Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 8 of 250
Found at i:2314585 original size:29 final size:30
Alignment explanation
Indices: 2314526--2314583 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2314516 TCCGAGCCTT
*
2314526 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
2314556 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
2314584 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:2314813 original size:13 final size:13
Alignment explanation
Indices: 2314795--2314826 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2314785 TTTCCAGCAA
2314795 TTATGAATTTATT
1 TTATGAATTTATT
2314808 TTATGAATTTATT
1 TTATGAATTTATT
*
2314821 TGATGA
1 TTATGA
2314827 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2315043 original size:50 final size:50
Alignment explanation
Indices: 2314920--2315113 Score: 280
Period size: 51 Copynumber: 3.8 Consensus size: 50
2314910 ATTTGGGTAA
*
2314920 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG-ATG
*
2314971 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
2315021 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
2315071 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
2315114 TGTTATTATC
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 49 0.38
51 79 0.62
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:2315112 original size:101 final size:101
Alignment explanation
Indices: 2314932--2315113 Score: 296
Period size: 101 Copynumber: 1.8 Consensus size: 101
2314922 AGATCCCATG
* **
2314932 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAATGAGAGGTCCCATGTAAGACCATGTCTG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGAATGAGACATCCCATGTAAGACCATGTCTG
2314997 GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
66 GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
2315033 TAAGACCATGTCTGGGACATGGCATGGGCACC-A-ACATGAGAACATCCCATGTAAGACCATGTC
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGA-ATGAG-ACATCCCATGTAAGACCATGTC
*
2315096 TGGGACATGGCTTTGGCA
64 TGGGACATGGCGTTGGCA
2315114 TGTTATTATC
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
99 1 0.01
100 6 0.08
101 68 0.91
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (101 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGAATGAGACATCCCATGTAAGACCATGTCTG
GGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
Found at i:2322109 original size:29 final size:30
Alignment explanation
Indices: 2322050--2322107 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2322040 TCCGAGCCTT
*
2322050 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
2322080 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
2322108 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:2322337 original size:13 final size:13
Alignment explanation
Indices: 2322319--2322350 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2322309 TTTCCAGCAA
2322319 TTATGAATTTATT
1 TTATGAATTTATT
2322332 TTATGAATTTATT
1 TTATGAATTTATT
*
2322345 TGATGA
1 TTATGA
2322351 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2322541 original size:56 final size:51
Alignment explanation
Indices: 2322445--2322643 Score: 249
Period size: 50 Copynumber: 3.8 Consensus size: 51
2322435 ATTTGGGTAA
2322445 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC---AGA-CATG
* * * *
2322501 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCACC-GAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGACATG
* * *
2322551 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCA-ACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGACATG
* *
2322601 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
2322644 TGTTATTATC
Statistics
Matches: 127, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
50 49 0.39
51 37 0.29
55 2 0.02
56 39 0.31
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (51 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAGACATG
Found at i:2333391 original size:24 final size:24
Alignment explanation
Indices: 2333349--2333398 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2333339 TTCCAGAAGG
* *
2333349 TAAAAGTGGGGCCTATGTATTTTT
1 TAAAAGTGGGCCCTATGTACTTTT
2333373 TAAAAGTGGGCCC-ATTGTACTTTT
1 TAAAAGTGGGCCCTA-TGTACTTTT
2333397 TA
1 TA
2333399 GGGATTACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (24 bp):
TAAAAGTGGGCCCTATGTACTTTT
Found at i:2338164 original size:39 final size:39
Alignment explanation
Indices: 2338068--2338201 Score: 169
Period size: 40 Copynumber: 3.4 Consensus size: 39
2338058 TAAATAACAG
* * * * *
2338068 GCTTTGTGCTAGTATATTTATCGGGCTTTGTGCTTAGCA
1 GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
* *
2338107 GACTTTGTGCTGGTGTGTTTATTGGGCTTTATGCCTAGTA
1 G-CTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
*
2338147 GCTTTATGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
1 GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
*
2338186 TGCCTTGTGCTGGTGT
1 -GCTTTGTGCTGGTGT
2338202 TGTCTATCAG
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
39 36 0.44
40 45 0.56
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.44
Consensus pattern (39 bp):
GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
Found at i:2340025 original size:33 final size:33
Alignment explanation
Indices: 2339965--2340028 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2339955 GAACTATCTT
* * * *
2339965 TGTGTTTATTGTCCTAGCAGACTTTCTCTATTC
1 TGTGTTTATTGTCCCAACAAACATTCTCTATTC
2339998 TGTGTTTATTGTCCCAACAAACATTCTCTAT
1 TGTGTTTATTGTCCCAACAAACATTCTCTAT
2340029 GGGTTTCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.45
Consensus pattern (33 bp):
TGTGTTTATTGTCCCAACAAACATTCTCTATTC
Found at i:2344376 original size:32 final size:32
Alignment explanation
Indices: 2344339--2344402 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2344329 TTAAAGGGAG
** *
2344339 ATAGTTTGTTGTGGATAATATAGTAAGAGCTC
1 ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
*
2344371 ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
1 ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
2344403 CTTTTAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (32 bp):
ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
Found at i:2349673 original size:22 final size:22
Alignment explanation
Indices: 2349645--2349686 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2349635 ATTATATTAA
2349645 GAGTTAGATTGCATTTTGCTAG
1 GAGTTAGATTGCATTTTGCTAG
2349667 GAGTTAGATTGCATTTTGCT
1 GAGTTAGATTGCATTTTGCT
2349687 CTCTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (22 bp):
GAGTTAGATTGCATTTTGCTAG
Found at i:2352178 original size:19 final size:19
Alignment explanation
Indices: 2352149--2352193 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
2352139 TTTTTTCTAA
2352149 AATTATTATAATATTA-TTAT
1 AATT-TTATAAT-TTATTTAT
2352169 AATTTTATAATTTATTTAT
1 AATTTTATAATTTATTTAT
2352188 AATTTT
1 AATTTT
2352194 CTAACAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTATAATTTATTTAT
Found at i:2352226 original size:24 final size:23
Alignment explanation
Indices: 2352199--2352262 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
2352189 ATTTTCTAAC
2352199 AAAATTTTAATAATTTATATTTTT
1 AAAATTTTAATAATTT-TATTTTT
2352223 AAAA--TT-AT-A-TTTATTTTT
1 AAAATTTTAATAATTTTATTTTT
2352241 -AAATTTTAATAACTTTTTATTT
1 AAAATTTTAATAA--TTTTATTT
2352263 AAATAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 4 0.12
20 3 0.09
21 3 0.09
22 2 0.06
24 11 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AAAATTTTAATAATTTTATTTTT
Found at i:2352232 original size:14 final size:16
Alignment explanation
Indices: 2352203--2352234 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2352193 TCTAACAAAA
2352203 TTTTAATAATTTATAT
1 TTTTAATAATTTATAT
2352219 TTTTAA-AA-TTATAT
1 TTTTAATAATTTATAT
2352233 TT
1 TT
2352235 ATTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATAATTTATAT
Found at i:2353270 original size:43 final size:43
Alignment explanation
Indices: 2353170--2353273 Score: 173
Period size: 43 Copynumber: 2.5 Consensus size: 43
2353160 TCAAAGTAAG
2353170 AATAAAATAATTAAA--AA--T-AATTTTATTTCAAAATAAAA
1 AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
2353208 AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
1 AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
2353251 AATAAAATAATTAAATTAAGGTG
1 AATAAAATAATTAAATTAAGGTG
2353274 TTGTTTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
38 15 0.25
40 2 0.03
42 1 0.02
43 43 0.70
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (43 bp):
AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
Found at i:2360826 original size:20 final size:21
Alignment explanation
Indices: 2360798--2360850 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
2360788 TTATTCAAAA
* *
2360798 AATATTTTTTAGATAA-TTTT
1 AATAATTTTTAAATAACTTTT
2360818 AATAATTTTTAAATAACTTTT
1 AATAATTTTTAAATAACTTTT
2360839 GAAT--TTTTTAAA
1 -AATAATTTTTAAA
2360851 ACTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 22 0.76
21 4 0.14
22 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
AATAATTTTTAAATAACTTTT
Found at i:2360857 original size:19 final size:19
Alignment explanation
Indices: 2360821--2360856 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2360811 TAATTTTAAT
2360821 AATTTTTAAATAACTTTTG
1 AATTTTTAAATAACTTTTG
*
2360840 AATTTTTTAA-AACTTTT
1 AATTTTTAAATAACTTTT
2360857 TAAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTTTAAATAACTTTTG
Found at i:2366774 original size:10 final size:10
Alignment explanation
Indices: 2366759--2366783 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2366749 ATGACTTCAT
2366759 TTTTTTTTTA
1 TTTTTTTTTA
2366769 TTTTTTTTTA
1 TTTTTTTTTA
2366779 TTTTT
1 TTTTT
2366784 ATAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:2367590 original size:39 final size:37
Alignment explanation
Indices: 2367523--2367615 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
2367513 ACCAGAATGG
* *
2367523 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
2367562 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
2367599 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
2367616 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:2367979 original size:3 final size:3
Alignment explanation
Indices: 2367971--2368015 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
2367961 ATTCCCACTC
* * * *
2367971 ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2368016 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2368016 original size:18 final size:18
Alignment explanation
Indices: 2367971--2368017 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2367961 ATTCCCACTC
*
2367971 ATAATAATAATAATACTA
1 ATAATAATACTAATACTA
2367989 ATAATAATACTAATACTA
1 ATAATAATACTAATACTA
*
2368007 ATATTAATACT
1 ATAATAATACT
2368018 TACCTCACAT
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:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATACTAATACTA
Found at i:2368017 original size:12 final size:12
Alignment explanation
Indices: 2367975--2368015 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
2367965 CCACTCATAA
2367975 TAATAATAATAC
1 TAATAATAATAC
2367987 TAATAATAATAC
1 TAATAATAATAC
* *
2367999 TAATACTAATAT
1 TAATAATAATAC
2368011 TAATA
1 TAATA
2368016 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:2368742 original size:16 final size:16
Alignment explanation
Indices: 2368723--2368757 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2368713 TTCTTTGTTC
2368723 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
*
2368739 TTTCTATTTTGTTTCT
1 TTTCTATTCTGTTTCT
2368755 TTT
1 TTT
2368758 TATATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:2368828 original size:28 final size:28
Alignment explanation
Indices: 2368756--2368829 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
2368746 TTTGTTTCTT
*
2368756 TTTATATATAATATAATATTTATAATGTAA
1 TTTATATAT-TTAT-ATATTTATAATGTAA
* * * *
2368786 TTAATTTAATAATATACTTTATAAT-TAA
1 TTTATATATTTATATA-TTTATAATGTAA
2368814 TTTATATATTTATATA
1 TTTATATATTTATATA
2368830 AATAATAATA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
28 18 0.53
29 10 0.29
30 6 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
TTTATATATTTATATATTTATAATGTAA
Found at i:2368835 original size:21 final size:20
Alignment explanation
Indices: 2368797--2368835 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2368787 TAATTTAATA
*
2368797 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
2368817 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
2368836 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:2369843 original size:43 final size:43
Alignment explanation
Indices: 2369780--2369861 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
2369770 AATGAAGGAA
* *
2369780 GTATTAGCAGCTTGCTTGCACCGGTTAGTTGTTTATCCACACT
1 GTATTAGCAGCTTGCTTGCACCGATTAGTGGTTTATCCACACT
*
2369823 GTATTAGTAGCTTG-TCTGCACCGATTAGTGGTTTATCCA
1 GTATTAGCAGCTTGCT-TGCACCGATTAGTGGTTTATCCA
2369862 TACCTATTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (43 bp):
GTATTAGCAGCTTGCTTGCACCGATTAGTGGTTTATCCACACT
Found at i:2371434 original size:18 final size:20
Alignment explanation
Indices: 2371402--2371448 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2371392 AGTGAGGGAT
* *
2371402 AAAAGCATAGCAATG-GTTA
1 AAAAGCATTGCAATGAGTGA
2371421 AAAAGCATTG-AATGAGTGA
1 AAAAGCATTGCAATGAGTGA
2371440 AAAA-CATTG
1 AAAAGCATTG
2371449 TGGGTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAAGCATTGCAATGAGTGA
Found at i:2372252 original size:18 final size:20
Alignment explanation
Indices: 2372224--2372268 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2372214 ATTTAATAGA
2372224 TTTTATTTTTAGTTT-A-GTT
1 TTTTA-TTTTAGTTTAATGTT
*
2372243 TTTTATTTTATTTTAATGTT
1 TTTTATTTTAGTTTAATGTT
2372263 TTTTAT
1 TTTTAT
2372269 GAATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTTATTTTAGTTTAATGTT
Found at i:2372264 original size:19 final size:19
Alignment explanation
Indices: 2372224--2372265 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
2372214 ATTTAATAGA
*
2372224 TTTTATTTTTAGTTTAGTT
1 TTTTATTTTTAGTTTAATT
*
2372243 TTTTA-TTTTATTTTAATGT
1 TTTTATTTTTAGTTTAAT-T
2372262 TTTT
1 TTTT
2372266 TATGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTATTTTTAGTTTAATT
Found at i:2374757 original size:37 final size:38
Alignment explanation
Indices: 2374716--2374793 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
2374706 TAAAATTTAT
** * *
2374716 TAAAAATTGGAATTTTTTTAT-AAAAATCCTAAAAAAA
1 TAAAAATTGGAAAATTTTAATAAAAAATCATAAAAAAA
*
2374753 TAAAAATTGTAAAATTTTAATAAAAAATCATAAAAAAA
1 TAAAAATTGGAAAATTTTAATAAAAAATCATAAAAAAA
2374791 TAA
1 TAA
2374794 CAACCCTAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 17 0.49
38 18 0.51
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (38 bp):
TAAAAATTGGAAAATTTTAATAAAAAATCATAAAAAAA
Found at i:2374989 original size:21 final size:21
Alignment explanation
Indices: 2374965--2375009 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2374955 AAAATTTATA
* *
2374965 TTTCTTTAC-ATTTTGTATAAT
1 TTTC-TTACGATTTTATAAAAT
2374986 TTTCTTACGATTTTATAAAAT
1 TTTCTTACGATTTTATAAAAT
2375007 TTT
1 TTT
2375010 ATATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTCTTACGATTTTATAAAAT
Found at i:2375017 original size:17 final size:18
Alignment explanation
Indices: 2374994--2375046 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
2374984 ATTTTCTTAC
2374994 GATTTTATAAAATTTTAT
1 GATTTTATAAAATTTTAT
**
2375012 -ATTTTATAACTTTTTAT
1 GATTTTATAAAATTTTAT
2375029 GATTTTTATAAAATTTTA
1 GA-TTTTATAAAATTTTA
2375047 CAATTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 15 0.52
18 1 0.03
19 13 0.45
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
GATTTTATAAAATTTTAT
Found at i:2375037 original size:19 final size:19
Alignment explanation
Indices: 2374969--2375054 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 19
2374959 TTTATATTTC
*
2374969 TTTAC-ATTTTGTATAATTT
1 TTTACGATTTT-TATAAATT
*
2374988 TCTTACGA-TTTTATAAAAT
1 T-TTACGATTTTTATAAATT
* *
2375007 TTTA-TA-TTTTATAACTT
1 TTTACGATTTTTATAAATT
* *
2375024 TTTATGATTTTTATAAAAT
1 TTTACGATTTTTATAAATT
*
2375043 TTTACAATTTTT
1 TTTACGATTTTT
2375055 CTAACTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.26
18 4 0.08
19 27 0.51
20 7 0.13
21 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTACGATTTTTATAAATT
Found at i:2375143 original size:9 final size:9
Alignment explanation
Indices: 2374996--2375145 Score: 58
Period size: 9 Copynumber: 16.6 Consensus size: 9
2374986 TTTCTTACGA
*
2374996 TTTTATAAAA
1 TTTTAT-AAT
2375006 TTTTAT-A-
1 TTTTATAAT
2375013 TTTTATAACT
1 TTTTATAA-T
*
2375023 TTTTATGAT
1 TTTTATAAT
*
2375032 TTTTATAAAA
1 TTTTAT-AAT
*
2375042 TTTTACAAT
1 TTTTATAAT
* *
2375051 TTTTCTAAC
1 TTTTATAAT
*
2375060 TTTTATAAA
1 TTTTATAAT
2375069 TTTTA-AAT
1 TTTTATAAT
* *
2375077 ATTT-GAAT
1 TTTTATAAT
*
2375085 TTTTATTAAAA
1 TTTTA-T-AAT
*
2375096 TTTAATAAT
1 TTTTATAAT
* **
2375105 ATTTATAGC
1 TTTTATAAT
*
2375114 TTTTATTGAT
1 TTTTA-TAAT
* *
2375124 TTTAAT-TT
1 TTTTATAAT
2375132 TTTTATAAT
1 TTTTATAAT
2375141 TTTTA
1 TTTTA
2375146 ATAAAAGCAA
Statistics
Matches: 101, Mismatches: 29, Indels: 21
0.67 0.19 0.14
Matches are distributed among these distances:
7 6 0.06
8 19 0.19
9 45 0.45
10 25 0.25
11 6 0.06
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2376124 original size:14 final size:14
Alignment explanation
Indices: 2376105--2376132 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2376095 TTTAGGATTT
2376105 TACCTAAAGTTGTC
1 TACCTAAAGTTGTC
2376119 TACCTAAAGTTGTC
1 TACCTAAAGTTGTC
2376133 AATCTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
TACCTAAAGTTGTC
Found at i:2379569 original size:8 final size:8
Alignment explanation
Indices: 2379543--2379572 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2379533 TGAAATGCCA
2379543 GCTTTTCG
1 GCTTTTCG
*
2379551 GCATTTCG
1 GCTTTTCG
2379559 GCTTTTCG
1 GCTTTTCG
2379567 GCTTTT
1 GCTTTT
2379573 GTCGATCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.23, G:0.23, T:0.50
Consensus pattern (8 bp):
GCTTTTCG
Found at i:2383711 original size:34 final size:34
Alignment explanation
Indices: 2383664--2383734 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
2383654 TCTCTACCTT
*
2383664 TTTTATTTGCATAATTAACATTGACCTTATAATA
1 TTTTATTTCCATAATTAACATTGACCTTATAATA
2383698 TTTTATTTCCATAATTAACATTGACCTTATAATA
1 TTTTATTTCCATAATTAACATTGACCTTATAATA
2383732 TTT
1 TTT
2383735 AGGTTCACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTTATTTCCATAATTAACATTGACCTTATAATA
Found at i:2384150 original size:25 final size:23
Alignment explanation
Indices: 2384086--2384150 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
2384076 ATTATCACAC
*
2384086 TTTTATAAC-ATATAAATTATTT
1 TTTTATAACTTTATAAATTATTT
*
2384108 TTTATAATAA-TTTCTAAATATATTT
1 TTT-T-ATAACTTTATAAAT-TATTT
2384133 TTGTTATAACTTTATAAA
1 TT-TTATAACTTTATAAA
2384151 ATGCATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 3 0.09
23 1 0.03
24 14 0.41
25 15 0.44
26 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAACTTTATAAATTATTT
Found at i:2385298 original size:24 final size:23
Alignment explanation
Indices: 2385252--2385310 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2385242 ACATTTATAG
2385252 AAATAAAATTAATTAAGTTAAATT
1 AAATAAAA-TAATTAAGTTAAATT
**
2385276 ATTTAAAATAATATAA-TTAAAATT
1 AAATAAAATAAT-TAAGTT-AAATT
2385300 AAATAAAATAA
1 AAATAAAATAA
2385311 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATAAAATAATTAAGTTAAATT
Found at i:2388223 original size:116 final size:116
Alignment explanation
Indices: 2388038--2388252 Score: 349
Period size: 116 Copynumber: 1.9 Consensus size: 116
2388028 ATACAAAGTA
* * *
2388038 TATTAATGTTATCCATGAATAATTTTATTAACCAATCTGTTTGAAAAAATTATAAGTGTACAAAT
1 TATTAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAT
*
2388103 GAATATACTACACTTAGGGTACCAGATCTAACAAGGACAACATACAAAAGG
66 GAATATACTACACTTAGGGCACCAGATCTAACAAGGACAACATACAAAAGG
* * *
2388154 TATTAATGTAATTCATGAATAATTTTACTAACTAGTCTGTTCGAAAAAATTATAAGTGTACAAAT
1 TATTAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAT
* *
2388219 GAATATACTACATTTAGGGCACTAGATCTAACAA
66 GAATATACTACACTTAGGGCACCAGATCTAACAA
2388253 TCTTCAACTT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 90 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (116 bp):
TATTAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAAT
GAATATACTACACTTAGGGCACCAGATCTAACAAGGACAACATACAAAAGG
Found at i:2394711 original size:54 final size:54
Alignment explanation
Indices: 2394652--2394764 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
2394642 CATGGCTGCT
2394652 AGAACAGATA-ATGAGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACC
1 AGAACAGATATATGAGACAGAGTCACCAGAT-CAGATAATCGTGGCAGAGCCACC
* * * * *
2394706 AGAACAGATATATGTGGCAGAGTCACCAGATCAGATATTTGTGGCATAGCCACC
1 AGAACAGATATATGAGACAGAGTCACCAGATCAGATAATCGTGGCAGAGCCACC
2394760 AGAAC
1 AGAAC
2394765 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (54 bp):
AGAACAGATATATGAGACAGAGTCACCAGATCAGATAATCGTGGCAGAGCCACC
Found at i:2394712 original size:27 final size:26
Alignment explanation
Indices: 2394652--2394764 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
2394642 CATGGCTGCT
* * *
2394652 AGAACAGATAATGAGACAGAGTCACC
1 AGAACAGATAATGTGGCAGAGCCACC
2394678 AGATACAGATAATCGTGGCAGAGCCACC
1 AGA-ACAGATAAT-GTGGCAGAGCCACC
*
2394706 AGAACAGATATATGTGGCAGAGTCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
* * *
2394733 AGATCAGATATTTGTGGCATAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
2394760 AGAAC
1 AGAAC
2394765 GCTTCCTCCA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.04
27 56 0.75
28 16 0.21
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (26 bp):
AGAACAGATAATGTGGCAGAGCCACC
Found at i:2396407 original size:26 final size:26
Alignment explanation
Indices: 2396371--2396505 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
2396361 CATGAAATTC
* *
2396371 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* *
2396397 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
2396423 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2396449 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2396474 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2396500 TTATCA
1 TTATCA
2396506 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 25 0.24
26 81 0.76
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:2399486 original size:17 final size:15
Alignment explanation
Indices: 2399455--2399484 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2399445 CGCAACAAAA
2399455 AAAATTTTGTTTTTG
1 AAAATTTTGTTTTTG
2399470 AAAATCTTTGTTTTT
1 AAAAT-TTTGTTTTT
2399485 TGTAAACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (15 bp):
AAAATTTTGTTTTTG
Found at i:2400489 original size:27 final size:26
Alignment explanation
Indices: 2400452--2400566 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
2400442 AGCATGGCTG
* *
2400452 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
2400478 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
2400506 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
2400533 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
2400560 CCAGAAC
1 CCAGAAC
2400567 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:2400511 original size:54 final size:54
Alignment explanation
Indices: 2400452--2400566 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
2400442 AGCATGGCTG
*
2400452 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
2400506 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
2400560 CCAGAAC
1 CCAGAAC
2400567 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:2402212 original size:26 final size:26
Alignment explanation
Indices: 2402176--2402284 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
2402166 CATGAAATTC
2402176 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2402202 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
2402228 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
2402253 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
2402279 TTATCA
1 TTATCA
2402285 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 24 0.30
26 56 0.70
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2402266 original size:51 final size:52
Alignment explanation
Indices: 2402176--2402284 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 52
2402166 CATGAAATTC
2402176 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
* * * *
2402228 TTATCATGGAACATTTA-CTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
2402279 TTATCA
1 TTATCA
2402285 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 37 0.70
52 16 0.30
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
Found at i:2410305 original size:28 final size:28
Alignment explanation
Indices: 2410265--2410322 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
2410255 AACGGTCTGT
*
2410265 ATCACCGGTACATAGTACCTGCTAAATG
1 ATCACCGGCACATAGTACCTGCTAAATG
* **
2410293 ATCACCTGCACATAGTACCTTTTAAATG
1 ATCACCGGCACATAGTACCTGCTAAATG
2410321 AT
1 AT
2410323 TACCAGCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (28 bp):
ATCACCGGCACATAGTACCTGCTAAATG
Found at i:2411716 original size:15 final size:16
Alignment explanation
Indices: 2411696--2411733 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2411686 ACTAACCACT
*
2411696 AATTCAATTAATT-AA
1 AATTCAATCAATTCAA
2411711 AATTC-ATCAATTCAA
1 AATTCAATCAATTCAA
2411726 AATTCAAT
1 AATTCAAT
2411734 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 12 0.60
16 2 0.10
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTCAATCAATTCAA
Found at i:2421884 original size:3 final size:3
Alignment explanation
Indices: 2421876--2421901 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2421866 GTTTGAAATG
2421876 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2421902 ATTTAAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2422192 original size:18 final size:19
Alignment explanation
Indices: 2422151--2422192 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
2422141 AAAAAAATTT
2422151 ATAAAATATTAAATTTTAG
1 ATAAAATATTAAATTTTAG
2422170 A-AAAATATTAAATTTTA-
1 ATAAAATATTAAATTTTAG
2422187 ATAAAA
1 ATAAAA
2422193 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATATTAAATTTTAG
Found at i:2422199 original size:19 final size:19
Alignment explanation
Indices: 2422153--2422205 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
2422143 AAAAATTTAT
*
2422153 AAAATATTAAATTTT-AGA
1 AAAATATTAAATTTTAAAA
2422171 AAAATATTAAATTTTAATAA
1 AAAATATTAAATTTTAA-AA
*
2422191 AAAAT-TTAAAATTTA
1 AAAATATTAAATTTTA
2422206 TTGAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATATTAAATTTTAAAA
Found at i:2422212 original size:19 final size:20
Alignment explanation
Indices: 2422153--2422212 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
2422143 AAAAATTTAT
*
2422153 AAAATATT-AAATTTTA-GA
1 AAAATATTAAAATTTAATGA
* *
2422171 AAAATATTAAATTTTAATAA
1 AAAATATTAAAATTTAATGA
*
2422191 AAAAT-TTAAAATTTATTGA
1 AAAATATTAAAATTTAATGA
2422210 AAA
1 AAA
2422213 TTAGATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.24
19 20 0.59
20 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAATATTAAAATTTAATGA
Found at i:2422453 original size:10 final size:10
Alignment explanation
Indices: 2422440--2422478 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2422430 TTTTATGAAA
2422440 TTTATATTTC
1 TTTATATTTC
* *
2422450 TTTACATTTT
1 TTTATATTTC
2422460 TTTATATTTC
1 TTTATATTTC
*
2422470 TATATATTT
1 TTTATATTT
2422479 TATAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTTC
Found at i:2422478 original size:20 final size:20
Alignment explanation
Indices: 2422440--2422499 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2422430 TTTTATGAAA
* *
2422440 TTTATATTTCTTTACATTTT
1 TTTATATTTCTATATATTTT
2422460 TTTATATTTCTATATATTTT
1 TTTATATTTCTATATATTTT
* *
2422480 ATAATATTT-TATAATATTTT
1 TTTATATTTCTAT-ATATTTT
2422500 GAAAGTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATTTCTATATATTTT
Found at i:2422486 original size:10 final size:10
Alignment explanation
Indices: 2422463--2422499 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2422453 ACATTTTTTT
2422463 ATATTTCTAT-
1 ATATTT-TATA
2422473 ATATTTTATA
1 ATATTTTATA
2422483 ATATTTTATA
1 ATATTTTATA
2422493 ATATTTT
1 ATATTTT
2422500 GAAAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 3 0.12
10 23 0.88
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATTTTATA
Found at i:2422647 original size:90 final size:88
Alignment explanation
Indices: 2422495--2422659 Score: 201
Period size: 90 Copynumber: 1.9 Consensus size: 88
2422485 ATTTTATAAT
* * * * * *
2422495 ATTTTGAAAGTTTAAGTACCTAATTGAGTGCAAAAAAAATGTAGGGGCTTAATTGCTTTTTTTGA
1 ATTTTAAAAATTTAAGTACCCAAATGAGTGCAAAAAAAATATAAGGGCTTAATTGCTTTTTTT--
2422560 AAAAATTTGAGAACCTTTTTTATGC
64 AAAAATTTGAGAACCTTTTTTATGC
*
2422585 ATTTTAAAAATTTAAGTACCCAAATGAGTGTCAAAAAAAA-ATAAGGG-TTCAATT-TTTATTTT
1 ATTTTAAAAATTTAAGTACCCAAATGAGTG-CAAAAAAAATATAAGGGCTT-AATTGCTT-TTTT
2422647 TAAAAATTTGAGA
63 TAAAAATTTGAGA
2422660 GATTTTTACA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
88 12 0.18
89 4 0.06
90 40 0.62
91 9 0.14
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (88 bp):
ATTTTAAAAATTTAAGTACCCAAATGAGTGCAAAAAAAATATAAGGGCTTAATTGCTTTTTTTAA
AAATTTGAGAACCTTTTTTATGC
Found at i:2426719 original size:3 final size:3
Alignment explanation
Indices: 2426713--2426756 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2426703 TAAAAAAGAA
2426713 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2426757 AAAAAAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:2432271 original size:252 final size:251
Alignment explanation
Indices: 2431627--2432759 Score: 1092
Period size: 252 Copynumber: 4.5 Consensus size: 251
2431617 CCTATCATCC
* *
2431627 ATTTATGTCATGGTGTCACTGAAAGTTAGGCTTTGTATAAGCTGCATTTGTTAATCCGAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTG-TAATCCGAGTTCGG
* * *
2431692 GTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGC
65 GTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGC
* * * * * * ** *
2431755 ATTTGTAATCCGAGTTCAAGTTCAGCTCTCATATAATAGATTTACGATATGGTGTCGTTCAAAGT
130 ATTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTAT-GTGTCACTGAAAGT
* * * * * * *
2431820 TAAGACTTTGTTTAAGCTGTATTTGTGATCCGAGTTCTGGTTTAGCCCTCATTTGATAG
194 T-AGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
* * * * * *
2431879 ATTTATGTTATTGAGTCGCTGAAAGTTAGACATTGTAGAAGCTGCATTTGTAATCTGAGTTCGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2431944 TTTGGCTCTCATATAATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
66 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGCA
*
2432009 TTTGTAACCCAATTTCGGGTTCAGCTCTCATATAATAGATTTATGTTATGATGTCACTGAAAGTT
131 TTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTATG-TGTCACTGAAAGTT
* * * * * *
2432074 AGACTTTGGACAAGCTGCATTTGTAATCCAAGTTCGGGTTCAGCTCTCATATAATAT
195 AGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
* * * *
2432131 ATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGCATTTGTAATCCAAGTTCAGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * * *
2432196 TTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCATGAGCTGCA
66 TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGCA
* * * * * * *
2432261 TTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTT
131 TTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTA-TGTGTCACTGAAAGTT
* * * * *
2432326 AAACTTTGCATGAGCTGCATTTATAA-CCTGAGTTCGGGCTT-AGCTCT-ATTGTAATAG
195 AGACTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGGG-TTCAGCCCTCA-TGTAATAG
* * ** * * * * * * *
2432383 ATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTTTATGAGTTGTATTTGTAATCCGATTTCAGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2432447 TTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAAAGTTAGACTTTGTGTGAGCTG
66 TTTAGCTC-TCATATAATAGA-TTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTG
* * ** ** *
2432511 CATTTGCAATCTGATTTTGGGATT-AGCTCTCGA-ATCATAGATTTATGTTATG-G----TG-AA
129 CATTTGTAACCCAATTTCAGG-TTCAGCTCTC-ATATAATAGATTTATGTTATGTGTCACTGAAA
* * * **
2432568 GTTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGGTTCAGCCCTCATGCCATAG
192 GTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
* * * ** * * * * *
2432628 ATTTGTCTTATGGTATCACTGCCACTTGGACTTTGTATGAGCTGCATTTCTAA-CCTCAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGG
* * * * * *
2432692 GTTTAGCTCTCAAATCATAGATTTATATTATGTTGTTGCTGAAAGTTAGACTTTGTATGTGCTGC
65 GTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGC
2432757 ATT
130 ATT
2432760 CGTACTAAGA
Statistics
Matches: 728, Mismatches: 136, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
244 2 0.00
245 98 0.13
246 58 0.08
250 1 0.00
251 96 0.13
252 374 0.51
253 99 0.14
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (251 bp):
ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
TTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGCA
TTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTATGTGTCACTGAAAGTTA
GACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
Found at i:2432627 original size:77 final size:76
Alignment explanation
Indices: 2432489--2432641 Score: 202
Period size: 77 Copynumber: 2.0 Consensus size: 76
2432479 GTGTTGCTGA
* * *
2432489 AAGTTAGACTTTGTGTGAGCTGCATTTGCAATCTGATTTTGGGATTAGCTCTCGAATCATAGATT
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATTAGCCCTC-AATCATAGATT
*
2432554 TATGTTATGGTG
65 TATCTTATGGTG
*
2432566 AAGTTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGG-TTCAGCCCTC-ATGCCATAGA
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATT-AGCCCTCAAT--CATAGA
*
2432629 TTTGTCTTATGGT
63 TTTATCTTATGGT
2432642 ATCACTGCCA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
75 2 0.03
76 2 0.03
77 63 0.94
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (76 bp):
AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATTAGCCCTCAATCATAGATTT
ATCTTATGGTG
Found at i:2432749 original size:84 final size:83
Alignment explanation
Indices: 2431599--2432759 Score: 982
Period size: 84 Copynumber: 13.9 Consensus size: 83
2431589 AAGGTAATCA
* * * * ** * * *
2431599 GAGTCCGGTTTTAGCTCTCCTATCATCCATTTATGTCATGGTGTCACTGAAAGTTAGGCTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2431664 TAAGCTGCATTTGTTAATCC
66 TGAGCTGCATTTG-TAA-CC
* *
2431684 GAGTTCGGGTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGTTAGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2431747 TAAGCTGCATTTGTAATCC
66 TGAGCTGCATTTGTAA-CC
** * * * * *
2431766 GAGTTCAAGTTCAGCTCTCATATAATAGATTTACGATATGGTGTCGTTCAAAGTTAAGACTTTGT
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTT-AGACTTTGT
* * * *
2431831 TTAAGCTGTATTTGTGATCC
65 ATGAGCTGCATTTGT-AACC
* * * * * * *
2431851 GAGTTCTGGTTTAGCCCTCATTTGATAGATTTATGTTATTGAGTCGCTGAAAGTTAGACATTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2431916 -GAAGCTGCATTTGTAATCT
66 TG-AGCTGCATTTGTAA-CC
* * *
2431935 GAGTTCGGGTTTGGCTCTCATATAATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
* *
2432000 TAAGCTGTATTTGTAACCC
66 TGAGCTGCATTTGTAA-CC
* * * * * *
2432019 AATTTCGGGTTCAGCTCTCATATAATAGATTTATGTTATGATGTCACTGAAAGTTAGACTTTGGA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
**
2432084 CAAGCTGCATTTGTAATCC
66 TGAGCTGCATTTGTAA-CC
* * * * *
2432103 AAGTTCGGGTTCAGCTCTCATATAATATATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
* *
2432168 TAAGTTGCATTTGTAATCC
66 TGAGCTGCATTTGTAA-CC
* * * * * * * *
2432187 AAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2432252 TGAGCTGCATTTATAACCC
66 TGAGCTGCATTTGTAA-CC
* * * * * * * * * * *
2432271 AAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTTAAACTTTGCA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2432336 TGAGCTGCATTTATAACC
66 TGAGCTGCATTTGTAACC
* * * * * * *
2432354 TGAGTTCGGGCTTAGCTCT-ATTGTAATAGATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTT
1 -GAGTTCGGGTTTAGCTCTCA-TATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTG
* *
2432417 TATGAGTTGTATTTGTAATCC
64 TATGAGCTGCATTTGTAA-CC
* * * * * *
2432438 GATTTCAGGTTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAAAGTTAGACTTTG
1 GAGTTCGGGTTTAGCTC-TCATATAATAGA-TTTATGTTATGGTGTCGCTGAAAGTTAGACTTTG
* * *
2432502 TGTGAGCTGCATTTGCAATCT
64 TATGAGCTGCATTTGTAA-CC
* * * *
2432523 GATTTTGGGATTAGCTCTCGA-ATCATAGATTTATGTTA---TG--G-TG-AAGTTAGACTTTGT
1 GAGTTCGGGTTTAGCTCTC-ATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGT
*
2432580 ATGAGCTGCATTTGTAATCT
65 ATGAGCTGCATTTGTAA-CC
* * * *** * * * * ** * *
2432600 GAGTTTGGGTTCAGCCCTCATGCCATAGATTTGTCTTATGGTATCACTGCCACTTGGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2432665 TGAGCTGCATTTCTAACC
66 TGAGCTGCATTTGTAACC
* * * * * *
2432683 TCAGTTCGGGTTTAGCTCTCAAATCATAGATTTATATTATGTTGTTGCTGAAAGTTAGACTTTGT
1 -GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGT
*
2432748 ATGTGCTGCATT
65 ATGAGCTGCATT
2432760 CGTACTAAGA
Statistics
Matches: 891, Mismatches: 161, Indels: 49
0.81 0.15 0.04
Matches are distributed among these distances:
76 1 0.00
77 60 0.07
78 2 0.00
79 1 0.00
80 1 0.00
81 2 0.00
82 33 0.04
83 105 0.12
84 534 0.60
85 151 0.17
86 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (83 bp):
GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
TGAGCTGCATTTGTAACC
Found at i:2439076 original size:17 final size:18
Alignment explanation
Indices: 2439048--2439081 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2439038 TTAAAAATAA
2439048 TTTAACAATAATAAATTT
1 TTTAACAATAATAAATTT
*
2439066 TTTAA-AATAATTAATT
1 TTTAACAATAATAAATT
2439082 CGATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAACAATAATAAATTT
Found at i:2443239 original size:28 final size:26
Alignment explanation
Indices: 2443208--2443270 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2443198 TATTTTTTCA
*
2443208 ATTTTTAAATAATACTTTTAATTTATAT
1 ATTTTTAAATAATAATTTT--TTTATAT
* * **
2443236 ATTTATAATTTCTAATTTTTTTATAT
1 ATTTTTAAATAATAATTTTTTTATAT
2443262 ATTTTTAAA
1 ATTTTTAAA
2443271 AGTTTTGTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 14 0.50
28 14 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTAAATAATAATTTTTTTATAT
Found at i:2443303 original size:19 final size:19
Alignment explanation
Indices: 2443281--2443317 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2443271 AGTTTTGTGC
2443281 ATTTT-TTATTTCTATATAG
1 ATTTTATTATTT-TATATAG
2443300 ATTTTATTATTTTATATA
1 ATTTTATTATTTTATATA
2443318 TTTTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTATTATTTTATATAG
Found at i:2446255 original size:42 final size:42
Alignment explanation
Indices: 2446196--2446279 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2446186 CTTGCCTAAA
2446196 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
1 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
2446238 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
1 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
2446280 ACTTTAGTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.45
Consensus pattern (42 bp):
TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
Found at i:2450094 original size:38 final size:38
Alignment explanation
Indices: 2450013--2450165 Score: 155
Period size: 38 Copynumber: 4.1 Consensus size: 38
2450003 TTCAGGCTAT
** ** * **
2450013 GTGCCTAGTAGGCTTTGTGTCGGTGAT-TTCGGGCTAT
1 GTGCCTAACAGGCTTTGTACCGGTGATATTCGAGCTCC
* * * *
2450050 GTGCCTAGCAGGCTTTATGCCGGTAATATTCGAGCTCC
1 GTGCCTAACAGGCTTTGTACCGGTGATATTCGAGCTCC
* * *
2450088 GTGCCTAACAGACTTTGTACCAGTGATATTCGACCTCC
1 GTGCCTAACAGGCTTTGTACCGGTGATATTCGAGCTCC
* *
2450126 GTACCTAACAGGCTTTGTACCGGTGATATTCGGGCTCC
1 GTGCCTAACAGGCTTTGTACCGGTGATATTCGAGCTCC
2450164 GT
1 GT
2450166 ACCGGTGATA
Statistics
Matches: 96, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
37 23 0.24
38 73 0.76
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (38 bp):
GTGCCTAACAGGCTTTGTACCGGTGATATTCGAGCTCC
Found at i:2450167 original size:22 final size:22
Alignment explanation
Indices: 2450142--2450190 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2450132 AACAGGCTTT
*
2450142 GTACCGGTGATATTCGGGCTCC
1 GTACCGGTGATATTCAGGCTCC
*
2450164 GTACCGGTGATATTCAGGCTCT
1 GTACCGGTGATATTCAGGCTCC
2450186 GTACC
1 GTACC
2450191 TAACAGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (22 bp):
GTACCGGTGATATTCAGGCTCC
Found at i:2450197 original size:60 final size:63
Alignment explanation
Indices: 2450104--2450224 Score: 169
Period size: 60 Copynumber: 2.0 Consensus size: 63
2450094 AACAGACTTT
2450104 GTACCAGTGATATTCGACCTCCGTACCTAACAGGCTTTGTACCGGTG-A-TAT-TCGGGCTCC
1 GTACCAGTGATATTCGACCTCCGTACCTAACAGGCTTTGTACCGGTGTATTATATCGGGCTCC
* * * *
2450164 GTACCGGTGATATTC-AGGCTCTGTACCTAACAGGTTTTGTACCGGTGTATTATATCGGGCT
1 GTACCAGTGATATTCGA-CCTCCGTACCTAACAGGCTTTGTACCGGTGTATTATATCGGGCT
2450225 TTGTGCCTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
59 1 0.02
60 41 0.77
61 1 0.02
62 3 0.06
63 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (63 bp):
GTACCAGTGATATTCGACCTCCGTACCTAACAGGCTTTGTACCGGTGTATTATATCGGGCTCC
Found at i:2450272 original size:25 final size:25
Alignment explanation
Indices: 2450235--2450323 Score: 106
Period size: 25 Copynumber: 3.5 Consensus size: 25
2450225 TTGTGCCTAG
*
2450235 CAGGCTTCATGCCAGTGTACTATAT
1 CAGGCTTCGTGCCAGTGTACTATAT
* *
2450260 CGGGCTTTGTGCCAGTGTACTATAT
1 CAGGCTTCGTGCCAGTGTACTATAT
** *
2450285 CAGGCTTCGTGTGAGTGCACTATTAT
1 CAGGCTTCGTGCCAGTGTACTA-TAT
*
2450311 CAGGCTTGGTGCC
1 CAGGCTTCGTGCC
2450324 TAGTAGGCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 39 0.75
26 13 0.25
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (25 bp):
CAGGCTTCGTGCCAGTGTACTATAT
Found at i:2488826 original size:19 final size:19
Alignment explanation
Indices: 2488783--2488819 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2488773 ATTTTCAATT
2488783 TTTTATATTTTTTAATTATA
1 TTTT-TATTTTTTAATTATA
2488803 TTTTTATTTTTT-ATTAT
1 TTTTTATTTTTTAATTAT
2488820 TGTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTAATTATA
Found at i:2492322 original size:7 final size:7
Alignment explanation
Indices: 2492302--2492346 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
2492292 TTAAGGTTGG
2492302 AATT-AA
1 AATTAAA
2492308 AA-TAAA
1 AATTAAA
2492314 AATTAAA
1 AATTAAA
2492321 AATTAAA
1 AATTAAA
2492328 AA-TAAA
1 AATTAAA
*
2492334 AATTTAA
1 AATTAAA
2492341 AATTAA
1 AATTAA
2492347 GGGATCTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 1 0.03
6 12 0.35
7 21 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:2492331 original size:20 final size:20
Alignment explanation
Indices: 2492302--2492346 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2492292 TTAAGGTTGG
2492302 AATT-AAAATAAAAATTAAA
1 AATTAAAAATAAAAATTAAA
*
2492321 AATTAAAAATAAAAATTTAA
1 AATTAAAAATAAAAATTAAA
2492341 AATTAA
1 AATTAA
2492347 GGGATCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTAAAAATAAAAATTAAA
Found at i:2500326 original size:6 final size:6
Alignment explanation
Indices: 2500307--2500402 Score: 102
Period size: 6 Copynumber: 16.0 Consensus size: 6
2500297 GCTTAAGTTT
* * * * *
2500307 TTCTTC TTCCTC TTCTTC TTCTGC TTCTGC TTCTGC TTCTGC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * *
2500355 TTCTTC TTCTTC TTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
2500403 GGATTCTCCA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.00, C:0.40, G:0.04, T:0.56
Consensus pattern (6 bp):
TTCTTC
Found at i:2511062 original size:5 final size:6
Alignment explanation
Indices: 2511046--2511072 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2511036 AAAGCTCACC
2511046 ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATT
2511073 CTCTGCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:2512001 original size:3 final size:3
Alignment explanation
Indices: 2511995--2512024 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2511985 GGCGGAGGTA
*
2511995 TGG TGG TGC TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
2512025 CAGGCCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.63, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:2513134 original size:19 final size:20
Alignment explanation
Indices: 2513110--2513159 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2513100 AAATATAAAT
*
2513110 TTTGGAATTTTTAT-AATTA
1 TTTGGAATTTTTATAAATCA
*
2513129 TTTGG-ATTTTAATAAATCA
1 TTTGGAATTTTTATAAATCA
*
2513148 TTTTGAATTTTT
1 TTTGGAATTTTT
2513160 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTGGAATTTTTATAAATCA
Found at i:2513157 original size:20 final size:19
Alignment explanation
Indices: 2513108--2513158 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
2513098 TTAAATATAA
* *
2513108 ATTTTGGAATTTTTATAATT
1 ATTTT-GAATTTTAATAATC
*
2513128 A-TTTGGATTTTAATAAATC
1 ATTTTGAATTTTAAT-AATC
2513147 ATTTTGAATTTT
1 ATTTTGAATTTT
2513159 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTAATAATC
Found at i:2515468 original size:18 final size:18
Alignment explanation
Indices: 2515433--2515468 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2515423 GTTTGTGATG
* *
2515433 TTTTATATTATGTTATTT
1 TTTTATATTATATAATTT
2515451 TTTTATATTATATAATTT
1 TTTTATATTATATAATTT
2515469 ATAACACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATATTATATAATTT
Found at i:2515574 original size:30 final size:26
Alignment explanation
Indices: 2515521--2515587 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 26
2515511 TAATATGGCT
*
2515521 ATATATAAAATTTTAATAAATTAAAAA
1 ATATATAAATTTTTAATAAATT-AAAA
2515548 ATATATAAATTTATTAAATCAAATTAAAA
1 ATATATAAATTT-TT-AAT-AAATTAAAA
2515577 ATAATATAAAT
1 AT-ATATAAAT
2515588 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 11 0.31
28 2 0.06
29 9 0.26
30 13 0.37
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATATAAATTTTTAATAAATTAAAA
Found at i:2529468 original size:16 final size:17
Alignment explanation
Indices: 2529447--2529482 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2529437 TTATGCTTAA
*
2529447 TTAATAATTT-TTATTT
1 TTAATAATTTATTAATT
2529463 TTAATAATTTATTAATT
1 TTAATAATTTATTAATT
2529480 TTA
1 TTA
2529483 TTTTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATAATTTATTAATT
Found at i:2532341 original size:13 final size:14
Alignment explanation
Indices: 2532327--2532381 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
2532317 GTACCCTTCT
*
2532327 ACGA-TACCTTCCT
1 ACGAGTACCTTCCC
*
2532340 ACGAGTACCCTCCC
1 ACGAGTACCTTCCC
*
2532354 ATGAGTACCTTCCC
1 ACGAGTACCTTCCC
*
2532368 ACGACTACC-TCCC
1 ACGAGTACCTTCCC
2532381 A
1 A
2532382 AAGTACCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.24, C:0.44, G:0.11, T:0.22
Consensus pattern (14 bp):
ACGAGTACCTTCCC
Found at i:2532391 original size:27 final size:28
Alignment explanation
Indices: 2532331--2532393 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
2532321 CCTTCTACGA
* * *
2532331 TACCTTCCTACGAGTACCCTCCCATGAG
1 TACCTTCCCACGACTACCCTCCCATAAG
2532359 TACCTTCCCACGACTA-CCTCCCA-AAG
1 TACCTTCCCACGACTACCCTCCCATAAG
2532385 TACCCTTCC
1 TA-CCTTCC
2532394 ACGGAACCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 13 0.42
28 14 0.45
ACGTcount: A:0.22, C:0.44, G:0.10, T:0.24
Consensus pattern (28 bp):
TACCTTCCCACGACTACCCTCCCATAAG
Found at i:2536293 original size:26 final size:26
Alignment explanation
Indices: 2536257--2536308 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2536247 TAAACTAGAC
2536257 TGCCTGTATATCTGTTTCAAATATAT
1 TGCCTGTATATCTGTTTCAAATATAT
2536283 TGCCTGTATATCTGTTTCAAATATAT
1 TGCCTGTATATCTGTTTCAAATATAT
2536309 CTTTGAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TGCCTGTATATCTGTTTCAAATATAT
Found at i:2540653 original size:19 final size:22
Alignment explanation
Indices: 2540612--2540656 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2540602 GTAAAATGAC
*
2540612 TTATTCTTTTGAAAAGCGTAAT
1 TTATTCTTTTGAAAAGAGTAAT
2540634 TTATT-TTTTGAAAA-AG-AAT
1 TTATTCTTTTGAAAAGAGTAAT
2540653 TTAT
1 TTAT
2540657 CTATGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 9 0.41
22 5 0.23
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (22 bp):
TTATTCTTTTGAAAAGAGTAAT
Found at i:2540973 original size:28 final size:28
Alignment explanation
Indices: 2540941--2541004 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
2540931 TATATGATTA
2540941 AATAAATA-ATAATTAT-ATAATATTAAAT
1 AATAAATATATAATT-TCATAAT-TTAAAT
*
2540969 AATAAA-ATATAATTTCATAATTTTAAT
1 AATAAATATATAATTTCATAATTTAAAT
2540996 AATAAATAT
1 AATAAATAT
2541005 TTTATCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
AATAAATATATAATTTCATAATTTAAAT
Found at i:2544414 original size:16 final size:16
Alignment explanation
Indices: 2544393--2544425 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2544383 ACATGGATAT
2544393 GTTCAAAATTTTAAGA
1 GTTCAAAATTTTAAGA
2544409 GTTCAAAATTTTAAGA
1 GTTCAAAATTTTAAGA
2544425 G
1 G
2544426 ACGTCTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (16 bp):
GTTCAAAATTTTAAGA
Found at i:2547161 original size:77 final size:76
Alignment explanation
Indices: 2547058--2547207 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 76
2547048 GCTAGTCTTC
* * * * *
2547058 AAGAAACTCGATAATGATTCTGATACTCAAGCAACTGGCAGTCAAGAAGCTTTATCTCAGACTGT
1 AAGAAACTCGACAATGATTCTGATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACTGT
2547123 CTGAAAGTTGG
66 CTGAAAGTTGG
** *
2547134 AAGAAACTCAGACAATGATT-TGGATACTTGAGCAACCGGCAGTCGAGAAGCTTCATCACAAACT
1 AAGAAACTC-GACAATGATTCT-GATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACT
2547198 GTCTGAAAGT
64 GTCTGAAAGT
2547208 GAATAACTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
76 10 0.16
77 54 0.84
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
AAGAAACTCGACAATGATTCTGATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACTGT
CTGAAAGTTGG
Found at i:2548186 original size:10 final size:10
Alignment explanation
Indices: 2548171--2548200 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2548161 TGCCTTTGTG
2548171 ATAAAATTTT
1 ATAAAATTTT
2548181 ATAAAATTTT
1 ATAAAATTTT
2548191 A-AAAATTTT
1 ATAAAATTTT
2548200 A
1 A
2548201 ACCCTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAAAATTTT
Found at i:2552119 original size:27 final size:27
Alignment explanation
Indices: 2552089--2552150 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2552079 GAAAAGATGA
2552089 AGAATCAAAGGAAGTAAAGGAAGGAGT
1 AGAATCAAAGGAAGTAAAGGAAGGAGT
2552116 AGAATCAAAGGAAGTAAAGGAAGGAGT
1 AGAATCAAAGGAAGTAAAGGAAGGAGT
*
2552143 AGCATCAA
1 AGAATCAA
2552151 TAGCGTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.52, C:0.06, G:0.31, T:0.11
Consensus pattern (27 bp):
AGAATCAAAGGAAGTAAAGGAAGGAGT
Found at i:2552573 original size:28 final size:29
Alignment explanation
Indices: 2552529--2552583 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2552519 TCTAAGAAGG
*
2552529 TGAATCAATTGGTTCC-TCTACTATTACA
1 TGAATCAATTAGTTCCTTCTACTATTACA
*
2552557 TGAATCAATTTAG-TCCTTTTACTATTA
1 TGAATCAA-TTAGTTCCTTCTACTATTA
2552584 AAAGGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (29 bp):
TGAATCAATTAGTTCCTTCTACTATTACA
Found at i:2553321 original size:2 final size:2
Alignment explanation
Indices: 2553314--2553344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2553304 TTCCACAAAA
2553314 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2553345 ACACACACAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2562468 original size:18 final size:20
Alignment explanation
Indices: 2562445--2562488 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2562435 AAATTCTTTT
*
2562445 TTTTGCT-ATTTT-TTACTA
1 TTTTGCTCATTTTCTCACTA
2562463 TTTTGCTGCATTTTCTCACTA
1 TTTTGCT-CATTTTCTCACTA
2562484 TTTTG
1 TTTTG
2562489 TTACCATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTTGCTCATTTTCTCACTA
Found at i:2564411 original size:25 final size:25
Alignment explanation
Indices: 2564379--2564534 Score: 129
Period size: 25 Copynumber: 6.3 Consensus size: 25
2564369 GCCCTCTCTT
2564379 GAGCCATATAATAGGAAGCTCATCA
1 GAGCCATATAATAGGAAGCTCATCA
* *
2564404 GAGCCATATAATAGGAAGCTTATCC
1 GAGCCATATAATAGGAAGCTCATCA
* ** * *
2564429 GAGCTATATAACGGGAAGCTTATAA
1 GAGCCATATAATAGGAAGCTCATCA
* * **
2564454 GAGCCATA-ATTGGGAAGCTCATGT
1 GAGCCATATAATAGGAAGCTCATCA
* *
2564478 GAGCCATA-AATAGGAAGCTTATCC
1 GAGCCATATAATAGGAAGCTCATCA
* ** *
2564502 GGGTTATATAAT-GAGAAGCTCATAA
1 GAGCCATATAATAG-GAAGCTCATCA
2564527 GAGCCATA
1 GAGCCATA
2564535 ATTGGGAAGT
Statistics
Matches: 102, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
24 36 0.35
25 66 0.65
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
GAGCCATATAATAGGAAGCTCATCA
Found at i:2564481 original size:24 final size:24
Alignment explanation
Indices: 2564378--2564556 Score: 97
Period size: 25 Copynumber: 7.3 Consensus size: 24
2564368 AGCCCTCTCT
* *
2564378 TGAGCCATATAATAGGAAGCTCATC
1 TGAGCCATA-AATGGGAAGCTCATG
* * * *
2564403 AGAGCCATATAATAGGAAGCTTATC
1 TGAGCCATA-AATGGGAAGCTCATG
* * * * *
2564428 CGAGCTATATAACGGGAAGCTTATA
1 TGAGCCATA-AATGGGAAGCTCATG
* *
2564453 AGAGCCATAATTGGGAAGCTCATG
1 TGAGCCATAAATGGGAAGCTCATG
* * *
2564477 TGAGCCATAAATAGGAAGCTTATC
1 TGAGCCATAAATGGGAAGCTCATG
* * ** * *
2564501 CGGGTTATATAATGAGAAGCTCATA
1 TGAGCCATA-AATGGGAAGCTCATG
* * *
2564526 AGAGCCATAATTGGGAAGTTCATG
1 TGAGCCATAAATGGGAAGCTCATG
2564550 TGAGCCA
1 TGAGCCA
2564557 ATAACAGGTA
Statistics
Matches: 118, Mismatches: 35, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
24 52 0.44
25 66 0.56
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (24 bp):
TGAGCCATAAATGGGAAGCTCATG
Found at i:2564498 original size:73 final size:74
Alignment explanation
Indices: 2564392--2564569 Score: 252
Period size: 73 Copynumber: 2.4 Consensus size: 74
2564382 CCATATAATA
** * *
2564392 GGAAGCTCATCAGAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGGGAAGCTTATAAGAG
1 GGAAGCTCATGTGAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGAGAAGCTCATAAGAG
2564457 CCATAATTG
66 CCATAATTG
* * *
2564466 GGAAGCTCATGTGAGCCATA-AATAGGAAGCTTATCCGGGTTATATAATGAGAAGCTCATAAGAG
1 GGAAGCTCATGTGAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGAGAAGCTCATAAGAG
2564530 CCATAATTG
66 CCATAATTG
* * *
2564539 GGAAGTTCATGTGAGCCA-ATAACAGGTAGCT
1 GGAAGCTCATGTGAGCCATATAATAGGAAGCT
2564570 CCAAAGAGCC
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.01
73 74 0.80
74 18 0.19
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (74 bp):
GGAAGCTCATGTGAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGAGAAGCTCATAAGAG
CCATAATTG
Found at i:2564683 original size:26 final size:26
Alignment explanation
Indices: 2564654--2564704 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2564644 TGGAGAACCA
2564654 TTAATCAGGAAGCTCACAAAGAGCCT
1 TTAATCAGGAAGCTCACAAAGAGCCT
* **
2564680 TTAATCGGGAAGCTCATGAAGAGCC
1 TTAATCAGGAAGCTCACAAAGAGCC
2564705 ATATAACGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAGAGCCT
Found at i:2565180 original size:10 final size:10
Alignment explanation
Indices: 2565166--2565209 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2565156 TAAATTTAGC
2565166 TCAATTTAAT
1 TCAATTTAAT
* *
2565176 ACAATCTATAT
1 TCAATTTA-AT
2565187 TCAATTTAAT
1 TCAATTTAAT
*
2565197 TCAATTCAAT
1 TCAATTTAAT
2565207 TCA
1 TCA
2565210 CATCATGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (10 bp):
TCAATTTAAT
Found at i:2567129 original size:34 final size:34
Alignment explanation
Indices: 2567006--2567124 Score: 114
Period size: 34 Copynumber: 3.5 Consensus size: 34
2566996 TTCTGATATG
* * * **
2567006 ATATAACATTTTGATATATTATATGTTTCTAAAA
1 ATATGACATTCTGATATAGTATATGTTTCTGGAA
* *
2567040 ATATGACATTCTAATCTAGTATATGTTTCTGGAA
1 ATATGACATTCTGATATAGTATATGTTTCTGGAA
* * * *
2567074 ATATGACATTTTGGT-TTGATATATGTTTCTGGTA
1 ATATGACATTCTGATATAG-TATATGTTTCTGGAA
*
2567108 ATCTGACATTCTGATAT
1 ATATGACATTCTGATAT
2567125 GATATTGTAT
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
33 2 0.03
34 65 0.96
35 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (34 bp):
ATATGACATTCTGATATAGTATATGTTTCTGGAA
Found at i:2575125 original size:15 final size:15
Alignment explanation
Indices: 2575105--2575170 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
2575095 ACTGCAAAAA
2575105 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
2575120 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
2575139 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
2575154 ATTCA-TATTAA-AT
1 ATTTATTATTAATAT
2575167 ATTT
1 ATTT
2575171 TCAATAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 13 0.31
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:2575217 original size:16 final size:16
Alignment explanation
Indices: 2575189--2575225 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2575179 ATGTGAAGAA
2575189 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
2575205 TATT-TTTACAAATTAT
1 TATTATTTA-AAATTAT
2575221 TATTA
1 TATTA
2575226 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:2576836 original size:13 final size:13
Alignment explanation
Indices: 2576818--2576842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2576808 ATTTCACAAG
2576818 ATAAAAATAAAAA
1 ATAAAAATAAAAA
2576831 ATAAAAATAAAA
1 ATAAAAATAAAA
2576843 CCCCCTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:2579803 original size:7 final size:7
Alignment explanation
Indices: 2579791--2579830 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
2579781 ATTTCCGATC
2579791 GGCAAAT
1 GGCAAAT
2579798 GGCAAAT
1 GGCAAAT
2579805 GGCAAAT
1 GGCAAAT
2579812 GGCAAAT
1 GGCAAAT
2579819 GGCAAAT
1 GGCAAAT
2579826 GGCAA
1 GGCAA
2579831 TGAGGGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.30, T:0.12
Consensus pattern (7 bp):
GGCAAAT
Found at i:2580079 original size:34 final size:34
Alignment explanation
Indices: 2580036--2580105 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
2580026 TGACCTTTGT
*
2580036 TACACTCTTTGAAGATGAAGGATGAACGTATATA
1 TACACTCTTTGAAGATGAAGGATGAACATATATA
2580070 TACACTCTTTGAAGATGAAGGATGAACATATATA
1 TACACTCTTTGAAGATGAAGGATGAACATATATA
2580104 TA
1 TA
2580106 TATACACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (34 bp):
TACACTCTTTGAAGATGAAGGATGAACATATATA
Found at i:2580116 original size:6 final size:6
Alignment explanation
Indices: 2580107--2580131 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2580097 ATATATATAT
2580107 ATACAC ATACAC ATACAC ATACAC A
1 ATACAC ATACAC ATACAC ATACAC A
2580132 GGGACCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ATACAC
Found at i:2583441 original size:21 final size:21
Alignment explanation
Indices: 2583417--2583456 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2583407 CACAGGTTGA
* *
2583417 TGTGGCTTAACATAAGGCTAT
1 TGTGGCTCAACACAAGGCTAT
2583438 TGTGGCTCAACACAAGGCT
1 TGTGGCTCAACACAAGGCT
2583457 GTGTGTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
TGTGGCTCAACACAAGGCTAT
Found at i:2588024 original size:168 final size:168
Alignment explanation
Indices: 2587735--2588078 Score: 607
Period size: 168 Copynumber: 2.0 Consensus size: 168
2587725 CCTAGAACAT
*
2587735 GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACGCGGCCTA
1 GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
2587800 AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATGATGACATCATAGTCAGAGAGT
66 AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATGATGACATCATAGTCAGAGAGT
2587865 TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
131 TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
* * **
2587903 GGGTGTGTGCCTAGGCCGTGTGAAGTCTGCACCTGATTTTAGAATTTAATTCACCACACGGCCTA
1 GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
* **
2587968 AGCACACGAGTGTGTGATTTGGCCGTGTGACCTTATTTTGGATGATGAGGTCATAGTCAGAGAGT
66 AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATGATGACATCATAGTCAGAGAGT
*
2588033 TACACGGGTTGAGGACACGGGCGTGTCCCAAACCACAC
131 TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
2588071 GGGCGTGT
1 GGGCGTGT
2588079 ATGACCACAC
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
168 166 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (168 bp):
GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATGATGACATCATAGTCAGAGAGT
TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
Found at i:2589040 original size:11 final size:11
Alignment explanation
Indices: 2589026--2589080 Score: 76
Period size: 11 Copynumber: 5.1 Consensus size: 11
2589016 GACAAAAAGT
*
2589026 AGCAGCAAAAC
1 AGCAACAAAAC
*
2589037 AGCACCAAAAC
1 AGCAACAAAAC
2589048 AGCAACAAAAC
1 AGCAACAAAAC
*
2589059 AGC-ACCAAAC
1 AGCAACAAAAC
2589069 AGCAACAAAAC
1 AGCAACAAAAC
2589080 A
1 A
2589081 ACACAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.23
11 30 0.77
ACGTcount: A:0.58, C:0.31, G:0.11, T:0.00
Consensus pattern (11 bp):
AGCAACAAAAC
Found at i:2589070 original size:21 final size:22
Alignment explanation
Indices: 2589026--2589089 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 22
2589016 GACAAAAAGT
*
2589026 AGCAGCAAAACAGCACCAAAAC
1 AGCAACAAAACAGCACCAAAAC
2589048 AGCAACAAAACAGCACC-AAAC
1 AGCAACAAAACAGCACCAAAAC
* *
2589069 AGCAACAAAACAACACAAAAA
1 AGCAACAAAACAGCACCAAAA
2589090 ACAACATCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.61, C:0.30, G:0.09, T:0.00
Consensus pattern (22 bp):
AGCAACAAAACAGCACCAAAAC
Found at i:2589982 original size:26 final size:26
Alignment explanation
Indices: 2589953--2590008 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
2589943 TGATAAAAAT
2589953 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2589979 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2590005 TGAT
1 TGAT
2590009 GGGCATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2591516 original size:26 final size:26
Alignment explanation
Indices: 2591487--2591539 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2591477 TTTACAGTTT
2591487 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
2591513 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
2591539 T
1 T
2591540 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:2595272 original size:19 final size:20
Alignment explanation
Indices: 2595243--2595280 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2595233 TCTCTGCAAA
*
2595243 ATATAAATATTTTTAATTAG
1 ATATAAATATTTTAAATTAG
2595263 ATAT-AATATTTTAAATTA
1 ATATAAATATTTTAAATTA
2595281 TCTTGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATATTTTAAATTAG
Found at i:2595387 original size:13 final size:13
Alignment explanation
Indices: 2595369--2595395 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2595359 GTGTTTGTTT
2595369 TAAAGACATCAAA
1 TAAAGACATCAAA
2595382 TAAAGACATCAAA
1 TAAAGACATCAAA
2595395 T
1 T
2595396 TGTTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.15, G:0.07, T:0.19
Consensus pattern (13 bp):
TAAAGACATCAAA
Found at i:2598547 original size:3 final size:3
Alignment explanation
Indices: 2598539--2598870 Score: 77
Period size: 3 Copynumber: 112.0 Consensus size: 3
2598529 CAATTCAATC
* * * *
2598539 TAT TAT TAT TAAC TAT TAT T-T TAC TAT TAT TAT CA- AAT ATAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * * * *
2598584 CAT TAT CT-C TAT TAT TAC T-T TAT TAT TGT AACT TAA TA- TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * * ** * *
2598628 TAT TA- TAT TAC TAT CAT TAT TAT TAT TAT TAC CGT TAG CAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2598674 TCAT TAC TAT TA- TAT T-T TAT TGAT TA- TAT TAC TA- TATT TGT TA-
1 T-AT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT
* * * * * * * *
2598717 TAT TAT CAT TAT CAT TCT TAC TAT TGT TAT TAT TAC TAC TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
2598765 TCT TAT TAA CA- TAT TAT TAT TAT TTT TAC TA- TAC TAT TAT TAT TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
2598811 T-T T-T TTT TCACT TAT TAA TAT TAT TGA- TAT TAA CAT ATAT TAAT
1 TAT TAT TAT T-A-T TAT TAT TAT TAT T-AT TAT TAT TAT -TAT T-AT
2598855 GTAT TAT TAT TAT TAT
1 -TAT TAT TAT TAT TAT
2598871 CTTATTTTAC
Statistics
Matches: 234, Mismatches: 66, Indels: 58
0.65 0.18 0.16
Matches are distributed among these distances:
2 29 0.12
3 181 0.77
4 21 0.09
5 3 0.01
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:2598566 original size:11 final size:13
Alignment explanation
Indices: 2598538--2598571 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
2598528 TCAATTCAAT
2598538 CTATTATTATTAA
1 CTATTATTATTAA
2598551 CTATTATT-TT-A
1 CTATTATTATTAA
2598562 CTATTATTAT
1 CTATTATTAT
2598572 CAAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 3 0.15
13 8 0.40
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (13 bp):
CTATTATTATTAA
Found at i:2598802 original size:20 final size:20
Alignment explanation
Indices: 2598735--2598808 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
2598725 TTATCATTCT
* *
2598735 TACTATTGTTATTATTACTA
1 TACTATTATTATTTTTACTA
* *
2598755 CTACTATTATTCTTATTAAC-A
1 -TACTATTATTATT-TTTACTA
*
2598776 TATTATTATTATTTTTACTA
1 TACTATTATTATTTTTACTA
2598796 TACTATTATTATT
1 TACTATTATTATT
2598809 CTTTTTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.09
20 24 0.56
21 12 0.28
22 3 0.07
ACGTcount: A:0.31, C:0.11, G:0.01, T:0.57
Consensus pattern (20 bp):
TACTATTATTATTTTTACTA
Found at i:2598802 original size:23 final size:23
Alignment explanation
Indices: 2598750--2598814 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
2598740 TTGTTATTAT
* * * *
2598750 TACTACTACTATTATTCTTATTA
1 TACTATTATTATTATTTTTACTA
2598773 -ACATATTATTATTATTTTTACTA
1 TAC-TATTATTATTATTTTTACTA
*
2598796 TACTATTATTATTCTTTTT
1 TACTATTATTATTATTTTT
2598815 TTTTCACTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 2 0.06
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (23 bp):
TACTATTATTATTATTTTTACTA
Found at i:2599328 original size:3 final size:3
Alignment explanation
Indices: 2599322--2599369 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
2599312 TGTATTTCAA
*
2599322 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
2599368 TA
1 TA
2599370 GTGTATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2599374 original size:154 final size:153
Alignment explanation
Indices: 2599197--2599655 Score: 572
Period size: 154 Copynumber: 3.0 Consensus size: 153
2599187 TATTTTCATC
*
2599197 TTATTATTATTATATATTAGTGTATATTTTCATTATATATGTATATGTATATATATTTGTATATA
1 TTATTATTATTATATATTAGTGTATATTTTCATTATATATGTATATGTATATATATTTATATATA
2599262 GTATTATTTTTATTA-TTTATTTTAATATTTTTATTATATTTGCTTTTTTTTGTATTTCAATATT
66 GTATTATTTTTATTACTTTATTTTAATATTTTTATTATATTT--TTTTTTTTGTATTTCAATATT
2599326 ATTACTATTATTATTATTATTATTA
129 ATTACTATTATTATTATTATTATTA
* * * *
2599351 TTATTATTATTATATATTAGTGTATATTTTTATTGTATAGGTATATGTATATATATTTATATCTA
1 TTATTATTATTATATATTAGTGTATATTTTCATTATATATGTATATGTATATATATTTATATATA
* * * *
2599416 GTATTACTTTTTATTACTTTATTTTAATATTTATATTATA---TATATTTTGTATTCCAATATTA
66 GTATTA-TTTTTATTACTTTATTTTAATATTTTTATTATATTTTTTTTTTTGTATTTCAATATTA
*
2599478 TTAC------------CATTATTA
130 TTACTATTATTATTATTATTATTA
*
2599490 TTATTATTATTATATATTAGTCTATATTTTCATTATATATGTATATGTATATATATATTTATATA
1 TTATTATTATTATATATTAGTGTATATTTTCATTATATATGTATATG--TATATATATTTATATA
* *
2599555 TAGTATTATTTTTAATTACTTTATTTCAATATTTTTATTGTATTATATTTGCTTTTTGTATTTCA
64 TAGTATTATTTTT-ATTACTTTATTTTAATATTTTTATTATATT-T-TTT--TTTTTGTATTTCA
* *
2599620 ATATTATTGCTATTATTATTATTGTTATTA
124 ATATTATTACTATTATTATTATTATTATTA
*
2599650 CTATTA
1 TTATTA
2599656 GTGTATATTT
Statistics
Matches: 256, Mismatches: 25, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
139 50 0.20
140 5 0.02
141 48 0.19
146 2 0.01
148 20 0.08
151 23 0.09
154 66 0.26
155 9 0.04
156 22 0.09
160 11 0.04
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (153 bp):
TTATTATTATTATATATTAGTGTATATTTTCATTATATATGTATATGTATATATATTTATATATA
GTATTATTTTTATTACTTTATTTTAATATTTTTATTATATTTTTTTTTTTGTATTTCAATATTAT
TACTATTATTATTATTATTATTA
Done.