Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013594.1 Kokia drynarioides strain JFW-HI SEQ_128621, 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: 188289
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 204 characters in sequence are not A, C, G, or T
Found at i:1955 original size:43 final size:43
Alignment explanation
Indices: 1897--2037 Score: 210
Period size: 43 Copynumber: 3.3 Consensus size: 43
1887 TGGAAAGTGG
* *
1897 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGC
* * * *
1940 AAAGTGCCGCTAAAGACCATGTTTTTTAGCGGCATTTGTGGCC
1 AAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGC
* *
1983 ATAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGC
1 AAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGC
2026 AAAGCGCCGCTA
1 AAAGCGCCGCTA
2038 TCTTAAGCGG
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGC
Found at i:2101 original size:43 final size:43
Alignment explanation
Indices: 2038--2174 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
2028 AGCGCCGCTA
* * *
2038 TCTTAAGCGGTGTTTTTGGGAAAAGCGTCGGTAAAAACCATGT
1 TCTTAAGCGGTGTTTATGGGAAAAGCGCCGCTAAAAACCATGT
* * * * *
2081 TCTTAAGCGGTGTTTGTGGGAGAAGCACCACTAAAGACCATGT
1 TCTTAAGCGGTGTTTATGGGAAAAGCGCCGCTAAAAACCATGT
* * * *
2124 TATTTAGCAGTGTTTAT-GAAAAAGCGCCGCTAAAAACCATGT
1 TCTTAAGCGGTGTTTATGGGAAAAGCGCCGCTAAAAACCATGT
*
2166 TCTTTAGCG
1 TCTTAAGCG
2175 CGTTATCTTT
Statistics
Matches: 76, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
42 27 0.36
43 49 0.64
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
TCTTAAGCGGTGTTTATGGGAAAAGCGCCGCTAAAAACCATGT
Found at i:3506 original size:3 final size:3
Alignment explanation
Indices: 3500--3544 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
3490 ATTATTATTA
* * *
3500 TTG TTG TTG TTG TTG TTC TTC TTG TTG TTC TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
3545 GTGGTGGTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.07, G:0.27, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:5512 original size:30 final size:30
Alignment explanation
Indices: 5480--5633 Score: 100
Period size: 30 Copynumber: 5.2 Consensus size: 30
5470 ATTTTATCCA
*
5480 AAAAT-ATATATTGACCCCCAAACTTTTCC
1 AAAATCATATATTAACCCCCAAACTTTTCC
*
5509 AAAATCATATTTTAACCCCCAAAC-TTTCTC
1 AAAATCATATATTAACCCCCAAACTTTTC-C
* * *** *
5539 AAAATCACT-TTTTGATTGCCAAAATTTTCC
1 AAAATCA-TATATTAACCCCCAAACTTTTCC
** * * *
5569 AAAATTTTATTTTAATCCCTAAACTTTTCC
1 AAAATCATATATTAACCCCCAAACTTTTCC
* * **
5599 AAAATTATAT-TTTACCCCCTAAACTTACCC
1 AAAATCATATATTAACCCCC-AAACTTTTCC
5629 AAAAT
1 AAAAT
5634 TACATTTTGA
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
29 16 0.16
30 78 0.79
31 5 0.05
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATCATATATTAACCCCCAAACTTTTCC
Found at i:5634 original size:30 final size:28
Alignment explanation
Indices: 5567--5671 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 28
5557 CCAAAATTTT
** * *
5567 CCAAAATTTTATTTTAATCCCTAAACTTTT
1 CCAAAATTACATTTT-ACCCCTAAAC-TTC
*
5597 CCAAAATTATATTTTACCCCCTAAACTTAC
1 CCAAAATTACATTTTA-CCCCTAAACTT-C
*
5627 CCAAAATTACATTTTGACCCTTAAACTTC
1 CCAAAATTACATTTT-ACCCCTAAACTTC
5656 CCTAAAATTACATTTT
1 CC-AAAATTACATTTT
5672 GCCCGAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.09
30 59 0.89
31 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (28 bp):
CCAAAATTACATTTTACCCCTAAACTTC
Found at i:5663 original size:90 final size:89
Alignment explanation
Indices: 5499--5664 Score: 201
Period size: 90 Copynumber: 1.8 Consensus size: 89
5489 ATTGACCCCC
* * * * *
5499 AAACTTTTCCAAAATCATATTTTAACCCCCAAACTTTCTCAAAATCACTTTTTGATTGCCAAAAT
1 AAACTTTTCCAAAATCATATTTTAACCCCCAAACTTACCCAAAATCACATTTTGA-TCCCAAAAC
*
5564 TTTCCAAAATTTTATTTTAATCCCT
65 TTCCCAAAATTTTATTTTAATCCCT
* * *
5589 AAACTTTTCCAAAATTATATTTT-ACCCCCTAAACTTACCCAAAATTACATTTTGA-CCCTTAAA
1 AAACTTTTCCAAAATCATATTTTAACCCCC-AAACTTACCCAAAATCACATTTTGATCCC-AAAA
5652 CTTCCCTAAAATT
64 CTTCCC-AAAATT
5665 ACATTTTGCC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
88 2 0.03
89 13 0.20
90 49 0.77
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (89 bp):
AAACTTTTCCAAAATCATATTTTAACCCCCAAACTTACCCAAAATCACATTTTGATCCCAAAACT
TCCCAAAATTTTATTTTAATCCCT
Found at i:5672 original size:30 final size:31
Alignment explanation
Indices: 5585--5672 Score: 110
Period size: 30 Copynumber: 2.9 Consensus size: 31
5575 TTATTTTAAT
** *
5585 CCCTAAACTTTTCCAAAATTATATTTT-ACC
1 CCCTAAACTTACCCAAAATTACATTTTGACC
5615 CCCTAAACTTACCCAAAATTACATTTTGA-C
1 CCCTAAACTTACCCAAAATTACATTTTGACC
*
5645 CCTTAAACTT-CCCTAAAATTACATTTTG
1 CCCTAAACTTACCC-AAAATTACATTTTG
5673 CCCGAAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.06
30 48 0.92
31 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (31 bp):
CCCTAAACTTACCCAAAATTACATTTTGACC
Found at i:6622 original size:8 final size:8
Alignment explanation
Indices: 6609--6636 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
6599 CACACACACA
6609 AAAAAAAG
1 AAAAAAAG
6617 AAAAAAAG
1 AAAAAAAG
6625 AAAAAAAG
1 AAAAAAAG
6633 AAAA
1 AAAA
6637 TCCCACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:10170 original size:73 final size:73
Alignment explanation
Indices: 10051--10192 Score: 257
Period size: 73 Copynumber: 1.9 Consensus size: 73
10041 TAATTAAGTT
* * *
10051 TAGTTTGGATGGGAGGTGAGATTAGTTTTGATAAGATTAAAAATAATTGTTGTGAGGGGATTAGT
1 TAGTTTGGATGGAAGGTGAGATTAGTTTCGATAAGATTAAAAATAATTGTTGTGAGGGGATTAAT
10116 CACTATAA
66 CACTATAA
10124 TAGTTTGGATGGAAGGTGAGATTAGTTTCGATAAGATTAAAAATAATTGTTGTGAGGGGATTAAT
1 TAGTTTGGATGGAAGGTGAGATTAGTTTCGATAAGATTAAAAATAATTGTTGTGAGGGGATTAAT
10189 CACT
66 CACT
10193 GGTGAATTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (73 bp):
TAGTTTGGATGGAAGGTGAGATTAGTTTCGATAAGATTAAAAATAATTGTTGTGAGGGGATTAAT
CACTATAA
Found at i:10871 original size:24 final size:24
Alignment explanation
Indices: 10838--10909 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
10828 AGAAATAATA
* *
10838 TTTCAGTTAAACTCTGGTTATTTG
1 TTTCAATTAAACTCTAGTTATTTG
*
10862 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTAGTTATTTG
* * * *
10886 CTTGAGTCAAACTCTAGATTATTT
1 TTTCAATTAAACTCTAG-TTATTT
10910 TATTATGATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 33 0.85
25 6 0.15
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAATTAAACTCTAGTTATTTG
Found at i:12581 original size:24 final size:24
Alignment explanation
Indices: 12553--12603 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12543 TGGTCAACTC
* * *
12553 TTTCATTTAAACTTTGCTTATTTG
1 TTTCAATTAAACTCTACTTATTTG
*
12577 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTACTTATTTG
12601 TTT
1 TTT
12604 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTACTTATTTG
Found at i:12612 original size:24 final size:24
Alignment explanation
Indices: 12570--12615 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12560 TAAACTTTGC
*
12570 TTATTTGTTTCAATTAAACTCTAT
1 TTATTTGTTTCAATCAAACTCTAT
* *
12594 TTATTTGTTTGAGTCAAACTCT
1 TTATTTGTTTCAATCAAACTCT
12616 TATTACGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (24 bp):
TTATTTGTTTCAATCAAACTCTAT
Found at i:25055 original size:34 final size:34
Alignment explanation
Indices: 25017--25154 Score: 162
Period size: 34 Copynumber: 4.2 Consensus size: 34
25007 CTGTGAAGTG
** *
25017 CGAGCTCATCAAGTGTGTAAGCTCACTAAGACTT
1 CGAGCTCATCAAGTGTGCGAGCTCACCAAGACTT
*
25051 CGAGCTCATCAAGTATGCGAGCTCACCAAGACTT
1 CGAGCTCATCAAGTGTGCGAGCTCACCAAGACTT
* * *
25085 TGAGGTTATCAAGTGTGCGAGCTCACCAAGAC-T
1 CGAGCTCATCAAGTGTGCGAGCTCACCAAGACTT
25118 ---GC-CATCAAGTGTGCGAGCTCACCAAGA-TT
1 CGAGCTCATCAAGTGTGCGAGCTCACCAAGACTT
25147 GCGAGCTC
1 -CGAGCTC
25155 GTCTGTTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
29 25 0.28
30 1 0.01
33 3 0.03
34 59 0.67
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (34 bp):
CGAGCTCATCAAGTGTGCGAGCTCACCAAGACTT
Found at i:25114 original size:17 final size:17
Alignment explanation
Indices: 25014--25154 Score: 60
Period size: 17 Copynumber: 8.6 Consensus size: 17
25004 GAACTGTGAA
*
25014 GTGCGAGCTCATCAAGT
1 GTGCGAGCTCACCAAGT
** * *
25031 GTGTAAGCTCACTAAGA
1 GTGCGAGCTCACCAAGT
* * *
25048 CTTCGAGCTCATCAAGT
1 GTGCGAGCTCACCAAGT
* *
25065 ATGCGAGCTCACCAAGA
1 GTGCGAGCTCACCAAGT
* ** * * *
25082 CTTTGAGGTTATCAAGT
1 GTGCGAGCTCACCAAGT
25099 GTGCGAGCTCACCAA--
1 GTGCGAGCTCACCAAGT
* * *
25114 G-AC-TGC-CATCAAGT
1 GTGCGAGCTCACCAAGT
25128 GTGCGAGCTCACCAAGAT
1 GTGCGAGCTCACCAAG-T
25146 -TGCGAGCTC
1 GTGCGAGCTC
25155 GTCTGTTAAA
Statistics
Matches: 83, Mismatches: 35, Indels: 12
0.64 0.27 0.09
Matches are distributed among these distances:
12 5 0.06
13 2 0.02
14 2 0.02
15 2 0.02
16 2 0.02
17 69 0.83
18 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.23
Consensus pattern (17 bp):
GTGCGAGCTCACCAAGT
Found at i:27897 original size:90 final size:89
Alignment explanation
Indices: 27722--27931 Score: 332
Period size: 90 Copynumber: 2.4 Consensus size: 89
27712 ACTACAATTC
* *
27722 AAAATTTTCATATTATTTTTGTATTTGTAAATCAATTTTAGTCGTATTATTTGTTTGTCGAATTT
1 AAAATGTTCGTATTATTTTTGTATTTGTAAATCAATTTTAGTCGTATTATTTGTTTGTCGAATTT
*
27787 TATATTTTTGTATATCAAGTTTCT
66 TATATTTTCGTATATCAAGTTTCT
* *
27811 AAAATGTTCGTATTATTTTTGTATTTGTAAATCAATTTTAGCTTGTATTATTTGTTTGTTGAATT
1 AAAATGTTCGTATTATTTTTGTATTTGTAAATCAATTTTAG-TCGTATTATTTGTTTGTCGAATT
*
27876 TTATATTTTCGTATATTAAGTTTCT
65 TTATATTTTCGTATATCAAGTTTCT
* *
27901 AAAATGTTTGTATT-TTCTTGTATTTGTAAAT
1 AAAATGTTCGTATTATTTTTGTATTTGTAAAT
27932 ATTGTTTGTT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
89 55 0.49
90 57 0.51
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (89 bp):
AAAATGTTCGTATTATTTTTGTATTTGTAAATCAATTTTAGTCGTATTATTTGTTTGTCGAATTT
TATATTTTCGTATATCAAGTTTCT
Found at i:31382 original size:117 final size:116
Alignment explanation
Indices: 31219--31475 Score: 287
Period size: 117 Copynumber: 2.2 Consensus size: 116
31209 AAAAAAATTA
* * * *
31219 ATTTTTTTAT-TCA-AT-AAAGTTGATGCCAACCATTAGTGTCTCAAAACCCTAAAAAAAAAAAT
1 ATTTTTTTATATCAGATAAAAGTTGGTACCAACCATTAATGTCTCAAAACCCCAAAAAAAAAAAT
* * * * * * *
31281 TT-ATTCTC-GAAAAAGATGGTGTCAATCATCTATCACTCAAAATCCA-AATAAT
66 TTGATTC-CAAAAAAAG-TGATGCCAACCATCTATCACCCAAAA--CAGAAAAAG
* *
31333 ATTTTTTTATATCAGATAAAAGTTGGTATCAACTATTAATGT-TCTAAAACCCCAAAAAAAAAAA
1 ATTTTTTTATATCAGATAAAAGTTGGTACCAACCATTAATGTCTC-AAAACCCCAAAAAAAAAAA
31397 TTTGATTCCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACATGAAAAAG
65 TTTGATTCCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACA-GAAAAAG
31450 A-TTTTTTATATCAGATAAAAGTTGGT
1 ATTTTTTTATATCAGATAAAAGTTGGT
31476 GCCAGGCATT
Statistics
Matches: 122, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
114 10 0.08
115 5 0.04
116 29 0.24
117 68 0.56
118 10 0.08
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (116 bp):
ATTTTTTTATATCAGATAAAAGTTGGTACCAACCATTAATGTCTCAAAACCCCAAAAAAAAAAAT
TTGATTCCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACAGAAAAAG
Found at i:31861 original size:116 final size:113
Alignment explanation
Indices: 31655--31907 Score: 286
Period size: 116 Copynumber: 2.2 Consensus size: 113
31645 AAAAAAATTA
* * * * *
31655 ATTTTTTTAT-TCA-AT-AAAGTTGATGCCAATCATTAGTGTTTCAAAACCCTAAAAAAAAATTA
1 ATTTTTTTATATCAGATAAAAGTTGGTACCAACCATTAATGTTTCAAAACCCAAAAAAAAAATTA
* * * * *
31717 TTCTCAAAAAAAGTGGTGTCAATCATCTATCACTCAAAATCCA-AATAAT
66 TTCTCAAAAAAAGTGATGCCAACCATCTATCACCCAAAA--CAGAAAAAT
*
31766 ATTTTTTTATATCAGATAAAAGTTGGTATCAACCATTAATG-TTCTAAAACCCCAAAAAAAAAAT
1 ATTTTTTTATATCAGATAAAAGTTGGTACCAACCATTAATGTTTC-AAAA-CCCAAAAAAAAAA-
*
31830 TTGGTTC-CAAAAAAAGTGATGCCAACCATCTATCACCCAAAACATGAAAAAT
63 TT-ATTCTCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACA-GAAAAAT
31882 A-TTTTTTATATCAGATAAAAGTTGGT
1 ATTTTTTTATATCAGATAAAAGTTGGT
31908 GCCGAGCATT
Statistics
Matches: 121, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
111 10 0.08
112 3 0.02
113 5 0.04
114 24 0.20
115 37 0.31
116 39 0.32
117 3 0.02
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (113 bp):
ATTTTTTTATATCAGATAAAAGTTGGTACCAACCATTAATGTTTCAAAACCCAAAAAAAAAATTA
TTCTCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACAGAAAAAT
Found at i:31918 original size:115 final size:113
Alignment explanation
Indices: 31646--31919 Score: 292
Period size: 115 Copynumber: 2.4 Consensus size: 113
31636 AAAATCCTAA
* * * *
31646 AAAAAATTAATTTTTTTAT-TCA-AT-AAAGTTGATGCCAATCATTAGTGTTTCAAAACCCTAAA
1 AAAAAA-T-ATTTTTTTATATCAGATAAAAGTTGGTGCCAACCATTAATGTTTCAAAACCCAAAA
* * * *
31708 AAAAAATTATTCTCAAAAAAAGTGGTGTCAATCATCTATCACTCAAAATCC
64 AAAAAATTATTCTCAAAAAAAGTGATGCCAACCATCTATCACCCAAAA-CC
* **
31759 AAATAATATTTTTTTATATCAGATAAAAGTTGGTATCAACCATTAATG-TTCTAAAACCCCAAAA
1 AAAAAATATTTTTTTATATCAGATAAAAGTTGGTGCCAACCATTAATGTTTC-AAAA-CCCAAAA
*
31823 AAAAAATTTGGTTC-CAAAAAAAGTGATGCCAACCATCTATCACCCAAAA-C
64 AAAAAA-TT-ATTCTCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACC
* *
31873 ATGAAAAATA-TTTTTTATATCAGATAAAAGTTGGTGCCGAGCATTAA
1 A--AAAAATATTTTTTTATATCAGATAAAAGTTGGTGCCAACCATTAA
31920 ATGGCAAGCA
Statistics
Matches: 135, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
111 10 0.07
112 4 0.03
113 10 0.07
114 24 0.18
115 45 0.33
116 39 0.29
117 3 0.02
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (113 bp):
AAAAAATATTTTTTTATATCAGATAAAAGTTGGTGCCAACCATTAATGTTTCAAAACCCAAAAAA
AAAATTATTCTCAAAAAAAGTGATGCCAACCATCTATCACCCAAAACC
Found at i:31994 original size:51 final size:51
Alignment explanation
Indices: 31898--31994 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
31888 TATATCAGAT
* * *
31898 AAAAGTTGGTGCCGAGCATTAAATGGCAAGCACCCAAATTTTTTTTATTTA
1 AAAAGTTGGTGCCGACCATTAAACGGCAAGCACCCAAATTGTTTTTATTTA
* * *
31949 AAAAGTTGGTGCCGACCATTACACGGCCAGCACTTC-AATTGTTTTT
1 AAAAGTTGGTGCCGACCATTAAACGGCAAGCAC-CCAAATTGTTTTT
31995 TTCAAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 38 0.97
52 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (51 bp):
AAAAGTTGGTGCCGACCATTAAACGGCAAGCACCCAAATTGTTTTTATTTA
Found at i:32617 original size:21 final size:22
Alignment explanation
Indices: 32591--32631 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
32581 GTATCATTAG
32591 TTTTTAA-AAAAATTATAAATA
1 TTTTTAATAAAAATTATAAATA
*
32612 TTTTTAATAAAAATTTTAAA
1 TTTTTAATAAAAATTATAAA
32632 ATATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTTTAATAAAAATTATAAATA
Found at i:37900 original size:36 final size:36
Alignment explanation
Indices: 37850--37924 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
37840 AACAAGAATT
*
37850 TAAACCAAATAACACTGGGTTAGGAAGCATAAAAAC
1 TAAACCAAACAACACTGGGTTAGGAAGCATAAAAAC
37886 TAAACCAAACAACACTGGGTTAGGAAGCATAAAAAC
1 TAAACCAAACAACACTGGGTTAGGAAGCATAAAAAC
37922 TAA
1 TAA
37925 GTATGAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (36 bp):
TAAACCAAACAACACTGGGTTAGGAAGCATAAAAAC
Found at i:40282 original size:15 final size:14
Alignment explanation
Indices: 40255--40289 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
40245 TATTTCATTT
*
40255 AAAAAATAGAAAAG
1 AAAAAATAAAAAAG
40269 AAAATAATAAAAAAG
1 AAAA-AATAAAAAAG
40284 AAAAAA
1 AAAAAA
40290 CAGGAGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAAATAAAAAAG
Found at i:41278 original size:93 final size:92
Alignment explanation
Indices: 41149--41654 Score: 430
Period size: 93 Copynumber: 5.4 Consensus size: 92
41139 TTAAAAAGTA
* * *
41149 GATCTCAATCTCCCTAAGATTACAGTGGAATGGAGTGAAGCACTAAATCCTATATCCTTGAGGTT
1 GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCTTGAGGTT
41214 ACTGCTGATCGGATTAAAATGAGTAATG
66 ACTG-TGATCGGATTAAAATGAGTAATG
* * * *
41242 GATCTCAATCTCCTTAAGGTTACAATGGAATGGAGTGAAGTACAACACCATATCCTATA-CCATT
1 GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG-----CACCAAATCCTATATCC-TT
* * * *
41306 GAAGTTGTAATG-GGTCGGATTAAAA--AG-CAT-
60 G-AGGT-TACTGTGATCGGATTAAAATGAGTAATG
* * * *
41336 -ATCTCAATCTCCCTGAGGTTACAGTGGAATGTAATGAAGAACCAAATCCTATATCCCTGAGGTT
1 GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCTTGAGGTT
*** **
41400 ACAACGAATTAGATTAAAATGAGTAATG
66 ACTGTG-ATCGGATTAAAATGAGTAATG
* * * * *
41428 GATCTCAATCTCCCTGAGGTTATAATGGAATAGAGTGAAGTATAACACCAAATCCTATACCCCTG
1 GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAG-----CACCAAATCCTATATCCTTG
* * * * *
41493 AAGTT-GTAGTAGGTCAGATTAAAA--AGCAA--
61 AGGTTACT-GT-GATCGGATTAAAATGAGTAATG
*
41522 -ATCTCAATCTCCCTGAGGTTATAGTGGAATGGAGTGAAGCACCAAATCCTATAT-CTCT-ATGG
1 GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCT-TGA-GG
*
41584 TTACAGTGGATCGGATTAAAATGAGTAATG
64 TTACTGT-GATCGGATTAAAATGAGTAATG
*
41614 GATCTCAATCTCGCTGAGGTTACAGTGGAATGGAGTGAAGC
1 GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGC
41655 TACGATAACA
Statistics
Matches: 329, Mismatches: 53, Indels: 62
0.74 0.12 0.14
Matches are distributed among these distances:
86 2 0.01
87 6 0.02
88 54 0.16
89 2 0.01
90 6 0.02
91 2 0.01
93 180 0.55
95 2 0.01
96 6 0.02
97 2 0.01
98 59 0.18
99 4 0.01
100 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (92 bp):
GATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCTTGAGGTT
ACTGTGATCGGATTAAAATGAGTAATG
Found at i:41417 original size:186 final size:183
Alignment explanation
Indices: 41095--41653 Score: 760
Period size: 186 Copynumber: 3.0 Consensus size: 183
41085 TGATGGATCG
* ** * *
41095 AGTAAACACCAAATGCTATACCCTTGAAGTTACAGTGGGTCAGATTAAAAAGTAGATCTCAATCT
1 AGTAAACACCAAATCCTATACCCTTGAAGTTGTAGTGGGTCAGATTAAAAAGCAAATCTCAATCT
* * * * *
41160 CCCTAAGATTACAGTGGAATGGAGTGAAGCACTAAATCCTATATCCTTGAGGTTACTGCTGATCG
66 CCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGAGGTTACAGC-GATCG
*
41225 GATTAAAATGAGTAATGGATCTCAATCTCCTTAAGGTTACAATGGAATGGAGTGA
130 GATTAAAATGAGTAATGGATCTCAATCTCC-TGAGGTTACAATGGAATGGAGTGA
* * * * *
41280 AGTACAACACCATATCCTATACCATTGAAGTTGTAATGGGTCGGATTAAAAAGCATATCTCAATC
1 AGTA-AACACCAAATCCTATACCCTTGAAGTTGTAGTGGGTCAGATTAAAAAGCAAATCTCAATC
* * * * *
41345 TCCCTGAGGTTACAGTGGAATGTAATGAAGAACCAAATCCTATATCCCTGAGGTTACAACGAATT
65 TCCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGAGGTTACAGCG-ATC
* * *
41410 AGATTAAAATGAGTAATGGATCTCAATCTCCCTGAGGTTATAATGGAATAGAGTGA
129 GGATTAAAATGAGTAATGGATCTCAATCT-CCTGAGGTTACAATGGAATGGAGTGA
* *
41466 AGTATAACACCAAATCCTATACCCCTGAAGTTGTAGTAGGTCAGATTAAAAAGCAAATCTCAATC
1 AGTA-AACACCAAATCCTATACCCTTGAAGTTGTAGTGGGTCAGATTAAAAAGCAAATCTCAATC
* * *
41531 TCCCTGAGGTTATAGTGGAATGGAGTGAAGCACCAAATCCTATATCTCT-ATGGTTACAGTGGAT
65 TCCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGA-GGTTACAG-CGAT
*
41595 CGGATTAAAATGAGTAATGGATCTCAATCTCGCTGAGGTTACAGTGGAATGGAGTGA
128 CGGATTAAAATGAGTAATGGATCTCAATCTC-CTGAGGTTACAATGGAATGGAGTGA
41652 AG
1 AG
41654 CTACGATAAC
Statistics
Matches: 325, Mismatches: 43, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
185 7 0.02
186 315 0.97
187 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (183 bp):
AGTAAACACCAAATCCTATACCCTTGAAGTTGTAGTGGGTCAGATTAAAAAGCAAATCTCAATCT
CCCTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGAGGTTACAGCGATCGG
ATTAAAATGAGTAATGGATCTCAATCTCCTGAGGTTACAATGGAATGGAGTGA
Found at i:43622 original size:19 final size:18
Alignment explanation
Indices: 43598--43641 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43588 TGAGGTATAC
43598 TATTTTTTACTCATATTTT
1 TATTTTTTA-TCATATTTT
* *
43617 TATTTTGTATTATATTTT
1 TATTTTTTATCATATTTT
*
43635 TCTTTTT
1 TATTTTT
43642 ATTTTCGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (18 bp):
TATTTTTTATCATATTTT
Found at i:44774 original size:22 final size:22
Alignment explanation
Indices: 44739--44793 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
44729 CTTATTTTGG
* **
44739 TTTTTTATTAAATCCTTTTATA
1 TTTTTAATTAAATCCCATTATA
* *
44761 TTTTTAATTTAATCCCATTATT
1 TTTTTAATTAAATCCCATTATA
44783 TTTTTAATTAA
1 TTTTTAATTAA
44794 TTTAATCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTAATTAAATCCCATTATA
Found at i:45127 original size:27 final size:26
Alignment explanation
Indices: 45097--45151 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
45087 AAATTAAAAT
45097 ATATGAAGTTTGGAATAAAAATCAAGA
1 ATAT-AAGTTTGGAATAAAAATCAAGA
**
45124 ATATTCGTTTGGAATAAAAATCAAGA
1 ATATAAGTTTGGAATAAAAATCAAGA
45150 AT
1 AT
45152 GCTCGATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.29
Consensus pattern (26 bp):
ATATAAGTTTGGAATAAAAATCAAGA
Found at i:52672 original size:37 final size:37
Alignment explanation
Indices: 52621--52800 Score: 218
Period size: 37 Copynumber: 4.9 Consensus size: 37
52611 TTGCATCTAA
* * *
52621 GTATTCGGGGTATGTGCCTAGCAGGCTTCATGTTGGT
1 GTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCTGGT
* * * *
52658 GTATTCGGGCTATGTGTCTAGCGGGCTTCGTACTAGT
1 GTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCTGGT
*
52695 GTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGT
1 GTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCTGGT
* **
52732 GTATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCAGT
1 GTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCTGGT
* * *
52769 GTATTTGGGCTAT-TCACCTAGCAAGCTTCGTG
1 GTATTCGGGCTATGT-GCCTAGCAGGCTTCGTG
52801 TCGATGGAAG
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
36 1 0.01
37 123 0.99
ACGTcount: A:0.14, C:0.21, G:0.32, T:0.33
Consensus pattern (37 bp):
GTATTCGGGCTATGTGCCTAGCAGGCTTCGTGCTGGT
Found at i:57912 original size:19 final size:19
Alignment explanation
Indices: 57884--57921 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
57874 CCACTGTCAA
*
57884 CCACCGTAATCAAATTTGT
1 CCACCATAATCAAATTTGT
57903 CCACCATAATCAAATTTGT
1 CCACCATAATCAAATTTGT
57922 TATTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (19 bp):
CCACCATAATCAAATTTGT
Found at i:58016 original size:31 final size:30
Alignment explanation
Indices: 57978--58058 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
57968 ATACCAAAAC
* *
57978 TATACATGAA-TTATGGTTTAATGTGTAATTG
1 TATACATGAACTTATGATTT--TGTGCAATTG
* *
58009 TATACATGAACTTTTGATTTTGTGCAATTT
1 TATACATGAACTTATGATTTTGTGCAATTG
* *
58039 TATACATGAAATTTTGATTT
1 TATACATGAACTTATGATTT
58059 GATCCAATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 27 0.61
31 10 0.23
32 7 0.16
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (30 bp):
TATACATGAACTTATGATTTTGTGCAATTG
Found at i:58045 original size:30 final size:30
Alignment explanation
Indices: 57999--58058 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
57989 TATGGTTTAA
* *
57999 TGTGTAATTGTATACATGAACTTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
*
58029 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
58059 GATCCAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:58067 original size:30 final size:30
Alignment explanation
Indices: 58004--58067 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
57994 TTTAATGTGT
* *
58004 AATTGTATACATGAACTTTTGATTTTGTGC
1 AATTGTATACATGAAATTTTGATTTTGTCC
*
58034 AATTTTATACATGAAATTTTGA-TTTGATCC
1 AATTGTATACATGAAATTTTGATTTTG-TCC
58064 AATT
1 AATT
58068 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (30 bp):
AATTGTATACATGAAATTTTGATTTTGTCC
Found at i:66300 original size:21 final size:21
Alignment explanation
Indices: 66274--66325 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
66264 CAGAAGGCGA
66274 TGTCGCGACACACAGGAGCCG
1 TGTCGCGACACACAGGAGCCG
66295 TGTCGCGACACACAGGAGCCG
1 TGTCGCGACACACAGGAGCCG
66316 TGTCGCGACA
1 TGTCGCGACA
66326 TAGAACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.33, T:0.12
Consensus pattern (21 bp):
TGTCGCGACACACAGGAGCCG
Found at i:71588 original size:26 final size:26
Alignment explanation
Indices: 71558--71746 Score: 195
Period size: 26 Copynumber: 7.3 Consensus size: 26
71548 TTACAGAAGT
*
71558 TTAGCTCATATGAGCCCAGACAGA-A
1 TTAGCTCTTATGAGCCCAGACAGAGA
* * *
71583 TTTAGCTCTTATAAGCCCAAACAAAGA
1 -TTAGCTCTTATGAGCCCAGACAGAGA
** *
71610 TTAGCTCTTACT-AGCTTAGATAGAGA
1 TTAGCTCTTA-TGAGCCCAGACAGAGA
* *
71636 TTAGCTCATACGAGCCCAGACAGAGA
1 TTAGCTCTTATGAGCCCAGACAGAGA
*
71662 TTAGCTCTTACT-AGCCCAGATAGAGA
1 TTAGCTCTTA-TGAGCCCAGACAGAGA
*
71688 TTAGCTCTTATGAGCCTAGACAGAGA
1 TTAGCTCTTATGAGCCCAGACAGAGA
* * * *
71714 TTAGCTCTTACGAGCCCAAACAAAGT
1 TTAGCTCTTATGAGCCCAGACAGAGA
71740 TTAGCTC
1 TTAGCTC
71747 ATGCGAGCCT
Statistics
Matches: 134, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.01
26 131 0.98
27 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (26 bp):
TTAGCTCTTATGAGCCCAGACAGAGA
Found at i:71689 original size:78 final size:78
Alignment explanation
Indices: 71558--71746 Score: 240
Period size: 78 Copynumber: 2.4 Consensus size: 78
71548 TTACAGAAGT
*
71558 TTAGCTCATATGAGCCCAGACAGA-ATTTAGCTCTTATAAGCCCAAACAAAGATTAGCTCTTACT
1 TTAGCTCATACGAGCCCAGACAGAGA-TTAGCTCTTATAAGCCCAAACAAAGATTAGCTCTTA-T
* *
71622 -AGCTTAGATAGAGA
64 GAGCCTAGACAGAGA
* * *
71636 TTAGCTCATACGAGCCCAGACAGAGATTAGCTCTTACT-AGCCCAGATAGAGATTAGCTCTTATG
1 TTAGCTCATACGAGCCCAGACAGAGATTAGCTCTTA-TAAGCCCAAACAAAGATTAGCTCTTATG
71700 AGCCTAGACAGAGA
65 AGCCTAGACAGAGA
* * * *
71714 TTAGCTCTTACGAGCCCAAACAAAGTTTAGCTC
1 TTAGCTCATACGAGCCCAGACAGAGATTAGCTC
71747 ATGCGAGCCT
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
77 1 0.01
78 95 0.97
79 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (78 bp):
TTAGCTCATACGAGCCCAGACAGAGATTAGCTCTTATAAGCCCAAACAAAGATTAGCTCTTATGA
GCCTAGACAGAGA
Found at i:71753 original size:26 final size:26
Alignment explanation
Indices: 71554--71765 Score: 111
Period size: 26 Copynumber: 8.2 Consensus size: 26
71544 GTCGTTACAG
* *
71554 AAGTTTAGCTCATATGAGCCCAGACA
1 AAGTTTAGCTCATACGAGCCCAAACA
* **
71580 GAA-TTTAGCTCTTATAAGCCCAAACA
1 -AAGTTTAGCTCATACGAGCCCAAACA
* * * ** * *
71606 AAGATTAGCTCTTACTAGCTTAGATA
1 AAGTTTAGCTCATACGAGCCCAAACA
* * *
71632 GAGATTAGCTCATACGAGCCCAGACA
1 AAGTTTAGCTCATACGAGCCCAAACA
* * * * * *
71658 GAGATTAGCTCTTACTAGCCCAGATA
1 AAGTTTAGCTCATACGAGCCCAAACA
* * * * * *
71684 GAGATTAGCTCTTATGAGCCTAGACA
1 AAGTTTAGCTCATACGAGCCCAAACA
* * *
71710 GAGATTAGCTCTTACGAGCCCAAACA
1 AAGTTTAGCTCATACGAGCCCAAACA
* * *
71736 AAGTTTAGCTCATGCGAGCCTAGACA
1 AAGTTTAGCTCATACGAGCCCAAACA
71762 AAGT
1 AAGT
71766 CACGCTCTTA
Statistics
Matches: 152, Mismatches: 32, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
25 2 0.01
26 148 0.97
27 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (26 bp):
AAGTTTAGCTCATACGAGCCCAAACA
Found at i:71773 original size:78 final size:78
Alignment explanation
Indices: 71558--71782 Score: 204
Period size: 78 Copynumber: 2.9 Consensus size: 78
71548 TTACAGAAGT
* * * * ** * *
71558 TTAGCTCATATGAGCCCAGACAGAA-TTTAGCTCTTATAAGCCCAAACAAAGATTAGCTCTTACT
1 TTAGCTCATACGAGCCCAAACA-AAGATTAGCTCATACGAGCCCAGACAAAGATCAGCTCTTA-T
* *
71622 -AGCTTAGATAGAGA
64 GAGCCTAGACAGAGA
* * * * * * *
71636 TTAGCTCATACGAGCCCAGACAGAGATTAGCTCTTACTAGCCCAGATAGAGATTAGCTCTTATGA
1 TTAGCTCATACGAGCCCAAACAAAGATTAGCTCATACGAGCCCAGACAAAGATCAGCTCTTATGA
71701 GCCTAGACAGAGA
66 GCCTAGACAGAGA
* * * *
71714 TTAGCTCTTACGAGCCCAAACAAAGTTTAGCTCATGCGAGCCTAGACAAAG-TCACGCTCTTATC
1 TTAGCTCATACGAGCCCAAACAAAGATTAGCTCATACGAGCCCAGACAAAGATCA-GCTCTTAT-
71778 GAGCC
64 GAGCC
71783 AGAATTTAGA
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
77 4 0.03
78 113 0.93
79 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (78 bp):
TTAGCTCATACGAGCCCAAACAAAGATTAGCTCATACGAGCCCAGACAAAGATCAGCTCTTATGA
GCCTAGACAGAGA
Found at i:71775 original size:52 final size:52
Alignment explanation
Indices: 71633--71761 Score: 177
Period size: 52 Copynumber: 2.5 Consensus size: 52
71623 GCTTAGATAG
* * * * *
71633 AGATTAGCTCATACGAGCCCAGACAGAGATTAGCTCTTACTAGCCCAGATAG
1 AGATTAGCTCATACGAGCCTAGACAGAGATTAGCTCTTACGAGCCCAAACAA
* *
71685 AGATTAGCTCTTATGAGCCTAGACAGAGATTAGCTCTTACGAGCCCAAACAA
1 AGATTAGCTCATACGAGCCTAGACAGAGATTAGCTCTTACGAGCCCAAACAA
* *
71737 AGTTTAGCTCATGCGAGCCTAGACA
1 AGATTAGCTCATACGAGCCTAGACA
71762 AAGTCACGCT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (52 bp):
AGATTAGCTCATACGAGCCTAGACAGAGATTAGCTCTTACGAGCCCAAACAA
Found at i:79377 original size:12 final size:12
Alignment explanation
Indices: 79356--79406 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
79346 AATATGCAAG
79356 AAAA-AAAACTA
1 AAAATAAAACTA
*
79367 AAACTAAAACTA
1 AAAATAAAACTA
79379 AAAAT-AAA-T-
1 AAAATAAAACTA
79388 AAAAT-AAA-TA
1 AAAATAAAACTA
79398 AAAATAAAA
1 AAAATAAAA
79407 TTGGGTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 9 0.26
10 6 0.17
11 9 0.26
12 11 0.31
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAACTA
Found at i:79401 original size:10 final size:10
Alignment explanation
Indices: 79377--79405 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
79367 AAACTAAAAC
79377 TAAAAATAAA
1 TAAAAATAAA
79387 T-AAAATAAA
1 TAAAAATAAA
79396 TAAAAATAAA
1 TAAAAATAAA
79406 ATTGGGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:79402 original size:15 final size:15
Alignment explanation
Indices: 79365--79407 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
79355 GAAAAAAAAC
*
79365 TAAAACTAAAACTAAA
1 TAAAAATAAAA-TAAA
79381 -AATAAATAAAATAAA
1 TAA-AAATAAAATAAA
79396 TAAAAATAAAAT
1 TAAAAATAAAAT
79408 TGGGTTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAATAAAATAAA
Found at i:84273 original size:13 final size:14
Alignment explanation
Indices: 84234--84268 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
84224 CCTAGGTCAC
84234 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
84248 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
84262 AAGAAAA
1 AA-AAAA
84269 GGAAAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:84275 original size:18 final size:18
Alignment explanation
Indices: 84234--84268 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
84224 CCTAGGTCAC
84234 AAAAAA-AAAGAAAGAAA
1 AAAAAAGAAAGAAAGAAA
84251 AAAAAAGAAAG-AAGAAA
1 AAAAAAGAAAGAAAGAAA
84268 A
1 A
84269 GGAAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAGAAA
Found at i:85987 original size:42 final size:42
Alignment explanation
Indices: 85936--86348 Score: 461
Period size: 42 Copynumber: 9.7 Consensus size: 42
85926 AAATCTAGAA
* *
85936 AGGGTAGATTGATGCCACCATCCAATCTTTTACCCCAACCAG
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* * *
85978 AGGGTAGATTGAAACCACCATCCAATCTCTTACCCCAACCAG
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* *
86020 AGGGCAAATTGAAGCCACCATCCAATCTTTTACCCCAACAAG
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* * * *
86062 AGGGCAGATAGAAG--ACCATCCAATCTATTACCCTAACTAG
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* * *
86102 AGGGCAGATTAAAGACACCATCCAATCTTTTACCCCAACCAA
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* * *
86144 AGGACAGATTGGAGCCACCATCCAATCTTTTACCCCAACCAA
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* * * *
86186 AGGACAGATTGGAGCCACCATCCAATCTTTTACTCTAACCAG
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
* * **
86228 AGGGCAGATTGAAGTCACCATCCAATCTTTTACCCAAAATTTAG
1 AGGGCAGATTGAAGCCACCATCCAATCTTTTACCC-CAA-CCAG
* * * *
86272 AGGGGCAGATTGAAGCCACTATCCAATCTTATACCTCAAATTCAG
1 A-GGGCAGATTGAAGCCACCATCCAATCTTTTACC-CCAA-CCAG
* *
86317 ATGGGCAAATTGAGGCCATCACATCCAATCTT
1 A-GGGCAGATTGAAGCCA-C-CATCCAATCTT
86349 ACAAACAAGA
Statistics
Matches: 322, Mismatches: 41, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
40 35 0.11
42 218 0.68
43 2 0.01
44 3 0.01
45 52 0.16
46 2 0.01
47 10 0.03
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (42 bp):
AGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCAACCAG
Found at i:86232 original size:166 final size:170
Alignment explanation
Indices: 85951--86306 Score: 486
Period size: 166 Copynumber: 2.1 Consensus size: 170
85941 AGATTGATGC
* **
85951 CACCATCCAATCTTTTACCCCAACCAGAGGGTAGATTGAAACCACCATCCAATCTCTTACCCCAA
1 CACCATCCAATCTTTTACCCCAACCAAAGGACAGATTGAAACCACCATCCAATCTCTTACCCCAA
* *
86016 CCAGAGGGCAAATTGAAGCCACCATCCAATCTTTTACCCCAACAAGAGGGCAGATAGAAG-ACCA
66 CCAAAGGACAAATTGAAGCCACCATCCAATCTTTTACCCCAACAAGAGGGCAGATAGAAGCACCA
*
86080 TCCAATCTATTACCC-TAA-CTAGA-GGGCAGATTAAAGA
131 TCCAATCTATTACCCAAAATCTAGAGGGGCAGATTAAAGA
* * *
86117 CACCATCCAATCTTTTACCCCAACCAAAGGACAGATTGGAGCCACCATCCAATCTTTTACCCCAA
1 CACCATCCAATCTTTTACCCCAACCAAAGGACAGATTGAAACCACCATCCAATCTCTTACCCCAA
* * * * * *
86182 CCAAAGGACAGATTGGAGCCACCATCCAATCTTTTACTCTAACCAGAGGGCAGATTGAAGTCACC
66 CCAAAGGACAAATTGAAGCCACCATCCAATCTTTTACCCCAACAAGAGGGCAGATAGAAG-CACC
* * * *
86247 ATCCAATCTTTTACCCAAAATTTAGAGGGGCAGATTGAAGC
130 ATCCAATCTATTACCCAAAATCTAGAGGGGCAGATTAAAGA
* *
86288 CACTATCCAATCTTATACC
1 CACCATCCAATCTTTTACC
86307 TCAAATTCAG
Statistics
Matches: 164, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
166 111 0.68
168 18 0.11
169 2 0.01
170 4 0.02
171 29 0.18
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (170 bp):
CACCATCCAATCTTTTACCCCAACCAAAGGACAGATTGAAACCACCATCCAATCTCTTACCCCAA
CCAAAGGACAAATTGAAGCCACCATCCAATCTTTTACCCCAACAAGAGGGCAGATAGAAGCACCA
TCCAATCTATTACCCAAAATCTAGAGGGGCAGATTAAAGA
Found at i:86410 original size:93 final size:93
Alignment explanation
Indices: 86312--86497 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
86302 ATACCTCAAA
* * *
86312 TTCAGATGGGCAAATTGAGGCCATCACATCCAATCTTACAAACAAGAGTGAACAAAGAGGGGCAG
1 TTCAGAAGGGAAAATTGAAGCCATCACATCCAATCTTACAAACAAGAGTGAACAAAGAGGGGCAG
*
86377 CTGTAGAGCCCCAATTTTATTCGGCCCT
66 CTGTAGAGCCCAAATTTTATTCGGCCCT
*
86405 TTCAGAAGGGAAAATTGAAGCCATCACATCCAATCTTACAAACAAGAGTGAGCAAAGAGGGGCAG
1 TTCAGAAGGGAAAATTGAAGCCATCACATCCAATCTTACAAACAAGAGTGAACAAAGAGGGGCAG
86470 CTGTAGAGCCCAAATTTTATTCGGCCCT
66 CTGTAGAGCCCAAATTTTATTCGGCCCT
86498 AAACAAAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (93 bp):
TTCAGAAGGGAAAATTGAAGCCATCACATCCAATCTTACAAACAAGAGTGAACAAAGAGGGGCAG
CTGTAGAGCCCAAATTTTATTCGGCCCT
Found at i:86915 original size:15 final size:15
Alignment explanation
Indices: 86885--86914 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
86875 CTTATACATA
86885 TATTTGTTTTTATTT
1 TATTTGTTTTTATTT
86900 TATTT-TTTTTATTT
1 TATTTGTTTTTATTT
86914 T
1 T
86915 TTCATTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TATTTGTTTTTATTT
Found at i:94911 original size:22 final size:21
Alignment explanation
Indices: 94885--94930 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
94875 TACTTAATCG
94885 ATCTT-TAAAATATTTTCATATT
1 ATCTTCTAAAATA-TTTC-TATT
94907 ATCTTCGTAAAATATTTCTATT
1 ATCTTC-TAAAATATTTCTATT
94929 AT
1 AT
94931 ACCTTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.50
23 4 0.18
24 7 0.32
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCTTCTAAAATATTTCTATT
Found at i:99144 original size:42 final size:42
Alignment explanation
Indices: 99081--99219 Score: 138
Period size: 43 Copynumber: 3.3 Consensus size: 42
99071 TCTGTTAATG
** *
99081 TTAGCGGCATTTGTGGAAAAAGCGTTGCTAAAGACCTTG-TCT
1 TTAGCGGCATTTGTGG-AAAAGCGCCGCTAAAGACCATGTTCT
* * *
99123 TTAGCAGCATTCGTGAGAAAAGCGCCGCTAAAGATCATGTTCT
1 TTAGCGGCATTTGTG-GAAAAGCGCCGCTAAAGACCATGTTCT
* * *
99166 TTAGCGGCATTTGTGGAAAAAACGCCACTAAATACCATGTT-T
1 TTAGCGGCATTTGTGG-AAAAGCGCCGCTAAAGACCATGTTCT
*
99208 TATAGTGGCATT
1 T-TAGCGGCATT
99220 CTTTACTCAA
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
42 34 0.43
43 46 0.57
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (42 bp):
TTAGCGGCATTTGTGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:100644 original size:26 final size:26
Alignment explanation
Indices: 100615--100675 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
100605 ATTGCTTTAT
100615 TATAATTTA-ATTCCTTAGATTGAAAC
1 TATAATTTATATT-CTTAGATTGAAAC
* *
100641 TATAATTTATTTATTTTTAGATTGAAAT
1 TATAATTTA--TATTCTTAGATTGAAAC
100669 TATAATT
1 TATAATT
100676 GACTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.30
28 18 0.60
29 3 0.10
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (26 bp):
TATAATTTATATTCTTAGATTGAAAC
Found at i:101045 original size:22 final size:21
Alignment explanation
Indices: 101010--101050 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
101000 CCTGATTAAA
* *
101010 TTAAAATTTTTAGTTATTATAT
1 TTAAAATCTATAGTT-TTATAT
101032 TTAAAATCTATAGTTTTAT
1 TTAAAATCTATAGTTTTAT
101051 GTTTGCAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
TTAAAATCTATAGTTTTATAT
Found at i:102321 original size:17 final size:17
Alignment explanation
Indices: 102299--102333 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
102289 AATAGGGAAA
102299 GTAATCTTAGAAGATTT
1 GTAATCTTAGAAGATTT
*
102316 GTAATCTTATAAGATTT
1 GTAATCTTAGAAGATTT
102333 G
1 G
102334 ATTTTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (17 bp):
GTAATCTTAGAAGATTT
Found at i:103733 original size:14 final size:15
Alignment explanation
Indices: 103702--103746 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
103692 ATCGGACCTT
103702 CATCGTCACCACCAC
1 CATCGTCACCACCAC
* *
103717 CATCG-CACCGCCGC
1 CATCGTCACCACCAC
103731 CATCG--ACCACCAC
1 CATCGTCACCACCAC
103744 CAT
1 CAT
103747 TTTTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.24, C:0.53, G:0.11, T:0.11
Consensus pattern (15 bp):
CATCGTCACCACCAC
Found at i:105531 original size:15 final size:17
Alignment explanation
Indices: 105507--105538 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
105497 TACTGATTTG
105507 TTTCTTTTTCT-GTTGT
1 TTTCTTTTTCTAGTTGT
105523 TTTC-TTTTCTAGTTGT
1 TTTCTTTTTCTAGTTGT
105539 GTAGATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.03, C:0.12, G:0.12, T:0.72
Consensus pattern (17 bp):
TTTCTTTTTCTAGTTGT
Found at i:110420 original size:74 final size:74
Alignment explanation
Indices: 110299--110448 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 74
110289 GTTGCTGTTG
110299 ACTACGTCTCAAAGTGGATTGAAGTTATTACGATGCTAAGAGACGATGCTTGGATAGTGTTGAAG
1 ACTACGTCTCAAAGTGGATTGAAGTTATTACGATGCTAAGAGACGATGCTTGGATAGTGTTGAAG
110364 TTCTTTCAC
66 TTCTTTCAC
*
110373 ACTACGTCTCAAAGTGGATTGAAGTTATTATGATGCTAAGAGACGATGCTTGGATAGTGTTGAAG
1 ACTACGTCTCAAAGTGGATTGAAGTTATTACGATGCTAAGAGACGATGCTTGGATAGTGTTGAAG
110438 TTCTTTCAC
66 TTCTTTCAC
110447 AC
1 AC
110449 ATACATCCTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (74 bp):
ACTACGTCTCAAAGTGGATTGAAGTTATTACGATGCTAAGAGACGATGCTTGGATAGTGTTGAAG
TTCTTTCAC
Found at i:118348 original size:6 final size:7
Alignment explanation
Indices: 118333--118358 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
118323 TCTACTCATC
118333 TTTTCTT
1 TTTTCTT
118340 TTTTCTT
1 TTTTCTT
118347 TTTTCTT
1 TTTTCTT
118354 TTTTC
1 TTTTC
118359 AGATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:120383 original size:15 final size:14
Alignment explanation
Indices: 120365--120447 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 14
120355 CAATATATTT
120365 TTTCTTTTTTTCTC
1 TTTCTTTTTTTCTC
*
120379 ATTTCTTCTTCTTTCTT
1 -TTTCTT-TT-TTTCTC
* *
120396 TTTCTTCTCTTTCTT
1 TTTCTT-TTTTTCTC
*
120411 TTTCTCATTTCTTCTTC
1 TTTCT--TTTTTTC-TC
120428 TTTCTTTTTCTTCTC
1 TTTCTTTTT-TTCTC
120443 TTTCT
1 TTTCT
120448 ATCTTATAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 27 0.48
16 17 0.30
17 12 0.21
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTTTTTTTCTC
Found at i:120387 original size:10 final size:9
Alignment explanation
Indices: 120374--120447 Score: 50
Period size: 10 Copynumber: 8.1 Consensus size: 9
120364 TTTTCTTTTT
120374 TTCTCATTTC
1 TTCTC-TTTC
120384 TTCTTCTTTC
1 TTC-TCTTTC
*
120394 TTTTTCTTCTC
1 -TTCTCTT-TC
120405 TT-TCTTT-
1 TTCTCTTTC
120412 TTCTCATTTC
1 TTCTC-TTTC
120422 TTCTTCTTTC
1 TTC-TCTTTC
120432 -T-T-TTTC
1 TTCTCTTTC
120438 TTCTCTTTC
1 TTCTCTTTC
120447 T
1 T
120448 ATCTTATAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 21
0.71 0.01 0.28
Matches are distributed among these distances:
6 4 0.08
7 4 0.08
8 4 0.08
9 13 0.25
10 20 0.38
11 8 0.15
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (9 bp):
TTCTCTTTC
Found at i:120393 original size:25 final size:25
Alignment explanation
Indices: 120365--120447 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
120355 CAATATATTT
120365 TTTCTTTTT-TTCTCATTTCTTCTTC
1 TTTCTTTTTCTTCTC-TTTCTTCTTC
*
120390 TTTCTTTTTCTTCTCTTTCTTTTTCTC
1 TTTCTTTTTCTTCTCTTTC-TTCT-TC
* *
120417 ATTTCTTCTTCTTTCTTTTTCTTC-TC
1 -TTTCTTTTTC-TTCTCTTTCTTCTTC
120443 TTTCT
1 TTTCT
120448 ATCTTATAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
25 18 0.37
26 10 0.20
27 2 0.04
28 11 0.22
29 8 0.16
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTCTTTTTCTTCTCTTTCTTCTTC
Found at i:120400 original size:13 final size:13
Alignment explanation
Indices: 120384--120441 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
120374 TTCTCATTTC
120384 TTCTTCTTTCTTT
1 TTCTTCTTTCTTT
120397 TTCTTCTCTTTCTTT
1 TTC-T-TCTTTCTTT
120412 TTC-TCATTTC---
1 TTCTTC-TTTCTTT
120422 TTCTTCTTTCTTT
1 TTCTTCTTTCTTT
120435 TTCTTCT
1 TTCTTCT
120442 CTTTCTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
12 2 0.05
13 14 0.37
14 1 0.03
15 12 0.32
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCTTTCTTT
Found at i:120409 original size:19 final size:19
Alignment explanation
Indices: 120387--120452 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
120377 TCATTTCTTC
120387 TTCTTTCTTTTTCTTCTCT
1 TTCTTTCTTTTTCTTCTCT
*
120406 TTC-TT-TTTCTCATT-TCTT
1 TTCTTTCTTTTTC-TTCTC-T
120424 CTTCTTTCTTTTTCTTCTCT
1 -TTCTTTCTTTTTCTTCTCT
*
120444 TTCTATCTT
1 TTCTTTCTT
120453 ATAAGTGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
17 7 0.18
18 5 0.13
19 14 0.37
20 5 0.13
21 7 0.18
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCTTTCTTTTTCTTCTCT
Found at i:120417 original size:38 final size:38
Alignment explanation
Indices: 120371--120447 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
120361 ATTTTTTCTT
120371 TTTTTCTCATTTCTTCTTCTTTCTTTTTCTTCTCTTTC
1 TTTTTCTCATTTCTTCTTCTTTCTTTTTCTTCTCTTTC
120409 TTTTTCTCATTTCTTCTTCTTTCTTTTTCTTCTCTTTC
1 TTTTTCTCATTTCTTCTTCTTTCTTTTTCTTCTCTTTC
120447 T
1 T
120448 ATCTTATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (38 bp):
TTTTTCTCATTTCTTCTTCTTTCTTTTTCTTCTCTTTC
Found at i:120433 original size:23 final size:22
Alignment explanation
Indices: 120396--120438 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
120386 CTTCTTTCTT
120396 TTTCTTCTCTTTCTTTTTCTCA
1 TTTCTTCTCTTTCTTTTTCTCA
120418 TTTCTTCTTCTTTCTTTTTCT
1 TTTCTTC-TCTTTCTTTTTCT
120439 TCTCTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTCTTCTCTTTCTTTTTCTCA
Found at i:121041 original size:17 final size:18
Alignment explanation
Indices: 121021--121062 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
121011 ACTACAATGC
121021 AAATGCACTAACAAAT-A
1 AAATGCACTAACAAATAA
* *
121038 AAATGCAGTGACAAATAA
1 AAATGCACTAACAAATAA
121056 AAATGCA
1 AAATGCA
121063 ATGACAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (18 bp):
AAATGCACTAACAAATAA
Found at i:121060 original size:18 final size:18
Alignment explanation
Indices: 121021--121074 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
121011 ACTACAATGC
* *
121021 AAATGCACTAACAAAT-A
1 AAATGCAATGACAAATAA
*
121038 AAATGCAGTGACAAATAA
1 AAATGCAATGACAAATAA
*
121056 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
121074 A
1 A
121075 TGCTGTGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:121496 original size:15 final size:15
Alignment explanation
Indices: 121476--121507 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
121466 TGTCGGGGCA
121476 TCTTCCTTCTCTTCT
1 TCTTCCTTCTCTTCT
*
121491 TCTTCCTTTTCTTCT
1 TCTTCCTTCTCTTCT
121506 TC
1 TC
121508 ATTTTCCTTT
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:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCCTTCTCTTCT
Found at i:123376 original size:17 final size:16
Alignment explanation
Indices: 123343--123392 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
123333 CATGGAATCT
*
123343 AAAAGAAAT-AGATAA
1 AAAAGAAATAAAATAA
123358 AAGAAGAAATAAAATAA
1 AA-AAGAAATAAAATAA
123375 AAAAGAAATAAACATAA
1 AAAAGAAATAAA-ATAA
123392 A
1 A
123393 TGTAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 2 0.06
16 17 0.55
17 12 0.39
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (16 bp):
AAAAGAAATAAAATAA
Found at i:148732 original size:17 final size:18
Alignment explanation
Indices: 148697--148732 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
148687 AAATTTAAAC
*
148697 AAATAAAGAAAAGATGAA
1 AAATAAACAAAAGATGAA
148715 AAATAAACAAAA-ATGAA
1 AAATAAACAAAAGATGAA
148732 A
1 A
148733 TAACAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
AAATAAACAAAAGATGAA
Found at i:148735 original size:15 final size:16
Alignment explanation
Indices: 148714--148751 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
148704 GAAAAGATGA
148714 AAAATAAAC-AAAAAT
1 AAAATAAACAAAAAAT
*
148729 GAAAT-AACAAAAAAT
1 AAAATAAACAAAAAAT
148744 AAAATAAA
1 AAAATAAA
148752 GTAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 3 0.16
15 14 0.74
16 2 0.11
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAATAAACAAAAAAT
Found at i:159816 original size:10 final size:10
Alignment explanation
Indices: 159803--159828 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
159793 AATTCAAAAA
159803 AAGAAAGAAT
1 AAGAAAGAAT
159813 AAGAAAGAAT
1 AAGAAAGAAT
159823 AAGAAA
1 AAGAAA
159829 AGAGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (10 bp):
AAGAAAGAAT
Found at i:179553 original size:12 final size:12
Alignment explanation
Indices: 179506--179557 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
179496 CAGGTTCTGT
*
179506 TTCTTCCTTCTC
1 TTCTTCCTTTTC
*
179518 TTCTTCCTTTCC
1 TTCTTCCTTTTC
179530 TTCTTCTTCTTTTC
1 TTCTTC--CTTTTC
*
179544 TTCATCCTTTTC
1 TTCTTCCTTTTC
179556 TT
1 TT
179558 GATCACCTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 24 0.71
14 10 0.29
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCCTTTTC
Done.