Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 26
Found at i:4649721 original size:140 final size:140
Alignment explanation
Indices: 4649469--4649880 Score: 711
Period size: 129 Copynumber: 3.0 Consensus size: 140
4649459 TTGCGTTGCG
* *
4649469 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAAAAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTAAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
4649534 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
4649599 AATACACATA
131 AATACACATA
*
4649609 ATAGTCAAATTCGCGTTGCGATAGTAAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTAAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
4649674 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAG--T-----T--
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
4649730 --TACACATA
131 AATACACATA
4649738 ATAGTCAAATTCGCGTTGCGATATTAAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTAAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
4649803 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
4649868 AATACACAAA
131 AATACACATA
4649878 ATA
1 ATA
4649881 CAACGTTTGC
Statistics
Matches: 256, Mismatches: 5, Indels: 22
0.90 0.02 0.08
Matches are distributed among these distances:
129 126 0.49
131 1 0.00
133 1 0.00
136 1 0.00
138 1 0.00
140 126 0.49
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTAAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:4651883 original size:14 final size:14
Alignment explanation
Indices: 4651864--4651900 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4651854 TCCCTTGGCA
4651864 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
4651878 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
4651892 TTCTTCTTC
1 TT-TTCTTC
4651901 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:4652124 original size:24 final size:24
Alignment explanation
Indices: 4652090--4652143 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4652080 CTGAAACATC
4652090 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
4652114 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4652138 ATCAAA
1 ATCAAA
4652144 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4652989 original size:20 final size:20
Alignment explanation
Indices: 4652964--4653051 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
4652954 GAAATTCAGT
* *
4652964 GTTGCGACAGTTAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
4652984 GTTGCGATGGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGC
* **
4653004 GTTGCAATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
4653025 GTTGTGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
4653045 GTTGCGA
1 GTTGCGA
4653052 ATCTGGAAAC
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.04
20 36 0.71
21 11 0.22
22 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:4653089 original size:20 final size:19
Alignment explanation
Indices: 4653066--4653111 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4653056 GGAAACTGAT
* *
4653066 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
4653086 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
4653105 TTGCGAT
1 TTGCGAT
4653112 TTTATTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:4653101 original size:19 final size:19
Alignment explanation
Indices: 4653077--4653113 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4653067 TGCGATACTG
*
4653077 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
4653096 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
4653114 TATTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:4657363 original size:54 final size:54
Alignment explanation
Indices: 4657233--4657344 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
4657223 ATGCCAGTCC
* * * * *
4657233 CAATCTTAAATCTAAACCCTAATCTATGCAAAATAAGATAAAATAATATAATCT
1 CAATCCTAAACCTAAACTCTAATATATGCAAAATAAAATAAAATAATATAATCT
*
4657287 CAATCCTAAACCTAAACTCTAATATATGCAAAATAAAATAAAAT-ATCATGATCT
1 CAATCCTAAACCTAAACTCTAATATATGCAAAATAAAATAAAATAAT-ATAATCT
4657341 CAAT
1 CAAT
4657345 TTCAATCTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.29
Consensus pattern (54 bp):
CAATCCTAAACCTAAACTCTAATATATGCAAAATAAAATAAAATAATATAATCT
Found at i:4662388 original size:13 final size:12
Alignment explanation
Indices: 4662369--4662423 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
4662359 GGTAATAAAC
4662369 AAAATTAACAAA
1 AAAATTAACAAA
4662381 ATAAATTAAC-AA
1 A-AAATTAACAAA
* *
4662393 AAAGTT--CAAT
1 AAAATTAACAAA
4662403 AAAATTAACAAA
1 AAAATTAACAAA
4662415 ATAAATTAA
1 A-AAATTAA
4662424 ATATTAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
9 1 0.03
10 6 0.18
11 4 0.12
12 8 0.24
13 15 0.44
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (12 bp):
AAAATTAACAAA
Found at i:4662632 original size:15 final size:15
Alignment explanation
Indices: 4662614--4662645 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4662604 ATCATCACCA
4662614 TCATCGTCGTCGTCG
1 TCATCGTCGTCGTCG
*
4662629 TCATCTTCGTCGTCG
1 TCATCGTCGTCGTCG
4662644 TC
1 TC
4662646 GTCAGGAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.34, G:0.22, T:0.38
Consensus pattern (15 bp):
TCATCGTCGTCGTCG
Found at i:4662638 original size:18 final size:18
Alignment explanation
Indices: 4662612--4662649 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4662602 TCATCATCAC
4662612 CATCATCGTCGTCGTCGT
1 CATCATCGTCGTCGTCGT
*
4662630 CATCTTCGTCGTCGTCGT
1 CATCATCGTCGTCGTCGT
4662648 CA
1 CA
4662650 GGAGCAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.34, G:0.21, T:0.34
Consensus pattern (18 bp):
CATCATCGTCGTCGTCGT
Found at i:4664715 original size:28 final size:31
Alignment explanation
Indices: 4664678--4664741 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 31
4664668 TGCACAAAAA
* *
4664678 AAATTATTAAATAAAATA-TTA-AAAAT-TT
1 AAATAATTAAATAAAATACTAACAAAATATT
4664706 AAATAATTAAATAAAATACTAACAAAATATT
1 AAATAATTAAATAAAATACTAACAAAATATT
4664737 AAATA
1 AAATA
4664742 TAGTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 17 0.55
29 2 0.06
30 5 0.16
31 7 0.23
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (31 bp):
AAATAATTAAATAAAATACTAACAAAATATT
Found at i:4671354 original size:16 final size:15
Alignment explanation
Indices: 4671335--4671380 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
4671325 GAATAAATGA
4671335 AAAAAAAATAAAGAAT
1 AAAAAAAATAAA-AAT
*
4671351 AAAAATAAGTAAAAAT
1 AAAAA-AAATAAAAAT
4671367 AAATAAAAATAAAA
1 AAA-AAAAATAAAA
4671381 GGCAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAAAAAATAAAAAT
Found at i:4671365 original size:10 final size:10
Alignment explanation
Indices: 4671348--4671379 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
4671338 AAAAATAAAG
4671348 AATAAAAATA
1 AATAAAAATA
*
4671358 AGTAAAAATA
1 AATAAAAATA
4671368 AATAAAAATA
1 AATAAAAATA
4671378 AA
1 AA
4671380 AGGCAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
AATAAAAATA
Found at i:4671715 original size:2 final size:2
Alignment explanation
Indices: 4671710--4671791 Score: 86
Period size: 2 Copynumber: 44.0 Consensus size: 2
4671700 TTAAAAAAAG
4671710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
4671751 TA -A TA TC TA -A AA AA TA TA TG TA TA TA TA -A TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4671788 TA TA
1 TA TA
4671792 GTGTAAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4671775 original size:35 final size:37
Alignment explanation
Indices: 4671727--4671804 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
4671717 ATATATATAT
4671727 ATATATATATATATATATATATAATA-ATA-TCTAAAAA
1 ATATATATATATATA-ATA-ATAATATATAGTCTAAAAA
* *
4671764 ATATATGTATATATAATAATAATATATAGTGTAAAAA
1 ATATATATATATATAATAATAATATATAGTCTAAAAA
4671801 ATAT
1 ATAT
4671805 CAATTGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
35 6 0.16
36 6 0.16
37 25 0.68
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (37 bp):
ATATATATATATATAATAATAATATATAGTCTAAAAA
Found at i:4672308 original size:37 final size:37
Alignment explanation
Indices: 4672267--4672371 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
4672257 GTGCTTGTGG
* *
4672267 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * *
4672304 ATCCTATTTTTAGGAGTTTTAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
4672341 ATCCTATTTTTAAGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
4672372 GACTAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:4672744 original size:22 final size:22
Alignment explanation
Indices: 4672718--4672780 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
4672708 ACCAAAGCAC
4672718 GGCATTTGATGCTCAAAGGTTT
1 GGCATTTGATGCTCAAAGGTTT
4672740 GGCATTTGATGCTCAAAGGTTT
1 GGCATTTGATGCTCAAAGGTTT
*
4672762 GGTATTTGATGCTCAAAGG
1 GGCATTTGATGCTCAAAGG
4672781 ATTGATGGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.35
Consensus pattern (22 bp):
GGCATTTGATGCTCAAAGGTTT
Found at i:4673431 original size:20 final size:20
Alignment explanation
Indices: 4673406--4673459 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 20
4673396 TTTTTGCTTA
*
4673406 TTTTCTTTTTTGTTCTTGTT
1 TTTTCTTTTTTGTTCTTGTC
4673426 TTTTCTTTTTTG---TT-TC
1 TTTTCTTTTTTGTTCTTGTC
4673442 TTTTCTTTTTTGTTCTTG
1 TTTTCTTTTTTGTTCTTG
4673460 ATTGAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 13 0.45
17 2 0.07
19 2 0.07
20 12 0.41
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTTGTTCTTGTC
Found at i:4673436 original size:36 final size:36
Alignment explanation
Indices: 4673390--4673459 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
4673380 TTTTTGTCCC
4673390 TTTTCCTTTTTGCTTATTTTCTTTTTTGTTCTTGTT
1 TTTTCCTTTTTGCTTATTTTCTTTTTTGTTCTTGTT
* * *
4673426 TTTTCTTTTTTGTTTCTTTTCTTTTTTGTTCTTG
1 TTTTCCTTTTTGCTTATTTTCTTTTTTGTTCTTG
4673460 ATTGAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.01, C:0.13, G:0.09, T:0.77
Consensus pattern (36 bp):
TTTTCCTTTTTGCTTATTTTCTTTTTTGTTCTTGTT
Found at i:4673447 original size:16 final size:16
Alignment explanation
Indices: 4673389--4673455 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
4673379 CTTTTTGTCC
* *
4673389 CTTTTCCTTTTTGCTT
1 CTTTTCTTTTTTGTTT
*
4673405 ATTTTCTTTTTTGTTCTTGT
1 CTTTTCTTTTTTG---TT-T
*
4673425 TTTTTCTTTTTTGTTT
1 CTTTTCTTTTTTGTTT
4673441 CTTTTCTTTTTTGTT
1 CTTTTCTTTTTTGTT
4673456 CTTGATTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 26 0.62
17 2 0.05
19 1 0.02
20 13 0.31
ACGTcount: A:0.01, C:0.13, G:0.07, T:0.78
Consensus pattern (16 bp):
CTTTTCTTTTTTGTTT
Found at i:4673458 original size:10 final size:10
Alignment explanation
Indices: 4673408--4673445 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
4673398 TTTGCTTATT
4673408 TTCTTTTTTG
1 TTCTTTTTTG
4673418 TTCTTGTTTT-
1 TTCTT-TTTTG
4673428 TTCTTTTTTG
1 TTCTTTTTTG
4673438 TTTCTTTT
1 -TTCTTTT
4673446 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.82
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:4678003 original size:18 final size:19
Alignment explanation
Indices: 4677966--4678003 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4677956 TGTTAGAGGG
*
4677966 AAAAAATGAATAAATGAAA
1 AAAAAATGAATAAATAAAA
*
4677985 AAAAAATGAA-GAATAAAA
1 AAAAAATGAATAAATAAAA
4678003 A
1 A
4678004 TGAGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAATGAATAAATAAAA
Found at i:4678020 original size:4 final size:4
Alignment explanation
Indices: 4678011--4678056 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
4678001 AAATGAGTAA
4678011 AAAT AAAT AAAT AAAT AAA- AGGAA- AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT -AAAT A
4678057 TTAATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.08
4 28 0.74
5 7 0.18
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:4678067 original size:2 final size:2
Alignment explanation
Indices: 4678060--4678088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4678050 TGAAATATTA
4678060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4678089 AATGAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4678319 original size:2 final size:2
Alignment explanation
Indices: 4678314--4678377 Score: 50
Period size: 2 Copynumber: 35.0 Consensus size: 2
4678304 TAAAAAAAAG
* * *
4678314 TA TA TA TA TA TA TA TA TA TA TA -A TA -A TA TC TA -A AA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4678353 TA TG TA TA TA TA -A TA -A TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4678378 GTGTAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
1 6 0.12
2 45 0.88
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Found at i:4678361 original size:37 final size:38
Alignment explanation
Indices: 4678307--4678387 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
4678297 AAATATTTAA
4678307 AAAAAAGTATATATATATATATATATATAATA-ATA-TCT
1 AAAAAAGTATATATATATATA-ATA-ATAATATATAGTCT
* *
4678345 AAAAAA-TATATGTATATATAATAATAATATATAGTGT
1 AAAAAAGTATATATATATATAATAATAATATATAGTCT
4678382 AAAAAA
1 AAAAAA
4678388 ATCAATTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 6 0.15
36 6 0.15
37 21 0.54
38 6 0.15
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (38 bp):
AAAAAAGTATATATATATATAATAATAATATATAGTCT
Found at i:4678892 original size:37 final size:37
Alignment explanation
Indices: 4678851--4678955 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
4678841 GTGCTTGTGG
* * *
4678851 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
4678888 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
4678925 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
4678956 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:4683190 original size:2 final size:2
Alignment explanation
Indices: 4683180--4683259 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
4683170 GTCTGCATTC
*
4683180 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4683222 AT GT 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
4683260 CATAGAAATG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4685620 original size:25 final size:25
Alignment explanation
Indices: 4685587--4685640 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
4685577 GTGCAGGTTT
4685587 AGCAGCAAGCATACCAGTTTGTTCC
1 AGCAGCAAGCATACCAGTTTGTTCC
4685612 AGCAGCAAGCATACCAGTTTGTTCC
1 AGCAGCAAGCATACCAGTTTGTTCC
4685637 AGCA
1 AGCA
4685641 ACCCTCGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (25 bp):
AGCAGCAAGCATACCAGTTTGTTCC
Found at i:4694410 original size:50 final size:50
Alignment explanation
Indices: 4694337--4694455 Score: 166
Period size: 50 Copynumber: 2.4 Consensus size: 50
4694327 ATTCTTCCAT
* * ** *
4694337 ACTCTTCCATAAGGTTCCGCACATATCTAGAATATTCCAGAGGATTCAAC
1 ACTCTTCCACAAGCTTCTACACATATCCAGAATATTCCAGAGGATTCAAC
* *
4694387 ACTCTTCCACAAGCTTCTACACATCTCCAGAATATTCCAGAGGATTCCAC
1 ACTCTTCCACAAGCTTCTACACATATCCAGAATATTCCAGAGGATTCAAC
*
4694437 ATTCTTCCACAAGCTTCTA
1 ACTCTTCCACAAGCTTCTA
4694456 GAGAGTTCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (50 bp):
ACTCTTCCACAAGCTTCTACACATATCCAGAATATTCCAGAGGATTCAAC
Found at i:4699125 original size:50 final size:50
Alignment explanation
Indices: 4699062--4699186 Score: 169
Period size: 50 Copynumber: 2.5 Consensus size: 50
4699052 TTTCATATTC
* * * * *
4699062 TTCCATACTCTTCCATAAGGTTCTACACAGCTCTAGAATATTCCAGAGGA
1 TTCCACACTCTTCCACAAGATTCTACACAGCTCCAGAATATTCCAGAAGA
* * *
4699112 TTTCACACTCTTCCACAAGCTTCTACACATCTCCAGAATATTCCAGAAGA
1 TTCCACACTCTTCCACAAGATTCTACACAGCTCCAGAATATTCCAGAAGA
*
4699162 TTCCATACTCTTCCACAAGATTCTA
1 TTCCACACTCTTCCACAAGATTCTA
4699187 GAGAATTCTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (50 bp):
TTCCACACTCTTCCACAAGATTCTACACAGCTCCAGAATATTCCAGAAGA
Found at i:4699269 original size:40 final size:40
Alignment explanation
Indices: 4699181--4699269 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
4699171 CTTCCACAAG
* *** *
4699181 ATTCTAGAGAATTCTACACTTCTCTAGAGTTCTCTGGAAT
1 ATTCTAGAAAATTCTACACTTCTCTAGAAAACTCTAGAAT
4699221 ATTCTAGAAAATTCTACACTTCTAC-AGAAAACTCTAGAAT
1 ATTCTAGAAAATTCTACACTTCT-CTAGAAAACTCTAGAAT
* *
4699261 TTTTTAGAA
1 ATTCTAGAA
4699270 CCTCTTCAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 40 0.98
41 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (40 bp):
ATTCTAGAAAATTCTACACTTCTCTAGAAAACTCTAGAAT
Found at i:4700479 original size:12 final size:13
Alignment explanation
Indices: 4700452--4700480 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4700442 TCAATTAGGA
4700452 TTTAAGATATTAT
1 TTTAAGATATTAT
4700465 TTTAA-ATATTAT
1 TTTAAGATATTAT
4700477 TTTA
1 TTTA
4700481 TCTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTAAGATATTAT
Found at i:4700528 original size:80 final size:82
Alignment explanation
Indices: 4700370--4700548 Score: 274
Period size: 80 Copynumber: 2.2 Consensus size: 82
4700360 AAACTCAAGT
* *
4700370 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTT
1 TTTAAGATATTATTTTAAACATTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTT
4700435 TAGTATTTCAATTAGGA
66 TAGTATTTCAATTAGGA
* *
4700452 TTTAAGATATTATTTTAAATA-T-TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTT
1 TTTAAGATATTATTTTAAACATTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTT
* *
4700514 TAAGTGTTTTAATTAGGA
66 T-AGTATTTCAATTAGGA
4700532 TTTAAGATATTATTTTA
1 TTTAAGATATTATTTTA
4700549 GGAATTATCT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
79 5 0.06
80 66 0.73
81 1 0.01
82 18 0.20
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.55
Consensus pattern (82 bp):
TTTAAGATATTATTTTAAACATTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATATGTTT
TAGTATTTCAATTAGGA
Found at i:4701154 original size:17 final size:17
Alignment explanation
Indices: 4701129--4701162 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4701119 CTTTATCCCA
*
4701129 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
4701146 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
4701163 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:4708799 original size:85 final size:84
Alignment explanation
Indices: 4708656--4708814 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 84
4708646 TTAAACGTTA
* **
4708656 TATTTTATCTTTTTTTTAGTATTTTAGTTTAAATAAGTTTTAGTATTTCAATTAGGATTT-AGGA
1 TATTTTATCTTTGTTTTAGTATTTTAGCCTAAATAAGTTTTAGTATTTCAATTAGGATTTGA-GA
4708720 TATTATTTTAAATATTATTT
65 TATTATTTTAAATATTATTT
* *
4708740 TATTTTATCTTTGTTTTAGGTATTTTAGCCTAAAT-AGTTTTAAGTGTTTTAATTAGGATTTGAG
1 TATTTTATCTTTGTTTTA-GTATTTTAGCCTAAATAAGTTTT-AGTATTTCAATTAGGATTTGAG
4708804 ATATTATTTTA
64 ATATTATTTTA
4708815 GGAATTATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
84 23 0.34
85 43 0.64
86 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (84 bp):
TATTTTATCTTTGTTTTAGTATTTTAGCCTAAATAAGTTTTAGTATTTCAATTAGGATTTGAGAT
ATTATTTTAAATATTATTT
Found at i:4711221 original size:14 final size:16
Alignment explanation
Indices: 4711198--4711231 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4711188 TGACATGATA
*
4711198 TTTATTATTATTATTAT
1 TTTATTAATA-TATTAT
4711215 TTTATTAATATATTAT
1 TTTATTAATATATTAT
4711231 T
1 T
4711232 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTAATATATTAT
Found at i:4712709 original size:23 final size:21
Alignment explanation
Indices: 4712682--4712724 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4712672 ATATAAAAAA
4712682 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
4712703 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
4712724 T
1 T
4712725 AATTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:4719760 original size:27 final size:27
Alignment explanation
Indices: 4719722--4719798 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
4719712 CCGACATTAC
* *
4719722 TTTCAAGCACTAATTCGATGATAAATG
1 TTTCAAGCACTAACTCGACGATAAATG
4719749 TTTCAAGCACTAACTCGACGATAAATG
1 TTTCAAGCACTAACTCGACGATAAATG
4719776 TTTCAAGCACTAACTCGACGATA
1 TTTCAAGCACTAACTCGACGATA
4719799 TAATATTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (27 bp):
TTTCAAGCACTAACTCGACGATAAATG
Found at i:4721396 original size:4 final size:4
Alignment explanation
Indices: 4721387--4722287 Score: 1788
Period size: 4 Copynumber: 225.8 Consensus size: 4
4721377 AGGATGTTAA
4721387 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721435 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721483 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721531 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721579 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721627 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721675 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721723 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721771 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721819 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721867 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721915 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4721963 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4722011 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4722059 ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4722105 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4722153 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4722201 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4722249 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
4722288 TATATATAAA
Statistics
Matches: 895, Mismatches: 0, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
2 2 0.00
4 893 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:4727964 original size:32 final size:32
Alignment explanation
Indices: 4727928--4727997 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
4727918 TAAGAAGACG
* *
4727928 AGGGTATTACTTTAT-TGTCTCAACAAAAGGTA
1 AGGGTATGACTTTATCTGTCTCAA-AAAAGATA
*
4727960 AGGGTATGACTTTTTCTGTCTCAAAAAAGATA
1 AGGGTATGACTTTATCTGTCTCAAAAAAGATA
*
4727992 AAGGTA
1 AGGGTA
4727998 GTATTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (32 bp):
AGGGTATGACTTTATCTGTCTCAAAAAAGATA
Found at i:4731981 original size:2 final size:2
Alignment explanation
Indices: 4731974--4732022 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4731964 TGTTAAATGC
4731974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4732016 AT AT AT A
1 AT AT AT A
4732023 AACATGCAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4732988 original size:16 final size:17
Alignment explanation
Indices: 4732958--4732991 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4732948 TCTATTTTTG
*
4732958 TTTTCTTTTTCTTTTCC
1 TTTTCCTTTTCTTTTCC
4732975 TTTTCCTTTT-TTTTCC
1 TTTTCCTTTTCTTTTCC
4732991 T
1 T
4732992 CCTCCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCCTTTTCTTTTCC
Found at i:4734819 original size:18 final size:16
Alignment explanation
Indices: 4734783--4734823 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
4734773 ATAATCTAAA
4734783 ATAAAAAATATTTTAT
1 ATAAAAAATATTTTAT
*
4734799 ATAAAAAATTATATTTTT
1 ATAAAAAA-TAT-TTTAT
4734817 ATAAAAA
1 ATAAAAA
4734824 TAAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAAAAATATTTTAT
Found at i:4735597 original size:3 final size:3
Alignment explanation
Indices: 4735589--4735624 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4735579 GATATCATCT
4735589 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4735625 AAGAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4739162 original size:15 final size:15
Alignment explanation
Indices: 4739131--4739164 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4739121 CATAAAAGTA
* *
4739131 AAAATTAAAATAGAT
1 AAAATTAAAAAAAAT
4739146 AAAATTAAAAAAAAT
1 AAAATTAAAAAAAAT
4739161 AAAA
1 AAAA
4739165 ACAAACGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATTAAAAAAAAT
Found at i:4739175 original size:21 final size:20
Alignment explanation
Indices: 4739151--4739203 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4739141 TAGATAAAAT
4739151 TAAAAAAAATAAAAACAAACG
1 TAAAAAAAAT-AAAACAAACG
* *
4739172 TAAAATAAAATTAAACAAATG
1 TAAAA-AAAATAAAACAAACG
4739193 TAAATAAAAAT
1 TAAA-AAAAAT
4739204 GTATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.19
Consensus pattern (20 bp):
TAAAAAAAATAAAACAAACG
Found at i:4740780 original size:18 final size:17
Alignment explanation
Indices: 4740744--4740787 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4740734 CTCTTAAAAG
4740744 TTTTAAATTTCTATATA
1 TTTTAAATTTCTATATA
* *
4740761 TTTTAAATATTTTTTATA
1 TTTTAAAT-TTCTATATA
*
4740779 TTTTTAATT
1 TTTTAAATT
4740788 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAAATTTCTATATA
Found at i:4749794 original size:2 final size:2
Alignment explanation
Indices: 4749789--4749819 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4749779 TGTGTGTATG
4749789 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4749820 GGTTTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4750685 original size:62 final size:62
Alignment explanation
Indices: 4750614--4750734 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
4750604 CATTTTCTCC
* * *
4750614 ATTTCCTCCTCATTTCCTTCTCCTTCTTCCTCTTCAAGTGTCATAGCTAAAGGTGAGTCCTT
1 ATTTCCTCCTCATTTCCTTCTCCTTCTACCTCTACAAATGTCATAGCTAAAGGTGAGTCCTT
*
4750676 ATTTCCTCCTCATTTGCTTCTCCTTCTACCTCTACAAATGTCATAGCTAAAGGTGAGTC
1 ATTTCCTCCTCATTTCCTTCTCCTTCTACCTCTACAAATGTCATAGCTAAAGGTGAGTC
4750735 ATTTGAGCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.40
Consensus pattern (62 bp):
ATTTCCTCCTCATTTCCTTCTCCTTCTACCTCTACAAATGTCATAGCTAAAGGTGAGTCCTT
Found at i:4751205 original size:32 final size:32
Alignment explanation
Indices: 4751169--4751233 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
4751159 CTTTGGGCTG
* * *
4751169 TAGTATCAATATTATTCTTGTAGTATCGATAC
1 TAGTATCAATATTATTCTTATACTATCAATAC
*
4751201 TAGTATCAATATTGTTCTTATACTATCAATAC
1 TAGTATCAATATTATTCTTATACTATCAATAC
4751233 T
1 T
4751234 CATCAATACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (32 bp):
TAGTATCAATATTATTCTTATACTATCAATAC
Found at i:4753494 original size:2 final size:2
Alignment explanation
Indices: 4753487--4753534 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
4753477 ATACACAATA
4753487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4753529 -T AT AT A
1 AT AT AT A
4753535 CTTTAATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4755861 original size:21 final size:20
Alignment explanation
Indices: 4755837--4755875 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4755827 CGTATATTTA
4755837 TAAATTAGTTAAATATAAAGG
1 TAAATTAGTTAAA-ATAAAGG
*
4755858 TAAATTATTTAAAATAAA
1 TAAATTAGTTAAAATAAA
4755876 ATATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAATTAGTTAAAATAAAGG
Found at i:4769075 original size:43 final size:42
Alignment explanation
Indices: 4769028--4769161 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 42
4769018 GCAGAAAAAT
4769028 GCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTCTTCACAAAC
1 GCCGCAATAGGTGTTGATGTTTAGCGGCGTTTT-TTCACAAAC
* * * *
4769071 GCCGCAATAGATGTTGATTTTTA-CTGACGTTTTTCCTACAAAC
1 GCCGCAATAGGTGTTGATGTTTAGC-GGCGTTTTTTC-ACAAAC
* * * *
4769114 GCCGCAATATGTATTGA-GATTTAGCGGTGTTTTTATCAAAAAC
1 GCCGCAATAGGTGTTGATG-TTTAGCGGCGTTTTT-TCACAAAC
4769157 GCCGC
1 GCCGC
4769162 TAAATGTATG
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
42 3 0.04
43 69 0.93
44 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
GCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTTTCACAAAC
Found at i:4769524 original size:21 final size:21
Alignment explanation
Indices: 4769500--4769576 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4769490 TTATATATTA
*
4769500 CTTCTCTCTGTGCTACCACTG
1 CTTCTCTCTGTGCTGCCACTG
* *
4769521 CTTCTCTCTGTACTGCCGCTG
1 CTTCTCTCTGTGCTGCCACTG
*
4769542 CCTCTCTCTGTGCTGCCACTG
1 CTTCTCTCTGTGCTGCCACTG
*
4769563 CTTCTCTCTCTGCT
1 CTTCTCTCTGTGCT
4769577 TCTGCTGCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.05, C:0.40, G:0.16, T:0.39
Consensus pattern (21 bp):
CTTCTCTCTGTGCTGCCACTG
Found at i:4769584 original size:21 final size:21
Alignment explanation
Indices: 4769500--4769629 Score: 102
Period size: 21 Copynumber: 6.2 Consensus size: 21
4769490 TTATATATTA
* * *
4769500 CTTCTCTCTGTGCTACCACTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
4769521 CTTCTCTCTGTACTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * * *
4769542 CCTCTCTCTGTGCTGCCACTG
1 CTTCTCTCTCTGCTTCCGCTG
*
4769563 CTTCTCTCTCTGCTTCTGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
4769584 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
4769605 -TTGCTCTCTCTGCTTCC-CTTG
1 CTT-CTCTCTCTGCTTCCGC-TG
4769626 CTTC
1 CTTC
4769630 ATTTTCCGCT
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.02
21 84 0.95
22 2 0.02
ACGTcount: A:0.04, C:0.39, G:0.17, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:4770769 original size:314 final size:315
Alignment explanation
Indices: 4770199--4770830 Score: 1175
Period size: 314 Copynumber: 2.0 Consensus size: 315
4770189 CCTCGTTACA
4770199 AGTATTTATGAAAAATACATCATACTGTCCTTTTTGAGAAACTCCAAAATCTGACTGCATCTTCC
1 AGTATTTATGAAAAATA-ATCATACTGTCCTTTTTGAGAAACTCCAAAATCTGACTGCATCTTCC
4770264 CATTGGTACCTGAGCATTCTGGTGGGACTGTTTGCAACTTCTCTTCAAGGCTGAGATCATTCTTG
65 CATTGGTACCTGAGCATTCTGGTGGGACTGTTTGCAACTTCTCTTCAAGGCTGAGATCATTCTTG
4770329 AAGTATTCTTCTTTAAGGAGCTCTTGTGGTCCCTCTATCTCTTCCCTAACGCTTGCTTCACATAA
130 AAGTATTCTTCTTTAAGGAGCTCTTGTGGTCCCTCTATCTCTTCCCTAACGCTTGCTTCACATAA
4770394 TCGTCAGAGACCTCTAAAACAAATTCTCCTATACAGCAAATAAGTGTGCACTGTAAGTATAAATT
195 TCGTCAGAGACCTCTAAAACAAATTCTCCTATACAGCAAATAAG-GTGCACTGTAAGTATAAATT
4770459 AGTATTGAATTTATATAG-GTATCTATTATAATGACA-TATTACCTTAACAAAATCC
259 AGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTACCTTAACAAAATCC
4770514 AGTATTTATGAAAAAT-ATCATACCTGTCCTTTTTGAG-AACTCCAAAATCTGACTGCATCTTCC
1 AGTATTTATGAAAAATAATCATA-CTGTCCTTTTTGAGAAACTCCAAAATCTGACTGCATCTTCC
4770577 CATTGGTACCTGAGCATTCCTGGTGGGACTGTTTGCAACTTCTCTTCAAGGCTGAGATCATTCTT
65 CATTGGTACCTGAGCATT-CTGGTGGGACTGTTTGCAACTTCTCTTCAAGGCTGAGATCATTCTT
4770642 GAAGTATTTCTTCTTTAAGGAGCTCTTGTGGTCCCCTCTATCTCTTCCCTAACGCTTGCTTCACA
129 GAAGTA-TTCTTCTTTAAGGAGCTCTTGTGGT-CCCTCTATCTCTTCCCTAACGCTTGCTTCACA
4770707 TAATCGTCAGAGACCTCTAAAACAAATTCTCCTATACAGCAAATAA-GTGCACTGTAAGTATAAA
192 TAATCGTCAGAGACCTCTAAAACAAATTCTCCTATACAGCAAATAAGGTGCACTGTAAGTATAAA
4770771 TTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTACCTTAACAAAATCC
257 TTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTACCTTAACAAAATCC
4770830 A
1 A
4770831 ACTCTTGATT
Statistics
Matches: 311, Mismatches: 0, Indels: 11
0.97 0.00 0.03
Matches are distributed among these distances:
313 50 0.16
314 104 0.33
315 59 0.19
316 98 0.32
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (315 bp):
AGTATTTATGAAAAATAATCATACTGTCCTTTTTGAGAAACTCCAAAATCTGACTGCATCTTCCC
ATTGGTACCTGAGCATTCTGGTGGGACTGTTTGCAACTTCTCTTCAAGGCTGAGATCATTCTTGA
AGTATTCTTCTTTAAGGAGCTCTTGTGGTCCCTCTATCTCTTCCCTAACGCTTGCTTCACATAAT
CGTCAGAGACCTCTAAAACAAATTCTCCTATACAGCAAATAAGGTGCACTGTAAGTATAAATTAG
TATTGAATTTATATAGAGTATCTATTATAATGACATTATTACCTTAACAAAATCC
Found at i:4778298 original size:83 final size:82
Alignment explanation
Indices: 4778173--4778327 Score: 204
Period size: 83 Copynumber: 1.9 Consensus size: 82
4778163 TACCATTAAT
* * * *
4778173 ACTCAATAGCGGCGTTTGTACAAAAACGTCGCTAAATGACTACTCTTTTACGGCGTTTGTTGATA
1 ACTCAATACCGGCGTTTGTACAAAAACGCCGCTAAATGACTACTCTATTACGGCATTTGTTGA-A
4778238 -AAACGCCACAATAAATA
65 GAAACGCCACAATAAATA
* * * * *
4778255 ACTCTATACCGGCGTTTGTTCCAAAAACGCCGCTAAATTACTACTCTATTGCGGCATTTTTTGAA
1 ACTCAATACCGGCGTTTG-TACAAAAACGCCGCTAAATGACTACTCTATTACGGCATTTGTTGAA
4778320 GAAACGCC
65 GAAACGCC
4778328 GCTATATTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 17 0.27
83 45 0.73
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (82 bp):
ACTCAATACCGGCGTTTGTACAAAAACGCCGCTAAATGACTACTCTATTACGGCATTTGTTGAAG
AAACGCCACAATAAATA
Found at i:4779248 original size:17 final size:18
Alignment explanation
Indices: 4779212--4779249 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4779202 GAATATAATT
* *
4779212 AAATTATATTTTTATTAA
1 AAATTATAATTATATTAA
4779230 AAATTATAATTAT-TTAA
1 AAATTATAATTATATTAA
4779247 AAA
1 AAA
4779250 AAATATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTATAATTATATTAA
Found at i:4781050 original size:60 final size:59
Alignment explanation
Indices: 4780963--4781123 Score: 195
Period size: 60 Copynumber: 2.7 Consensus size: 59
4780953 TTTTAAAATG
**
4780963 GTCCCTAAACTTTTAAATGTTCTAATTTCATCCCTAAACTATG-CTTATCATTCTAAATTA
1 GTCCCTAAACTTTTAAAACTTC-AATTTCATCCCTAAACTATGACTT-TCATTCTAAATTA
*
4781023 GT-CCTCAAACTTTTAAACACTTCAATTTCATCCCT-AACTATGACTTTCATTCTAAATTT
1 GTCCCT-AAACTTTTAAA-ACTTCAATTTCATCCCTAAACTATGACTTTCATTCTAAATTA
* *
4781082 GTCCCTAAACTTTTTGAATATTTCAATTTCATCCC-AAACTAT
1 GTCCCTAAAC-TTTT-AAAACTTCAATTTCATCCCTAAACTAT
4781124 ATTTATATAC
Statistics
Matches: 89, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
59 28 0.31
60 56 0.63
61 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (59 bp):
GTCCCTAAACTTTTAAAACTTCAATTTCATCCCTAAACTATGACTTTCATTCTAAATTA
Found at i:4781345 original size:60 final size:60
Alignment explanation
Indices: 4781249--4781385 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
4781239 GATGAATTTG
* * * *
4781249 GGGATGAAATTGGAATACTCAAAAGTTTAGAGACTAATATAGAA-AAGGGGTCATAGTTTA
1 GGGATGAAATTAGAATACTCAAAAGTTTAGAGACTAATATAGAATAA-GAGTCATAATCTA
** * * *
4781309 GGGATGAAATTAGAATTTTTAAAAGTTTA-AGAACTAATTTAGAATAAGAGTCATAATCTG
1 GGGATGAAATTAGAATACTCAAAAGTTTAGAG-ACTAATATAGAATAAGAGTCATAATCTA
*
4781369 GGGATGAAATTAAAATA
1 GGGATGAAATTAGAATA
4781386 TTACAATGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (60 bp):
GGGATGAAATTAGAATACTCAAAAGTTTAGAGACTAATATAGAATAAGAGTCATAATCTA
Found at i:4782624 original size:2 final size:2
Alignment explanation
Indices: 4782617--4782726 Score: 83
Period size: 2 Copynumber: 59.0 Consensus size: 2
4782607 TAAAAATAAT
4782617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
4782657 -A TA AA TT TA -A TT TA AA T- TA AA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
4782695 -A TA TT TA TA TA TT TA -A TT TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4782727 CCCAGCCCGA
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
1 8 0.10
2 74 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4782697 original size:38 final size:40
Alignment explanation
Indices: 4782645--4782726 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
4782635 TATATATATA
4782645 TATATAATATTAATAAATT-TA-ATTTAAATTAAAT-TATA
1 TATATAATATTAAT-AATTATATATTTAAATTAAATATATA
* *
4782683 TATAT-ATATATAATATTTATATATTTAATTTAAATATATA
1 TATATAATAT-TAATAATTATATATTTAAATTAAATATATA
4782723 TATA
1 TATA
4782727 CCCAGCCCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 7 0.18
38 11 0.29
39 12 0.32
40 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TATATAATATTAATAATTATATATTTAAATTAAATATATA
Found at i:4786508 original size:130 final size:131
Alignment explanation
Indices: 4786308--4786544 Score: 395
Period size: 130 Copynumber: 1.8 Consensus size: 131
4786298 TTAATATTGA
* *
4786308 AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGATAGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATAGCTTTAAGGCATGAGAGGTCAT
4786373 TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGAT
66 TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGAT
4786438 G
131 G
* * * * *
4786439 AAATAGTGATATCTCTTCATTTCGATTGG-GTAATAAATTATTGTTTTAAGGCATGAGAGGTTAT
1 AAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATAGCTTTAAGGCATGAGAGGTCAT
*
4786503 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTC
66 TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTC
4786545 TTAGAATTAT
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 72 0.73
131 26 0.27
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (131 bp):
AAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATAGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGAT
G
Found at i:4789848 original size:16 final size:16
Alignment explanation
Indices: 4789827--4789878 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
4789817 TACACTGTAG
*
4789827 AGTGTATCGATACACT
1 AGTGTATCGGTACACT
4789843 AGTGTATCGGTACACTAT
1 AGTGTATCGGTACAC--T
4789861 ATGTGTATCGGTACACT
1 A-GTGTATCGGTACACT
4789878 A
1 A
4789879 TAGGTGTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 14 0.44
17 2 0.06
18 2 0.06
19 14 0.44
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (16 bp):
AGTGTATCGGTACACT
Found at i:4789868 original size:19 final size:19
Alignment explanation
Indices: 4789808--4789907 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
4789798 TGCAGCCAGA
*
4789808 GTGTAT-GGATACACTGTAG
1 GTGTATCGG-TACACTATAG
*
4789827 AGTGTATCGATACAC--TA-
1 -GTGTATCGGTACACTATAG
*
4789844 GTGTATCGGTACACTATAT
1 GTGTATCGGTACACTATAG
4789863 GTGTATCGGTACACTATAG
1 GTGTATCGGTACACTATAG
**
4789882 GTGTATCATTACACTATAG
1 GTGTATCGGTACACTATAG
4789901 GTGTATC
1 GTGTATC
4789908 ATTACACTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
16 13 0.18
18 4 0.06
19 42 0.59
20 11 0.15
21 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (19 bp):
GTGTATCGGTACACTATAG
Found at i:4789908 original size:19 final size:19
Alignment explanation
Indices: 4789853--4789916 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
4789843 AGTGTATCGG
* **
4789853 TACACTATATGTGTATCGG
1 TACACTATAGGTGTATCAT
4789872 TACACTATAGGTGTATCAT
1 TACACTATAGGTGTATCAT
4789891 TACACTATAGGTGTATCAT
1 TACACTATAGGTGTATCAT
4789910 TACACTA
1 TACACTA
4789917 ATTGTATTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (19 bp):
TACACTATAGGTGTATCAT
Found at i:4795036 original size:6 final size:6
Alignment explanation
Indices: 4795016--4795056 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
4795006 TGATACGAGA
4795016 TATAT- TATCATG TATATG TATATG TATATG TATATG TATAT
1 TATATG TAT-ATG TATATG TATATG TATATG TATATG TATAT
4795057 ATATCCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 3 0.09
6 28 0.82
7 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:4795046 original size:18 final size:18
Alignment explanation
Indices: 4795016--4795061 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
4795006 TGATACGAGA
4795016 TATATTATCATGTATATG
1 TATATTATCATGTATATG
4795034 TATATGTAT-ATGTATATG
1 TATAT-TATCATGTATATG
4795052 TATATATATC
1 TATAT-TATC
4795062 CTTTCGTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (18 bp):
TATATTATCATGTATATG
Found at i:4798555 original size:8 final size:8
Alignment explanation
Indices: 4798542--4798641 Score: 64
Period size: 8 Copynumber: 12.2 Consensus size: 8
4798532 TCGCTTGAAG
4798542 AAAGAAAA
1 AAAGAAAA
4798550 AAAG--AA
1 AAAGAAAA
4798556 AAAGAAAA
1 AAAGAAAA
*
4798564 AATGAATATA
1 AAAGAA-A-A
4798574 AAATGAAAA
1 AAA-GAAAA
*
4798583 AATGAAAA
1 AAAGAAAA
*
4798591 AATGAAAAA
1 AAAG-AAAA
4798600 AAAGAGAAA
1 AAAGA-AAA
4798609 AAGAGAAAA
1 AA-AGAAAA
*
4798618 AAA-AGAA
1 AAAGAAAA
*
4798625 CAAG-AAA
1 AAAGAAAA
*
4798632 AGAGAAAA
1 AAAGAAAA
4798640 AA
1 AA
4798642 TAAAATGGGG
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
6 6 0.08
7 9 0.12
8 26 0.36
9 21 0.29
10 7 0.10
11 3 0.04
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.06
Consensus pattern (8 bp):
AAAGAAAA
Found at i:4798563 original size:5 final size:6
Alignment explanation
Indices: 4798539--4798640 Score: 50
Period size: 6 Copynumber: 16.3 Consensus size: 6
4798529 ACTTCGCTTG
* * *
4798539 AAGAAA GAA-AAA AAGAAA AAGAAA AA-ATGAA TATAAA ATGAAAA AATGAAAA
1 AAGAAA -AAGAAA AAGAAA AAGAAA AAGA--AA AAGAAA AAG-AAA AA-G-AAA
* * *
4798591 AATGAAA AA-AAA GAGAAA AAGAGA AA-AAA AAGAAC AAGAAA AGAGAAA
1 AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A-AGAAA
4798639 AA
1 AA
4798641 ATAAAATGGG
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
5 11 0.15
6 34 0.45
7 20 0.27
8 10 0.13
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:4798584 original size:27 final size:26
Alignment explanation
Indices: 4798546--4798646 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 26
4798536 TTGAAGAAAG
4798546 AAAAAA-AG-AAAAAGAAAAAATGAA
1 AAAAAAGAGAAAAAAGAAAAAATGAA
* *
4798570 TATAAAATGA-AAAAATGAAAAAATGAA
1 -A-AAAAAGAGAAAAAAGAAAAAATGAA
*
4798597 AAAAAAGAGAAAAAGAGAAAAAAAAGAA
1 AAAAAAGAGAAAAA-AG-AAAAAATGAA
*
4798625 CAAGAAAAGAGAAAAAATAAAA
1 -AA-AAAAGAGAAAAAAGAAAA
4798647 TGGGGATTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
25 7 0.11
26 10 0.16
27 17 0.27
28 13 0.21
29 3 0.05
30 12 0.19
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (26 bp):
AAAAAAGAGAAAAAAGAAAAAATGAA
Found at i:4798608 original size:11 final size:11
Alignment explanation
Indices: 4798594--4798641 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
4798584 ATGAAAAAAT
4798594 GAAAAAAAAGA
1 GAAAAAAAAGA
4798605 G---AAAAAGA
1 GAAAAAAAAGA
4798613 GAAAAAAAAGA
1 GAAAAAAAAGA
*
4798624 -ACAAGAAAAGA
1 GA-AAAAAAAGA
4798635 GAAAAAA
1 GAAAAAA
4798642 TAAAATGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 8 0.27
10 1 0.03
11 20 0.67
12 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAGA
Found at i:4798629 original size:17 final size:18
Alignment explanation
Indices: 4798578--4798629 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
4798568 AATATAAAAT
*
4798578 GAAAAAATGA-AAAAATGA
1 GAAAAAAAGAGAAAAA-GA
4798596 -AAAAAAAGAGAAAAAGA
1 GAAAAAAAGAGAAAAAGA
*
4798613 GAAAAAAA-AGAACAAGA
1 GAAAAAAAGAGAAAAAGA
4798630 AAAGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (18 bp):
GAAAAAAAGAGAAAAAGA
Found at i:4800262 original size:133 final size:133
Alignment explanation
Indices: 4800024--4800355 Score: 416
Period size: 133 Copynumber: 2.5 Consensus size: 133
4800014 TCTTTTTCCA
* * * * *
4800024 GATTTGATCTTCCCTAAAGAAAAATTGAATAAATCAACATTTCCAGATCTGATCTTCCCTGAAGA
1 GATTTAATCTTCCCTAAAGAACAATAGAATAAATCAACGTTTCCAGATCTAATCTTCCCTGAAGA
* ** * *
4800089 AGCAGTGGAACAAATCACCTCTTTTTAGATTTGATCTTCCCTGAGTAGTAGTGGAACAAGTCTGC
66 AGCAGTAGAACAAATCACCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGC
4800154 CTC
131 CTC
* * * * *
4800157 GATTTAATCTTCCCTGAAGAACAATAGAATTAATCAACGTCTCCGGATCTAATTTTCCCTG-AGC
1 GATTTAATCTTCCCTAAAGAACAATAGAATAAATCAACGTTTCCAGATCTAATCTTCCCTGAAG-
* *
4800221 AAGCAGTAGAACAAATCCCCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTT
65 AAGCAGTAGAACAAATCACCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTG
*
4800286 CCTT
130 CCTC
* * * * * *
4800290 GATTCAATCTTTCCTAAAGAACAATAAAATGAAA-CAACGTTTCCAGATCTGATCTACCATGAAG
1 GATTTAATCTTCCCTAAAGAACAATAGAAT-AAATCAACGTTTCCAGATCTAATCTTCCCTGAAG
4800354 AA
65 AA
4800356 ACATCGGATC
Statistics
Matches: 167, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
132 2 0.01
133 161 0.96
134 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (133 bp):
GATTTAATCTTCCCTAAAGAACAATAGAATAAATCAACGTTTCCAGATCTAATCTTCCCTGAAGA
AGCAGTAGAACAAATCACCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGC
CTC
Found at i:4801957 original size:108 final size:107
Alignment explanation
Indices: 4801633--4801971 Score: 368
Period size: 108 Copynumber: 3.1 Consensus size: 107
4801623 CCCTAACTTA
* * * * *
4801633 AGCGTGTTTTTGCATGTTAGTCACCTATA-AGGATCGAACTT-TCTATTTACCCA-TTTTTATGC
1 AGCGTGTTTTTACATGTTAGTCACCTGTACA-CACCGAAGTTAT-TATTTACCCATTTTTTATGC
* * *
4801695 ATGCTTTATATTTTTGGGATATTTGTTGTTTAGTCCCCCATAGTTT
64 ATGCTATGTA-TTTTGGGATATTTGTTGTTTAGT-CCCCTTAGTTT
* * *** *
4801741 AGCATGTTTTTGCATGTTAGTCACCTGTAGGGACCGAAGTTATTATTTACCCATTTTTTATGTAT
1 AGCGTGTTTTTACATGTTAGTCACCTGTACACACCGAAGTTATTATTTACCCATTTTTTATGCAT
*
4801806 GCTATGTATTTTGGGATATTTGTTGTTTAGTCCCCTTATTTT
66 GCTATGTATTTTGGGATATTTGTTGTTTAGTCCCCTTAGTTT
* * *
4801848 AGTGTGTTTTTACATGTTAGTCACCTGTACACACCGGAA-TTGTTATTTA-CTAGCTTTTTTATG
1 AGCGTGTTTTTACATGTTAGTCACCTGTACACACC-GAAGTTATTATTTACCCA--TTTTTTATG
*
4801911 CAAGCTATGTATTTTGGGATATTT-TCTGTTTAGTCCCACTTA-TTT
63 CATGCTATGTATTTTGGGATATTTGT-TGTTTAGTCCC-CTTAGTTT
4801956 AGGCGTGTTTTTACAT
1 A-GCGTGTTTTTACAT
4801972 TTTGGTCATG
Statistics
Matches: 201, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
106 2 0.01
107 48 0.24
108 117 0.58
109 34 0.17
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (107 bp):
AGCGTGTTTTTACATGTTAGTCACCTGTACACACCGAAGTTATTATTTACCCATTTTTTATGCAT
GCTATGTATTTTGGGATATTTGTTGTTTAGTCCCCTTAGTTT
Found at i:4803776 original size:2 final size:2
Alignment explanation
Indices: 4803769--4803860 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
4803759 GTATAAAATA
4803769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4803811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4803853 AT AT AT AT
1 AT AT AT AT
4803861 TCTATCTAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4805257 original size:2 final size:2
Alignment explanation
Indices: 4805205--4805237 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4805195 ATACCTCATA
4805205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4805238 ACAAAATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4809083 original size:6 final size:6
Alignment explanation
Indices: 4809072--4809116 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
4809062 TTGTCCCTCT
4809072 AATGTG AATGTG AATGTG AATGTG AATGTG AATGTG AATGTG AAT
1 AATGTG AATGTG AATGTG AATGTG AATGTG AATGTG AATGTG AAT
4809117 ATTTCTAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (6 bp):
AATGTG
Found at i:4809156 original size:19 final size:19
Alignment explanation
Indices: 4809134--4809171 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4809124 AGGAAAAGAA
4809134 AAATTTCCTTGAGCTGGAT
1 AAATTTCCTTGAGCTGGAT
4809153 AAATTTCCTTGAGCTGGAT
1 AAATTTCCTTGAGCTGGAT
4809172 GGTTTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATTTCCTTGAGCTGGAT
Found at i:4812595 original size:29 final size:29
Alignment explanation
Indices: 4812538--4812595 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
4812528 TTATTTCGAA
* *
4812538 TTAACCACTGATTTTTATTTTCTTGTATT
1 TTAACCACTGATATTTATTTTATTGTATT
4812567 TTAACCACTGTTATATTTA-TTTATT-TATT
1 TTAACCACTG--ATATTTATTTTATTGTATT
4812596 GCTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 14 0.56
30 5 0.20
31 6 0.24
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (29 bp):
TTAACCACTGATATTTATTTTATTGTATT
Found at i:4816969 original size:16 final size:16
Alignment explanation
Indices: 4816950--4816980 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4816940 TACATTTGCA
4816950 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
4816966 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
4816981 CATTACGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTATTTTTTAT
Found at i:4820094 original size:21 final size:20
Alignment explanation
Indices: 4820070--4820117 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
4820060 AAAATAAATA
4820070 AAAAGAGAGATAAAAAAGAAG
1 AAAAGAGA-ATAAAAAAGAAG
*
4820091 -AAA-AGAATGAAAAAGAAG
1 AAAAGAGAATAAAAAAGAAG
4820109 AAAAGAGAA
1 AAAAGAGAA
4820118 AAAGAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.46
19 6 0.25
20 7 0.29
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (20 bp):
AAAAGAGAATAAAAAAGAAG
Found at i:4820104 original size:10 final size:9
Alignment explanation
Indices: 4820082--4820128 Score: 57
Period size: 8 Copynumber: 5.6 Consensus size: 9
4820072 AAGAGAGATA
4820082 AAAAAGAAG
1 AAAAAGAAG
4820091 -AAAAGAATG
1 AAAAAGAA-G
4820100 AAAAAGAAG
1 AAAAAGAAG
4820109 -AAAAG-AG
1 AAAAAGAAG
4820116 AAAAAG-AG
1 AAAAAGAAG
4820124 AAAAA
1 AAAAA
4820129 AATTGAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 2 0.06
8 24 0.69
9 2 0.06
10 7 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:4820105 original size:18 final size:16
Alignment explanation
Indices: 4820082--4820127 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 16
4820072 AAGAGAGATA
4820082 AAAAAGAAGAAAAGAATG
1 AAAAAGAAGAAAAG-A-G
4820100 AAAAAGAAGAAAAGAG
1 AAAAAGAAGAAAAGAG
4820116 AAAAAG-AGAAAA
1 AAAAAGAAGAAAA
4820128 AAATTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.21
16 7 0.25
17 1 0.04
18 14 0.50
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
AAAAAGAAGAAAAGAG
Found at i:4820130 original size:18 final size:18
Alignment explanation
Indices: 4820069--4820130 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
4820059 AAAAATAAAT
*
4820069 AAAAAGAGAGATAAAAAAG
1 AAAAAAAGAGAT-AAAAAG
*
4820088 AAGAAAAGA-ATGAAAAAG
1 AAAAAAAGAGAT-AAAAAG
*
4820106 AAGAAAAGAGA-AAAAGAG
1 AAAAAAAGAGATAAAA-AG
4820124 AAAAAAA
1 AAAAAAA
4820131 TTGAAATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 25 0.68
19 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAGATAAAAAG
Found at i:4820136 original size:18 final size:17
Alignment explanation
Indices: 4820082--4820136 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
4820072 AAGAGAGATA
*
4820082 AAAAAGAAGAAAAGAATG
1 AAAAAG-AGAAAAAAATG
*
4820100 AAAAAGA-AGAAAAGA-G
1 AAAAAGAGA-AAAAAATG
4820116 AAAAAGAGAAAAAAATTG
1 AAAAAGAGAAAAAAA-TG
4820134 AAA
1 AAA
4820137 TGAGGGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 14 0.47
17 6 0.20
18 10 0.33
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (17 bp):
AAAAAGAGAAAAAAATG
Found at i:4822438 original size:36 final size:36
Alignment explanation
Indices: 4822368--4822440 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
4822358 AAATTTTCAA
*
4822368 ATTGTTTCACTCAAAACAAAATTTATCTTACTTGAG
1 ATTGTTTCACTCAAAACAAAATTTATCTCACTTGAG
* *
4822404 ATTGTTTTC-CTCAAAAC-CAATTTCATCTCGCTTGAG
1 ATTG-TTTCACTCAAAACAAAATTT-ATCTCACTTGAG
4822440 A
1 A
4822441 CAATTTTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.16
36 23 0.72
37 4 0.12
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (36 bp):
ATTGTTTCACTCAAAACAAAATTTATCTCACTTGAG
Found at i:4822465 original size:103 final size:103
Alignment explanation
Indices: 4822255--4822496 Score: 362
Period size: 102 Copynumber: 2.4 Consensus size: 103
4822245 AATTTCCTTT
* * *
4822255 AAATTTTGAAATTGTTTCACTCGAAACAAAATTGATCTTACTTGAGATTGTTTTTTCTTAAAACC
1 AAATTTTGAAATTGTTTCACTCGAAACAAAATTTATCTTACTTGAGATTGTTTTTCCTCAAAACC
** *
4822320 AATTTCATCTCGCTTGAGGGAGTTTTTCCTTAAAACAC
66 AATTTCATCTCGCTTGAGACAATTTTTCCTTAAAACAC
* *
4822358 AAATTTTCAAATTGTTTCACTCAAAACAAAATTTATCTTACTTGAGATTG-TTTTCCTCAAAACC
1 AAATTTTGAAATTGTTTCACTCGAAACAAAATTTATCTTACTTGAGATTGTTTTTCCTCAAAACC
**
4822422 AATTTCATCTCGCTTGAGACAATTTTTCCTTGGAACAC
66 AATTTCATCTCGCTTGAGACAATTTTTCCTTAAAACAC
* *
4822460 AAAATTTGAAATTG-TTCACTCGAAACCAAATTTATCT
1 AAATTTTGAAATTGTTTCACTCGAAACAAAATTTATCT
4822497 CACCTAATAT
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
101 21 0.17
102 57 0.46
103 47 0.38
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (103 bp):
AAATTTTGAAATTGTTTCACTCGAAACAAAATTTATCTTACTTGAGATTGTTTTTCCTCAAAACC
AATTTCATCTCGCTTGAGACAATTTTTCCTTAAAACAC
Found at i:4823091 original size:163 final size:158
Alignment explanation
Indices: 4822749--4823340 Score: 503
Period size: 163 Copynumber: 3.6 Consensus size: 158
4822739 GAGATTCAAA
** * ** *
4822749 TCCATCACAGAAGGAGGTGGATCAAAATTTCTAAAAGAGAGTTCATAATGTA-AAGAAATCATCC
1 TCCATCACA-AAGGAGGTGGATCAGTATTTCCAATGGAGAGTTCATAATG-AGAAGAACTCATCC
* * * * * * ** * ** *
4822813 ACAGAAGATAAAATAAGTTCAAAATGAGAAGAACTTGTTCAAACTTTTGCTCCACTCTATCTTAT
64 AAAG-AGA-GAGA-AAGTTCATAATGAGAAGAACTTGTTC-ACCCTTTGCTAGATTCTATCGCAG
* * * * *
4822878 AAGGAGATAGATCAGA-ATCAATATTTT-TCTCAAA
125 AAGAAGATAAATCA-ACATCAACATTTTAT-TCCAT
* *
4822912 TCCATCACAAAAGGAGGTGGGTC-GTCATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCC
1 TCCATCAC-AAAGGAGGTGGATCAGT-ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
*
4822976 AAAGAATGAGAGAAAGTTCATAATGAGAAGAACTTGTTCACCCTTTTTCTAGATTCTATCGCAGA
64 AAAG-A-GAGAGAAAGTTCATAATGAGAAGAACTTGTTCACCC-TTTGCTAGATTCTATCGCAGA
* *
4823041 ATAAGATAAATCAAGCATGAACATTTTATTCCAT
126 AGAAGATAAATCAA-CATCAACATTTTATTCCAT
* * *
4823075 TCCATCGCAGAAGGAGGTGGATCAGAATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCT
1 TCCATCACA-AAGGAGGTGGATCAGTATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCA
* *
4823140 AAGAGAGATAAAAGGTTCATAATGAGAAGAACGTT-TTCACCCTTTGCTAGATTCTATCGTAGAA
65 AAGAGAGA-GAAA-GTTCATAATGAGAAGAAC-TTGTTCACCCTTTGCTAGATTCTATCGCAGAA
** * * * **
4823204 GGGGATAGATCAACATCATCATTTTGTTTGAT
127 GAAGATAAATCAACATCAACATTTTATTCCAT
* * * * * *
4823236 TCCATCACAATAGGAGATGGATCAATATTTCCAATGAAAGGGTTCATAATGAGAAGAACTTATCT
1 TCCATCACAA-AGGAGGTGGATCAGTATTTCCAATG-GAGAGTTCATAATGAGAAGAACTCATCC
* *
4823301 GAAGAG-GAAGAATAATTTCATAATGAGAAGAACTTGTTCA
64 AAAGAGAG-AG-A-AAGTTCATAATGAGAAGAACTTGTTCA
4823341 ACTTTTTAGG
Statistics
Matches: 355, Mismatches: 55, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
160 1 0.00
161 54 0.15
162 136 0.38
163 157 0.44
164 7 0.02
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (158 bp):
TCCATCACAAAGGAGGTGGATCAGTATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAA
AGAGAGAGAAAGTTCATAATGAGAAGAACTTGTTCACCCTTTGCTAGATTCTATCGCAGAAGAAG
ATAAATCAACATCAACATTTTATTCCAT
Found at i:4823395 original size:74 final size:74
Alignment explanation
Indices: 4823274--4823421 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
4823264 TTCCAATGAA
* * * *
4823274 AGGGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAATAATTTCATAATGAGAAGAACTTGTT
1 AGGGTTCATAATGAAAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
4823339 CAACTTTTT
66 CAACTTTTT
4823348 AGGGTTCATAATGAAAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGGGTTCATAATGAAAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
4823413 CAATTTTTT
66 CAACTTTTT
4823422 GCTTGAATCT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (74 bp):
AGGGTTCATAATGAAAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTT
Found at i:4823571 original size:237 final size:236
Alignment explanation
Indices: 4823115--4823574 Score: 556
Period size: 237 Copynumber: 1.9 Consensus size: 236
4823105 CCAATGGAGA
* *
4823115 GTTCATAATGAGAAGAACTCATCCTAAGAGAGATAAAAGGTTCATAATGAGAAGAACGTTTTCAC
1 GTTCATAATGAAAAGAACTCATCCTAAGAGAGATAAAAAGTTCATAATGAGAAGAACGTTTTCAC
* * * * * ** *
4823180 CCTTTGCTAGATTCTATCGTAGAAGGGGATAGATCAACATCATCATTTTGTTTGATTCCATCACA
66 CCTTTGCTAGAATCTATCGCAAAAGGAGATAGATCAACATCATCATTTTGATCAAATCCATCACA
* * * *
4823245 ATAGGAGATGGATCAATATTTCCAATGAAAGGGTTCATAATGAGAAGAACTTATCTGAAGAGGAA
131 AAAGGAGATGGATCAATATTTCCAATGAAAGGGTTCATAATGAGAAGAACTCACCCGAAGAGGAA
* * *
4823310 GAATAATTTCATAATGAGAAGAACTTGTTCAACTTTTTAGG
196 GAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTTTAGG
4823351 GTTCATAATGAAAAGAACTCAT-CTGAAGAG-GA-AGAAGAAGTTCATAATGAGAAGAAC-TTGT
1 GTTCATAATGAAAAGAACTCATCCT-AAGAGAGATA-AA-AAGTTCATAATGAGAAGAACGTT-T
*** * * *
4823412 TCAATTTTTTGCTTGAATCTATCGCAAAATGAGATAGATCATCATCAAT-ATTTTGATCAAATCC
62 TC-ACCCTTTGCTAGAATCTATCGCAAAAGGAGATAGATCAACATC-ATCATTTTGATCAAATCC
* *
4823476 ATCACAAAAGGAGGTGGATCATTATTTCCAAT-AGAAGGGTTCATAATGAGAAGAACTCACCCGA
125 ATCACAAAAGGAGATGGATCAATATTTCCAATGA-AAGGGTTCATAATGAGAAGAACTCACCCGA
* *
4823540 AGA-GAGAGGAGAAGTTCATACTGAAAAGAACTTGT
189 AGAGGA-AGAAGAAGTTCATAATGAAAAGAACTTGT
4823575 AGCTCAAGAA
Statistics
Matches: 189, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
234 1 0.01
235 8 0.04
236 51 0.27
237 127 0.67
238 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (236 bp):
GTTCATAATGAAAAGAACTCATCCTAAGAGAGATAAAAAGTTCATAATGAGAAGAACGTTTTCAC
CCTTTGCTAGAATCTATCGCAAAAGGAGATAGATCAACATCATCATTTTGATCAAATCCATCACA
AAAGGAGATGGATCAATATTTCCAATGAAAGGGTTCATAATGAGAAGAACTCACCCGAAGAGGAA
GAAGAAGTTCATAATGAAAAGAACTTGTTCAACTTTTTAGG
Found at i:4824885 original size:12 final size:13
Alignment explanation
Indices: 4824863--4824893 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
4824853 TTTTAACCAC
4824863 TATTATATTTATT
1 TATTATATTTATT
4824876 TATT-TATTTATT
1 TATTATATTTATT
4824888 TATTAT
1 TATTAT
4824894 TATTATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATATTTATT
Found at i:4825197 original size:14 final size:14
Alignment explanation
Indices: 4825178--4825213 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4825168 TTTTTATTTA
*
4825178 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
4825192 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
4825206 TTTAATTT
1 TTTAATTT
4825214 TTTGTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:4827747 original size:3 final size:3
Alignment explanation
Indices: 4827739--4827910 Score: 226
Period size: 3 Copynumber: 58.0 Consensus size: 3
4827729 CTCGTCTAAT
4827739 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
4827787 AGA AGA AG- AGAA AGA AAA AG- AGA AGA AGA AGA AGA AGA AGA ATA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * *
4827831 ATA AGA AGA AGA AGA AGA AGA A-A AAA AAA AGA AAA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
4827878 AGA AGA AGA ACCA A-A AGA AGA AGA TGA AGA AGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA
4827911 TGATGATGAT
Statistics
Matches: 153, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
2 8 0.05
3 141 0.92
4 4 0.03
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:4830200 original size:42 final size:42
Alignment explanation
Indices: 4830089--4830200 Score: 102
Period size: 42 Copynumber: 2.7 Consensus size: 42
4830079 TCTTGATTGG
* ** * *
4830089 TAAGTCCTTTGGGCCATCGGTAAGTCTTTCGAGCATGATGAT
1 TAAGTTCTTTGGGCCATCCATAAGCCTTTCGAGCAAGATGAT
* ** * *
4830131 TAA-ATCTTTCGGGTTATCTATAAGCCTTTTGAGCAAGATGA-
1 TAAGTTCTTT-GGGCCATCCATAAGCCTTTCGAGCAAGATGAT
4830172 TAAGTTCTTTGGGCCATCCATAAGGCCTT
1 TAAGTTCTTTGGGCCATCCATAA-GCCTT
4830201 CGGGTAGGAT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
41 17 0.31
42 37 0.69
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAGTTCTTTGGGCCATCCATAAGCCTTTCGAGCAAGATGAT
Found at i:4830528 original size:231 final size:231
Alignment explanation
Indices: 4830084--4830545 Score: 565
Period size: 231 Copynumber: 2.0 Consensus size: 231
4830074 GGGTTTCTTG
* * * * *
4830084 ATTGGTAAGTCCTTTGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTTATC
1 ATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCATTCGGGTCATC
* * * * * * * * * *
4830149 TATAAGCCTTTTGAGCAAGATGATAAGTTCTTTGGGCCATCCATAAGGCCTTCGGGTAGGATGTT
66 TACAAGCCATTAGAACAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGCT
*
4830214 TTCACATGATTTTCGAGAAATGAGAAAATGATTTCCAAAGTTTCTCATTTAAATCTTTTCTAAAA
131 TTCACATGATTTTCGAGAAATGAGAAAATGATTTCCAAAGTTTCTCATTTAAATATTTTCTAAAA
*
4830279 AATAATTGTTTGAAAAGTAAGAAAACGATTTTCAAA
196 AATAATTGTTTGAAAAGTAAGAAAACGATTTACAAA
* *
4830315 ATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATTATGATTAAATCATTCGGGTCCTC
1 ATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCATTCGGGTCATC
* * * * * *
4830380 TGCCAGTCATTAGAACAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAATATGCT
66 TACAAGCCATTAGAACAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGCT
* * *
4830445 TTCATATGATAATTT-GA-AAGATGAGAAAATGATTTTCAAAGTTTCTCATTT-AGTATTTTC-A
131 TTCACATGAT--TTTCGAGAA-ATGAGAAAATGATTTCCAAAGTTTCTCATTTAAATATTTTCTA
* * *
4830506 GAAAATTAAATT-TTTTAAAAGTAAGAAAGCGATTTACAAA
193 -AAAAAT-AATTGTTTGAAAAGTAAGAAAACGATTTACAAA
4830546 GTTTCTTACC
Statistics
Matches: 195, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
230 1 0.01
231 155 0.79
232 36 0.18
233 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (231 bp):
ATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCATTCGGGTCATC
TACAAGCCATTAGAACAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGCT
TTCACATGATTTTCGAGAAATGAGAAAATGATTTCCAAAGTTTCTCATTTAAATATTTTCTAAAA
AATAATTGTTTGAAAAGTAAGAAAACGATTTACAAA
Found at i:4832169 original size:14 final size:14
Alignment explanation
Indices: 4832150--4832186 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
4832140 TTATTTTTCA
4832150 TATATTTATTTGAT
1 TATATTTATTTGAT
4832164 TATATTTATTTGAT
1 TATATTTATTTGAT
4832178 TATATTTAT
1 TATATTTAT
4832187 ATTTCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TATATTTATTTGAT
Found at i:4832495 original size:19 final size:16
Alignment explanation
Indices: 4832461--4832491 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4832451 AAGTTAGTCT
4832461 AATAATTCATAATATA
1 AATAATTCATAATATA
*
4832477 AATAATTCATTATAT
1 AATAATTCATAATAT
4832492 TATATTATAT
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:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:4835226 original size:36 final size:36
Alignment explanation
Indices: 4835177--4835290 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
4835167 AAGTCTCTAC
4835177 AGGTTCAGA-TCTGATCAAGCTGGTAATTCCTTATAT
1 AGGTTCA-ACTCTGATCAAGCTGGTAATTCCTTATAT
* * * *
4835213 AGGTTCAACTCTGACCAACCTGGTAATTTCTTATAC
1 AGGTTCAACTCTGATCAAGCTGGTAATTCCTTATAT
* * ** *
4835249 AAGTTCAGCATC-GAT-TGGTTGGTAATTCCTTATAT
1 AGGTTCAAC-TCTGATCAAGCTGGTAATTCCTTATAT
4835284 AGGTTCA
1 AGGTTCA
4835291 GAACCAATCA
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
35 21 0.34
36 39 0.63
37 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (36 bp):
AGGTTCAACTCTGATCAAGCTGGTAATTCCTTATAT
Found at i:4837467 original size:5 final size:5
Alignment explanation
Indices: 4837457--4837484 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4837447 TGAGGGGATC
4837457 TTAAA TTAAA TTAAA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTA
4837485 TAACTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:4837789 original size:3 final size:3
Alignment explanation
Indices: 4837781--4837820 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4837771 CCTTAAAAAG
4837781 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4837821 GTGAAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4843899 original size:20 final size:20
Alignment explanation
Indices: 4843874--4843926 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
4843864 AGCACTGCTA
*
4843874 AGCACCACTAACGCTTAACG
1 AGCACCACTAACGCTCAACG
*
4843894 AGCACCAGTAACGCTCAACG
1 AGCACCACTAACGCTCAACG
*
4843914 AGCATCACTAACG
1 AGCACCACTAACG
4843927 ATAAGCATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.17, T:0.13
Consensus pattern (20 bp):
AGCACCACTAACGCTCAACG
Found at i:4844586 original size:7 final size:7
Alignment explanation
Indices: 4844574--4844607 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
4844564 ATCGAATCTC
4844574 ATTATTT
1 ATTATTT
4844581 ATTATTT
1 ATTATTT
4844588 ATTATTT
1 ATTATTT
4844595 ATTATTT
1 ATTATTT
4844602 A-TATTT
1 ATTATTT
4844608 TCCATTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:4854668 original size:3 final size:3
Alignment explanation
Indices: 4854660--4854717 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
4854650 CCAAACTACA
* *
4854660 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4854708 AAT AA- AAT AA
1 AAT AAT AAT AA
4854718 ACAACAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4859877 original size:10 final size:10
Alignment explanation
Indices: 4859858--4859893 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
4859848 AGCTTCATAA
4859858 CAGC-ACATT
1 CAGCTACATT
4859867 CAGCTACATT
1 CAGCTACATT
4859877 CAGCTACATT
1 CAGCTACATT
4859887 CAGCTAC
1 CAGCTAC
4859894 CATTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.25
Consensus pattern (10 bp):
CAGCTACATT
Found at i:4870502 original size:20 final size:20
Alignment explanation
Indices: 4870474--4870518 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4870464 TTCTTTTAAT
* *
4870474 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
* *
4870494 ATTTAATTTCATAGATAAAA
1 ATTTAATTTCAAAAATAAAA
4870514 ATTTA
1 ATTTA
4870519 TTAAAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:4871105 original size:14 final size:14
Alignment explanation
Indices: 4871086--4871140 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
4871076 CAATTTAAAT
4871086 TTAAATAAATTTAA
1 TTAAATAAATTTAA
**
4871100 TTAAATAACGTTAA
1 TTAAATAAATTTAA
4871114 -TAAAT-AATTTAA
1 TTAAATAAATTTAA
*
4871126 TTAATTTAAATTTAA
1 TTAA-ATAAATTTAA
4871141 ATAACTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
12 5 0.15
13 8 0.24
14 13 0.39
15 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
TTAAATAAATTTAA
Found at i:4871566 original size:26 final size:28
Alignment explanation
Indices: 4871505--4871567 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
4871495 CGAGTATTGC
*
4871505 TGAGCTCGACTCGACTTGAAAACTCTGAAA
1 TGAGCTCGACTCGACTCGAAAACTCTG--A
4871535 TGGAGCTCGACTCGACTCGAAAACTC-G-
1 T-GAGCTCGACTCGACTCGAAAACTCTGA
4871562 TGAGCT
1 TGAGCT
4871568 TAAAATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 5 0.16
27 1 0.03
30 2 0.06
31 23 0.74
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTCTGA
Found at i:4877065 original size:22 final size:22
Alignment explanation
Indices: 4877040--4877091 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
4877030 TATTTTCTTT
* *
4877040 GATTTAGGTATTTG-GATTTAGG
1 GATTTAGGT-TTTGAAATTTAAG
4877062 GATTT-GAGTTTTGAAATTTAAG
1 GATTTAG-GTTTTGAAATTTAAG
4877084 GATTTAGG
1 GATTTAGG
4877092 AGATGGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 5 0.20
22 19 0.76
23 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (22 bp):
GATTTAGGTTTTGAAATTTAAG
Found at i:4880576 original size:16 final size:17
Alignment explanation
Indices: 4880535--4880656 Score: 80
Period size: 16 Copynumber: 7.5 Consensus size: 17
4880525 TTTAATGTAT
*
4880535 TTAATTATATTATAAAA
1 TTAATTATATTATAATA
* *
4880552 ATAA-AATA-TATAATA
1 TTAATTATATTATAATA
*
4880567 TTAATTATATTA-ATTA
1 TTAATTATATTATAATA
* *
4880583 CTT-ATTAAATTAGAATA
1 -TTAATTATATTATAATA
4880600 TT-ATTATATTATAATA
1 TTAATTATATTATAATA
* *
4880616 TTAATTAGATTA-ATTA
1 TTAATTATATTATAATA
* *
4880632 CTT-ATTAAATTAGAATA
1 -TTAATTATATTATAATA
4880649 TT-ATTATA
1 TTAATTATA
4880657 ATATTTAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
15 9 0.11
16 51 0.61
17 23 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAATTATATTATAATA
Found at i:4880618 original size:49 final size:49
Alignment explanation
Indices: 4880560--4880656 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
4880550 AAATAAAATA
*
4880560 TATAATATTAATTATATTAATTACTTATTAAATTAGAATATTATTATAT
1 TATAATATTAATTAGATTAATTACTTATTAAATTAGAATATTATTATAT
4880609 TATAATATTAATTAGATTAATTACTTATTAAATTAGAATATTATTATA
1 TATAATATTAATTAGATTAATTACTTATTAAATTAGAATATTATTATA
4880657 ATATTTAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (49 bp):
TATAATATTAATTAGATTAATTACTTATTAAATTAGAATATTATTATAT
Found at i:4881396 original size:151 final size:153
Alignment explanation
Indices: 4881177--4881481 Score: 562
Period size: 151 Copynumber: 2.0 Consensus size: 153
4881167 AAGTCATTTT
*
4881177 TCAAAAAATGAAAAAGAAATTCTGTTGACCAGGAAAATAAATTTTATTGACTATATATTTTTCAC
1 TCAAAAAATG-AAAAGAAATTCTGTTGACCAGGAAAATAAATTATATTGACTATATATTTTTCAC
4881242 CAACCTAACACTGAAAAATAACGAAAACATTTTCTATAAAACCAATTACTGTCGGAACGTCCCTT
65 CAACCTAACACTGAAAAATAACGAAAACATTTTCTATAAAACCAATTACTGTCGGAACGTCCCTT
4881307 AAACTTTTTAGGGTTTATGACAGGG
130 AAACTTTTTAGGG-TTATGACAGGG
4881332 TCAAAAAATG-AAAGAAATTCTGTTGACCA-GAAAAT-AATTATATTGACTATATATTTTTCACC
1 TCAAAAAATGAAAAGAAATTCTGTTGACCAGGAAAATAAATTATATTGACTATATATTTTTCACC
4881394 AACCTAACACTGAAAAATAACGAAAACATTTTCTATAAAACCAATTACTGTCGGAACGTCCCTTA
66 AACCTAACACTGAAAAATAACGAAAACATTTTCTATAAAACCAATTACTGTCGGAACGTCCCTTA
4881459 AACTTTTTAGGGTTATGACAGGG
131 AACTTTTTAGGGTTATGACAGGG
4881482 AGCGATCCAA
Statistics
Matches: 149, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
150 11 0.07
151 103 0.69
152 6 0.04
153 19 0.13
155 10 0.07
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (153 bp):
TCAAAAAATGAAAAGAAATTCTGTTGACCAGGAAAATAAATTATATTGACTATATATTTTTCACC
AACCTAACACTGAAAAATAACGAAAACATTTTCTATAAAACCAATTACTGTCGGAACGTCCCTTA
AACTTTTTAGGGTTATGACAGGG
Found at i:4885454 original size:18 final size:18
Alignment explanation
Indices: 4885428--4885474 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
4885418 TTTTAACTTG
4885428 AGACCCCCTTTGGTTTCA
1 AGACCCCCTTTGGTTTCA
*
4885446 AGACGCCCTTTGGTTTCA
1 AGACCCCCTTTGGTTTCA
*
4885464 AGACTCCCTTT
1 AGACCCCCTTT
4885475 ACAGATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (18 bp):
AGACCCCCTTTGGTTTCA
Found at i:4885540 original size:12 final size:12
Alignment explanation
Indices: 4885519--4885555 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
4885509 CTTTATTTTT
*
4885519 TTTTCATTTTCA
1 TTTTCTTTTTCA
4885531 TTTTCTTTTTCA
1 TTTTCTTTTTCA
4885543 -TTTCTTTTT-A
1 TTTTCTTTTTCA
4885553 TTT
1 TTT
4885556 ATTCAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 11 0.48
12 11 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:4885560 original size:18 final size:17
Alignment explanation
Indices: 4885498--4885560 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
4885488 TTGAACCCCC
4885498 TTTTATTTATTC-TTT-A
1 TTTTATTT-TTCATTTCA
4885514 TTTT-TTTTTCATTTTCA
1 TTTTATTTTTCA-TTTCA
* *
4885531 TTTTCTTTTTCATTTCT
1 TTTTATTTTTCATTTCA
4885548 TTTTATTTATTCA
1 TTTTATTT-TTCA
4885561 GAAAAAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 3 0.08
15 3 0.08
16 7 0.17
17 16 0.40
18 11 0.28
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTCATTTCA
Found at i:4894304 original size:14 final size:14
Alignment explanation
Indices: 4894284--4894317 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4894274 ATGGAGAGAG
4894284 AGAAATAAAAATAA
1 AGAAATAAAAATAA
* *
4894298 GGAAATAAAATTAA
1 AGAAATAAAAATAA
4894312 AGAAAT
1 AGAAAT
4894318 GAATAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (14 bp):
AGAAATAAAAATAA
Found at i:4894464 original size:10 final size:11
Alignment explanation
Indices: 4894442--4894475 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4894432 ATTATTCGGG
4894442 AAAAAGATAAA
1 AAAAAGATAAA
4894453 AAAAAGATAAA
1 AAAAAGATAAA
*
4894464 AATAAAAATAAA
1 AA-AAAGATAAA
4894476 TTCATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (11 bp):
AAAAAGATAAA
Found at i:4899545 original size:20 final size:21
Alignment explanation
Indices: 4899516--4899562 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
4899506 ATAACAAGTT
4899516 TGCATGGC-ATTAATTCATGA
1 TGCATGGCAATTAATTCATGA
* *
4899536 TGCATTGCATATTAATTCATGT
1 TGCATGGCA-ATTAATTCATGA
4899558 TGCAT
1 TGCAT
4899563 ATTCATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGCATGGCAATTAATTCATGA
Found at i:4903007 original size:13 final size:13
Alignment explanation
Indices: 4902943--4903010 Score: 82
Period size: 13 Copynumber: 5.2 Consensus size: 13
4902933 TGTGTCATAA
4902943 ATTTATGACGCAC
1 ATTTATGACGCAC
* *
4902956 ATTTACGACACAC
1 ATTTATGACGCAC
*
4902969 ATTTATGACACAC
1 ATTTATGACGCAC
* *
4902982 ATTTATGATGCGC
1 ATTTATGACGCAC
*
4902995 ATTTATGACGCGC
1 ATTTATGACGCAC
4903008 ATT
1 ATT
4903011 GCGTGTCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (13 bp):
ATTTATGACGCAC
Done.