Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020609.1 Corchorus olitorius cultivar O-4 contig20642, 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: 30732
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:142 original size:22 final size:22
Alignment explanation
Indices: 31--237 Score: 129
Period size: 22 Copynumber: 9.5 Consensus size: 22
21 TATTTTTATG
* *
31 AAATTTTGATTA-CTATCCTATT
1 AAATTTTGATAACCTA-CCTATA
* *
53 AAATTTTGATAATC-ACGCTATG
1 AAATTTTGATAACCTAC-CTATA
* *
75 AAATTTTGATAA-TTACCTATG
1 AAATTTTGATAACCTACCTATA
* * *
96 AAATTGTGATAAACT-CCATAGA
1 AAATTTTGATAACCTACC-TATA
*
118 AAATTTTGATAACCTAACTATA
1 AAATTTTGATAACCTACCTATA
* *
140 AAATTTTAATAAACCTTCCTATA
1 AAATTTTGAT-AACCTACCTATA
*
163 AAATTTTG-TAACCTTCCTAT-
1 AAATTTTGATAACCTACCTATA
* * * *
183 GATTTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTACCTATA
* * * *
205 AGATTTTGTTAATCTCCCTATA
1 AAATTTTGATAACCTACCTATA
**
227 ATTTTTTGATA
1 AAATTTTGATA
238 TTATAATATG
Statistics
Matches: 149, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.04
21 41 0.28
22 83 0.56
23 19 0.13
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACCTACCTATA
Found at i:161 original size:23 final size:21
Alignment explanation
Indices: 117--182 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
107 AACTCCATAG
**
117 AAAATTTTGATAACCTAACTAT
1 AAAATTTT-ATAACCTTCCTAT
139 AAAATTTTAATAAACCTTCCTAT
1 AAAATTTT-AT-AACCTTCCTAT
*
162 AAAATTTTGTAACCTTCCTAT
1 AAAATTTTATAACCTTCCTAT
183 GATTTTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
21 11 0.28
22 11 0.28
23 17 0.44
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (21 bp):
AAAATTTTATAACCTTCCTAT
Found at i:524 original size:45 final size:46
Alignment explanation
Indices: 474--567 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 46
464 TACAATCTAA
474 TCCGGTTTAACTCT-TATAGTATGATTATACGTTTAAAAATTCAAC
1 TCCGGTTTAACTCTATATAGTATGATTATACGTTTAAAAATTCAAC
**
519 TCCGGTTTAGTTCTAAATATAGTATGATTATACGTTTAAAAATTCAAC
1 TCCGGTTTAACTCT--ATATAGTATGATTATACGTTTAAAAATTCAAC
567 T
1 T
568 TCTTTGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 12 0.27
48 32 0.73
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (46 bp):
TCCGGTTTAACTCTATATAGTATGATTATACGTTTAAAAATTCAAC
Found at i:1849 original size:22 final size:21
Alignment explanation
Indices: 1820--1963 Score: 119
Period size: 22 Copynumber: 6.6 Consensus size: 21
1810 TGAATATTTT
1820 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTA-CC
*
1842 TATTAAATTTTGATAA-TCACGC
1 TATGAAATTTTGATAACT-AC-C
* * *
1864 TCTGGAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* *
1885 TATGAAATTGTGATAAACTACA
1 TATGAAATTTTGAT-AACTACC
* **
1907 TATGAAACTTTGATAACCTAAA
1 TATGAAATTTTGATAA-CTACC
* *
1929 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AA-CTACC
1952 TATGAAATTTTG
1 TATGAAATTTTG
1964 CAACGTTCTT
Statistics
Matches: 98, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
21 16 0.16
22 65 0.66
23 17 0.17
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:1997 original size:21 final size:20
Alignment explanation
Indices: 1944--2005 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1934 AATTTTAATA
1944 AACCTTCCTATGAAATTTTGC
1 AACCTTCCTATG-AATTTTGC
* * * *
1965 AACGTTCTTATGATTTTTGAT
1 AACCTTCCTATGAATTTTG-C
1986 AACCTTCCTATGAGATTTTG
1 AACCTTCCTATGA-ATTTTG
2006 TTAATTTCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 6 0.19
21 21 0.66
22 5 0.16
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (20 bp):
AACCTTCCTATGAATTTTGC
Found at i:3787 original size:84 final size:84
Alignment explanation
Indices: 3637--3964 Score: 516
Period size: 84 Copynumber: 3.9 Consensus size: 84
3627 AATAACCAAA
* * *
3637 AAGTCCCCAAACACATATATAACATAGAGGCAATTCTATTCCAAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATA
*
3702 ACATAGAGGCACCTATATCC
65 ACACAGAGGCACCTATATCC
*
3722 AAGTCCCCAAACACATATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATA
*
3786 ACACAGAGGCACCTATATTC
65 ACACAGAGGCACCTATATCC
3806 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
1 AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
* ** *
3871 CACAGAGACATTTATATCA
66 CACAGAGGCACCTATATCC
*
3890 AAGTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACAGATATATA
1 AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATATA
3954 ACACAGAGGCA
65 ACACAGAGGCA
3965 TTTCTCCTTA
Statistics
Matches: 226, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
83 4 0.02
84 185 0.82
85 35 0.15
86 2 0.01
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (84 bp):
AAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAA
CACAGAGGCACCTATATCC
Found at i:3965 original size:43 final size:43
Alignment explanation
Indices: 3636--3965 Score: 392
Period size: 43 Copynumber: 7.8 Consensus size: 43
3626 CAATAACCAA
* *
3636 AAAGTCCCCAAACACATATATAACATAGAGGCAAT-TCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
* *
3679 AAAAGTCCTCAAACACATATATAACATAGAGGCA-C-CTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
* * * *
3721 CAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
3764 AAAGTCCTCAAACACATATATAACACAGAGGCACCTATATT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
3806 -AAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
* *
3848 AAAGTCCTCAAACACATATATAACACAGAGACAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
3889 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
3932 AAAGTCCTCAAACAGATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
3966 TTCTCCTTAT
Statistics
Matches: 250, Mismatches: 24, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.01
41 98 0.39
42 12 0.05
43 103 0.41
44 35 0.14
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:5680 original size:18 final size:18
Alignment explanation
Indices: 5657--5691 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5647 TGCAACAATC
5657 ATATATTTATCATCATCT
1 ATATATTTATCATCATCT
*
5675 ATATATTTATTATCATC
1 ATATATTTATCATCATC
5692 ATTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATATTTATCATCATCT
Found at i:7266 original size:2 final size:2
Alignment explanation
Indices: 7259--7298 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
7249 TTCGTACTTT
*
7259 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7299 TACATTACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7572 original size:19 final size:20
Alignment explanation
Indices: 7529--7572 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
7519 AAAAAAAAAA
7529 GAAAAGGGAAAAGAGAGGC-
1 GAAAAGGGAAAAGAGAGGCG
* * *
7548 GAAAAAGGAAATGAGAGGGG
1 GAAAAGGGAAAAGAGAGGCG
7568 GAAAA
1 GAAAA
7573 TATTTCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.41, T:0.02
Consensus pattern (20 bp):
GAAAAGGGAAAAGAGAGGCG
Found at i:7572 original size:20 final size:19
Alignment explanation
Indices: 7529--7565 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7519 AAAAAAAAAA
*
7529 GAAAAGGGAAAAGAGAGGC
1 GAAAAAGGAAAAGAGAGGC
*
7548 GAAAAAGGAAATGAGAGG
1 GAAAAAGGAAAAGAGAGG
7566 GGGAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.41, T:0.03
Consensus pattern (19 bp):
GAAAAAGGAAAAGAGAGGC
Found at i:10641 original size:30 final size:30
Alignment explanation
Indices: 10597--10665 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
10587 TTGATTATTT
* * *
10597 ACCAAAAC-TTTTTTTGGTACATAATTATA
1 ACCAAAACTTTTTTTTAGAAAATAATTATA
*
10626 AGCAAAACTTTTTTTTAGAAAATAATTATA
1 ACCAAAACTTTTTTTTAGAAAATAATTATA
10656 ACCAAAACTT
1 ACCAAAACTT
10666 AAAAGTACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (30 bp):
ACCAAAACTTTTTTTTAGAAAATAATTATA
Found at i:11552 original size:178 final size:178
Alignment explanation
Indices: 11240--11577 Score: 459
Period size: 178 Copynumber: 1.9 Consensus size: 178
11230 TTCCACCATA
* * *
11240 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCCTTAG
1 AGCACAAATTATATAATATTAAGTAGACCGTCTATATCCGTTAACCGAAACAACAAATTCCTTAG
* *
11305 AAGTATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGCCATTAATGAAAGTTGTAGATCAT
66 AAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGCCATTAATGAAAGTTGTAGATCAT
*
11370 GGAACAACCTATCAAGAGACACTTGAATCATCTCAATCAGACATCTGG
131 GGAACAACCTATCAAGAGACACTTAAATCATCTCAATCAGACATCTGG
* ** **
11418 AGCA-AAAGTTATATAATATTAAGTGGACCGTCTA-ATCCTGTTAACTTAAACAACAAATTTTTT
1 AGCACAAA-TTATATAATATTAAGTAGACCGTCTATATCC-GTTAACCGAAACAACAAATTCCTT
* *
11481 GGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCC-TTCATGAAAGTTGTAGA
64 AGAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAG-CCATTAATGAAAGTTGTAGA
* * * *
11544 TCATGGAACAATCTTTTAATAGACACTTAAATCA
127 TCATGGAACAACCTATCAAGAGACACTTAAATCA
11578 CCTTAATTGG
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
177 10 0.07
178 127 0.91
179 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAAGTAGACCGTCTATATCCGTTAACCGAAACAACAAATTCCTTAG
AAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGCCATTAATGAAAGTTGTAGATCAT
GGAACAACCTATCAAGAGACACTTAAATCATCTCAATCAGACATCTGG
Found at i:12788 original size:24 final size:25
Alignment explanation
Indices: 12738--12788 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
12728 TATATTTCTA
* *
12738 AATTTCTATTATTAAAATTTAGTAT
1 AATTTCTATTATTAAAAATTAGAAT
12763 AATTT-TATTATTTAAAAATTA-AAT
1 AATTTCTATTA-TTAAAAATTAGAAT
12787 AA
1 AA
12789 AAATTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
AATTTCTATTATTAAAAATTAGAAT
Found at i:13127 original size:44 final size:43
Alignment explanation
Indices: 13072--13241 Score: 146
Period size: 44 Copynumber: 3.9 Consensus size: 43
13062 GTCTCTGTGT
* * * *
13072 GGTTATAAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAGGATGGTTACTAAAATTTCAT-AGGA
* * * *
13116 GGTTATCAAAATTCCATCGTG-TGGTTACCAAAATTTTATATGGA
1 GGTTATCAAAATTTCATAG-GATGGTTACTAAAATTTCATA-GGA
* * * *
13160 AGTTATCAAAATTTCATGGGAAGGTTACT-AAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGGATGGTTACTAAAATTTCATAG-GA
* *
13203 GGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC
1 GGTTATCAAAATTTCATAGGAT--GGTTACTAAAATTTC
13242 TTAGAAAGAT
Statistics
Matches: 99, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 30 0.30
44 54 0.55
45 7 0.07
46 7 0.07
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGATGGTTACTAAAATTTCATAGGA
Found at i:13186 original size:22 final size:22
Alignment explanation
Indices: 13072--13241 Score: 89
Period size: 22 Copynumber: 7.7 Consensus size: 22
13062 GTCTCTGTGT
* ** *
13072 GGTTATAAAAATTTCATAAGAT
1 GGTTATCAAAATTTCATGGGAA
* *
13094 GGTTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCATG-GGAA
* * *
13116 GGTTATCAAAATTCCATCGTG-T
1 GGTTATCAAAATTTCAT-GGGAA
* * *
13138 GGTTACCAAAATTTTATATGGAA
1 GGTTATCAAAATTTCAT-GGGAA
13161 -GTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATGGGAA
* * *
13182 GGTTA-CTAAATTTCATAGTG-T
1 GGTTATCAAAATTTCAT-GGGAA
* *
13203 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATGGGA--A
*
13227 GGTTATTAAAATTTC
1 GGTTATCAAAATTTC
13242 TTAGAAAGAT
Statistics
Matches: 110, Mismatches: 29, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
21 20 0.18
22 75 0.68
23 2 0.02
24 13 0.12
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATTTCATGGGAA
Found at i:13275 original size:68 final size:64
Alignment explanation
Indices: 13135--13302 Score: 183
Period size: 68 Copynumber: 2.5 Consensus size: 64
13125 AATTCCATCG
* * * *
13135 TGTGGTTACCAAAATTTTATATGGAAGTTATCAAAATTTCATGGGAAGGTTACTAAATTTCATAG
1 TGTGGTTACCAAAATTTTATA-GGAAGTTATCAAAATTTCATAGAAAGATTACTAAATTTCATAA
* * * *
13200 TGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGAAAGATTATTGAAATTTCA
1 TGTGGTTACCAAAATTTTATAGGA--A-GTTATCAAAATTTCATAGAAAGATTACT-AAATTTCA
13265 TAA
62 TAA
* * *
13268 TGTGGTTATCACAATTTTATAGAAAGGTTATCAAA
1 TGTGGTTACCAAAATTTTATAGGAA-GTTATCAAA
13303 GAGATTATCA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 3 0.03
65 20 0.23
66 11 0.13
67 22 0.26
68 30 0.35
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (64 bp):
TGTGGTTACCAAAATTTTATAGGAAGTTATCAAAATTTCATAGAAAGATTACTAAATTTCATAA
Found at i:13614 original size:66 final size:65
Alignment explanation
Indices: 13458--13879 Score: 238
Period size: 67 Copynumber: 6.5 Consensus size: 65
13448 CTATGGAGTA
* * * * * *
13458 ATCAAAATTTCA-GGGAGGATATCAAAATTTCATATGAAGATTATCAAAATTTCATAGTTTAG-T
1 ATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATA-ATGAGAT
13521 T
65 T
* * * * * *
13522 TTCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 ATCAAAATTTCATAGGAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGAT
13587 T
65 T
** * * *
13588 ATCAAAACATCATAGAGAGGTTATCAAAA-TT--T--GTAG-TTATCAAGATTTCATAAGGAGAT
1 ATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGAT
13647 T
65 T
* * * * * * *
13648 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGCGAGGTTATCACAATTTCATAGTGTGA
1 ATCAAAATTTCATA-GGAGG-TTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGA
13713 TT
64 TT
* * * * * * * * * *
13715 ATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATGTAGGTTTTTTAAAATTTCATAACGT
1 ATCAAAATTTCATAG-GAGGTTATC-AA-AATTTCATAGGGA-GATTATCAAAATTTCATAATGA
13778 GATT
62 GATT
* * * * * ** ***
13782 ATCAATATATCATATAGAGGTTATCAACATCTCATAGTGTTGATTATCAAAATTTCATTCGGA-A
1 ATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAG-GGAGATTATCAAAATTTCATAATGAGA
13846 GTT
64 -TT
13849 ATCAAAATTTCATAGTGAGGTCT-TCAAAATT
1 ATCAAAATTTCATAG-GAGGT-TATCAAAATT
13880 CTTTAGAGAT
Statistics
Matches: 267, Mismatches: 68, Indels: 43
0.71 0.18 0.11
Matches are distributed among these distances:
60 35 0.13
61 13 0.05
62 2 0.01
63 1 0.00
64 12 0.04
65 9 0.03
66 70 0.26
67 121 0.45
68 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (65 bp):
ATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGATT
Found at i:13668 original size:82 final size:83
Alignment explanation
Indices: 13544--13702 Score: 212
Period size: 82 Copynumber: 1.9 Consensus size: 83
13534 TAGTATGTAG
* *
13544 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG-TTATCAAAACATCATAGAGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAACATCATAGAGAGG
13608 TTATCAAAATTTGTAGTT
66 TTATCAAAATTTGTAGTT
* * * * ** * *
13626 ATCAAGATTTCATAAGGAGATTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGCGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAACATCATAGAGAGG
*
13691 TTATCACAATTT
66 TTATCAAAATTT
13703 CATAGTGTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
82 36 0.55
83 29 0.45
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (83 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAACATCATAGAGAGG
TTATCAAAATTTGTAGTT
Found at i:13707 original size:22 final size:21
Alignment explanation
Indices: 13307--14009 Score: 233
Period size: 22 Copynumber: 32.4 Consensus size: 21
13297 ATCAAAGAGA
* *
13307 TTATCAAAATGTCATAGCAAGG
1 TTATCAAAATTTCATAG-GAGG
*
13329 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
* *
13351 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
13373 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
**
13395 TTATCAAAATTTCATACTATGG
1 TTATCAAAATTTCATAGGA-GG
* *
13417 TTA-CTAAA--T--TAGGAAGC
1 TTATCAAAATTTCATAGG-AGG
* * *
13434 TTATTAAACTTTTACTATGGA-G
1 TTATCAAAATTTCA-TA-GGAGG
* *
13456 TAATCAAAATTTCA-GGGAGG
1 TTATCAAAATTTCATAGGAGG
* * *
13476 ATATCAAAATTTCATATGAAGA
1 TTATCAAAATTTCATA-GGAGG
*
13498 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG--GAGG
* * *
13520 TTTTCAAAATTTCATAGTATG
1 TTATCAAAATTTCATAGGAGG
* *
13541 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATA-GGAGG
* *
13564 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCAT-AGGAGG
**
13586 TTATCAAAACATCATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
*
13608 TTATCAAAA-TT--T-GTA-G
1 TTATCAAAATTTCATAGGAGG
* *
13624 TTATCAAGATTTCATAAGGAGA
1 TTATCAAAATTTCAT-AGGAGG
*
13646 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
13668 TTTATCAAAATTTTATAGCGAGG
1 -TTATCAAAATTTCATAG-GAGG
* * *
13691 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
* * *
13713 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
*
13735 TTA-CTAACAA-TTCATATGTAGG
1 TTATC-AA-AATTTCATA-GGAGG
* * * * *
13757 TTTTTTAAAATTTCATAACGTGA
1 -TTATCAAAATTTCAT-AGGAGG
* * *
13780 TTATCAATATATCATATAGAGG
1 TTATCAAAATTTCATA-GGAGG
* * * *
13802 TTATCAACATCTCATAGTGTTGA
1 TTATCAAAATTTCATAG-G-AGG
* *
13825 TTATCAAAATTTCATTCGGAAG
1 TTATCAAAATTTCA-TAGGAGG
13847 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
13869 TCT-TCAAAA-TTCTTTAGAGATG
1 T-TATCAAAATTTC-ATAG-GAGG
* *
13891 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
** **
13913 TTAAAAAAAATTT-ATAAAAAGG
1 TT-ATCAAAATTTCAT-AGGAGG
* * *
13935 TTCTCAAAA-TTCGATAGTATCG
1 TTATCAAAATTTC-ATAGGA-GG
* *
13957 TTATTAAAGTTTCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* *
13979 TTATTAAAATTTTATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
14001 TCATCAAAA
1 TTATCAAAA
14010 ATAGTGTAAT
Statistics
Matches: 505, Mismatches: 119, Indels: 114
0.68 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 9 0.02
18 4 0.01
19 6 0.01
20 18 0.04
21 30 0.06
22 342 0.68
23 82 0.16
24 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:14127 original size:2 final size:2
Alignment explanation
Indices: 14120--14155 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14110 TTAAAACTAG
14120 TA TA TA TA TA TA TA TA TA TA 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
14156 GACCAAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14441 original size:2 final size:2
Alignment explanation
Indices: 14434--14458 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14424 GTCCTCATGG
14434 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
14459 ATATTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:15427 original size:25 final size:25
Alignment explanation
Indices: 15390--15438 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
15380 GATTGGTTTG
*
15390 TAGAGACCGGGCGAGAGTGCTCAAA
1 TAGAGACCAGGCGAGAGTGCTCAAA
15415 TAGAGACCAGGCGAGAGTGCTCAA
1 TAGAGACCAGGCGAGAGTGCTCAA
15439 GATTATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (25 bp):
TAGAGACCAGGCGAGAGTGCTCAAA
Found at i:16172 original size:2 final size:2
Alignment explanation
Indices: 16165--16190 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16155 AAATCAAATT
16165 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16191 ATTAAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17244 original size:42 final size:43
Alignment explanation
Indices: 17168--17248 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 43
17158 TAAGTACCAA
* *
17168 CAATAAGTATAATTTGGTATCGCCTGAAATTGTTAGAATTAGC
1 CAATAAGTACAATTTGGTAACGCCTGAAATTGTTAGAATTAGC
* * *
17211 CAATTAGTACAATTT-GTAACGCTTGAATTTGTTAGAAT
1 CAATAAGTACAATTTGGTAACGCCTGAAATTGTTAGAAT
17249 CACCTAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 20 0.61
43 13 0.39
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (43 bp):
CAATAAGTACAATTTGGTAACGCCTGAAATTGTTAGAATTAGC
Found at i:17258 original size:42 final size:43
Alignment explanation
Indices: 17168--17264 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 43
17158 TAAGTACCAA
* * * *
17168 CAATAAGTATAATTTGGTATCGCCTGAAATTGTTAGAATTAGC
1 CAATTAGTACAATTTGGTAACGCCTGAAATTGTTAGAATCAGC
* *
17211 CAATTAGTACAATTT-GTAACGCTTGAATTTGTTAGAATCA-C
1 CAATTAGTACAATTTGGTAACGCCTGAAATTGTTAGAATCAGC
*
17252 CTAATTAATACAA
1 C-AATTAGTACAA
17265 CCTGTAACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.04
42 31 0.67
43 13 0.28
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (43 bp):
CAATTAGTACAATTTGGTAACGCCTGAAATTGTTAGAATCAGC
Found at i:17998 original size:42 final size:43
Alignment explanation
Indices: 17938--18020 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
17928 ATTAGGCCCT
* *
17938 TGAAAATGTATAAAATCAACCAGCCACTACAAATTGTAACGCC
1 TGAAAATATATAAAATCAACCAACCACTACAAATTGTAACGCC
* * *
17981 TGAAAATAT-TAAAATCAACTAACCAGTACAATTTGTAACG
1 TGAAAATATATAAAATCAACCAACCACTACAAATTGTAACG
18021 GATGAAAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 27 0.77
43 8 0.23
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (43 bp):
TGAAAATATATAAAATCAACCAACCACTACAAATTGTAACGCC
Found at i:18132 original size:42 final size:42
Alignment explanation
Indices: 18079--18227 Score: 163
Period size: 42 Copynumber: 3.5 Consensus size: 42
18069 ACCTGACTGC
* * *
18079 TACAATATGTAACGCCTAAAAATGTTAGAATTAGCCAAATAG
1 TACAATTTGTAACGCCTGAAAATGTTAGAATTAACCAAATAG
* * *
18121 TACAATTTGTAACGCCTGAAAATGTTAGAATTATCTAAACAG
1 TACAATTTGTAACGCCTGAAAATGTTAGAATTAACCAAATAG
* * ** * * *
18163 TACAATTTGTAATGCTTGAAAATACTAGAATCAACCAACTAC
1 TACAATTTGTAACGCCTGAAAATGTTAGAATTAACCAAATAG
* *
18205 TACAACTTGTAACGCGTGAAAAT
1 TACAATTTGTAACGCCTGAAAAT
18228 CAACCAACCA
Statistics
Matches: 89, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (42 bp):
TACAATTTGTAACGCCTGAAAATGTTAGAATTAACCAAATAG
Found at i:18234 original size:34 final size:34
Alignment explanation
Indices: 18191--18285 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 34
18181 AAAATACTAG
* * * *
18191 AATCAACCAACTACTACAACTTGTAACGCGTGAA
1 AATCAACCAACCAATACAACTTGTAACGCATAAA
*
18225 AATCAACCAACCAATACAATTTGTAACGCATAAA
1 AATCAACCAACCAATACAACTTGTAACGCATAAA
* * *
18259 AATCAGCAAAGCAATACAA-TATGTAAC
1 AATCAACCAACCAATACAACT-TGTAAC
18286 TCTTGAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 1 0.02
34 51 0.98
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.20
Consensus pattern (34 bp):
AATCAACCAACCAATACAACTTGTAACGCATAAA
Found at i:19016 original size:42 final size:42
Alignment explanation
Indices: 18959--19074 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 42
18949 ATCACCTGAC
* * *
18959 CAATATAATATGTAACGCCTAAAAATGTTAGAATTAGCCAAA
1 CAATACAATTTGTAACGCCTGAAAATGTTAGAATTAGCCAAA
*
19001 CAGTACAATTTGTAACGCCTGAAAATGTTAGAATTAGCCAAA
1 CAATACAATTTGTAACGCCTGAAAATGTTAGAATTAGCCAAA
* *
19043 CAATACAATTTGTAACGCTTGAAAATGCTAGA
1 CAATACAATTTGTAACGCCTGAAAATGTTAGA
19075 GTCAACAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (42 bp):
CAATACAATTTGTAACGCCTGAAAATGTTAGAATTAGCCAAA
Found at i:19092 original size:42 final size:42
Alignment explanation
Indices: 18969--19110 Score: 142
Period size: 42 Copynumber: 3.4 Consensus size: 42
18959 CAATATAATA
* * * *
18969 TGTAACGCCTAAAAATGTTAGAATTAGCCAAACAGTACAATT
1 TGTAACGCCTGAAAATGCTAGAATCAGACAAACAGTACAATT
* * * *
19011 TGTAACGCCTGAAAATGTTAGAATTAGCCAAACAATACAATT
1 TGTAACGCCTGAAAATGCTAGAATCAGACAAACAGTACAATT
* * * **
19053 TGTAACGCTTGAAAATGCTAGAGTCA-ACAAACTTGTACAACC
1 TGTAACGCCTGAAAATGCTAGAATCAGACAAAC-AGTACAATT
*
19095 TGTAACGCGTGAAAAT
1 TGTAACGCCTGAAAAT
19111 CAACCAACTA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 5 0.06
42 82 0.94
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (42 bp):
TGTAACGCCTGAAAATGCTAGAATCAGACAAACAGTACAATT
Found at i:19296 original size:112 final size:111
Alignment explanation
Indices: 19088--19402 Score: 280
Period size: 112 Copynumber: 2.8 Consensus size: 111
19078 AACAAACTTG
* * * * ** *
19088 TACAACCTGTAACGCGTGAAAATCAACCAACTAGTACAATTTGTAA-AGCCTAA-AAATCAGCAA
1 TACAATCTGTAACGCATGAAAATCAACCAACTAGTACAATTTGTAACTG-ATAATGCATCACCAA
* * * * * **
19151 AGCAATACAATATTTAACTCTTGAAAAACTTAGAATC-GGCTAGCCAA
65 ACCAATACAATATGTAACGCATGAAAAACTTAGAATCTGAC-AAACAA
* * *
19198 TACAATCTCTGTAACACATGAAAATCAGCCAACTAGTACAATTTGTAACTGATAATGCATCACCT
1 TACAA--TCTGTAACGCATGAAAATCAACCAACTAGTACAATTTGTAACTGATAATGCATCACCA
* * *
19263 AACCAATACAATATGTAACGCATG-GAAAGTTAGAATCTGACAAATAA
64 AACCAATACAATATGTAACGCATGAAAAACTTAGAATCTGACAAACAA
* * * * * * *
19310 TACAATATGTAATGCCTG-AAATCAATCAACCAATACAATTTGTAACGCTTGAAAATGCATCACC
1 TACAATCTGTAACGCATGAAAATCAACCAACTAGTACAATTTGTAA--C-TGATAATGCATCACC
*
19374 CAACCAATACAATATGTAACGCATGAAAA
63 AAACCAATACAATATGTAACGCATGAAAA
19403 TCAACGAACC
Statistics
Matches: 165, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
109 23 0.14
110 14 0.08
111 1 0.01
112 97 0.59
113 30 0.18
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (111 bp):
TACAATCTGTAACGCATGAAAATCAACCAACTAGTACAATTTGTAACTGATAATGCATCACCAAA
CCAATACAATATGTAACGCATGAAAAACTTAGAATCTGACAAACAA
Found at i:19392 original size:38 final size:37
Alignment explanation
Indices: 19251--19493 Score: 148
Period size: 38 Copynumber: 6.6 Consensus size: 37
19241 TGTAACTGAT
*
19251 AATGCATCACCTAACCAATACAATATGTAACGCATGGAA
1 AATGCATCACC-AACCAATACAATATGTAACGC-TTGAA
* * ** * *
19290 AGTTAGAATCTGA-CAAATAATACAATATGTAATGCCTG-A
1 A-AT-GCATC--ACCAACCAATACAATATGTAACGCTTGAA
* *
19329 AAT-CA--ATCAACCAATACAATTTGTAACGCTTGAA
1 AATGCATCACCAACCAATACAATATGTAACGCTTGAA
*
19363 AATGCATCACCCAACCAATACAATATGTAACGCATGAA
1 AATGCATCA-CCAACCAATACAATATGTAACGCTTGAA
* * * * *
19401 AAT-CA--ACGAACCAATAAAATTTATAATGCTTGAA
1 AATGCATCACCAACCAATACAATATGTAACGCTTGAA
* * * * *
19435 AATGCATCGTCCAACTAGTACAATTTGTAACGCAT-AA
1 AATGCATC-ACCAACCAATACAATATGTAACGCTTGAA
*
19472 AATCCA--ACCAACCAATACAATA
1 AATGCATCACCAACCAATACAATA
19494 ACGCCTAGGG
Statistics
Matches: 154, Mismatches: 36, Indels: 33
0.69 0.16 0.15
Matches are distributed among these distances:
32 1 0.01
33 20 0.13
34 41 0.27
35 5 0.03
36 1 0.01
37 10 0.06
38 47 0.31
39 3 0.02
40 2 0.01
41 22 0.14
42 1 0.01
43 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (37 bp):
AATGCATCACCAACCAATACAATATGTAACGCTTGAA
Found at i:19422 original size:72 final size:71
Alignment explanation
Indices: 19308--19488 Score: 222
Period size: 72 Copynumber: 2.5 Consensus size: 71
19298 TCTGACAAAT
* * * *
19308 AATACAATATGTAATGCCTG-AAATCAATCAACCAATACAATTTGTAACGCTTGAAAATGCATCA
1 AATACAATATGTAACGCATGAAAATCAA-CAACCAATAAAATTTATAACGCTTGAAAATGCATCA
19372 CCCAACC
65 CCCAACC
* *
19379 AATACAATATGTAACGCATGAAAATCAACGAACCAATAAAATTTATAATGCTTGAAAATGCATCG
1 AATACAATATGTAACGCATGAAAATCAAC-AACCAATAAAATTTATAACGCTTGAAAATGCATCA
* *
19444 TCCAACT
65 CCCAACC
* *
19451 AGTACAATTTGTAACGCAT-AAAATCCAACCAACCAATA
1 AATACAATATGTAACGCATGAAAAT-CAA-CAACCAATA
19489 CAATAACGCC
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
71 24 0.25
72 71 0.74
73 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.24
Consensus pattern (71 bp):
AATACAATATGTAACGCATGAAAATCAACAACCAATAAAATTTATAACGCTTGAAAATGCATCAC
CCAACC
Found at i:19435 original size:34 final size:34
Alignment explanation
Indices: 19308--19492 Score: 149
Period size: 38 Copynumber: 5.2 Consensus size: 34
19298 TCTGACAAAT
* * * *
19308 AATACAATATGTAATGCCTG-AAATCAATCAACC
1 AATACAATTTGTAACGCTTGAAAATCAACCAACC
19341 AATACAATTTGTAACGCTTGAAAATGCATCACCCAACC
1 AATACAATTTGTAACGCTTGAAAAT-CA--A-CCAACC
* * *
19379 AATACAATATGTAACGCATGAAAATCAACGAACC
1 AATACAATTTGTAACGCTTGAAAATCAACCAACC
* * * * *
19413 AATAAAATTTATAATGCTTGAAAATGCATCGTCCAACT
1 AATACAATTTGTAACGCTTGAAAAT-CA---ACCAACC
* *
19451 AGTACAATTTGTAACGCAT-AAAATCCAACCAACC
1 AATACAATTTGTAACGCTTGAAAAT-CAACCAACC
19485 AATACAAT
1 AATACAAT
19493 AACGCCTAGG
Statistics
Matches: 119, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
33 17 0.14
34 41 0.34
35 5 0.04
37 10 0.08
38 46 0.39
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.24
Consensus pattern (34 bp):
AATACAATTTGTAACGCTTGAAAATCAACCAACC
Found at i:20296 original size:2 final size:2
Alignment explanation
Indices: 20289--20313 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20279 TATAAAATTT
20289 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 T
20314 CCATTTGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22541 original size:2 final size:2
Alignment explanation
Indices: 22534--22580 Score: 76
Period size: 2 Copynumber: 22.5 Consensus size: 2
22524 GTACAATTTG
22534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
22578 TA T
1 TA T
22581 TATTTGAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 39 0.91
3 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25354 original size:114 final size:114
Alignment explanation
Indices: 25154--25368 Score: 358
Period size: 114 Copynumber: 1.9 Consensus size: 114
25144 TAAATTCTTA
* * * * *
25154 ATATATTAATATCAATAGAGAAAAGTTTCAAATGATAGAGCAACTCCTCGAGGGACGACAGTCTA
1 ATATATTAAGATCAATAAAGAAAAGTCTCAAATGATAGAGCAACTCCCCGAGGGACGACAATCTA
*
25219 GTGTGCAATTGTACTTAATTGGTATACTATTGCTGCGACAACATACTTC
66 ATGTGCAATTGTACTTAATTGGTATACTATTGCTGCGACAACATACTTC
*
25268 ATATATTAAGATCAATAAAGAAGAGTCTCAAATGATAGAGCAACTCCCCGAGGGACGACAATCTA
1 ATATATTAAGATCAATAAAGAAAAGTCTCAAATGATAGAGCAACTCCCCGAGGGACGACAATCTA
*
25333 ATGTGCAATTGTACTTAATTGGTATTCTATTGCTGC
66 ATGTGCAATTGTACTTAATTGGTATACTATTGCTGC
25369 AACATATCAT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (114 bp):
ATATATTAAGATCAATAAAGAAAAGTCTCAAATGATAGAGCAACTCCCCGAGGGACGACAATCTA
ATGTGCAATTGTACTTAATTGGTATACTATTGCTGCGACAACATACTTC
Found at i:30246 original size:25 final size:25
Alignment explanation
Indices: 30212--30260 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
30202 CCAAACAATC
30212 TTGAGCACTCTCGCTCGGTCTCTAA
1 TTGAGCACTCTCGCTCGGTCTCTAA
30237 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
30261 CAAACTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAA
Done.