126 Copynumber: 2.3 Consensus size: 126
29567789 GGCCAAACAT
* * *
29567799 GAGCTACTGTAGCAAAAGCGCATCCACTTAGGAGCTTTTTTCAGTACTTTTACTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTACTGACAAAGCATC
*
29567864 CTGTTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAA
66 CTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAA
* * * *
29567925 GAGCTACTGTAACAAAAACGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTTCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTACTGACAAAGCATC
*
29567990 CTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAG
66 CTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAA
* *
29568051 GAGCTACTGTAGGAAAAGCGCATCCATGTGGGAGCTT
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTT
29568088 TTTTAAATTA
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 149 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (126 bp):
GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTTTACTGACAAAGCATC
CTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAA
Found at i:29568332 original size:7 final size:7
Alignment explanation
Indices: 29568285--29568348 Score: 58
Period size: 7 Copynumber: 9.0 Consensus size: 7
29568275 ATTTTTCTTT
29568285 AAAACCC
1 AAAACCC
* *
29568292 TAAACCTA
1 AAAACC-C
29568300 AAAACCCC
1 AAAA-CCC
29568308 AAAACCC
1 AAAACCC
* *
29568315 -TAACCT
1 AAAACCC
*
29568321 TAAACCC
1 AAAACCC
29568328 AAAACCC
1 AAAACCC
29568335 AAAACCC
1 AAAACCC
29568342 AAAACCC
1 AAAACCC
29568349 TAACCATAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
6 4 0.09
7 32 0.71
8 7 0.16
9 2 0.04
ACGTcount: A:0.52, C:0.41, G:0.00, T:0.08
Consensus pattern (7 bp):
AAAACCC
Found at i:29569800 original size:13 final size:13
Alignment explanation
Indices: 29569782--29569806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29569772 TAAGTTATAT
29569782 GTGTGAAAATTTC
1 GTGTGAAAATTTC
29569795 GTGTGAAAATTT
1 GTGTGAAAATTT
29569807 GATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:29571507 original size:41 final size:41
Alignment explanation
Indices: 29571450--29571552 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
29571440 CTTAAAGCCT
* ** * *
29571450 AGCAGGCTTAAGGCCGGTGATGTAATTCGGACTTTATGTCC
1 AGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGTCC
*
29571491 AGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGTCT
1 AGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGTCC
29571532 AGCAGGC-TAATTGCCGGTGAA
1 AGCAGGCTTAA-TGCCGGTGAA
29571553 CTGAATAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 3 0.05
41 52 0.95
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (41 bp):
AGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGTCC
Found at i:29576278 original size:7 final size:8
Alignment explanation
Indices: 29576258--29576291 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
29576248 ATTATTTTCT
29576258 TAAAAATA
1 TAAAAATA
29576266 TAAAAATA
1 TAAAAATA
*
29576274 TAAAAAGA
1 TAAAAATA
*
29576282 TAAATATA
1 TAAAAATA
29576290 TA
1 TA
29576292 TTTTGTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:29590963 original size:12 final size:13
Alignment explanation
Indices: 29590939--29590967 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29590929 GGGCTATAAC
29590939 TATTGCATTTATT
1 TATTGCATTTATT
29590952 TATTGC-TTTATT
1 TATTGCATTTATT
29590964 TATT
1 TATT
29590968 CATGTATGAG
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:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:29604339 original size:17 final size:17
Alignment explanation
Indices: 29604317--29604352 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29604307 TTATCATAAA
29604317 TTTTACTATTATTTTAT
1 TTTTACTATTATTTTAT
29604334 TTTTACTATTATTTTAT
1 TTTTACTATTATTTTAT
29604351 TT
1 TT
29604353 AAGCGTTGGA
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:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTACTATTATTTTAT
Found at i:29605134 original size:31 final size:32
Alignment explanation
Indices: 29605098--29605162 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
29605088 CTTAGATAAT
29605098 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
29605129 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
29605161 TT
1 TT
29605163 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:29613017 original size:21 final size:21
Alignment explanation
Indices: 29612938--29613093 Score: 114
Period size: 21 Copynumber: 7.3 Consensus size: 21
29612928 CGTGTTTACT
* * *
29612938 TTCTGTTTAGCTCTCACGAGC
1 TTCTGTTTAACTCTTATGAGC
* *
29612959 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAACTCTTATGAGC
** * * *
29612980 TTCCATTCAGCTTTCTTTTGAGC
1 TTCTGTTTAAC--TCTTATGAGC
*
29613003 TTCTGTTTAACTCTTATGAGT
1 TTCTGTTTAACTCTTATGAGC
*
29613024 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTTAACTCTTATGAGC
* * * * *
29613045 TTCCGTTCAACCCTTATGGGT
1 TTCTGTTTAACTCTTATGAGC
* * *
29613066 TTCTGTTTAGCACTTATGTGC
1 TTCTGTTTAACTCTTATGAGC
29613087 TTCTGTT
1 TTCTGTT
29613094 CAGCCGTCGA
Statistics
Matches: 101, Mismatches: 32, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 87 0.86
23 14 0.14
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTGTTTAACTCTTATGAGC
Found at i:29613061 original size:42 final size:42
Alignment explanation
Indices: 29612937--29613095 Score: 174
Period size: 42 Copynumber: 3.7 Consensus size: 42
29612927 TCGTGTTTAC
* * * *
29612937 TTTCTGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
** * * *
29612979 TTTCCATTCAGCTTTCTTTTGAGCTTCTGTTTAACTCTTATGAG
1 TTTCTGTTTAGC--TCTTATGAGCTTCTGTTCAACTCTTATGAG
* * *
29613023 TTTCTGTTTAGCTCTTATGAGCTTCCGTTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* *
29613065 TTTCTGTTTAGCACTTATGTGCTTCTGTTCA
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCA
29613096 GCCGTCGAGC
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 62 0.64
44 35 0.36
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
Found at i:29615591 original size:26 final size:26
Alignment explanation
Indices: 29615544--29615614 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
29615534 AGTCATATCG
* *
29615544 GGAAGCTC-CGGAGAGCCATTAATTA
1 GGAAGCTCACGAAGAGCCATTAATCA
* *
29615569 GGAAGCTCA-GAAAGAGCCTTTAATCG
1 GGAAGCTCACG-AAGAGCCATTAATCA
29615595 GGAAGCTCACGAAGAGCCAT
1 GGAAGCTCACGAAGAGCCAT
29615615 ATAACGGAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 9 0.24
26 28 0.74
27 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCA
Found at i:29616081 original size:10 final size:10
Alignment explanation
Indices: 29616066--29616110 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
29616056 CTATACGAGT
*
29616066 AATTTAACTC
1 AATTTAATTC
*
29616076 AATTTAATAC
1 AATTTAATTC
29616086 AATTTATATTC
1 AATTTA-ATTC
*
29616097 AATTCAATTC
1 AATTTAATTC
29616107 AATT
1 AATT
29616111 CACATCTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTTAATTC
Found at i:29616100 original size:21 final size:20
Alignment explanation
Indices: 29616066--29616110 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
29616056 CTATACGAGT
*
29616066 AATTTAACTCAATTTAATAC
1 AATTTAACTCAATTCAATAC
* *
29616086 AATTTATATTCAATTCAATTC
1 AATTTA-ACTCAATTCAATAC
29616107 AATT
1 AATT
29616111 CACATCTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAACTCAATTCAATAC
Found at i:29619436 original size:15 final size:16
Alignment explanation
Indices: 29619411--29619446 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
29619401 AAAGCAAACC
29619411 ATTGAGGGTGCCATTG
1 ATTGAGGGTGCCATTG
29619427 ATTG-GGGTGCCATTG
1 ATTGAGGGTGCCATTG
29619442 ATTGA
1 ATTGA
29619447 TCTCTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.33
Consensus pattern (16 bp):
ATTGAGGGTGCCATTG
Found at i:29621062 original size:18 final size:18
Alignment explanation
Indices: 29621048--29621082 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29621038 GTTCTTTTCT
29621048 CCTTTAATTTTCTTTATG
1 CCTTTAATTTTCTTTATG
*
29621066 CCTTTATTTTTCTTTAT
1 CCTTTAATTTTCTTTAT
29621083 AGATTTTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.03, T:0.66
Consensus pattern (18 bp):
CCTTTAATTTTCTTTATG
Found at i:29630207 original size:50 final size:50
Alignment explanation
Indices: 29630149--29630264 Score: 187
Period size: 50 Copynumber: 2.3 Consensus size: 50
29630139 ATTTGGGTAA
* *
29630149 AGAGGTCCCATGTAAGACCATGTCTGGGTCATGGCGTTGGAACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGAACCAAGATG
* *
29630199 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGAACCAAGATG
*
29630249 AGAGGTCTCATGTAAG
1 AGAGGTCCCATGTAAG
29630265 TTATGATCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGAACCAAGATG
Found at i:29630637 original size:12 final size:12
Alignment explanation
Indices: 29630620--29630656 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29630610 TTTGATGATG
29630620 AATGGTTATTAA
1 AATGGTTATTAA
29630632 AATGGTTA--AA
1 AATGGTTATTAA
*
29630642 TATGGTTATTAA
1 AATGGTTATTAA
29630654 AAT
1 AAT
29630657 TGGCTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (12 bp):
AATGGTTATTAA
Found at i:29638500 original size:30 final size:30
Alignment explanation
Indices: 29638452--29638714 Score: 278
Period size: 30 Copynumber: 8.6 Consensus size: 30
29638442 TTGACAATAT
*
29638452 ATATGTATACAT-TACAAATCAATTCGGCA
1 ATATATATACATATACAAATCAATTCGGCA
29638481 ATATATATACATATACAAATCAATTCGGCA
1 ATATATATACATATACAAATCAATTCGGCA
* *
29638511 ATGTATAT-CTATATATAAATCAATTCGGCA
1 ATATATATAC-ATATACAAATCAATTCGGCA
* * * *
29638541 ATGTATATCCATATATAAATCAATTCGGCT
1 ATATATATACATATACAAATCAATTCGGCA
* * *
29638571 ATGTATATCCATATACAAATCAATTCGGTA
1 ATATATATACATATACAAATCAATTCGGCA
* *
29638601 ATGTATATCCATATACAAATCAATTCGGCTA
1 ATATATATACATATACAAATCAATTCGGC-A
* *
29638632 TATATATATATCTATATATAAATCAATTCGACA
1 -ATATATATA-C-ATATACAAATCAATTCGGCA
* **
29638665 ATATATATATCCATATACAAATAAATTTAGCA
1 ATATATATA--CATATACAAATCAATTCGGCA
*
29638697 ATATATAAAACATATACA
1 ATATAT-ATACATATACA
29638715 TTTGAATTCA
Statistics
Matches: 206, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
29 12 0.06
30 125 0.61
31 10 0.05
32 37 0.18
33 5 0.02
34 17 0.08
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (30 bp):
ATATATATACATATACAAATCAATTCGGCA
Found at i:29638591 original size:90 final size:92
Alignment explanation
Indices: 29638449--29638691 Score: 312
Period size: 90 Copynumber: 2.6 Consensus size: 92
29638439 AATTTGACAA
* * * * *
29638449 TATATATGTATACAT-TACAAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCAAT
1 TATATATATATCCATATATAAATCAATTCGGCTATATATATCCATATACAAATCAATTCGGCAAT
* *
29638513 GTATATCTATATATAAATCAATTCGGC
66 GTATATCCATATACAAATCAATTCGGC
* * *
29638540 -A-ATGTATATCCATATATAAATCAATTCGGCTATGTATATCCATATACAAATCAATTCGGTAAT
1 TATATATATATCCATATATAAATCAATTCGGCTATATATATCCATATACAAATCAATTCGGCAAT
29638603 GTATATCCATATACAAATCAATTCGGC
66 GTATATCCATATACAAATCAATTCGGC
* * *
29638630 TATATATATATATCTATATATAAATCAATTCGACAATATATATATCCATATACAAATAAATT
1 --TATATATATATCCATATATAAATCAATTCGGC--TATATATATCCATATACAAATCAATT
29638692 TAGCAATATA
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
89 9 0.07
90 70 0.54
93 1 0.01
94 26 0.20
96 24 0.18
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (92 bp):
TATATATATATCCATATATAAATCAATTCGGCTATATATATCCATATACAAATCAATTCGGCAAT
GTATATCCATATACAAATCAATTCGGC
Found at i:29638703 original size:34 final size:34
Alignment explanation
Indices: 29638574--29638703 Score: 112
Period size: 34 Copynumber: 4.0 Consensus size: 34
29638564 TTCGGCTATG
** *
29638574 TATATCCATATACAAATCAA-TT--CGGTA-ATG
1 TATATCCATATACAAATCAATTTAGCAATATATA
** *
29638604 TATATCCATATACAAATCAATTCGGCTATATATA
1 TATATCCATATACAAATCAATTTAGCAATATATA
* * *
29638638 TATATCTATATATAAATCAA-TTCG-ACA-ATATA
1 TATATCCATATACAAATCAATTTAGCA-ATATATA
*
29638670 TATATCCATATACAAATAAATTTAGCAATATATA
1 TATATCCATATACAAATCAATTTAGCAATATATA
29638704 AAACATATAC
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
30 20 0.25
31 1 0.01
32 22 0.28
33 10 0.13
34 26 0.33
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (34 bp):
TATATCCATATACAAATCAATTTAGCAATATATA
Found at i:29639038 original size:21 final size:21
Alignment explanation
Indices: 29638992--29639039 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29638982 TAAAACTTTC
*
29638992 ATTT-ATTTCATATTTCAACC
1 ATTTAATTTCATATTTCAACA
*
29639012 ACTTAATTTGCATATTTC-ACA
1 ATTTAATTT-CATATTTCAACA
29639033 ATTTAAT
1 ATTTAAT
29639040 CCCTATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTAATTTCATATTTCAACA
Found at i:29640697 original size:41 final size:41
Alignment explanation
Indices: 29640650--29640731 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
29640640 ATATTTTATT
29640650 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
*
29640691 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
29640732 CAATTAGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
Found at i:29644426 original size:19 final size:19
Alignment explanation
Indices: 29644402--29644442 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
29644392 TATTTTAAAG
*
29644402 TTATTTTGGTAGATAAAAC
1 TTATTTAGGTAGATAAAAC
*
29644421 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAAAC
29644440 TTA
1 TTA
29644443 GAATAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAAAC
Found at i:29644526 original size:41 final size:41
Alignment explanation
Indices: 29644480--29644560 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
29644470 ATATTTTATT
*
29644480 TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTCC
*
29644521 TTATCTTTTAGTAGTTTATTAGAACAAGGGAATTATTTTC
1 TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTC
29644561 TGAATTAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTCC
Found at i:29647195 original size:18 final size:18
Alignment explanation
Indices: 29647172--29647207 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29647162 TTTGTTGAAA
*
29647172 CAAATCGAATTGGCCAAC
1 CAAATCGAATCGGCCAAC
29647190 CAAATCGAATCGGCCAAC
1 CAAATCGAATCGGCCAAC
29647208 AACCCTCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.31, G:0.17, T:0.14
Consensus pattern (18 bp):
CAAATCGAATCGGCCAAC
Found at i:29650049 original size:46 final size:47
Alignment explanation
Indices: 29649945--29650054 Score: 132
Period size: 46 Copynumber: 2.4 Consensus size: 47
29649935 CATGTGCACA
*
29649945 TTAACAATTAATTAATTTTAAAAATATTTAAAATATATTTTTAATTT
1 TTAAAAATTAATTAATTTTAAAAATATTTAAAATATATTTTTAATTT
* ** * *** *
29649992 TTTAATTTTAATTATTTTTAATTTTA-TTAAAATATTTTTTTAATTT
1 TTAAAAATTAATTAATTTTAAAAATATTTAAAATATATTTTTAATTT
29650038 TTAAAAATTAATTAATT
1 TTAAAAATTAATTAATT
29650055 GCTTATGTGG
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
46 32 0.64
47 18 0.36
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (47 bp):
TTAAAAATTAATTAATTTTAAAAATATTTAAAATATATTTTTAATTT
Found at i:29655605 original size:69 final size:69
Alignment explanation
Indices: 29655429--29655605 Score: 196
Period size: 69 Copynumber: 2.6 Consensus size: 69
29655419 GGTTAGCTTG
* * * ** *
29655429 GCTATGAAAACCAATAGAGTCTATTGGGACAGTAAATACGGAGATTTCAAGGTGTAAAACCATAG
1 GCTATGACAACCAATAGAGTCTATTAGGACAGTAAACATAGAGATTTCAAGGTGTAAAAACATAG
29655494 CTCA
66 CTCA
* *
29655498 GCTATGACAACCAATAGAGT-TAGTTAGGATAGTAAACATAGAGATTTCAATGTGTAAAAACATA
1 GCTATGACAACCAATAGAGTCTA-TTAGGACAGTAAACATAGAGATTTCAAGGTGTAAAAACATA
*
29655562 GCTCG
65 GCTCA
* * * * *
29655567 GGTTTGGCAACCAATAGAGTCCATCT-GGACATTAAACAT
1 GCTATGACAACCAATAGAGTCTAT-TAGGACAGTAAACAT
29655606 GGGTTTATAC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
68 2 0.02
69 86 0.96
70 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (69 bp):
GCTATGACAACCAATAGAGTCTATTAGGACAGTAAACATAGAGATTTCAAGGTGTAAAAACATAG
CTCA
Found at i:29657700 original size:13 final size:13
Alignment explanation
Indices: 29657682--29657707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29657672 GGAATGATAT
29657682 TTTGAAAATTTCG
1 TTTGAAAATTTCG
29657695 TTTGAAAATTTCG
1 TTTGAAAATTTCG
29657708 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGAAAATTTCG
Found at i:29658269 original size:15 final size:15
Alignment explanation
Indices: 29658249--29658280 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29658239 AAAAGAGTAA
29658249 AACGACATAATCGGT
1 AACGACATAATCGGT
29658264 AACGACATAATCGGT
1 AACGACATAATCGGT
29658279 AA
1 AA
29658281 AAATACCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (15 bp):
AACGACATAATCGGT
Found at i:29658861 original size:50 final size:50
Alignment explanation
Indices: 29658783--29658968 Score: 246
Period size: 50 Copynumber: 3.7 Consensus size: 50
29658773 ATTTGGGTAA
*
29658783 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
29658833 AGAGGTCCCGTGTAAGATCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
29658883 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
29658933 AGAACATCCCATGTAAGACCATGTCTGGGGCATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
29658969 TTTAGCATGT
Statistics
Matches: 118, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 90 0.76
51 28 0.24
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:29664712 original size:49 final size:49
Alignment explanation
Indices: 29664617--29664712 Score: 131
Period size: 50 Copynumber: 2.0 Consensus size: 49
29664607 AAATAAAAAT
* *
29664617 TTATTAATTAAAAGATGAATTAAAAAAAAAAAACTTGAAAATAATATAA
1 TTATTAATTAAAACATGAATTAAAAAAAAAAAACTTGAAAACAATATAA
* * *
29664666 TTATTGATTAAAAACATTAATTAAAATAAAAAAACTTG-AAACAATAT
1 TTATTAATT-AAAACATGAATTAAAAAAAAAAAACTTGAAAACAATAT
29664713 GAAATAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 16 0.39
50 25 0.61
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.30
Consensus pattern (49 bp):
TTATTAATTAAAACATGAATTAAAAAAAAAAAACTTGAAAACAATATAA
Found at i:29665709 original size:16 final size:16
Alignment explanation
Indices: 29665663--29665734 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
29665653 GTTAATCATA
*
29665663 TAATATATTATTATGAT
1 TAATAAATTATTAT-AT
*
29665680 TAATATAATATATTATTT
1 TAATA-AAT-TATTATAT
29665698 TAATAAATTATT-TAAT
1 TAATAAATTATTAT-AT
*
29665714 T-TTAAAATT-TTATAT
1 TAAT-AAATTATTATAT
29665729 TAATAA
1 TAATAA
29665735 TAAATTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
15 9 0.20
16 13 0.30
17 8 0.18
18 8 0.18
19 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (16 bp):
TAATAAATTATTATAT
Found at i:29665836 original size:18 final size:18
Alignment explanation
Indices: 29665813--29665847 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29665803 TTTATATTAG
29665813 TGATTTAATAATAAATAA
1 TGATTTAATAATAAATAA
29665831 TGATTTAATAATAAATA
1 TGATTTAATAATAAATA
29665848 TTTTTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TGATTTAATAATAAATAA
Found at i:29665872 original size:24 final size:24
Alignment explanation
Indices: 29665844--29665897 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
29665834 TTTAATAATA
29665844 AATATTTTTATAGTATA-AAATATG
1 AATATTTTTA-AGTATATAAATATG
*
29665868 AATA-TTTTAATTATATAAATATG
1 AATATTTTTAAGTATATAAATATG
*
29665891 AGTATTT
1 AATATTT
29665898 GTTTAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 15 0.58
24 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (24 bp):
AATATTTTTAAGTATATAAATATG
Found at i:29666381 original size:2 final size:2
Alignment explanation
Indices: 29666374--29666413 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29666364 TGTTCTAGGA
29666374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29666414 GTTAGTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29671775 original size:19 final size:20
Alignment explanation
Indices: 29671742--29671785 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
29671732 ATTATTTGTT
29671742 ATTTGGAAGGGTTAA-GGC-
1 ATTTGGAAGGGTTAATGGCG
*
29671760 ATTTGGAATTGGTTAATGGCG
1 ATTTGGAA-GGGTTAATGGCG
29671781 ATTTG
1 ATTTG
29671786 AAAGTGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 3 0.14
21 5 0.23
ACGTcount: A:0.25, C:0.05, G:0.34, T:0.36
Consensus pattern (20 bp):
ATTTGGAAGGGTTAATGGCG
Found at i:29675430 original size:24 final size:23
Alignment explanation
Indices: 29675401--29675508 Score: 108
Period size: 24 Copynumber: 4.5 Consensus size: 23
29675391 TCCAGGCTAT
*
29675401 ATAACGGGAAGCTCATGCGAGCCA
1 ATAACGGGAAGCTC-TGAGAGCCA
* *
29675425 ATAACGGGTAGCTCTAAAGAGCCA
1 ATAACGGGAAGCTCT-GAGAGCCA
*
29675449 TTAACGGGAAGCTCTGAAGAGCCA
1 ATAACGGGAAGCTCTG-AGAGCCA
* *
29675473 TTAACGGGAAGCTCTGGATAGCCA
1 ATAACGGGAAGCTCT-GAGAGCCA
*
29675497 TATATCGGGAAG
1 -ATAACGGGAAG
29675509 TTCAAGCGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.01
24 60 0.85
25 10 0.14
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (23 bp):
ATAACGGGAAGCTCTGAGAGCCA
Found at i:29675496 original size:48 final size:49
Alignment explanation
Indices: 29675399--29675508 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
29675389 TATCCAGGCT
* *
29675399 ATATAACGGGAAGCTCATGCGAGCCAATAACGGGTAGCTCTAAAGAGCC
1 ATATAACGGGAAGCTCATGAGAGCCAATAACGGGAAGCTCTAAAGAGCC
* ** *
29675448 AT-TAACGGGAAGCTC-TGAAGAGCCATTAACGGGAAGCTCTGGATAGCC
1 ATATAACGGGAAGCTCATG-AGAGCCAATAACGGGAAGCTCTAAAGAGCC
*
29675496 ATATATCGGGAAG
1 ATATAACGGGAAG
29675509 TTCAAGCGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 2 0.04
48 39 0.75
49 11 0.21
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (49 bp):
ATATAACGGGAAGCTCATGAGAGCCAATAACGGGAAGCTCTAAAGAGCC
Found at i:29675557 original size:26 final size:26
Alignment explanation
Indices: 29675520--29675582 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
29675510 TCAAGCGAGT
*
29675520 TGGGAAGCTCACAAAGAGCC-TTTAA
1 TGGGAAGCTCACAAAGAGCCATATAA
29675545 TCGGGAAGCTCACAAAGAGCCATATAA
1 T-GGGAAGCTCACAAAGAGCCATATAA
*
29675572 TGGGATGCTCA
1 TGGGAAGCTCA
29675583 TAAGAGCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 1 0.03
26 28 0.82
27 5 0.15
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
TGGGAAGCTCACAAAGAGCCATATAA
Found at i:29676623 original size:30 final size:30
Alignment explanation
Indices: 29676589--29676646 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
29676579 TATTTTATTA
*
29676589 TTTATCATCTTTATTTTTC-ATTTTTCCAAT
1 TTTATCAT-TTTATTTTTCTAATTTTCCAAT
* *
29676619 TTTATCCTTTTCTTTTTCTAATTTTCCA
1 TTTATCATTTTATTTTTCTAATTTTCCA
29676647 TGAATGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTATCATTTTATTTTTCTAATTTTCCAAT
Found at i:29678475 original size:45 final size:45
Alignment explanation
Indices: 29678424--29678512 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
29678414 AAAATGTCAG
29678424 CTTAGCTTTTAACTCAGCTAAGATTGAGCCATCATCAAACAATGT
1 CTTAGCTTTTAACTCAGCTAAGATTGAGCCATCATCAAACAATGT
29678469 CTTAGCTTTTAACTCAGCTAAGATTGAGCCATCATCAAACAATG
1 CTTAGCTTTTAACTCAGCTAAGATTGAGCCATCATCAAACAATG
29678513 ATAATCGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (45 bp):
CTTAGCTTTTAACTCAGCTAAGATTGAGCCATCATCAAACAATGT
Found at i:29683235 original size:24 final size:25
Alignment explanation
Indices: 29683155--29683233 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 25
29683145 TGTATAACGT
29683155 GAAGCTCAT-AAGAGCCA-TAATCAG
1 GAAGCTCATGAAGAGCCATTAA-CAG
* * *
29683179 GAAGATCATG-TGAGCCAATAACAG
1 GAAGCTCATGAAGAGCCATTAACAG
*
29683203 GCAGCTC-TGAAGAGCCATTAACAG
1 GAAGCTCATGAAGAGCCATTAACAG
29683227 GAAGCTC
1 GAAGCTC
29683234 TGGATAGCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.04
24 40 0.89
25 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (25 bp):
GAAGCTCATGAAGAGCCATTAACAG
Found at i:29683242 original size:24 final size:24
Alignment explanation
Indices: 29683155--29683245 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
29683145 TGTATAACGT
29683155 GAAGCTCAT-AAGAGCCA-TAATCAG
1 GAAGCTC-TGAAGAGCCATTAA-CAG
* * *
29683179 GAAGATCATG-TGAGCCAATAACAG
1 GAAGCTC-TGAAGAGCCATTAACAG
*
29683203 GCAGCTCTGAAGAGCCATTAACAG
1 GAAGCTCTGAAGAGCCATTAACAG
* *
29683227 GAAGCTCTGGATAGCCATT
1 GAAGCTCTGAAGAGCCATT
29683246 TATTGGGAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
23 2 0.04
24 50 0.91
25 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (24 bp):
GAAGCTCTGAAGAGCCATTAACAG
Found at i:29683314 original size:26 final size:26
Alignment explanation
Indices: 29683273--29683360 Score: 108
Period size: 26 Copynumber: 3.4 Consensus size: 26
29683263 TAGCTATATT
* *
29683273 GGGAAGCTTACAAAGAGCCTTTAATAC
1 GGGAAGCTCACGAAGAGCCTTTAAT-C
29683300 -GGAAGCTCACGAAGAGCCTTTAATC
1 GGGAAGCTCACGAAGAGCCTTTAATC
*
29683325 GGGAAGCTCACGAAGAGCCATATAAT-
1 GGGAAGCTCACGAAGAGCC-TTTAATC
*
29683351 GGGATGCTCA
1 GGGAAGCTCA
29683361 TAAGAGCTGC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
25 1 0.02
26 49 0.89
27 5 0.09
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (26 bp):
GGGAAGCTCACGAAGAGCCTTTAATC
Found at i:29688758 original size:30 final size:30
Alignment explanation
Indices: 29688724--29688792 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
29688714 AAAAAATATC
* *
29688724 AATTTAACTCTTTTGAAAGGTTGATGGTCA
1 AATTTAACTCTTTTAAAAGGTTGATGGACA
**
29688754 AATTTGATTTCTTTTAAAAGGTTGATGGACA
1 AATTT-AACTCTTTTAAAAGGTTGATGGACA
29688785 AATTTAAC
1 AATTTAAC
29688793 AAAAAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACTCTTTTAAAAGGTTGATGGACA
Found at i:29690263 original size:14 final size:14
Alignment explanation
Indices: 29690244--29690271 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29690234 TAAAAGACAA
29690244 TGATTACTTAATGG
1 TGATTACTTAATGG
29690258 TGATTACTTAATGG
1 TGATTACTTAATGG
29690272 GGTTCTCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
TGATTACTTAATGG
Found at i:29690397 original size:27 final size:27
Alignment explanation
Indices: 29690358--29690668 Score: 293
Period size: 27 Copynumber: 11.5 Consensus size: 27
29690348 CACGATAGAT
* * *
29690358 AAGAATAGCCTTTATGGCATAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
29690385 AAGAAAAGTCTTTGTGGTGTAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * * *
29690412 AAGAAAATCATTTGTGGCATAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
*
29690439 AAGAAAAGCATTTGTGGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * * *
29690466 AATAATAGCCTTTGTGACGCAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
29690493 AAGAAAAAACCTTTGTGGCATAATATGT
1 AAG-AAAAGCCTTTGTGGCGTAATATGA
* *
29690521 ATGAAAAGCCTTTGTGACGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* *
29690548 AATAATAA-CCTTTGTAGCGTAATATGA
1 AAGAA-AAGCCTTTGTGGCGTAATATGA
* * *
29690575 AAGAAAAGTCTTTGTAGCATAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * **
29690602 AATAATAGCCTTTGTGATGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* **
29690629 AAGAATAGCCTTTGTGGCAAAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
29690656 AATG-AAAGCCTTT
1 AA-GAAAAGCCTTT
29690669 CTGGAAAACC
Statistics
Matches: 229, Mismatches: 51, Indels: 8
0.80 0.18 0.03
Matches are distributed among these distances:
26 2 0.01
27 204 0.89
28 23 0.10
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.31
Consensus pattern (27 bp):
AAGAAAAGCCTTTGTGGCGTAATATGA
Found at i:29690610 original size:136 final size:135
Alignment explanation
Indices: 29690366--29690668 Score: 378
Period size: 136 Copynumber: 2.2 Consensus size: 135
29690356 ATAAGAATAG
* * * ** * *
29690366 CCTTTATGGCATAATATGAAAGAAAAGTCTTTGTGGTGTAATATGTAAGAAAATCATTTGTGGCA
1 CCTTTGTGGCATAATATGAATGAAAAGCCTTTGTGACGTAATATGAAAGAAAATCATTTGTAGCA
* * *
29690431 TAATATGTAAGAAAAGCATTTGTGGCGTAATATGAAATAATAGCCTTTGTGACGCAATATGAAAG
66 TAATATGAAAGAAAAGCATTTGTAGCATAATATGAAATAATAGCCTTTGTGACGCAATATGAAAG
29690496 AAAAAA
131 -AAAAA
* * *
29690502 CCTTTGTGGCATAATATGTATGAAAAGCCTTTGTGACGTAATATGAAATAATAA-CCTTTGTAGC
1 CCTTTGTGGCATAATATGAATGAAAAGCCTTTGTGACGTAATATGAAAGAA-AATCATTTGTAGC
* * *
29690566 GTAATATGAAAGAAAAGTC-TTTGTAGCATAATATGAAATAATAGCCTTTGTGATGTAATATGAA
65 ATAATATGAAAGAAAAG-CATTTGTAGCATAATATGAAATAATAGCCTTTGTGACGCAATATGAA
* *
29690630 AGAATAG
129 AGAAAAA
*
29690637 CCTTTGTGGCAAAATATGAAATG-AAAGCCTTT
1 CCTTTGTGGCATAATATG-AATGAAAAGCCTTT
29690669 CTGGAAAACC
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
135 29 0.20
136 112 0.78
137 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (135 bp):
CCTTTGTGGCATAATATGAATGAAAAGCCTTTGTGACGTAATATGAAAGAAAATCATTTGTAGCA
TAATATGAAAGAAAAGCATTTGTAGCATAATATGAAATAATAGCCTTTGTGACGCAATATGAAAG
AAAAA
Found at i:29690682 original size:27 final size:26
Alignment explanation
Indices: 29690625--29690700 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
29690615 GTGATGTAAT
* *
29690625 ATGAAAGAATAGCCTTTGTGGCAAAAT
1 ATGAAAGAA-AGCCTTTCTGGCAAAAC
29690652 ATGAAATGAAAGCCTTTCTGG-AAAACC
1 ATGAAA-GAAAGCCTTTCTGGCAAAA-C
* *
29690679 ATGAAAAGAAAGTCTTTGTGGC
1 ATG-AAAGAAAGCCTTTCTGGC
29690701 GATCTCCCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.10
27 31 0.76
28 6 0.15
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (26 bp):
ATGAAAGAAAGCCTTTCTGGCAAAAC
Found at i:29692659 original size:41 final size:41
Alignment explanation
Indices: 29692602--29692823 Score: 320
Period size: 41 Copynumber: 5.4 Consensus size: 41
29692592 CTTTAATTAT
* *
29692602 TTTGTACTTTGGTACCCCAT-AATTGCACATACGTGCCCCTA
1 TTTGTACTTCGGTACCCC-TGAATTGCACATACGTGCCCCTG
* * * *
29692643 TTTGTACTTCGATACCCATGAATTGCACATACATGCCCTTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
*
29692684 TTTGTACTTCAGTACCCCTGAATTGCACATACGTGCCCCTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
* *
29692725 TTTGTACTTCGGTACCCTTAAATTGCACATACGTGCCCCTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
*
29692766 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCTCTG
1 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
* *
29692807 TTTATACTTCAGTACCC
1 TTTGTACTTCGGTACCC
29692824 TGTTTAGATT
Statistics
Matches: 161, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 1 0.01
41 160 0.99
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (41 bp):
TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCCCTG
Found at i:29692785 original size:20 final size:19
Alignment explanation
Indices: 29692682--29692785 Score: 55
Period size: 20 Copynumber: 5.1 Consensus size: 19
29692672 TACATGCCCT
29692682 TGTTTGTACTTCAGTACCCC
1 TGTTTGTACTTC-GTACCCC
* * * *
29692702 TGAATTGCACATACGTGCCCC
1 TG-TTTGTAC-TTCGTACCCC
*
29692723 TGTTTGTACTTCGGTACCCT
1 TGTTTGTACTTC-GTACCCC
** * * *
29692743 TAAATTGCACATACGTGCCCC
1 T-GTTTGTAC-TTCGTACCCC
29692764 TGTTTGTACTTCGGTACCCC
1 TGTTTGTACTTC-GTACCCC
29692784 TG
1 TG
29692786 AATTGCACAT
Statistics
Matches: 58, Mismatches: 20, Indels: 12
0.64 0.22 0.13
Matches are distributed among these distances:
19 4 0.07
20 26 0.45
21 24 0.41
22 4 0.07
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (19 bp):
TGTTTGTACTTCGTACCCC
Found at i:29697655 original size:36 final size:36
Alignment explanation
Indices: 29697614--29697682 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
29697604 AGAAGTTATG
*
29697614 ATAATTACACATTTAAAAATAATCACAATTTAATTA
1 ATAATTACACATTTAAAAATAATCAAAATTTAATTA
* * *
29697650 ATAATTATACATTTATAAATAATTAAAATTTAA
1 ATAATTACACATTTAAAAATAATCAAAATTTAA
29697683 ATTACAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (36 bp):
ATAATTACACATTTAAAAATAATCAAAATTTAATTA
Found at i:29697670 original size:18 final size:18
Alignment explanation
Indices: 29697614--29697674 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
29697604 AGAAGTTATG
*
29697614 ATAATTACACATTTAAAA
1 ATAATTACACATTTATAA
* *
29697632 ATAATCACA-ATTTAATTA
1 ATAATTACACATTT-ATAA
*
29697650 ATAATTATACATTTATAA
1 ATAATTACACATTTATAA
29697668 ATAATTA
1 ATAATTA
29697675 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.11
18 27 0.77
19 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTACACATTTATAA
Found at i:29697692 original size:36 final size:36
Alignment explanation
Indices: 29697616--29697693 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
29697606 AAGTTATGAT
* * *
29697616 AATTACACATTTAAAAATAATCACAATTTAATTAAT
1 AATTATACATTTAAAAATAATCAAAATTTAATTAAC
* *
29697652 AATTATACATTTATAAATAATTAAAATTTAAATT-AC
1 AATTATACATTTAAAAATAATCAAAATTT-AATTAAC
29697688 AATTAT
1 AATTAT
29697694 TCCTTAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (36 bp):
AATTATACATTTAAAAATAATCAAAATTTAATTAAC
Found at i:29703253 original size:2 final size:2
Alignment explanation
Indices: 29703246--29703272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29703236 ACGAGTATTT
29703246 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29703273 TGAATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29704073 original size:11 final size:11
Alignment explanation
Indices: 29704057--29704090 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29704047 TTCTCACTGA
29704057 TTTACTACTAT
1 TTTACTACTAT
*
29704068 TTTACTATTAT
1 TTTACTACTAT
*
29704079 GTTACTACTAT
1 TTTACTACTAT
29704090 T
1 T
29704091 ATGTTGTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (11 bp):
TTTACTACTAT
Found at i:29708565 original size:28 final size:28
Alignment explanation
Indices: 29708531--29708594 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
29708521 TTTTTAAAAA
* *
29708531 TAATTTTTATATTTTATAC-CTTTTTTAT
1 TAATTTTTAAATTTTAAACAC-TTTTTAT
29708559 TAATTTTTAAATTTTAAACACTTTTTAT
1 TAATTTTTAAATTTTAAACACTTTTTAT
*
29708587 AAATTTTT
1 TAATTTTT
29708595 TGAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (28 bp):
TAATTTTTAAATTTTAAACACTTTTTAT
Found at i:29711296 original size:41 final size:42
Alignment explanation
Indices: 29711239--29711321 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 42
29711229 TAGTCAAATG
*
29711239 GTCAAAAAGAAAAGAAAAGATGATTGGTCCTTCTCT-TCTCT
1 GTCAAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTCTCT
*
29711280 GTCAAAAAGAAAAGAAAATATGATTAGTCCTTCTCTGTCTCT
1 GTCAAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTCTCT
29711322 TTTTTCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 34 0.87
42 5 0.13
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (42 bp):
GTCAAAAAGAAAAGAAAAGATGATTAGTCCTTCTCTGTCTCT
Found at i:29713931 original size:9 final size:9
Alignment explanation
Indices: 29713917--29713953 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29713907 TATAGTTTGA
29713917 TATTCGAAT
1 TATTCGAAT
29713926 TATTCGAAT
1 TATTCGAAT
*
29713935 TATTCGAGT
1 TATTCGAAT
29713944 TATTCGAAT
1 TATTCGAAT
29713953 T
1 T
29713954 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29714022 original size:9 final size:9
Alignment explanation
Indices: 29714005--29714035 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29713995 TCGAGTTGAT
29714005 TCGAATAAC
1 TCGAATAAC
*
29714014 TCGATTAAC
1 TCGAATAAC
29714023 TCGAATAAC
1 TCGAATAAC
29714032 TCGA
1 TCGA
29714036 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:29715196 original size:14 final size:14
Alignment explanation
Indices: 29715177--29715207 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29715167 TTCCATTTTC
29715177 TCTTCTTCTCCTCT
1 TCTTCTTCTCCTCT
*
29715191 TCTTCTTTTCCTCT
1 TCTTCTTCTCCTCT
29715205 TCT
1 TCT
29715208 CCTCTATTTC
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:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTTCTTCTCCTCT
Found at i:29715229 original size:11 final size:11
Alignment explanation
Indices: 29715174--29715232 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
29715164 TCCTTCCATT
29715174 TTCTCTTCTTC
1 TTCTCTTCTTC
*
29715185 TCCTCTTCTTC
1 TTCTCTTCTTC
* *
29715196 TTTTCCTCTTC
1 TTCTCTTCTTC
*
29715207 TCCTCTAT-TTC
1 TTCTCT-TCTTC
*
29715218 TTCTCTTATTC
1 TTCTCTTCTTC
29715229 TTCT
1 TTCT
29715233 TCTACTGCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 1 0.03
11 36 0.95
12 1 0.03
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:29715229 original size:22 final size:22
Alignment explanation
Indices: 29715174--29715229 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
29715164 TCCTTCCATT
29715174 TTCTCTTCTTCTCCTCTTCTTC
1 TTCTCTTCTTCTCCTCTTCTTC
* *
29715196 TTTTCCTCTTCTCCTCTAT-TTC
1 TTCTCTTCTTCTCCTCT-TCTTC
*
29715218 TTCTCTTATTCT
1 TTCTCTTCTTCT
29715230 TCTTCTACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.04, C:0.36, G:0.00, T:0.61
Consensus pattern (22 bp):
TTCTCTTCTTCTCCTCTTCTTC
Found at i:29715567 original size:24 final size:24
Alignment explanation
Indices: 29715521--29715569 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29715511 ACATTTTTTT
**
29715521 ATTTGATTGAATTTTGCTATTAAA
1 ATTTGATTGAATTTTAATATTAAA
* *
29715545 ATTTGATTTAATTTTAATTTTAAA
1 ATTTGATTGAATTTTAATATTAAA
29715569 A
1 A
29715570 AAATTGAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (24 bp):
ATTTGATTGAATTTTAATATTAAA
Found at i:29715643 original size:24 final size:23
Alignment explanation
Indices: 29715616--29715661 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
29715606 AAATTTATTT
29715616 TAATAGCTAAAAATAATAATTAAG
1 TAATAGCTAAAAATAA-AATTAAG
** *
29715640 TAATATTTAAAATTAAAATTAA
1 TAATAGCTAAAAATAAAATTAA
29715662 CTATATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
TAATAGCTAAAAATAAAATTAAG
Found at i:29715659 original size:23 final size:25
Alignment explanation
Indices: 29715623--29715671 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
29715613 TTTTAATAGC
*
29715623 TAAAAATAATAATTAAGTA-ATATT
1 TAAAAATAATAATTAACTATATATT
*
29715647 TAAAATTAA-AATTAACTATATATT
1 TAAAAATAATAATTAACTATATATT
29715671 T
1 T
29715672 GAGTTGAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAAAATAATAATTAACTATATATT
Found at i:29719237 original size:27 final size:27
Alignment explanation
Indices: 29719196--29719251 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 27
29719186 TAGTCTTAAT
29719196 TTTTAAAATTAAAAAGTTA-AAAAAAAA
1 TTTTAAAATTAAAAA-TTAGAAAAAAAA
29719223 TTTT-AAATTAGAAAATTATGAAAAAAAA
1 TTTTAAAATTA-AAAATTA-GAAAAAAAA
29719251 T
1 T
29719252 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 9 0.35
27 8 0.31
28 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
TTTTAAAATTAAAAATTAGAAAAAAAA
Found at i:29721050 original size:43 final size:41
Alignment explanation
Indices: 29720991--29721122 Score: 111
Period size: 43 Copynumber: 3.1 Consensus size: 41
29720981 ACCACCAGTG
* * *
29720991 TTTGCAGATGAACTGCCAGTAGGTTATGGATGCACAACATA
1 TTTGCAAATAAACTGCCAGTAGGTTATGGATACACAACATA
* * * * * *
29721032 TTTGCAAATAAGAGCTGCCAATAAGTTTGTGGATAAACCATCAGTG
1 TTTGCAAATAA-A-CTGCCAGT-AGGTTATGGATACA-CAACA-TA
* * *
29721078 TTTGCAAATAAATTGCCAGTAGGTTATGAATACACAACGTA
1 TTTGCAAATAAACTGCCAGTAGGTTATGGATACACAACATA
29721119 TTTG
1 TTTG
29721123 TAGACAAAAG
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
41 14 0.21
42 4 0.06
43 17 0.25
44 16 0.24
45 5 0.07
46 12 0.18
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (41 bp):
TTTGCAAATAAACTGCCAGTAGGTTATGGATACACAACATA
Found at i:29721121 original size:87 final size:87
Alignment explanation
Indices: 29720974--29721170 Score: 232
Period size: 87 Copynumber: 2.3 Consensus size: 87
29720964 CTCCAATTTT
* * * * * *
29720974 TGGATGAACCACCAGTGTTTGCAGATGAACTGCCAGTAGGTTATGGATGCACAACATATTTGCAA
1 TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATATTTGCAA
* * * * *
29721039 ATAAGAGCTGCCAATAAGTTTG
66 ACAAAAGATGCCAATAAATTCG
* * * *
29721061 TGGATAAACCATCAGTGTTTGCAAATAAATTGCCAGTAGGTTATGAATACACAACGTATTTGTAG
1 TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATATTTGCAA
* *
29721126 ACAAAAGATGCTAGTAAATTCG
66 ACAAAAGATGCCAATAAATTCG
*
29721148 TGGATAAACCATTAGTGTTTGCA
1 TGGATAAACCATCAGTGTTTGCA
29721171 GATTATTAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
87 92 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (87 bp):
TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATATTTGCAA
ACAAAAGATGCCAATAAATTCG
Found at i:29724517 original size:53 final size:53
Alignment explanation
Indices: 29724447--29724583 Score: 184
Period size: 53 Copynumber: 2.6 Consensus size: 53
29724437 TGAAGAATCT
* *
29724447 TATCGTGTAAGACCGTAATTGGTGGGTTATGACATCATATGGAAAGAAGACCA
1 TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAGACCA
* *
29724500 TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAAATCA
1 TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAGACCA
** * ** *
29724553 TATAATGTAAGATTGTAACTGGTGGTTTATG
1 TATCGTGTAAAACCGTAACTGGTGGGTTATG
29724584 GGAAAAATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (53 bp):
TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAGACCA
Found at i:29724804 original size:61 final size:61
Alignment explanation
Indices: 29724705--29724859 Score: 213
Period size: 61 Copynumber: 2.5 Consensus size: 61
29724695 CAAGAAAGGA
* * *
29724705 AAGCCTTTTTGGCGAGTACTGAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACA-AG
1 AAGCCTTTGTGGCGAGTACTAAATGTAAATGAACGCCTTTGTAACAAAACTCTAGACATAG
* * * * *
29724765 AATGCCTTTGTGGAGAGTACTAAATGTAAATGAACGCCTTTGTAGCAAAATTCTGGACATGG
1 AA-GCCTTTGTGGCGAGTACTAAATGTAAATGAACGCCTTTGTAACAAAACTCTAGACATAG
*
29724827 AAGCTTTTGTGGCGAGTACTAAATGTAAATGAA
1 AAGCCTTTGTGGCGAGTACTAAATGTAAATGAA
29724860 TACCTTCGTG
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
60 2 0.02
61 78 0.94
62 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (61 bp):
AAGCCTTTGTGGCGAGTACTAAATGTAAATGAACGCCTTTGTAACAAAACTCTAGACATAG
Found at i:29727168 original size:27 final size:27
Alignment explanation
Indices: 29727138--29727191 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
29727128 AAAATAAAAC
29727138 AATGTTGATTACATGTGTATAGACCAT
1 AATGTTGATTACATGTGTATAGACCAT
29727165 AATGTTGATTACATGTGTATAGACCAT
1 AATGTTGATTACATGTGTATAGACCAT
29727192 GTATTGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (27 bp):
AATGTTGATTACATGTGTATAGACCAT
Found at i:29731633 original size:87 final size:87
Alignment explanation
Indices: 29731487--29731664 Score: 356
Period size: 87 Copynumber: 2.0 Consensus size: 87
29731477 ATATCAATTA
29731487 TACCAAATAAGTGTCACAAAACCACATTGCCCCGCATCTATTAGAAGACCTGTCCTAAACAACTA
1 TACCAAATAAGTGTCACAAAACCACATTGCCCCGCATCTATTAGAAGACCTGTCCTAAACAACTA
29731552 AATAGTTTTCCTTGAAGCACAT
66 AATAGTTTTCCTTGAAGCACAT
29731574 TACCAAATAAGTGTCACAAAACCACATTGCCCCGCATCTATTAGAAGACCTGTCCTAAACAACTA
1 TACCAAATAAGTGTCACAAAACCACATTGCCCCGCATCTATTAGAAGACCTGTCCTAAACAACTA
29731639 AATAGTTTTCCTTGAAGCACAT
66 AATAGTTTTCCTTGAAGCACAT
29731661 TACC
1 TACC
29731665 TTTGGCAAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (87 bp):
TACCAAATAAGTGTCACAAAACCACATTGCCCCGCATCTATTAGAAGACCTGTCCTAAACAACTA
AATAGTTTTCCTTGAAGCACAT
Found at i:29739340 original size:50 final size:52
Alignment explanation
Indices: 29739215--29739345 Score: 144
Period size: 50 Copynumber: 2.6 Consensus size: 52
29739205 TGAACAAATG
* *
29739215 AGTTACTTAATGCA-AGA-TTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTT-ATTTAATGATGCAGACTTAAACTAACATGGA
** * * *
29739267 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
29739317 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
29739346 CAGAATACAC
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
50 31 0.48
51 15 0.23
52 17 0.26
53 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:29743821 original size:63 final size:62
Alignment explanation
Indices: 29743750--29743920 Score: 207
Period size: 63 Copynumber: 2.7 Consensus size: 62
29743740 AAAAACATGT
* * *
29743750 GTGTGTCTAGCCCGTGTAACTCTTTGATTTCAGATTTGAGTCATACAGGCAAGACACACGGGC
1 GTGTGTCTAG-CCGTGTAACTCTCTGACTTCAGATTTGAGTCACACAGGCAAGACACACGGGC
* * * * * * *
29743813 GTGTGTCTAAGCCTTGTAACTCTCTAACTTCAGATTGGAGTTACACGGGTAAGACACACGGGT
1 GTGTGTCT-AGCCGTGTAACTCTCTGACTTCAGATTTGAGTCACACAGGCAAGACACACGGGC
* *
29743876 GTGTGTCTAGGCCGTGTAACTCACTGACTTCAGATTTGAGACACA
1 GTGTGTCTA-GCCGTGTAACTCTCTGACTTCAGATTTGAGTCACA
29743921 TGGGCGTGTG
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
62 1 0.01
63 87 0.97
64 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (62 bp):
GTGTGTCTAGCCGTGTAACTCTCTGACTTCAGATTTGAGTCACACAGGCAAGACACACGGGC
Found at i:29748033 original size:16 final size:16
Alignment explanation
Indices: 29748012--29748042 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29748002 CAATATCCAA
*
29748012 TTATCATATTTACACG
1 TTATCACATTTACACG
29748028 TTATCACATTTACAC
1 TTATCACATTTACAC
29748043 ATTCATTCAT
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:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATCACATTTACACG
Found at i:29748897 original size:2 final size:2
Alignment explanation
Indices: 29748890--29748976 Score: 75
Period size: 2 Copynumber: 47.5 Consensus size: 2
29748880 ATATTATAAC
* * *
29748890 AT AT AT AT AT AT TT CT -T AT -T AT AT A- AT AT A- AC AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29748927 AT AT AT A- AT A- AGT -T A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29748966 AT AT AT AT AT A
1 AT AT AT AT AT A
29748977 ATCATCATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
1 9 0.12
2 63 0.88
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29750401 original size:41 final size:39
Alignment explanation
Indices: 29750356--29750447 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
29750346 AGCGGTATTT
*
29750356 TTAGCGGCGTTTGGACAAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCGTTTCGA-AAAAAACGCCGCTAAAAA-TGAGCA
* * ** *
29750397 TTAGCGGCGCTTCTAGGAAAGCGCCGCTAAAAATGAGCA
1 TTAGCGGCGTTTCGAAAAAAACGCCGCTAAAAATGAGCA
29750436 TTAGCGGCGTTT
1 TTAGCGGCGTTT
29750448 TTTGGAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 17 0.39
40 15 0.34
41 12 0.27
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (39 bp):
TTAGCGGCGTTTCGAAAAAAACGCCGCTAAAAATGAGCA
Found at i:29750468 original size:39 final size:40
Alignment explanation
Indices: 29750373--29750468 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 40
29750363 CGTTTGGACA
*
29750373 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCTAGG
1 AAAAACGCCGC-AAAAAATGAGCATTAGCGGCGCTTCTAGG
* * * * *
29750414 -AAAGCGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCAAAAAATGAGCATTAGCGGCGCTTCTAGG
29750453 AAAAAC-CCGCAAAAAA
1 AAAAACGCCGCAAAAAA
29750469 CCTAAGCCCA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
39 33 0.72
40 13 0.28
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (40 bp):
AAAAACGCCGCAAAAAATGAGCATTAGCGGCGCTTCTAGG
Found at i:29750556 original size:41 final size:40
Alignment explanation
Indices: 29750511--29750693 Score: 258
Period size: 41 Copynumber: 4.4 Consensus size: 40
29750501 TTTAACGATA
* *
29750511 TTTTTGAGAAAGCGTCGCTAATGCTCGGGGCTTTAGCAGCG
1 TTTTTGA-AAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCG
29750552 TTTTTGAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCG
1 TTTTTGAA-AAGCGCCGCTAATGCTCGGGGCTTTAGCGGCG
** *
29750593 TTTTCCAAGAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCG
1 TTTTTGAA-AAGCGCCGCTAATGCTCGGGGCTTTAGCGGCG
*
29750634 TTTTTTGAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGTG
1 -TTTTTG-AAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCG
29750676 TTTTTGAAAAAGCGCCGC
1 TTTTTG-AAAAGCGCCGC
29750694 AAAAATATTT
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.01
41 93 0.72
42 34 0.26
43 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.28
Consensus pattern (40 bp):
TTTTTGAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCG
Found at i:29750669 original size:83 final size:82
Alignment explanation
Indices: 29750519--29750693 Score: 269
Period size: 83 Copynumber: 2.1 Consensus size: 82
29750509 TATTTTTGAG
* *
29750519 AAAGCGTCGCTAATGCTCGGGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGGCT
1 AAAGCGCCGCTAATGCTCGGGGCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGCT
29750584 TTAGCGGCGTTTTCCAA
66 TTAGCGGCGTTTTCCAA
* * *
29750601 GAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
1 AAAGCGCCGCTAATGCTCGGGGCTTTAGCAGCG-TTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* **
29750666 TTTAGCGGTGTTTTTGAA
65 TTTAGCGGCGTTTTCCAA
29750684 AAAGCGCCGC
1 AAAGCGCCGC
29750694 AAAAATATTT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 29 0.35
83 54 0.65
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.27
Consensus pattern (82 bp):
AAAGCGCCGCTAATGCTCGGGGCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGCT
TTAGCGGCGTTTTCCAA
Found at i:29751087 original size:14 final size:15
Alignment explanation
Indices: 29751052--29751091 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
29751042 TAGTGTAAGG
*
29751052 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
29751067 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
29751082 -TTAGGGATTA
1 TTTAGGGATTA
29751092 AGGTTTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:29751102 original size:15 final size:14
Alignment explanation
Indices: 29751047--29751098 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
29751037 GATAATAGTG
*
29751047 TAAGGTTTAGGGAG
1 TAAGGTTTAGGGAT
*
29751061 TATGGATTTAGGGAT
1 TAAGG-TTTAGGGAT
* *
29751076 TATGGATTAGGGAT
1 TAAGGTTTAGGGAT
29751090 TAAGGTTTA
1 TAAGGTTTA
29751099 AGGGTTAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (14 bp):
TAAGGTTTAGGGAT
Found at i:29751161 original size:21 final size:21
Alignment explanation
Indices: 29751121--29751161 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29751111 TAAGGTTTAG
* * *
29751121 AGGTTAGGGGTTAGGGGTTAA
1 AGGTTAAGGGTTAAGAGTTAA
29751142 AGGTTAAGGGTTAAGAGTTA
1 AGGTTAAGGGTTAAGAGTTA
29751162 GGGATTTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (21 bp):
AGGTTAAGGGTTAAGAGTTAA
Found at i:29754936 original size:42 final size:43
Alignment explanation
Indices: 29754890--29755082 Score: 239
Period size: 43 Copynumber: 4.5 Consensus size: 43
29754880 GAAGCGTTGT
* * **
29754890 TAAAGGT-TTGTTCTATAGTGGCGCTTGTGGGAAAAGCGCCGC
1 TAAAGGTCTTGATCTATAGCGGCATTTGTGGGAAAAGCGCCGC
** * **
29754932 TAAAGGTCTTGAGATATAGCGGCGTTTGTGAAAAAAGCGCCGC
1 TAAAGGTCTTGATCTATAGCGGCATTTGTGGGAAAAGCGCCGC
* *
29754975 TAAAGGTCTTGATCTATAGCGGCATTTGT-GCAAAAGCCCCGC
1 TAAAGGTCTTGATCTATAGCGGCATTTGTGGGAAAAGCGCCGC
*
29755017 TAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGCGCCGC
1 TAAAGGTCTTGATCTATAGCGGCATTTGTGGGAAAAGCGCCGC
*
29755060 TAAAGGTCAT-AGTCTATAGCGGC
1 TAAAGGTCTTGA-TCTATAGCGGC
29755083 GTTTATTTCT
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 46 0.35
43 85 0.65
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (43 bp):
TAAAGGTCTTGATCTATAGCGGCATTTGTGGGAAAAGCGCCGC
Found at i:29755010 original size:85 final size:86
Alignment explanation
Indices: 29754890--29755082 Score: 239
Period size: 85 Copynumber: 2.3 Consensus size: 86
29754880 GAAGCGTTGT
* * * * * *
29754890 TAAAGGT-TTGTTCTATAGTGGCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGATATAGCGG
1 TAAAGGTCTTGATCTATAGCGGCACTTGTGGCAAAAGCCCCGCTAAAGGTCCTGAGATATAGCGG
*
29754954 CGTTTGTGAAAAAAGCGCCGC
66 CATTTGTGAAAAAAGCGCCGC
* **
29754975 TAAAGGTCTTGATCTATAGCGGCATTTGT-GCAAAAGCCCCGCTAAAGGTCCTGATCTATAGCGG
1 TAAAGGTCTTGATCTATAGCGGCACTTGTGGCAAAAGCCCCGCTAAAGGTCCTGAGATATAGCGG
**
29755039 CATTTGTGGGAAAAGCGCCGC
66 CATTTGTGAAAAAAGCGCCGC
*
29755060 TAAAGGTCAT-AGTCTATAGCGGC
1 TAAAGGTCTTGA-TCTATAGCGGC
29755083 GTTTATTTCT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
84 1 0.01
85 75 0.81
86 17 0.18
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (86 bp):
TAAAGGTCTTGATCTATAGCGGCACTTGTGGCAAAAGCCCCGCTAAAGGTCCTGAGATATAGCGG
CATTTGTGAAAAAAGCGCCGC
Found at i:29756483 original size:14 final size:15
Alignment explanation
Indices: 29756464--29756494 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
29756454 TATTTTACTG
29756464 TTTTTGAAAAAT-GA
1 TTTTTGAAAAATAGA
29756478 TTTTTGAAAAATAGA
1 TTTTTGAAAAATAGA
29756493 TT
1 TT
29756495 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (15 bp):
TTTTTGAAAAATAGA
Found at i:29756520 original size:20 final size:21
Alignment explanation
Indices: 29756478--29756521 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
29756468 TGAAAAATGA
*
29756478 TTTTTGAAAAATAGATTAATT
1 TTTTTAAAAAATAGATTAATT
29756499 TTTTTAAAAAATAGA-T-ATT
1 TTTTTAAAAAATAGATTAATT
29756518 TTTT
1 TTTT
29756522 ATGTTTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTTAAAAAATAGATTAATT
Found at i:29756843 original size:24 final size:23
Alignment explanation
Indices: 29756816--29756862 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29756806 ACAAATACTC
29756816 ATATTTTATA-TAATTAAAATATTT
1 ATATTTTATACT-A-TAAAATATTT
*
29756840 ATATTTTGTACTATAAAATATTT
1 ATATTTTATACTATAAAATATTT
29756863 TTTAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 10 0.48
25 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTTTATACTATAAAATATTT
Found at i:29756860 original size:17 final size:18
Alignment explanation
Indices: 29756840--29756879 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
29756830 TAAAATATTT
*
29756840 ATATTTTGTACTATAA-A
1 ATATTTTGTAATATAATA
*
29756857 ATATTTTTTAATATAATA
1 ATATTTTGTAATATAATA
29756875 ATATT
1 ATATT
29756880 AAGCTTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTTTGTAATATAATA
Found at i:29760881 original size:95 final size:96
Alignment explanation
Indices: 29760777--29761055 Score: 305
Period size: 95 Copynumber: 2.9 Consensus size: 96
29760767 GTTTGTCAAT
* * * ** *
29760777 TAAATTAATTATAAATTTTT-CAAAATTGGATTAGGTTTCGTGTTTATTGTTTTTTAAGAAAAAA
1 TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGTTTAGTGTTTAAGGGTTTTTAAGAAAAAA
* * *
29760841 TCAATTAAATTAGGGTTTAGGGTTACTTGAG
66 TCAAATAAATTAGGGTTCAAGGTTACTTGAG
* * * *
29760872 TAATTTAA-T-TAATTTTATTAAAAAATTAGATTAGGATTTAGAG-TTAAGGGTTTTTAAGGAAA
1 TAAATTAATTATAAATTT-TTAAAAAATTAGATTAGG-TTTAGTGTTTAAGGGTTTTTAAGAAAA
29760934 AATCAAATAAATTAGGGTTCAAGGTTACTTGAG
64 AATCAAATAAATTAGGGTTCAAGGTTACTTGAG
*
29760967 TAAATTAATTATAAATTTTTATAAAATTAGATTAAGGTTTAGTGTTTAGGATTTAGGGTTTTTAA
1 TAAATTAATTATAAATTTTTAAAAAATTAGATT-AGGTTTAGTGTTT---A---AGGGTTTTTAA
* *
29761032 GTAAAACTCAAATAAATTAGGGTT
59 GAAAAAATCAAATAAATTAGGGTT
29761056 TGGGAAACTC
Statistics
Matches: 152, Mismatches: 19, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
93 6 0.04
94 3 0.02
95 72 0.47
96 26 0.17
97 11 0.07
100 1 0.01
103 33 0.22
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (96 bp):
TAAATTAATTATAAATTTTTAAAAAATTAGATTAGGTTTAGTGTTTAAGGGTTTTTAAGAAAAAA
TCAAATAAATTAGGGTTCAAGGTTACTTGAG
Found at i:29761052 original size:29 final size:27
Alignment explanation
Indices: 29761019--29761081 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 27
29761009 TGTTTAGGAT
*
29761019 TTAGGGTTTTTAAGTAAAACTCAAATAAA
1 TTAGGGTTTTT--GGAAAACTCAAATAAA
*
29761048 TTAGGG--TTTGGGAAACTCAAATAAA
1 TTAGGGTTTTTGGAAAACTCAAATAAA
29761073 TTAGGGTTT
1 TTAGGGTTT
29761082 GGGGTTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 20 0.67
27 4 0.13
29 6 0.20
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (27 bp):
TTAGGGTTTTTGGAAAACTCAAATAAA
Found at i:29761069 original size:25 final size:25
Alignment explanation
Indices: 29761035--29761084 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
29761025 TTTTTAAGTA
29761035 AAACTCAAATAAATTAGGGTTTGGG
1 AAACTCAAATAAATTAGGGTTTGGG
29761060 AAACTCAAATAAATTAGGGTTTGGG
1 AAACTCAAATAAATTAGGGTTTGGG
29761085 GTTTAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (25 bp):
AAACTCAAATAAATTAGGGTTTGGG
Found at i:29761294 original size:126 final size:127
Alignment explanation
Indices: 29761120--29761410 Score: 505
Period size: 126 Copynumber: 2.3 Consensus size: 127
29761110 TTGTTAATTT
* * * *
29761120 AAAGAAGCTCCCACGTGGATGCACTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACATGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
*
29761185 GTTTCTGAGCAAATAGTGTC-AAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGACCAAATAGTGTCAAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
29761246 AAAGAAGCTCCCACTTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACATGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
*
29761311 GTTTCTGACCAAATAGTGTCAAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTATTG
66 GTTTCTGACCAAATAGTGTCAAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
29761373 AAAGAAGCTCCCA-ATGGACGCGCTTTTGCTACAGTAGC
1 AAAGAAGCTCCCACATGGACGCGCTTTTGCTACAGTAGC
29761411 GCATGTTTGG
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
126 104 0.66
127 53 0.34
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (127 bp):
AAAGAAGCTCCCACATGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGACCAAATAGTGTCAAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:29765146 original size:25 final size:26
Alignment explanation
Indices: 29765075--29765127 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29765065 TATTTCTAAA
*
29765075 TATAAGTAAAATAAAGCTAATAATTT
1 TATAAGTAAAATAAAACTAATAATTT
29765101 TATAAGTAAAATAAAACTAATAATTT
1 TATAAGTAAAATAAAACTAATAATTT
29765127 T
1 T
29765128 TAGTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (26 bp):
TATAAGTAAAATAAAACTAATAATTT
Found at i:29766910 original size:31 final size:31
Alignment explanation
Indices: 29766850--29766913 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
29766840 GTTGAATACC
*
29766850 CAATAACTTAAATAAAAACTTCTGAATAGTT
1 CAATAACTTAAATAAAAACTTCTCAATAGTT
* *
29766881 CAATTACTTAAATGAAAACTT-TCATATAGTT
1 CAATAACTTAAATAAAAACTTCTCA-ATAGTT
29766912 CA
1 CA
29766914 GTAATCACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.34
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTCTCAATAGTT
Found at i:29771306 original size:17 final size:19
Alignment explanation
Indices: 29771273--29771313 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
29771263 CATGTTGCAT
29771273 GCCCATGTGGTCCCACAC-
1 GCCCATGTGGTCCCACACG
29771291 GCCCATGTGG-CCCACACG
1 GCCCATGTGGTCCCACACG
29771309 GCCCA
1 GCCCA
29771314 AAATGGCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.17, C:0.46, G:0.24, T:0.12
Consensus pattern (19 bp):
GCCCATGTGGTCCCACACG
Found at i:29776073 original size:340 final size:340
Alignment explanation
Indices: 29775453--29776136 Score: 1323
Period size: 340 Copynumber: 2.0 Consensus size: 340
29775443 AGGATGGAAA
* *
29775453 TATATATTGGTTATGAATCTCCTTCTATAATTAAGTATGTTAAACCATGTTAAGTATGAATCATG
1 TATATATTGGTTATGAATCTCATTCTATAATTAAGTATGTTAAACCATGTTAAGTATGAATCATA
*
29775518 TTTTAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCTGCTTATTTGTTTCAATCAAACTCTG
66 TTTCAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCTGCTTATTTGTTTCAATCAAACTCTG
29775583 ATTAGTCTAGATTATTTTATTATTATTTGACCTATAAATTTGGCCTATAAATAGGCTCTTTTACA
131 ATTAGTCTAGATTATTTTATTATTATTTGACCTATAAATTTGGCCTATAAATAGGCTCTTTTACA
29775648 ACCTTAGAAAATACACCCATTAGAGATTAGAACTCATAATACTTTTAGAGAATTTTGTGTTTACG
196 ACCTTAGAAAATACACCCATTAGAGATTAGAACTCATAATACTTTTAGAGAATTTTGTGTTTACG
29775713 TTTTGAGGGTTATTTGTTTTTGGGTTTTTACGGTTTAGTTTTTTTATCTCCATCTTTTGTACTCT
261 TTTTGAGGGTTATTTGTTTTTGGGTTTTTACGGTTTAGTTTTTTTATCTCCATCTTTTGTACTCT
29775778 TCATTCTTTTGCCAT
326 TCATTCTTTTGCCAT
*
29775793 TATATATTGGTTATGAATCTCATTCTATAATTAAGTATGTTAAACTATGTTAAGTATGAATCATA
1 TATATATTGGTTATGAATCTCATTCTATAATTAAGTATGTTAAACCATGTTAAGTATGAATCATA
29775858 TTTCAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCTGCTTATTTGTTTCAATCAAACTCTG
66 TTTCAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCTGCTTATTTGTTTCAATCAAACTCTG
29775923 ATTAGTCTAGATTATTTTATTATTATTTGACCTATAAATTTGGCCTATAAATAGGCTCTTTTACA
131 ATTAGTCTAGATTATTTTATTATTATTTGACCTATAAATTTGGCCTATAAATAGGCTCTTTTACA
29775988 ACCTTAGAAAATACACCCATTAGAGATTAGAACTCATAATACTTTTAGAGAATTTTGTGTTTACG
196 ACCTTAGAAAATACACCCATTAGAGATTAGAACTCATAATACTTTTAGAGAATTTTGTGTTTACG
*
29776053 TTTTGAGGGTTATTTGTTTTTGGGTTTTTACGGTTTAGTTTTTTTATCTCCATCTTTTGTATTCT
261 TTTTGAGGGTTATTTGTTTTTGGGTTTTTACGGTTTAGTTTTTTTATCTCCATCTTTTGTACTCT
29776118 TCATTCTTTTGCCAT
326 TCATTCTTTTGCCAT
29776133 TATA
1 TATA
29776137 GTAAAAGTAT
Statistics
Matches: 339, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
340 339 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (340 bp):
TATATATTGGTTATGAATCTCATTCTATAATTAAGTATGTTAAACCATGTTAAGTATGAATCATA
TTTCAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCTGCTTATTTGTTTCAATCAAACTCTG
ATTAGTCTAGATTATTTTATTATTATTTGACCTATAAATTTGGCCTATAAATAGGCTCTTTTACA
ACCTTAGAAAATACACCCATTAGAGATTAGAACTCATAATACTTTTAGAGAATTTTGTGTTTACG
TTTTGAGGGTTATTTGTTTTTGGGTTTTTACGGTTTAGTTTTTTTATCTCCATCTTTTGTACTCT
TCATTCTTTTGCCAT
Found at i:29786753 original size:9 final size:9
Alignment explanation
Indices: 29786739--29786771 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
29786729 GAGTTGAACG
29786739 ATTCGAGTT
1 ATTCGAGTT
29786748 ATTCGAGTT
1 ATTCGAGTT
29786757 AATT-GAGTT
1 -ATTCGAGTT
29786766 ATTCGA
1 ATTCGA
29786772 ATCAACTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 3 0.14
9 16 0.73
10 3 0.14
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (9 bp):
ATTCGAGTT
Found at i:29786842 original size:9 final size:9
Alignment explanation
Indices: 29786825--29786888 Score: 110
Period size: 9 Copynumber: 7.1 Consensus size: 9
29786815 TGAGTTTTCG
29786825 AATTCGAAT
1 AATTCGAAT
*
29786834 AACTCGAAT
1 AATTCGAAT
29786843 AATTCGAAT
1 AATTCGAAT
*
29786852 AACTCGAAT
1 AATTCGAAT
29786861 AATTCGAAT
1 AATTCGAAT
29786870 AATTCGAAT
1 AATTCGAAT
29786879 AATTCGAAT
1 AATTCGAAT
29786888 A
1 A
29786889 TCAAACTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.