Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002858.1 Kokia drynarioides strain JFW-HI SEQ_115257, 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: 209013
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:5445 original size:26 final size:27
Alignment explanation
Indices: 5399--5451 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
5389 ACTGTAACCC
5399 GGTACTCTTCTAACTTATGAACAACAT
1 GGTACTCTTCTAACTTATGAACAACAT
5426 GGTACTCTTC-AACTTATGAACAACAT
1 GGTACTCTTCTAACTTATGAACAACAT
5452 CACTTACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (27 bp):
GGTACTCTTCTAACTTATGAACAACAT
Found at i:10265 original size:74 final size:75
Alignment explanation
Indices: 10126--10275 Score: 205
Period size: 74 Copynumber: 2.0 Consensus size: 75
10116 TAATTTTGAT
* * * * * *
10126 GCAATCTAGAAGTGCTCATGTGGCGATAGTTTTTGGGCGCAATCTAGAGGTGCTCATGCGACGAC
1 GCAATCTAGAAGTGCTCATGCGACGATAGTGTTTGGGCACAATCTAGAAGTGCTCATGAGACGAC
*
10191 ATGTTTGGGC
66 ATGTTTAGGC
*
10201 GCAATCTAGAAGTGCTCATGCGACGATA-TGTTTGGGCATAATCTAGAAGTGCTCATGTAG-CGA
1 GCAATCTAGAAGTGCTCATGCGACGATAGTGTTTGGGCACAATCTAGAAGTGCTCATG-AGACGA
10264 CATGTTTAGGC
65 CATGTTTAGGC
10275 G
1 G
10276 TAATTCTGGA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 39 0.59
75 27 0.41
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (75 bp):
GCAATCTAGAAGTGCTCATGCGACGATAGTGTTTGGGCACAATCTAGAAGTGCTCATGAGACGAC
ATGTTTAGGC
Found at i:10269 original size:37 final size:37
Alignment explanation
Indices: 10126--10275 Score: 185
Period size: 37 Copynumber: 4.0 Consensus size: 37
10116 TAATTTTGAT
* * * *
10126 GCAATCTAGAAGTGCTCATGTGGCGATAGTTTTTGGGC
1 GCAATCTAGAAGTGCTCATGCGACGACA-TGTTTGGGC
*
10164 GCAATCTAGAGGTGCTCATGCGACGACATGTTTGGGC
1 GCAATCTAGAAGTGCTCATGCGACGACATGTTTGGGC
*
10201 GCAATCTAGAAGTGCTCATGCGACGATATGTTTGGGC
1 GCAATCTAGAAGTGCTCATGCGACGACATGTTTGGGC
** * *
10238 ATAATCTAGAAGTGCTCATG-TAGCGACATGTTTAGGC
1 GCAATCTAGAAGTGCTCATGCGA-CGACATGTTTGGGC
10275 G
1 G
10276 TAATTCTGGA
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.01
37 73 0.74
38 24 0.24
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
GCAATCTAGAAGTGCTCATGCGACGACATGTTTGGGC
Found at i:13767 original size:16 final size:16
Alignment explanation
Indices: 13746--13776 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13736 ATATTGTGAC
13746 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
13762 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
13777 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:14680 original size:38 final size:37
Alignment explanation
Indices: 14638--14712 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 37
14628 GGGTGCAACT
*
14638 GAATACTTATACAACGACAGTTCTTGATGCAATTTGAA
1 GAATACTTATACAACGACAGTT-TTGATGCAATCTGAA
* ** * *
14676 GAATATTTATGTAGCGACAGTTTTGGTGCAATCTGAA
1 GAATACTTATACAACGACAGTTTTGATGCAATCTGAA
14713 AGTGCTCATG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
37 13 0.42
38 18 0.58
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (37 bp):
GAATACTTATACAACGACAGTTTTGATGCAATCTGAA
Found at i:14737 original size:37 final size:36
Alignment explanation
Indices: 14689--14847 Score: 119
Period size: 37 Copynumber: 4.3 Consensus size: 36
14679 TATTTATGTA
*
14689 GCGACAG-TTTTGGTGCAATCTGAAAGTGCTCATGTG
1 GCGACAGTTTTTGGTGCAATCT-AAAGTGCTCATGCG
* *
14725 GCGACAGTTTTTGGCCGTAATCTAAAGGTGCTCATGCG
1 GCGACAGTTTTTGG-TGCAATCTAAA-GTGCTCATGCG
* * * *
14763 ACGACA-TGTTTGGGTACAATCTCAAAGTACTCATGCG
1 GCGACAGT-TTTTGGTGCAATCT-AAAGTGCTCATGCG
* * *
14800 GCGGCA-TGTTTGG-GCATAATCTAGAAGTGCTCATGCA
1 GCGACAGTTTTTGGTGC--AATCTA-AAGTGCTCATGCG
14837 GCGACATGTTT
1 GCGACA-GTTT
14848 GGGCGTAATT
Statistics
Matches: 95, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
35 1 0.01
36 12 0.13
37 51 0.54
38 29 0.31
39 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (36 bp):
GCGACAGTTTTTGGTGCAATCTAAAGTGCTCATGCG
Found at i:14756 original size:38 final size:36
Alignment explanation
Indices: 14684--14760 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 36
14674 AAGAATATTT
*
14684 ATGTAGCGACAGTTTTGGTGCAATCTGAAAGTGCTC
1 ATGTAGCGACAGTTTTGGCGCAATCTGAAAGTGCTC
* *
14720 ATGTGGCGACAGTTTTTGGCCGTAATCT-AAAGGTGCTC
1 ATGTAGCGACAG-TTTTGG-CGCAATCTGAAA-GTGCTC
14758 ATG
1 ATG
14761 CGACGACATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 11 0.31
37 9 0.26
38 15 0.43
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (36 bp):
ATGTAGCGACAGTTTTGGCGCAATCTGAAAGTGCTC
Found at i:14768 original size:74 final size:74
Alignment explanation
Indices: 14690--14850 Score: 193
Period size: 74 Copynumber: 2.2 Consensus size: 74
14680 ATTTATGTAG
* * * * * * *
14690 CGACA-GTTTTGGTGCAATCTGAAAGTGCTCATGTGGCGACAGTTTTTGGCCGTAATCTA-AAGG
1 CGACATGTTTGGGTACAATCTCAAAGTACTCATGCGGCGACA-TGTTTGGCCATAATCTAGAA-G
14753 TGCTCATGCGA
64 TGCTCATGCGA
* *
14764 CGACATGTTTGGGTACAATCTCAAAGTACTCATGCGGCGGCATGTTTGGGCATAATCTAGAAGTG
1 CGACATGTTTGGGTACAATCTCAAAGTACTCATGCGGCGACATGTTTGGCCATAATCTAGAAGTG
14829 CTCATGC-A
66 CTCATGCGA
14837 GCGACATGTTTGGG
1 -CGACATGTTTGGG
14851 CGTAATTTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
73 1 0.01
74 42 0.56
75 32 0.43
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (74 bp):
CGACATGTTTGGGTACAATCTCAAAGTACTCATGCGGCGACATGTTTGGCCATAATCTAGAAGTG
CTCATGCGA
Found at i:14848 original size:37 final size:36
Alignment explanation
Indices: 14705--14856 Score: 160
Period size: 37 Copynumber: 4.1 Consensus size: 36
14695 GTTTTGGTGC
* * * *
14705 AATCTGAAAGTGCTCATGTGGCGACAGTTTTTGGCCGT
1 AATCT-AAAGTGCTCATGCGGCGACA-TGTTTGGGCAT
* * *
14743 AATCTAAAGGTGCTCATGCGACGACATGTTTGGGTAC
1 AATCTAAA-GTGCTCATGCGGCGACATGTTTGGGCAT
* *
14780 AATCTCAAAGTACTCATGCGGCGGCATGTTTGGGCAT
1 AATCT-AAAGTGCTCATGCGGCGACATGTTTGGGCAT
* *
14817 AATCTAGAAGTGCTCATGCAGCGACATGTTTGGGCGT
1 AATCTA-AAGTGCTCATGCGGCGACATGTTTGGGCAT
14854 AAT
1 AAT
14857 TTTGGATTAA
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
36 1 0.01
37 71 0.75
38 23 0.24
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (36 bp):
AATCTAAAGTGCTCATGCGGCGACATGTTTGGGCAT
Found at i:20478 original size:17 final size:18
Alignment explanation
Indices: 20456--20493 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20446 GGGCATATAA
* *
20456 AAATATGAACATG-AATT
1 AAATATAAACAAGCAATT
20473 AAATATAAACAAGCAATT
1 AAATATAAACAAGCAATT
20491 AAA
1 AAA
20494 CACAATCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATATAAACAAGCAATT
Found at i:22037 original size:6 final size:6
Alignment explanation
Indices: 22026--22065 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
22016 CATATGCTTC
22026 CTTTTT CTTTTT CTTTTT C--TTT -TTTTT CTTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
22066 ATTCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.10
5 3 0.10
6 25 0.81
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:22053 original size:15 final size:15
Alignment explanation
Indices: 22033--22064 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22023 TTCCTTTTTC
22033 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
22048 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
22063 TT
1 TT
22065 CATTCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:23409 original size:18 final size:18
Alignment explanation
Indices: 23388--23428 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
23378 TTCCATAGGA
23388 TCTTCCTCAGGATCTTCT
1 TCTTCCTCAGGATCTTCT
*
23406 TCTTCTTCAGGATCTTCT
1 TCTTCCTCAGGATCTTCT
23424 TCTTC
1 TCTTC
23429 AATTTGCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.32, G:0.10, T:0.49
Consensus pattern (18 bp):
TCTTCCTCAGGATCTTCT
Found at i:24701 original size:20 final size:20
Alignment explanation
Indices: 24676--24884 Score: 278
Period size: 20 Copynumber: 10.4 Consensus size: 20
24666 ACCTAAGTAT
* **
24676 TCAGGCTTTATGCTGGTAAA
1 TCAGGCTTTATGCCGGTGTA
*
24696 TCAGGCTTTATGTCGGTG-A
1 TCAGGCTTTATGCCGGTGTA
*
24715 TTCAGGCTTTGTGCCGGTG-A
1 -TCAGGCTTTATGCCGGTGTA
*
24735 TTCAGGCTTTGTGCCGGTGTA
1 -TCAGGCTTTATGCCGGTGTA
*
24756 TCAGGCTTTATGTCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
*
24776 TCAGGCTTTGTGCCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
24796 TCAGGCTTTATGCCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
*
24816 TCAGACTTTATGCCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
*
24836 TCAGGCTTTATACCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
*
24856 TCAGGCTTTGTGCCGGTGTA
1 TCAGGCTTTATGCCGGTGTA
*
24876 ACAGGCTTT
1 TCAGGCTTT
24885 GTGCAGGATA
Statistics
Matches: 171, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
19 1 0.01
20 169 0.99
21 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (20 bp):
TCAGGCTTTATGCCGGTGTA
Found at i:34524 original size:166 final size:167
Alignment explanation
Indices: 34250--34582 Score: 623
Period size: 166 Copynumber: 2.0 Consensus size: 167
34240 TACATGAGTG
* *
34250 CACAGCTAGACTGTAATAAACTTTTACAGCTGCAATTGGATCTGTATCTGAGGAGAGAGAAGGTT
1 CACAGCTAAACTGTAACAAACTTTTACAGCTGCAATTGGATCTGTATCTGAGGAGAGAGAAGGTT
34315 TACCATTCTTGAAGCCTATAAATTGAGGAAAAAAGATGAAGAAAAATATCAAGAGGTAAAGGAAT
66 TACCATTCTTGAAGCCTATAAATTGAGGAAAAAAGATGAAGAAAAATATCAAGAGGTAAAGGAAT
34380 TAAATTTGC-TTACTTTGTGTTTTTGGAGATTTTACT
131 TAAATTTGCATTACTTTGTGTTTTTGGAGATTTTACT
34416 CACAGCTAAACTGTAACAAACTTTTACAGCTGCAATTGGATCTGTATCTGAGGAGAGAGAAGGTT
1 CACAGCTAAACTGTAACAAACTTTTACAGCTGCAATTGGATCTGTATCTGAGGAGAGAGAAGGTT
*
34481 TACCATTCTTGAAGCCTATAAATTGAGGAAAAAAGATGAAGAAAAATATCAAGAGGTAGAGGAAT
66 TACCATTCTTGAAGCCTATAAATTGAGGAAAAAAGATGAAGAAAAATATCAAGAGGTAAAGGAAT
34546 TAAATTTGCAATTACTTTGTGTTTTTGGAGATTTTAC
131 TAAATTTGC-ATTACTTTGTGTTTTTGGAGATTTTAC
34583 ACTGGAACGG
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
166 136 0.84
168 26 0.16
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (167 bp):
CACAGCTAAACTGTAACAAACTTTTACAGCTGCAATTGGATCTGTATCTGAGGAGAGAGAAGGTT
TACCATTCTTGAAGCCTATAAATTGAGGAAAAAAGATGAAGAAAAATATCAAGAGGTAAAGGAAT
TAAATTTGCATTACTTTGTGTTTTTGGAGATTTTACT
Found at i:44982 original size:304 final size:304
Alignment explanation
Indices: 44433--45042 Score: 1184
Period size: 304 Copynumber: 2.0 Consensus size: 304
44423 TTAGAAGATT
44433 ATACATGCACAAATTAAATAGTATGTCCATTAACCACAATTTCAATGCGCTTAAATGATTAATTC
1 ATACATGCACAAATTAAATAGTATGTCCATTAACCACAATTTCAATGCGCTTAAATGATTAATTC
*
44498 AATACTTATATCACACGGGTAATGTAATAATAACTTAAGGATGATAATATTTAATTAAATAGAAT
66 AATACTTATATCACACGGGTAATGTAATAATAACTTAAGAATGATAATATTTAATTAAATAGAAT
44563 ATTCAGGGCCTATAACAATACGAACATAAATGAAATATAAACAAGCAATTAAACACAATCAACCC
131 ATTCAGGGCCTATAACAATACGAACATAAATGAAATATAAACAAGCAATTAAACACAATCAACCC
44628 AACACTTAAAGAATTTAAGTCATTTCAATTAAATAAATAATAACATTCATAATAGCATTCATCAT
196 AACACTTAAAGAATTTAAGTCATTTCAATTAAATAAATAATAACATTCATAATAGCATTCATCAT
44693 AATAACAAACAAGAATCTAAAATAAAGAAAAATAATAGGATTAA
261 AATAACAAACAAGAATCTAAAATAAAGAAAAATAATAGGATTAA
* *
44737 ATACATGCACAAATTAAATAGTTTGTCCATTAACCACAATTTCAATGCGTTTAAATGATTAATTC
1 ATACATGCACAAATTAAATAGTATGTCCATTAACCACAATTTCAATGCGCTTAAATGATTAATTC
*
44802 AATAGTTATATCACACGGGTAATGTAATAATAACTTAAGAATGATAATATTTAATTAAATAGAAT
66 AATACTTATATCACACGGGTAATGTAATAATAACTTAAGAATGATAATATTTAATTAAATAGAAT
44867 ATTCAGGGCCTATAACAATACGAACATAAATGAAATATAAACAAGCAATTAAACACAATCAACCC
131 ATTCAGGGCCTATAACAATACGAACATAAATGAAATATAAACAAGCAATTAAACACAATCAACCC
44932 AACACTTAAAGAATTTAAGTCATTTCAATTAAATAAATAATAACATTCATAATAGCATTCATCAT
196 AACACTTAAAGAATTTAAGTCATTTCAATTAAATAAATAATAACATTCATAATAGCATTCATCAT
44997 AATAACAAACAAGAATCTAAAATAAAGAAAAATAATAGGATTAA
261 AATAACAAACAAGAATCTAAAATAAAGAAAAATAATAGGATTAA
45041 AT
1 AT
45043 CCGTCGATTT
Statistics
Matches: 302, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
304 302 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (304 bp):
ATACATGCACAAATTAAATAGTATGTCCATTAACCACAATTTCAATGCGCTTAAATGATTAATTC
AATACTTATATCACACGGGTAATGTAATAATAACTTAAGAATGATAATATTTAATTAAATAGAAT
ATTCAGGGCCTATAACAATACGAACATAAATGAAATATAAACAAGCAATTAAACACAATCAACCC
AACACTTAAAGAATTTAAGTCATTTCAATTAAATAAATAATAACATTCATAATAGCATTCATCAT
AATAACAAACAAGAATCTAAAATAAAGAAAAATAATAGGATTAA
Found at i:50510 original size:30 final size:32
Alignment explanation
Indices: 50474--50536 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
50464 TGTAAAAACA
* *
50474 ATATATGT-GA-ATATAAAATAGTGTGTATAT
1 ATATATGTAGATATATAAAAAAATGTGTATAT
*
50504 ATATATGTATATATATAAAAAAATGTGTATAT
1 ATATATGTAGATATATAAAAAAATGTGTATAT
50536 A
1 A
50537 ACATTGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 8 0.29
31 1 0.04
32 19 0.68
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.40
Consensus pattern (32 bp):
ATATATGTAGATATATAAAAAAATGTGTATAT
Found at i:50545 original size:32 final size:32
Alignment explanation
Indices: 50484--50546 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
50474 ATATATGTGA
* * *
50484 ATATAAAATAGTGTGTATATATATATGTATAT
1 ATATAAAAAAATGTGTATATACATATGTATAT
50516 ATATAAAAAAATGTGTATATAACAT-TGTATA
1 ATATAAAAAAATGTGTATAT-ACATATGTATA
50547 AGTTTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (32 bp):
ATATAAAAAAATGTGTATATACATATGTATAT
Found at i:51871 original size:124 final size:124
Alignment explanation
Indices: 51651--51899 Score: 489
Period size: 124 Copynumber: 2.0 Consensus size: 124
51641 ACCAAGATAC
51651 AAGCATGTTGCCTAAAAATTGACAAGTTCCGGAAGTGCTTTTTCTATCCAACTTGCATCCACCAA
1 AAGCATGTTGCCTAAAAATTGACAAGTTCCGGAAGTGCTTTTTCTATCCAACTTGCATCCACCAA
51716 AATTCACATTAGAGTAAGCATGTAAACTAAATGATGAATCTCTGGGATACCAAAGTCCT
66 AATTCACATTAGAGTAAGCATGTAAACTAAATGATGAATCTCTGGGATACCAAAGTCCT
51775 AAGCATGTTGCCTAAAAATTGACAAGTTCCGGAAGTGCTTTTTCTATCCAACTTGCATCCACCAA
1 AAGCATGTTGCCTAAAAATTGACAAGTTCCGGAAGTGCTTTTTCTATCCAACTTGCATCCACCAA
*
51840 AATTCACATTAGAGTAAGCATGTAAACTAAATGATGAATCTTTGGGATACCAAAGTCCT
66 AATTCACATTAGAGTAAGCATGTAAACTAAATGATGAATCTCTGGGATACCAAAGTCCT
51899 A
1 A
51900 GGTTTGAAGT
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (124 bp):
AAGCATGTTGCCTAAAAATTGACAAGTTCCGGAAGTGCTTTTTCTATCCAACTTGCATCCACCAA
AATTCACATTAGAGTAAGCATGTAAACTAAATGATGAATCTCTGGGATACCAAAGTCCT
Found at i:55420 original size:20 final size:20
Alignment explanation
Indices: 55395--55439 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
55385 AATCATTTGA
*
55395 ATTTCCTTGCGAACATAGTC
1 ATTTCCTTGCGAACATAGCC
*
55415 ATTTCCTTGTGAACATAGCC
1 ATTTCCTTGCGAACATAGCC
55435 ATTTC
1 ATTTC
55440 TTCCTAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (20 bp):
ATTTCCTTGCGAACATAGCC
Found at i:56497 original size:13 final size:13
Alignment explanation
Indices: 56479--56505 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56469 AATCCACTAG
56479 ATTTGAACCTTTA
1 ATTTGAACCTTTA
56492 ATTTGAACCTTTA
1 ATTTGAACCTTTA
56505 A
1 A
56506 GGGCAAGGTT
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTTGAACCTTTA
Found at i:58055 original size:25 final size:25
Alignment explanation
Indices: 58025--58105 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
58015 AGCTTAAATG
58025 TTCTGTCTGACATGACTATTCTAAT
1 TTCTGTCTGACATGACTATTCTAAT
* * *
58050 TTCTGTATAGCCGATGAGC--TT-AAAT
1 TTCTGTCT-GAC-ATGA-CTATTCTAAT
*
58075 GTTCTGTCTAACATGACTATTCTAAT
1 -TTCTGTCTGACATGACTATTCTAAT
58101 TTCTG
1 TTCTG
58106 AATAGCTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
23 1 0.02
24 4 0.10
25 18 0.43
26 14 0.33
27 4 0.10
28 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (25 bp):
TTCTGTCTGACATGACTATTCTAAT
Found at i:58056 original size:51 final size:51
Alignment explanation
Indices: 57999--58105 Score: 169
Period size: 51 Copynumber: 2.1 Consensus size: 51
57989 TTCTTTTTTA
** *
57999 TTCTGTATAATTGAGGAGCTTAAATGTTCTGTCTGACATGACTATTCTAAT
1 TTCTGTATAACCGAGGAGCTTAAATGTTCTGTCTAACATGACTATTCTAAT
* *
58050 TTCTGTATAGCCGATGAGCTTAAATGTTCTGTCTAACATGACTATTCTAAT
1 TTCTGTATAACCGAGGAGCTTAAATGTTCTGTCTAACATGACTATTCTAAT
58101 TTCTG
1 TTCTG
58106 AATAGCTAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (51 bp):
TTCTGTATAACCGAGGAGCTTAAATGTTCTGTCTAACATGACTATTCTAAT
Found at i:58111 original size:51 final size:51
Alignment explanation
Indices: 58014--58130 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
58004 TATAATTGAG
* * * *
58014 GAGCTTAAATGTTCTGTCTGACATGACTATTCTAATTTCTGTATAGCCGAT
1 GAGCTTAAATGTTCTGTCTAACATGACTATTCTAATTTCTGAATAGCCAAC
*
58065 GAGCTTAAATGTTCTGTCTAACATGACTATTCTAATTTCTGAATAGCTAAC
1 GAGCTTAAATGTTCTGTCTAACATGACTATTCTAATTTCTGAATAGCCAAC
*
58116 GAGCTTAAACGTTCT
1 GAGCTTAAATGTTCT
58131 ATCTGTTACG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (51 bp):
GAGCTTAAATGTTCTGTCTAACATGACTATTCTAATTTCTGAATAGCCAAC
Found at i:65350 original size:30 final size:30
Alignment explanation
Indices: 65307--65373 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
65297 ATTTTTTTTC
** *
65307 AATTTTTTTATAATTGTTAA-AGATTTCTAT
1 AATTTTTAAATAATTATTAATA-ATTTCTAT
* *
65337 TATTTTTAAATAATTATTAATATTTTCTAT
1 AATTTTTAAATAATTATTAATAATTTCTAT
65367 AATTTTT
1 AATTTTT
65374 TATTTTTAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
AATTTTTAAATAATTATTAATAATTTCTAT
Found at i:73516 original size:16 final size:17
Alignment explanation
Indices: 73484--73516 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
73474 AAAGTTAAAA
*
73484 TATTTATTTTATGATCT
1 TATTTATTTTATAATCT
73501 TATTTA-TTTATAATCT
1 TATTTATTTTATAATCT
73517 ATACAAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTATTTTATAATCT
Found at i:74074 original size:23 final size:23
Alignment explanation
Indices: 74044--74090 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
74034 ATCTAAAAAA
74044 AATATAGGTTAAAAAAATAGGAG
1 AATATAGGTTAAAAAAATAGGAG
74067 AATATAGGTTAAAAAAATAGGAG
1 AATATAGGTTAAAAAAATAGGAG
74090 A
1 A
74091 TTGTTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (23 bp):
AATATAGGTTAAAAAAATAGGAG
Found at i:75009 original size:21 final size:21
Alignment explanation
Indices: 74948--75009 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
74938 AAGGGTGCGG
* **
74948 TACCTCTTGAGTAGGGTGCAA
1 TACCTCTTGAGAAGGGTGTTA
* * *
74969 TACCTGGTTG-GAAAGTTGTTA
1 TACCT-CTTGAGAAGGGTGTTA
74990 TACCTCTTGAGAAGGGTGTT
1 TACCTCTTGAGAAGGGTGTT
75010 GCACCTCTGT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.34
Consensus pattern (21 bp):
TACCTCTTGAGAAGGGTGTTA
Found at i:76512 original size:13 final size:13
Alignment explanation
Indices: 76496--76547 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
76486 TTAGAATAAA
*
76496 TCTAACCTTAAGT
1 TCTAAACTTAAGT
76509 TCTAAACTTAAG-
1 TCTAAACTTAAGT
* * * *
76521 TCTAATCCTGAGG
1 TCTAAACTTAAGT
76534 TCTAAACTTAAGT
1 TCTAAACTTAAGT
76547 T
1 T
76548 AAGTTCTAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (13 bp):
TCTAAACTTAAGT
Found at i:76524 original size:25 final size:25
Alignment explanation
Indices: 76496--76546 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
76486 TTAGAATAAA
*
76496 TCTAA-CCTTAAGTTCTAAACTTAAG
1 TCTAATCC-TAAGGTCTAAACTTAAG
*
76521 TCTAATCCTGAGGTCTAAACTTAAG
1 TCTAATCCTAAGGTCTAAACTTAAG
76546 T
1 T
76547 TAAGTTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (25 bp):
TCTAATCCTAAGGTCTAAACTTAAG
Found at i:80706 original size:25 final size:25
Alignment explanation
Indices: 80678--80728 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
80668 TTATTCGAAG
80678 TTAATAGTTAACTTGCTAGTAACAT
1 TTAATAGTTAACTTGCTAGTAACAT
80703 TTAATAGTTAACTTGCTAGTAACAT
1 TTAATAGTTAACTTGCTAGTAACAT
80728 T
1 T
80729 CGAAAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (25 bp):
TTAATAGTTAACTTGCTAGTAACAT
Found at i:81648 original size:20 final size:19
Alignment explanation
Indices: 81625--81670 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
81615 GACTCTTATA
81625 ATTTTTGATACTCACCTCAT
1 ATTTTTGATACTC-CCTCAT
*
81645 ATTTTTTGATATTCCCTCAT
1 A-TTTTTGATACTCCCTCAT
81665 ATTTTT
1 ATTTTT
81671 TAGTATTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 8 0.33
21 11 0.46
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (19 bp):
ATTTTTGATACTCCCTCAT
Found at i:81671 original size:20 final size:21
Alignment explanation
Indices: 81626--81671 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
81616 ACTCTTATAA
81626 TTTTTGATACTCACCTCATAT
1 TTTTTGATACTCACCTCATAT
*
81647 TTTTTGATATTC-CCTCATAT
1 TTTTTGATACTCACCTCATAT
81667 TTTTT
1 TTTTT
81672 AGTATTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTGATACTCACCTCATAT
Found at i:84604 original size:21 final size:20
Alignment explanation
Indices: 84579--84635 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
84569 ATAATCTTTT
84579 ATAATTTTTAGTACTCGCCTC
1 ATAATTTTTAGTACTC-CCTC
* *
84600 ATAATTTTTTTGTACTCCTTC
1 ATAA-TTTTTAGTACTCCCTC
84621 AT-ATATTTTAGTACT
1 ATAAT-TTTTAGTACT
84636 TCAAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 10 0.32
21 9 0.29
22 11 0.35
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (20 bp):
ATAATTTTTAGTACTCCCTC
Found at i:84634 original size:20 final size:22
Alignment explanation
Indices: 84579--84635 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
84569 ATAATCTTTT
84579 ATAAT-TTTTAGTACTCGCCTC
1 ATAATATTTTAGTACTCGCCTC
* * *
84600 ATAATTTTTTTGTACTC-CTTC
1 ATAATATTTTAGTACTCGCCTC
84621 AT-ATATTTTAGTACT
1 ATAATATTTTAGTACT
84636 TCAAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 11 0.35
21 10 0.32
22 10 0.32
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (22 bp):
ATAATATTTTAGTACTCGCCTC
Found at i:85072 original size:20 final size:19
Alignment explanation
Indices: 85049--85097 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
85039 TAAATTTCAC
*
85049 CAAAAAATAGAATAATAAA
1 CAAAAAATAGAACAATAAA
* *
85068 TCAAATATTAGAACAATAAA
1 -CAAAAAATAGAACAATAAA
85088 CAAGAAAATA
1 CAA-AAAATA
85098 AGGAAGATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.18
Consensus pattern (19 bp):
CAAAAAATAGAACAATAAA
Found at i:87820 original size:43 final size:41
Alignment explanation
Indices: 87768--87921 Score: 200
Period size: 41 Copynumber: 3.7 Consensus size: 41
87758 AGTCTCACGT
* * *
87768 TCATTTCGAGACATGAGTCTTCCATTTATACGTAATCTCATGC
1 TCATCTCGAGACATGAGTCTTCC-TTT-TACATAATCTCATAC
*
87811 TCGTCTCGAGACATGAGTCTTCCTTTTACATAATCTCATAC
1 TCATCTCGAGACATGAGTCTTCCTTTTACATAATCTCATAC
* *
87852 TCATCCCGAGACATGAGTCTTCCTTTTACATAATCTCATTC
1 TCATCTCGAGACATGAGTCTTCCTTTTACATAATCTCATAC
** * *
87893 TCATCAAGAGAGAAGAGTCTTCCTTTTAC
1 TCATCTCGAGACATGAGTCTTCCTTTTAC
87922 TTTTGAGTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 76 0.76
42 3 0.03
43 21 0.21
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (41 bp):
TCATCTCGAGACATGAGTCTTCCTTTTACATAATCTCATAC
Found at i:94270 original size:24 final size:24
Alignment explanation
Indices: 94215--94271 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
94205 CAAGTATTCT
*
94215 AACTACCAATACAAACATGCAAAG
1 AACTACCGATACAAACATGCAAAG
*
94239 TACTACCGATACAAACATGCAAAG
1 AACTACCGATACAAACATGCAAAG
94263 AACTACCGA
1 AACTACCGA
94272 AACTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.14
Consensus pattern (24 bp):
AACTACCGATACAAACATGCAAAG
Found at i:94852 original size:41 final size:41
Alignment explanation
Indices: 94773--94852 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 41
94763 ACATTTAACA
* * *
94773 ATCGAGTCATAAATCTTTCTTTTTAAACAATCTTATGCTCC
1 ATCGAGTCATAAATCTTTCTCTTAAAACAATCTCATGCTCC
*
94814 ATCGAGTCATAAGTC-TTC-CTTAAAACATAGTCTCATGCT
1 ATCGAGTCATAAATCTTTCTCTTAAAACA-A-TCTCATGCT
94853 TATTTCGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
39 7 0.21
40 4 0.12
41 22 0.67
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (41 bp):
ATCGAGTCATAAATCTTTCTCTTAAAACAATCTCATGCTCC
Found at i:98031 original size:27 final size:27
Alignment explanation
Indices: 98001--98052 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
97991 AAAGATTCTC
*
98001 AAAACTCTTCTAAAAG-AAAACTCAATA
1 AAAACTCTT-GAAAAGAAAAACTCAATA
*
98028 AAAAGTCTTGAAAAGAAAAACTCAA
1 AAAACTCTTGAAAAGAAAAACTCAA
98053 AGGTAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (27 bp):
AAAACTCTTGAAAAGAAAAACTCAATA
Found at i:100425 original size:24 final size:24
Alignment explanation
Indices: 100393--100481 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 24
100383 AATAAGTTGA
100393 CGAGCGTAAACGTGTGCAAGCTGG
1 CGAGCGTAAACGTGTGCAAGCTGG
* ** *
100417 CGAGTGTAAACGCAAATGACTAAGCTGA
1 CGAGCGTAAACG--TGTG-C-AAGCTGG
*
100445 CGAGCGTAAACATGTGCAAGCTGG
1 CGAGCGTAAACGTGTGCAAGCTGG
* *
100469 TGAGTGTAAACGT
1 CGAGCGTAAACGT
100482 AAATGAATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
24 27 0.55
25 1 0.02
26 4 0.08
27 1 0.02
28 16 0.33
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.19
Consensus pattern (24 bp):
CGAGCGTAAACGTGTGCAAGCTGG
Found at i:100426 original size:52 final size:52
Alignment explanation
Indices: 100358--100506 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 52
100348 ACAAATGAAT
* * *
100358 AAGCTGGCGAAG-GTAAATGCAAATGAATAAGTTGACGAGCGTAAACGTGTGC
1 AAGCTGGCG-AGTGTAAACGCAAATGAATAAGCTGACGAGCGTAAACATGTGC
*
100410 AAGCTGGCGAGTGTAAACGCAAATGACTAAGCTGACGAGCGTAAACATGTGC
1 AAGCTGGCGAGTGTAAACGCAAATGAATAAGCTGACGAGCGTAAACATGTGC
* * * *
100462 AAGCTGGTGAGTGTAAACGTAAATGAATAAGCTGGCGAGTGTAAA
1 AAGCTGGCGAGTGTAAACGCAAATGAATAAGCTGACGAGCGTAAA
100507 TGCAAATGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.19
Consensus pattern (52 bp):
AAGCTGGCGAGTGTAAACGCAAATGAATAAGCTGACGAGCGTAAACATGTGC
Found at i:100453 original size:28 final size:28
Alignment explanation
Indices: 100343--100673 Score: 165
Period size: 28 Copynumber: 12.2 Consensus size: 28
100333 AACTTTGAAT
*
100343 TAAACACAAATGAATAAGCTGGCGAAG-G
1 TAAACGCAAATGAATAAGCTGGCG-AGCG
* * *
100371 TAAATGCAAATGAATAAGTTGACGAGCG
1 TAAACGCAAATGAATAAGCTGGCGAGCG
*** *
100399 TAAACG----TGTGCAAGCTGGCGAGTG
1 TAAACGCAAATGAATAAGCTGGCGAGCG
* *
100423 TAAACGCAAATGACTAAGCTGACGAGCG
1 TAAACGCAAATGAATAAGCTGGCGAGCG
*** * *
100451 TAAA--C--ATGTGCAAGCTGGTGAGTG
1 TAAACGCAAATGAATAAGCTGGCGAGCG
* *
100475 TAAACGTAAATGAATAAGCTGGCGAGTG
1 TAAACGCAAATGAATAAGCTGGCGAGCG
* ** *
100503 TAAATGCAAATGAATAAGCTAACGAGCA
1 TAAACGCAAATGAATAAGCTGGCGAGCG
* * * *
100531 TAAATG----TGTACAAGTTGGCGAGCG
1 TAAACGCAAATGAATAAGCTGGCGAGCG
* *
100555 TAAACACATAA-GTATAAGCTGGCGAGCG
1 TAAACGCA-AATGAATAAGCTGGCGAGCG
* *
100583 TAAACGCGTAA-GTATAAGCTGGCGAGCG
1 TAAACGC-AAATGAATAAGCTGGCGAGCG
* * *
100611 TAAACGCGTAA-GTATAAGCTGGCAAGCG
1 TAAACGC-AAATGAATAAGCTGGCGAGCG
* * * * *
100639 AAAACGCGTAA-GTATAAGCTAGCAAGCG
1 TAAACGC-AAATGAATAAGCTGGCGAGCG
100667 TAAACGC
1 TAAACGC
100674 GTACGTATAA
Statistics
Matches: 239, Mismatches: 49, Indels: 30
0.75 0.15 0.09
Matches are distributed among these distances:
24 51 0.21
26 1 0.00
27 2 0.01
28 185 0.77
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (28 bp):
TAAACGCAAATGAATAAGCTGGCGAGCG
Found at i:100494 original size:80 final size:79
Alignment explanation
Indices: 100410--100615 Score: 218
Period size: 80 Copynumber: 2.6 Consensus size: 79
100400 AAACGTGTGC
* * *
100410 AAGCTGGCGAGTGTAAACGCAAATGACTAAGCTGACGAGCGTAAACATGTGCAAGCTGGTGAGTG
1 AAGCTGGCGAGTGTAAACGCAAATGA-TAAGCTGACGAGCGTAAACATGTACAAGCTGGCGAGCG
**
100475 TAAACGTA-AATGAAT
65 TAAACACATAA-GAAT
* * * ** *
100490 AAGCTGGCGAGTGTAAATGCAAATGAATAAGCTAACGAGCATAAATGTGTACAAGTTGGCGAGCG
1 AAGCTGGCGAGTGTAAACGCAAATG-ATAAGCTGACGAGCGTAAACATGTACAAGCTGGCGAGCG
*
100555 TAAACACATAAGTAT
65 TAAACACATAAGAAT
* * *
100570 AAGCTGGCGAGCGTAAACGCGTAA-GTATAAGCTGGCGAGCGTAAAC
1 AAGCTGGCGAGTGTAAACGC-AAATG-ATAAGCTGACGAGCGTAAAC
100616 GCGTAAGTAT
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
80 98 0.95
81 5 0.05
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (79 bp):
AAGCTGGCGAGTGTAAACGCAAATGATAAGCTGACGAGCGTAAACATGTACAAGCTGGCGAGCGT
AAACACATAAGAAT
Found at i:100572 original size:52 final size:54
Alignment explanation
Indices: 100490--100630 Score: 126
Period size: 52 Copynumber: 2.6 Consensus size: 54
100480 GTAAATGAAT
* ** * *
100490 AAGCTGGCGAGTGTAAATGCA-AATGAATAAGCTAACGAGCATAAA-TGT-GTAC
1 AAGCTGGCGAGCGTAAACACATAA-GTATAAGCTAACGAGCATAAACCGTAGTAC
* ** * *
100542 AAGTTGGCGAGCGTAAACACATAAGTATAAGCTGGCGAGCGTAAACGCGTAAGTAT
1 AAGCTGGCGAGCGTAAACACATAAGTATAAGCTAACGAGCATAAAC-CGT-AGTAC
* *
100598 AAGCTGGCGAGCGTAAACGCGTAAGTATAAGCT
1 AAGCTGGCGAGCGTAAACACATAAGTATAAGCT
100631 GGCAAGCGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
52 34 0.48
53 2 0.03
54 2 0.03
56 33 0.46
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.20
Consensus pattern (54 bp):
AAGCTGGCGAGCGTAAACACATAAGTATAAGCTAACGAGCATAAACCGTAGTAC
Found at i:100694 original size:28 final size:28
Alignment explanation
Indices: 100546--100694 Score: 217
Period size: 28 Copynumber: 5.3 Consensus size: 28
100536 GTGTACAAGT
* *
100546 TGGCGAGCGTAAACACATAAGTATAAGC
1 TGGCGAGCGTAAACGCGTAAGTATAAGC
100574 TGGCGAGCGTAAACGCGTAAGTATAAGC
1 TGGCGAGCGTAAACGCGTAAGTATAAGC
100602 TGGCGAGCGTAAACGCGTAAGTATAAGC
1 TGGCGAGCGTAAACGCGTAAGTATAAGC
* *
100630 TGGCAAGCGAAAACGCGTAAGTATAAGC
1 TGGCGAGCGTAAACGCGTAAGTATAAGC
* * * *
100658 TAGCAAGCGTAAACGCGTACGTATAAAC
1 TGGCGAGCGTAAACGCGTAAGTATAAGC
*
100686 TGGTGAGCG
1 TGGCGAGCG
100695 AAAATGCATA
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 110 1.00
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (28 bp):
TGGCGAGCGTAAACGCGTAAGTATAAGC
Found at i:106820 original size:21 final size:21
Alignment explanation
Indices: 106769--106820 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
106759 GGAGTTTTTA
106769 GTATCGGTAGAAGCATGACGT
1 GTATCGGTAGAAGCATGACGT
* *
106790 GTTTCGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACGT
*
106811 GTATCAGTAG
1 GTATCGGTAG
106821 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACGT
Found at i:112142 original size:49 final size:48
Alignment explanation
Indices: 112024--112144 Score: 118
Period size: 49 Copynumber: 2.5 Consensus size: 48
112014 ACCGTCTTAC
* *
112024 AAGCCTGCTAAGCCGAAGGTTGAGTCATTTCTCTACTTCACCGACTCTA
1 AAGCCTGCTAAG-CGAAGCTTGAGTCATTTCTCTACTTCACCGACTCAA
* * * * * *
112073 AAGCCTGCTAAGACGTAGCTTGGGTTATTTCATCT-TTTCATCGGCTCAA
1 AAGCCTGCTAAG-CGAAGCTTGAGTCATTTC-TCTACTTCACCGACTCAA
*
112122 AATCCTGCTAAGCTGAAGCTTGA
1 AAGCCTGCTAAGC-GAAGCTTGA
112145 TACGTTTCAC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
48 1 0.02
49 54 0.93
50 3 0.05
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (48 bp):
AAGCCTGCTAAGCGAAGCTTGAGTCATTTCTCTACTTCACCGACTCAA
Found at i:112170 original size:41 final size:41
Alignment explanation
Indices: 112115--112193 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
112105 TCTTTTCATC
* *
112115 GGCTCAAAATCCTGCTAAGCTGAAGCTTGATACGTTTCACA
1 GGCTCAAAAACCTGCTAAGCCGAAGCTTGATACGTTTCACA
112156 GGCTCAAAAACCTGCTAAGCCGAAGCTTGATACGTTTC
1 GGCTCAAAAACCTGCTAAGCCGAAGCTTGATACGTTTC
112194 GTATTACCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (41 bp):
GGCTCAAAAACCTGCTAAGCCGAAGCTTGATACGTTTCACA
Found at i:114064 original size:20 final size:20
Alignment explanation
Indices: 113997--114066 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
113987 TTTCCAAATC
* *
113997 ATACCAAAAATTTTGAGGGT
1 ATACAAAAAATTTTGAGGGA
*
114017 ATACTAAAAAA-TATGA-GGA
1 ATAC-AAAAAATTTTGAGGGA
114036 AGTGA-AAAAAATTTTGAGGGA
1 A-T-ACAAAAAATTTTGAGGGA
114057 ATACAAAAAA
1 ATACAAAAAA
114067 AAAGTACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
19 10 0.25
20 20 0.50
21 10 0.25
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.23
Consensus pattern (20 bp):
ATACAAAAAATTTTGAGGGA
Found at i:114152 original size:20 final size:20
Alignment explanation
Indices: 114074--114269 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
114064 AAAAAAGTAC
*
114074 AAAAACATGAGGAACCACCA
1 AAAAACATGAGGAACTACCA
** **
114094 AAAATTATGAGTGAA-TATAA
1 AAAAACATGAG-GAACTACCA
** ** *
114114 AAAAATTTGATAAAGTACCA
1 AAAAACATGAGGAACTACCA
114134 AAAAACATGAGGAACTACCA
1 AAAAACATGAGGAACTACCA
*
114154 AAAAACATGATGGGGAAATACCA
1 AAAAACATGA---GGAACTACCA
** * *
114177 AAAATGATAAGGGAA-TA-TA
1 AAAAACATGA-GGAACTACCA
* * *
114196 AAAAAAATGAGGCACCACCA
1 AAAAACATGAGGAACTACCA
*
114216 AAATAACATGAGGAAGTA--A
1 AAA-AACATGAGGAACTACCA
* * *
114235 AAAATATATAAGGAAGTACCA
1 AAAA-ACATGAGGAACTACCA
* *
114256 AAACATATGAGGAA
1 AAAAACATGAGGAA
114270 GTATAAAAAA
Statistics
Matches: 130, Mismatches: 35, Indels: 22
0.70 0.19 0.12
Matches are distributed among these distances:
18 4 0.03
19 26 0.20
20 62 0.48
21 22 0.17
23 16 0.12
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAAACATGAGGAACTACCA
Found at i:114284 original size:20 final size:20
Alignment explanation
Indices: 114223--114861 Score: 122
Period size: 20 Copynumber: 32.9 Consensus size: 20
114213 CCAAAATAAC
114223 ATGAGGAAGT--AAAAAATAT
1 ATGAGGAAGTACAAAAAAT-T
* *
114242 ATAAGGAAGTACCAAAACA-T
1 ATGAGGAAGTA-CAAAAAATT
*
114262 ATGAGGAAGTATAAAAAATT
1 ATGAGGAAGTACAAAAAATT
*
114282 ATG-GTAGAA-TATC-AAGAATT
1 ATGAG--GAAGTA-CAAAAAATT
* *
114302 ATGAGAAAGTGCCAAAAAA--
1 ATGAGGAAGT-ACAAAAAATT
* * * *
114321 ATGAAGAAATACCAAAACTT
1 ATGAGGAAGTACAAAAAATT
* *
114341 ATGA-AAATGTGTC-AAAAATT
1 ATGAGGAA-GT-ACAAAAAATT
* * *
114361 ATTAGGAAGTTCCAAAAA-T
1 ATGAGGAAGTACAAAAAATT
* *
114380 ACGAGGAATTACAAAAAATT
1 ATGAGGAAGTACAAAAAATT
* *
114400 ATGAGGGAGTACCAAAAATT
1 ATGAGGAAGTACAAAAAATT
* * * *
114420 ATAAGTACGTAC-CAAAATT
1 ATGAGGAAGTACAAAAAATT
* *
114439 -T-A-GATGTATAAAAAATT
1 ATGAGGAAGTACAAAAAATT
* *
114456 ATGA-GAA-TGCTAAAAAA-C
1 ATGAGGAAGTAC-AAAAAATT
* *
114474 ATGATGAAGTACAAAAAAAT
1 ATGAGGAAGTACAAAAAATT
* *
114494 ATGAGCAAATACAAAAAATT
1 ATGAGGAAGTACAAAAAATT
* *
114514 ATGAGGGA-TACCAAAAAA-A
1 ATGAGGAAGTA-CAAAAAATT
* * *
114533 ATAAGGATGTAC-CAAAATT
1 ATGAGGAAGTACAAAAAATT
*
114552 ATGAGAGAA-TACACAAAA-T
1 ATGAG-GAAGTACAAAAAATT
* *
114571 AT----AAGTATAAAAAATC
1 ATGAGGAAGTACAAAAAATT
* * *
114587 ATGAGAGAA-TATCATAAGA-C
1 ATGAG-GAAGTA-CAAAAAATT
*
114607 CTGAGGAAGTATC-AAAAA--
1 ATGAGGAAGTA-CAAAAAATT
* * *
114625 ATGAGGATGTAC-CAAAA-C
1 ATGAGGAAGTACAAAAAATT
114643 ATGAGGAAGTACAAAAAATTT
1 ATGAGGAAGTACAAAAAA-TT
* *
114664 ATGAGAGAAGAACAAAAAAAT
1 ATGAG-GAAGTACAAAAAATT
* ** **
114685 CTGACTAAGTACAACAAAAAA
1 ATGAGGAAGTACAA-AAAATT
*
114706 AT-A--ATGTA-ACAAAAATT
1 ATGAGGAAGTACA-AAAAATT
* * * * *
114723 A-CACTGAAATATTAAAAAAAT
1 ATGA-GGAAGTA-CAAAAAATT
*
114744 ATGAGGAAGTACTAAAAATT
1 ATGAGGAAGTACAAAAAATT
* ** *
114764 ATAAGAGAA-TATCTTAAAGTT
1 ATGAG-GAAGTA-CAAAAAATT
*
114785 -TGAGGAAGTGCAAAAAATT
1 ATGAGGAAGTACAAAAAATT
* *
114804 AT-AAGAATGTACCAAAACA-T
1 ATGAGGAA-GTA-CAAAAAATT
* *
114824 AAGAGGAAGTACCAAAAATT
1 ATGAGGAAGTACAAAAAATT
**
114844 ATGAGGAAAAACAAAAAA
1 ATGAGGAAGTACAAAAAA
114862 AAAAAAATCT
Statistics
Matches: 445, Mismatches: 114, Indels: 121
0.65 0.17 0.18
Matches are distributed among these distances:
14 2 0.00
15 7 0.02
16 6 0.01
17 19 0.04
18 41 0.09
19 112 0.25
20 175 0.39
21 64 0.14
22 19 0.04
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGAGGAAGTACAAAAAATT
Found at i:114402 original size:59 final size:57
Alignment explanation
Indices: 114234--114570 Score: 162
Period size: 59 Copynumber: 5.8 Consensus size: 57
114224 TGAGGAAGTA
* * *
114234 AAAAATATATAAGGAAGTACCAAAACATATGAGGAAGTATAAAAAATTATGGTAGAATATC
1 AAAAAT-TATAAGGAAGTACCAAAA-ATATGAGGAAATACAAAAAATTAT-G-AAAATATC
* * * * * * * * *
114295 AAGAATTATGAGAAAGTGCCAAAAAAATGAAGAAATACCAAAACTTATGAAAATGTGTC
1 AAAAATTATAAGGAAGTACCAAAAATATGAGGAAATACAAAAAATTATGAAAA--TATC
* * * * * * *
114354 AAAAATTATTAGGAAGTTCCAAAAATACGAGGAATTACAAAAAATTATGAGGGAGTACC
1 AAAAATTATAAGGAAGTACCAAAAATATGAGGAAATACAAAAAATTATGA--AAATATC
* * * ** * * *
114413 AAAAATTATAAGTACGTACC-AAAAT-TTA-GATGTATAAAAAATTATGAGAAT-GC
1 AAAAATTATAAGGAAGTACCAAAAATATGAGGAAATACAAAAAATTATGAAAATATC
** * * * * ** *
114466 TAAAAAACATGATGAAGTACAAAAAAATATGAGCAAATACAAAAAATTATGAGGGATACC
1 -AAAAATTATAAGGAAGTAC-CAAAAATATGAGGAAATACAAAAAATTATGA-AAATATC
** * * *
114526 AAAAAAAATAAGGATGTACCAAAATTATGA-GAGAATACACAAAAT
1 AAAAATTATAAGGAAGTACCAAAAATATGAGGA-AATACAAAAAAT
114571 ATAAGTATAA
Statistics
Matches: 205, Mismatches: 59, Indels: 27
0.70 0.20 0.09
Matches are distributed among these distances:
53 1 0.00
54 16 0.08
56 21 0.10
57 7 0.03
58 41 0.20
59 97 0.47
60 16 0.08
61 6 0.03
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.22
Consensus pattern (57 bp):
AAAAATTATAAGGAAGTACCAAAAATATGAGGAAATACAAAAAATTATGAAAATATC
Found at i:114555 original size:58 final size:57
Alignment explanation
Indices: 114364--114570 Score: 159
Period size: 58 Copynumber: 3.6 Consensus size: 57
114354 AAAAATTATT
* * * * **
114364 AGGAAGTTCCAAAAATACGAGGAATTACAAAAAATTATGAGGGAGTACCAAAAATTATA
1 AGGAAGTACCAAAATTATGA-GAAATACAAAAAATTATGAGGGA-TACCAAAAAAAATA
* * ** * * * * * *
114423 AGTACGTACCAAAATT-T-AGATGTATAAAAAATTATGA-GAATGCTAAAAAACATG
1 AGGAAGTACCAAAATTATGAGAAATACAAAAAATTATGAGGGATACCAAAAAAAATA
* * *
114477 ATGAAGTACAAAAAAATATGAGCAAATACAAAAAATTATGAGGGATACCAAAAAAAATA
1 AGGAAGTAC-CAAAATTATGAG-AAATACAAAAAATTATGAGGGATACCAAAAAAAATA
* *
114536 AGGATGTACCAAAATTATGAGAGAATACACAAAAT
1 AGGAAGTACCAAAATTATGAGA-AATACAAAAAAT
114571 ATAAGTATAA
Statistics
Matches: 110, Mismatches: 32, Indels: 13
0.71 0.21 0.08
Matches are distributed among these distances:
54 15 0.14
55 7 0.06
56 17 0.15
57 4 0.04
58 36 0.33
59 31 0.28
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.21
Consensus pattern (57 bp):
AGGAAGTACCAAAATTATGAGAAATACAAAAAATTATGAGGGATACCAAAAAAAATA
Found at i:114657 original size:17 final size:18
Alignment explanation
Indices: 114608--114661 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
114598 TCATAAGACC
*
114608 TGAGGAAGTATCAAAAAA
1 TGAGGAAGTACCAAAAAA
* *
114626 TGAGGATGTACCAAAACA
1 TGAGGAAGTACCAAAAAA
114644 TGAGGAAGTA-CAAAAAA
1 TGAGGAAGTACCAAAAAA
114661 T
1 T
114662 TTATGAGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.52, C:0.09, G:0.22, T:0.17
Consensus pattern (18 bp):
TGAGGAAGTACCAAAAAA
Found at i:116002 original size:18 final size:18
Alignment explanation
Indices: 115979--116019 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
115969 AAATCATTGA
115979 AGAAGAAG-AAGAAGAAAG
1 AGAAGAAGAAAG-AGAAAG
*
115997 AGAAGAAGAAAGGGAAAG
1 AGAAGAAGAAAGAGAAAG
116015 AGAAG
1 AGAAG
116020 GAGGAGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAGAGAAAG
Found at i:121170 original size:3 final size:3
Alignment explanation
Indices: 121162--121196 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
121152 CCAAAATCAA
*
121162 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
121197 ATAGTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:122284 original size:7 final size:7
Alignment explanation
Indices: 122261--122345 Score: 86
Period size: 7 Copynumber: 12.6 Consensus size: 7
122251 TTTGAAAAAA
122261 ATCAACG
1 ATCAACG
* *
122268 GTCAA-A
1 ATCAACG
*
122274 ATCAACT
1 ATCAACG
122281 ATCAACG
1 ATCAACG
122288 ATCAACG
1 ATCAACG
**
122295 AT-AAAA
1 ATCAACG
122301 ATCAACG
1 ATCAACG
122308 ATCAACG
1 ATCAACG
122315 ATCAACG
1 ATCAACG
**
122322 AT-AAAA
1 ATCAACG
122328 ATCAACG
1 ATCAACG
122335 ATCAACG
1 ATCAACG
122342 ATCA
1 ATCA
122346 GTCATAATTT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
6 12 0.19
7 50 0.81
ACGTcount: A:0.49, C:0.24, G:0.11, T:0.16
Consensus pattern (7 bp):
ATCAACG
Found at i:122352 original size:27 final size:27
Alignment explanation
Indices: 122261--122345 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
122251 TTTGAAAAAA
* * *
122261 ATCAACGGTCAAAATCAACTATCAACG
1 ATCAACGATAAAAATCAACGATCAACG
122288 ATCAACGATAAAAATCAACGATCAACG
1 ATCAACGATAAAAATCAACGATCAACG
122315 ATCAACGATAAAAATCAACGATCAACG
1 ATCAACGATAAAAATCAACGATCAACG
122342 ATCA
1 ATCA
122346 GTCATAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.49, C:0.24, G:0.11, T:0.16
Consensus pattern (27 bp):
ATCAACGATAAAAATCAACGATCAACG
Found at i:124067 original size:31 final size:30
Alignment explanation
Indices: 124032--124089 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
124022 TAATAACTAC
124032 TAAA-TTCATTAAGTTAAATTATATTATTTTT
1 TAAATTTCA-TAAGTTAAA-TATATTATTTTT
* *
124063 TAAATTTGATATGTTAAATATATTATT
1 TAAATTTCATAAGTTAAATATATTATT
124090 ATATGTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.38
31 12 0.50
32 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
TAAATTTCATAAGTTAAATATATTATTTTT
Found at i:127851 original size:24 final size:24
Alignment explanation
Indices: 127783--127857 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
127773 AGAAATAATC
* * * *
127783 TTTCAGTTAGACTCTGTTTAATTA
1 TTTCAATTAAACTCTGTTTATTTG
*
127807 TTTCAATTGAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
127831 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
127855 TTT
1 TTT
127858 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:127866 original size:24 final size:24
Alignment explanation
Indices: 127793--127869 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
127783 TTTCAGTTAG
* * **
127793 ACTCTGTTTAATTATTTCAATTGA
1 ACTCTGTTTATTTGTTTCAATCAA
*
127817 ACTCTGTTTATTTGTTTCAATTAA
1 ACTCTGTTTATTTGTTTCAATCAA
* *
127841 ACTCTGTTTATTTGTTTGAGTCAA
1 ACTCTGTTTATTTGTTTCAATCAA
127865 ACTCT
1 ACTCT
127870 TATTAGTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
ACTCTGTTTATTTGTTTCAATCAA
Found at i:128983 original size:13 final size:13
Alignment explanation
Indices: 128965--128990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128955 ATAGAGCTAG
128965 AAATAAATTTTCT
1 AAATAAATTTTCT
128978 AAATAAATTTTCT
1 AAATAAATTTTCT
128991 TACTTTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAAATTTTCT
Found at i:132082 original size:21 final size:21
Alignment explanation
Indices: 132058--132098 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
132048 TGAATTGAGA
* *
132058 GGAGGAGGCTTTGAAATAGTG
1 GGAGAAGGCTCTGAAATAGTG
132079 GGAGAAGGCTCTGAAATAGT
1 GGAGAAGGCTCTGAAATAGT
132099 AAGAAGAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.39, T:0.22
Consensus pattern (21 bp):
GGAGAAGGCTCTGAAATAGTG
Found at i:133135 original size:26 final size:26
Alignment explanation
Indices: 133106--133158 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
133096 ACCGTCACTA
*
133106 AATCTAACCTTTAGTTCCCTTAGGAG
1 AATCTAACCTTCAGTTCCCTTAGGAG
133132 AATCTAACCTTCAGTTCCCTTAGGAG
1 AATCTAACCTTCAGTTCCCTTAGGAG
133158 A
1 A
133159 TTAAACATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (26 bp):
AATCTAACCTTCAGTTCCCTTAGGAG
Found at i:134578 original size:148 final size:149
Alignment explanation
Indices: 134334--134637 Score: 531
Period size: 148 Copynumber: 2.0 Consensus size: 149
134324 CTAAGAATTT
*
134334 GCATGAATTTGAGTTAAAAAAGGTATGAAAAATCTATATATTTTCATTGTTCCACATCCCAAACT
1 GCATAAATTTGAGTTAAAAAAGGTATGAAAAATCTATATATTTTCATTGTTCCACATCCCAAACT
* *
134399 TAATTAATTGCTCGTCTCGAGTAATGCACAAATCACGAAAGAGTTTATCATTTCTCCTCGTACTT
66 TAATTAATTGCTCGTCTCGAGTAATGCACAAATCACAAAAGAGTTTATCATTTCTCCTCATACTT
*
134464 ATGAATTTAAAATAATTAA
131 AGGAATTTAAAATAATTAA
134483 GCATAAATTTGAGTTAAAAAAGGTATGAAAAATCTATATATTTTCATT-TTCCACATCCCAAACT
1 GCATAAATTTGAGTTAAAAAAGGTATGAAAAATCTATATATTTTCATTGTTCCACATCCCAAACT
*
134547 TAATTCATTGCTCGTCTTC-AGTAATGCACAAATCACAAAAGAGTTTATCATTTCTCCTCATACT
66 TAATTAATTGCTCGTC-TCGAGTAATGCACAAATCACAAAAGAGTTTATCATTTCTCCTCATACT
*
134611 TAGGAATTTAAAATAATTTA
130 TAGGAATTTAAAATAATTAA
134631 GCATAAA
1 GCATAAA
134638 AACAAGAATT
Statistics
Matches: 148, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
148 99 0.67
149 49 0.33
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (149 bp):
GCATAAATTTGAGTTAAAAAAGGTATGAAAAATCTATATATTTTCATTGTTCCACATCCCAAACT
TAATTAATTGCTCGTCTCGAGTAATGCACAAATCACAAAAGAGTTTATCATTTCTCCTCATACTT
AGGAATTTAAAATAATTAA
Found at i:136394 original size:3 final size:3
Alignment explanation
Indices: 136388--136416 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
136378 TTCTTTAGTA
136388 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
136417 AACTTGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:137329 original size:26 final size:25
Alignment explanation
Indices: 137300--137349 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
137290 GTATAAAGTC
*
137300 TTAACAATTTAAAATAAATTAAAAAG
1 TTAACAAATT-AAATAAATTAAAAAG
*
137326 TTAATAAATTAAATAAATTAAAAA
1 TTAACAAATTAAATAAATTAAAAA
137350 ATTAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
TTAACAAATTAAATAAATTAAAAAG
Found at i:137342 original size:9 final size:9
Alignment explanation
Indices: 137311--137353 Score: 56
Period size: 8 Copynumber: 5.1 Consensus size: 9
137301 TAACAATTTA
137311 AAATAAATT
1 AAATAAATT
*
137320 AAA-AAGTT
1 AAATAAATT
137328 -AATAAATT
1 AAATAAATT
137336 AAATAAATT
1 AAATAAATT
137345 AAA-AAATT
1 AAATAAATT
137353 A
1 A
137354 GAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 2 0.07
8 14 0.47
9 14 0.47
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAATAAATT
Found at i:137358 original size:9 final size:8
Alignment explanation
Indices: 137315--137359 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
137305 AATTTAAAAT
137315 AAATTAAA
1 AAATTAAA
* *
137323 AAGTTAAT
1 AAATTAAA
137331 AAATTAAA
1 AAATTAAA
137339 TAAATTAAA
1 -AAATTAAA
*
137348 AAATTAGA
1 AAATTAAA
137356 AAAT
1 AAAT
137360 AAATTTCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 23 0.74
9 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (8 bp):
AAATTAAA
Found at i:137359 original size:25 final size:24
Alignment explanation
Indices: 137311--137363 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
137301 TAACAATTTA
*
137311 AAATAAATTAAAAAGTTAATAAATT
1 AAATAAATTAAAAAATTAATAAA-T
137336 AAATAAATTAAAAAATTAGA-AAAT
1 AAATAAATTAAAAAATTA-ATAAAT
137360 AAAT
1 AAAT
137364 TTCTTACCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 20 0.77
26 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
AAATAAATTAAAAAATTAATAAAT
Found at i:138011 original size:4 final size:4
Alignment explanation
Indices: 138002--138047 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
137992 ATCAATTTTA
138002 AAAT AAAT AAAAT AAAT AACAT -AA- AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AA
138048 CTTTTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.08
4 29 0.76
5 6 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:138014 original size:9 final size:9
Alignment explanation
Indices: 138000--138047 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
137990 TTATCAATTT
138000 TAAAATAAA
1 TAAAATAAA
138009 TAAAATAAA
1 TAAAATAAA
*
138018 TAACATAAA
1 TAAAATAAA
*
138027 AATAAATAAA
1 TA-AAATAAA
138037 T-AAATAAA
1 TAAAATAAA
138045 TAA
1 TAA
138048 CTTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 8 0.24
9 19 0.58
10 6 0.18
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAAATAAA
Found at i:138035 original size:19 final size:19
Alignment explanation
Indices: 138006--138044 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
137996 ATTTTAAAAT
138006 AAATAAAATAAATAACATAA
1 AAATAAAATAAATAA-ATAA
138026 AAAT-AAATAAATAAATAA
1 AAATAAAATAAATAAATAA
138044 A
1 A
138045 TAACTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 10 0.53
20 4 0.21
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (19 bp):
AAATAAAATAAATAAATAA
Found at i:138101 original size:31 final size:29
Alignment explanation
Indices: 138066--138134 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 29
138056 TTTTTAGCTG
*
138066 TTTTAAAATATTTACAGAAAA-AGACAACTAA
1 TTTTAAAA-ATTTACA-AAAAGA-ACAACAAA
138097 TTTT-AAAATTTACAAAAAGAACAACAAA
1 TTTTAAAAATTTACAAAAAGAACAACAAA
138125 TTTTACAAAA
1 TTTTA-AAAA
138135 AATTCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 15 0.44
29 8 0.24
30 7 0.21
31 4 0.12
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (29 bp):
TTTTAAAAATTTACAAAAAGAACAACAAA
Found at i:138789 original size:43 final size:43
Alignment explanation
Indices: 138723--138808 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
138713 GTCATAAGAG
*
138723 AATGTTCAGAATTATTCTAACTCATTGAGCTGAAGCATTCGTT
1 AATGCTCAGAATTATTCTAACTCATTGAGCTGAAGCATTCGTT
138766 AATGCTCAGAATTATTCTAACTCATTGAGCTGAAGCATTCGTT
1 AATGCTCAGAATTATTCTAACTCATTGAGCTGAAGCATTCGTT
138809 TCTCTTTAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (43 bp):
AATGCTCAGAATTATTCTAACTCATTGAGCTGAAGCATTCGTT
Found at i:139758 original size:36 final size:36
Alignment explanation
Indices: 139718--139825 Score: 198
Period size: 36 Copynumber: 3.0 Consensus size: 36
139708 AGCTAAGTAG
139718 TTAGTAAAATTAGCAAACTAAGGGGTGTTATGACTT
1 TTAGTAAAATTAGCAAACTAAGGGGTGTTATGACTT
139754 TTAGTAAAATTAGCAAACTAAGGGGTGTTATGACTT
1 TTAGTAAAATTAGCAAACTAAGGGGTGTTATGACTT
* *
139790 TTAGTAAAATTAGCAAACCAAAGGGTGTTATGACTT
1 TTAGTAAAATTAGCAAACTAAGGGGTGTTATGACTT
139826 ACATTGAGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (36 bp):
TTAGTAAAATTAGCAAACTAAGGGGTGTTATGACTT
Found at i:148132 original size:13 final size:14
Alignment explanation
Indices: 148116--148147 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
148106 ATATTTTTTG
148116 TTTTTTA-ATTTAA
1 TTTTTTACATTTAA
148129 -TTTTTACATTTAA
1 TTTTTTACATTTAA
148142 TTTTTT
1 TTTTTT
148148 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTACATTTAA
Found at i:148134 original size:12 final size:13
Alignment explanation
Indices: 148117--148146 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
148107 TATTTTTTGT
148117 TTTTTA-ATTTAA
1 TTTTTACATTTAA
148129 TTTTTACATTTAA
1 TTTTTACATTTAA
148142 TTTTT
1 TTTTT
148147 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:150253 original size:17 final size:18
Alignment explanation
Indices: 150228--150270 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
150218 TTTTCTTAGT
150228 TTTTAATTTTTA-GTTTTA
1 TTTT-ATTTTTATGTTTTA
*
150246 TTTTA-TTTTATTTTTTA
1 TTTTATTTTTATGTTTTA
150263 TTTTATTT
1 TTTTATTT
150271 GATTATGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 6 0.27
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTATGTTTTA
Found at i:150261 original size:12 final size:12
Alignment explanation
Indices: 150196--150270 Score: 57
Period size: 12 Copynumber: 6.0 Consensus size: 12
150186 AATTAGTACA
150196 TTTATTTTCA-TT
1 TTTATTTT-ATTT
*
150208 TTCATTTTCATTT
1 TTTATTTT-ATTT
*
150221 TCTTAGTTTTTAATT
1 T-TTA--TTTTATTT
150236 TTTAGTTTTA--T
1 TTTA-TTTTATTT
150247 TTTATTTTATTT
1 TTTATTTTATTT
150259 TTTATTTTATTT
1 TTTATTTTATTT
150271 GATTATGCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
10 5 0.09
11 5 0.09
12 22 0.42
13 8 0.15
14 5 0.09
15 4 0.08
16 4 0.08
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:150623 original size:57 final size:57
Alignment explanation
Indices: 150550--150659 Score: 193
Period size: 57 Copynumber: 1.9 Consensus size: 57
150540 TATAATTGTG
*
150550 ATAAAATCCCTAAATTATTTATTGTGTTTAAGTAATTTTCTCATATCCCATTAGAGT
1 ATAAAATCCCTAAATTATTTATTGTGTTTAAGTAATTTTCTCATACCCCATTAGAGT
* *
150607 ATAAAATCTCTGAATTATTTATTGTGTTTAAGTAATTTTCTCATACCCCATTA
1 ATAAAATCCCTAAATTATTTATTGTGTTTAAGTAATTTTCTCATACCCCATTA
150660 AAGTGAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.45
Consensus pattern (57 bp):
ATAAAATCCCTAAATTATTTATTGTGTTTAAGTAATTTTCTCATACCCCATTAGAGT
Found at i:151271 original size:9 final size:8
Alignment explanation
Indices: 151259--151297 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
151249 GAAAAAGAAA
151259 AAAAAATTG
1 AAAAAA-TG
151268 AAAAAATG
1 AAAAAATG
151276 AAAAAATG
1 AAAAAATG
151284 -AAAAATGG
1 AAAAAAT-G
151292 AAAAAA
1 AAAAAA
151298 GAAGAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 11 0.39
9 11 0.39
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:152325 original size:23 final size:25
Alignment explanation
Indices: 152299--152344 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
152289 CCAATTAGGG
152299 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
152322 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
152345 TGGATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:164486 original size:15 final size:16
Alignment explanation
Indices: 164466--164501 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
164456 TTCTCTCCCT
164466 TCTTCCCTCACCT-TG
1 TCTTCCCTCACCTCTG
*
164481 TCTTCCCTCCCCTCTG
1 TCTTCCCTCACCTCTG
164497 TCTTC
1 TCTTC
164502 TCAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.03, C:0.50, G:0.06, T:0.42
Consensus pattern (16 bp):
TCTTCCCTCACCTCTG
Found at i:164525 original size:9 final size:9
Alignment explanation
Indices: 164504--164558 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
164494 CTGTCTTCTC
*
164504 AAAAAGAAG
1 AAAAAAAAG
164513 AAAAAAGAA-
1 AAAAAA-AAG
164522 AAAAAATAAG
1 AAAAAA-AAG
164532 AAAAGAAAAG
1 AAAA-AAAAG
*
164542 AAATAAAAG
1 AAAAAAAAG
164551 AAAAAAAA
1 AAAAAAAA
164559 AGTAAATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 25 0.64
10 12 0.31
11 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:164532 original size:19 final size:19
Alignment explanation
Indices: 164504--164559 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
164494 CTGTCTTCTC
*
164504 AAAAAGAAGAAAAAAGAAA
1 AAAAATAAGAAAAAAGAAA
164523 AAAAATAAG--AAAAGAAA
1 AAAAATAAGAAAAAAGAAA
*
164540 AGAAATAA-AAGAAAA-AAA
1 AAAAATAAGAA-AAAAGAAA
164558 AA
1 AA
164560 GTAAATGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 15 0.48
18 4 0.13
19 12 0.39
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (19 bp):
AAAAATAAGAAAAAAGAAA
Found at i:164534 original size:12 final size:12
Alignment explanation
Indices: 164510--164556 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
164500 TCTCAAAAAG
164510 AAGAAAAAAGAA
1 AAGAAAAAAGAA
164522 AA-AAAATAAGAA
1 AAGAAAA-AAGAA
*
164534 AAGAAAAGAAATAA
1 AAG-AAA-AAAGAA
164548 AAGAAAAAA
1 AAGAAAAAA
164557 AAAGTAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 4 0.13
12 12 0.40
13 3 0.10
14 10 0.33
15 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:164540 original size:22 final size:22
Alignment explanation
Indices: 164507--164549 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
164497 TCTTCTCAAA
164507 AAGAAGAAAAAAGAAAAAAAAT
1 AAGAAGAAAAAAGAAAAAAAAT
*
164529 AAGAA-AAGAAAAGAAATAAAA
1 AAGAAGAA-AAAAGAAAAAAAA
164550 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (22 bp):
AAGAAGAAAAAAGAAAAAAAAT
Found at i:164559 original size:10 final size:10
Alignment explanation
Indices: 164504--164560 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
164494 CTGTCTTCTC
*
164504 AAAAAGAAGA
1 AAAAAGAAAA
164514 AAAAAGAAAAA
1 AAAAAG-AAAA
164525 AAATAAGAAAA
1 AAA-AAGAAAA
*
164536 GAAAAG-AAA
1 AAAAAGAAAA
*
164545 TAAAAGAAAA
1 AAAAAGAAAA
164555 AAAAAG
1 AAAAAG
164561 TAAATGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.20
10 17 0.43
11 12 0.30
12 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:165319 original size:18 final size:19
Alignment explanation
Indices: 165275--165319 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
165265 CTGAACATCC
* *
165275 TAACTAACAATGAACTACT
1 TAACAAACAATAAACTACT
165294 TAACAAACAATAAACTACT
1 TAACAAACAATAAACTACT
165313 T-ACAAAC
1 TAACAAAC
165320 TAATTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.22
Consensus pattern (19 bp):
TAACAAACAATAAACTACT
Found at i:168870 original size:19 final size:19
Alignment explanation
Indices: 168846--168902 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
168836 GTACGATAAT
168846 TTTTATAATTTTTTATGAA
1 TTTTATAATTTTTTATGAA
** *
168865 TTTTAT-ATTTATTTACCAG
1 TTTTATAATTT-TTTATGAA
168884 TTTTATAATTTTCTTATGA
1 TTTTATAATTTT-TTATGA
168903 CCTTATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 4 0.13
19 18 0.60
20 8 0.27
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTTATGAA
Found at i:168989 original size:23 final size:24
Alignment explanation
Indices: 168950--169000 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
168940 TATTTTATAA
* *
168950 TTTTTTACAATTATTTATACTTTT
1 TTTTTTACAATTATTTATAATTCT
168974 TTTTTTACAATT-TTTATAATTCT
1 TTTTTTACAATTATTTATAATTCT
168997 TTTT
1 TTTT
169001 CTAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTTACAATTATTTATAATTCT
Found at i:168999 original size:21 final size:20
Alignment explanation
Indices: 168942--169010 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 20
168932 TTTCTATATA
168942 TTTTATAA-TTTTTTACAAT
1 TTTTATAATTTTTTTACAAT
*
168961 TATTTATACTTTTTTTTTTACAAT
1 T-TTTATA---ATTTTTTTACAAT
168985 TTTTATAATTCTTTTT-CTAAT
1 TTTTATAATT-TTTTTAC-AAT
169006 TTTTA
1 TTTTA
169011 ATAAAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
19 1 0.02
20 9 0.22
21 13 0.32
23 6 0.15
24 12 0.29
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAT
Found at i:169028 original size:29 final size:29
Alignment explanation
Indices: 168996--169056 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
168986 TTTATAATTC
168996 TTTTTCTA-ATTTTTAATAAAATTTAA-A
1 TTTTTCTATATTTTTAATAAAATTTAATA
*
169023 TATTTTCTATATTTTTATTAAAATTTAATA
1 T-TTTTCTATATTTTTAATAAAATTTAATA
169053 TTTT
1 TTTT
169057 ATAACTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 1 0.03
28 7 0.23
29 20 0.67
30 2 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTTCTATATTTTTAATAAAATTTAATA
Found at i:169037 original size:28 final size:27
Alignment explanation
Indices: 168997--169066 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
168987 TTATAATTCT
168997 TTTTCTAATTTTTAATAAAATTTAAATA
1 TTTTCTAATTTTTAATAAAATTT-AATA
*
169025 TTTTCTATATTTTTATTAAAATTTAATA
1 TTTTCTA-ATTTTTAATAAAATTTAATA
* *
169053 TTTTATAACTTTTA
1 TTTTCTAATTTTTA
169067 TTGATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.16
28 17 0.45
29 15 0.39
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCTAATTTTTAATAAAATTTAATA
Found at i:169340 original size:95 final size:95
Alignment explanation
Indices: 169199--169388 Score: 247
Period size: 95 Copynumber: 2.0 Consensus size: 95
169189 TTAATGACTA
* * * *
169199 TTTTTGAAAAAGTTTAAGGGTTTTCTTGATGCATTTTTAAAATTCAAGTATTCAATTGAGTGCAA
1 TTTTTGAAAAAGTTTAAGGGTTTTCTTGATACATTTTGAAAATTCAAGTATCCAAGTGAGTGCAA
* *
169264 ATTAAAAGCAGGGGCTCAATTGCTTTTTTT
66 AATAAAAGCAGGAGCTCAATTGCTTTTTTT
* * * *
169294 TTTTTGAAAAAGTTTGAGGGTCTTT-TTTATATATTTTGAAAGTTCAAGTATCCAAGTGAGTGCA
1 TTTTTGAAAAAGTTTAAGGGT-TTTCTTGATACATTTTGAAAATTCAAGTATCCAAGTGAGTGCA
* * *
169358 AAATAAAAGTATGAGCTTAATTGCTTTTTTT
65 AAATAAAAGCAGGAGCTCAATTGCTTTTTTT
169389 AAAAAAATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 78 0.96
96 3 0.04
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (95 bp):
TTTTTGAAAAAGTTTAAGGGTTTTCTTGATACATTTTGAAAATTCAAGTATCCAAGTGAGTGCAA
AATAAAAGCAGGAGCTCAATTGCTTTTTTT
Found at i:180233 original size:17 final size:18
Alignment explanation
Indices: 180211--180250 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
180201 CAAGTTTTAA
180211 TGCATTTT-TATTATCAC
1 TGCATTTTATATTATCAC
*
180228 TGCATTTTATGTTATCAC
1 TGCATTTTATATTATCAC
180246 TGCAT
1 TGCAT
180251 CATTTTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (18 bp):
TGCATTTTATATTATCAC
Found at i:184930 original size:10 final size:11
Alignment explanation
Indices: 184915--184955 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
184905 GTTGCCTTTG
184915 CACCACCATT-
1 CACCACCATTC
184925 CACCACCATGTC
1 CACCACCAT-TC
*
184937 CACCACC-TTG
1 CACCACCATTC
184947 CACCACCAT
1 CACCACCAT
184956 CAATAATACC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 17 0.63
11 3 0.11
12 7 0.26
ACGTcount: A:0.27, C:0.51, G:0.05, T:0.17
Consensus pattern (11 bp):
CACCACCATTC
Found at i:190451 original size:31 final size:32
Alignment explanation
Indices: 190389--190457 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
190379 TGTGACAAGT
190389 CGTGTGAACATGCAAAATTACCCTCACATGCC
1 CGTGTGAACATGCAAAATTACCCTCACATGCC
*
190421 CGTGTGAACATGCGAAATTACCC-CACATGCC
1 CGTGTGAACATGCAAAATTACCCTCACATGCC
190452 CGTGTG
1 CGTGTG
190458 TCAAACCCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 14 0.39
32 22 0.61
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (32 bp):
CGTGTGAACATGCAAAATTACCCTCACATGCC
Found at i:199002 original size:29 final size:29
Alignment explanation
Indices: 198969--199031 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
198959 TTGAAGAAGA
* *
198969 AGGAACAAATACTATGTCTTCATCGAATG
1 AGGAACAAATACTATGTCTGCACCGAATG
198998 AGGAACAAATACTATGTCTGCACCGAATG
1 AGGAACAAATACTATGTCTGCACCGAATG
199027 AGGAA
1 AGGAA
199032 TAAGTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (29 bp):
AGGAACAAATACTATGTCTGCACCGAATG
Found at i:201159 original size:37 final size:38
Alignment explanation
Indices: 201083--201163 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
201073 AAGACTGTTA
*
201083 CTGCATAAATATTCTTCAAATTGCATCCAGAACTATCG
1 CTGCATAAATATTCTTCAAATTGCACCCAGAACTATCG
*
201121 CTGCA-AAAGTATTCTTC-AATTGCACCCAGGAA-TGTCG
1 CTGCATAAA-TATTCTTCAAATTGCACCCA-GAACTATCG
201158 CTGCAT
1 CTGCAT
201164 GAACATGTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 22 0.58
38 16 0.42
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (38 bp):
CTGCATAAATATTCTTCAAATTGCACCCAGAACTATCG
Found at i:201986 original size:16 final size:16
Alignment explanation
Indices: 201965--201995 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
201955 TTGTGGATCT
201965 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
201981 CATTTTATCTTTATT
1 CATTTTACCTTTATT
201996 TTCACAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:203204 original size:18 final size:18
Alignment explanation
Indices: 203191--203225 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
203181 AGCATACAGG
203191 CTCGTTTGAGCATACTAA
1 CTCGTTTGAGCATACTAA
*
203209 CTCGTTTGACCATACTA
1 CTCGTTTGAGCATACTA
203226 GCTCATCAGA
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:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (18 bp):
CTCGTTTGAGCATACTAA
Found at i:203961 original size:21 final size:21
Alignment explanation
Indices: 203919--203969 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
203909 ATGAATTGTT
* * *
203919 TCGGTAGAAATATCGCTTGTA
1 TCGGTAGAAACATCCCTAGTA
*
203940 TCGGTAGAACCATCCCTAGTA
1 TCGGTAGAAACATCCCTAGTA
*
203961 TCGTTAGAA
1 TCGGTAGAA
203970 GTCTACTGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TCGGTAGAAACATCCCTAGTA
Found at i:207324 original size:201 final size:200
Alignment explanation
Indices: 206979--207379 Score: 633
Period size: 201 Copynumber: 2.0 Consensus size: 200
206969 GTTATTACTA
* * *
206979 TCGATTTGTTAAGGATTTTTCTATCATAACCTAGTCGATAATGAAGTTACTTCAGAAGAATGCTC
1 TCGATTTGTTAAGGATTTTTCTATCATAACCTAGCCGATAATGAAGTTACTCCAGAAGAATACTC
* * *
207044 AATTTGTCTGGATTGAGAAATGTCAGCAGAGTTTTGACTAGTTAAAGAAAATGTTAACAGAGGCC
66 AATTTGTCTGGACTGAGAAATGTCAGCAGAGTTTTGACCAGTTAAAGAAAATATTAACAGAGGCC
*
207109 TCAGTTTCGACACAACCAAAGACAGGAACAGAGTTTATCGTTTACAAGTGACGTGCCATTGAACG
131 TCAGTTTCGACACAACCAAAGACAGGAACAGAGTTTATCGTTTAC-AGTGACGCGCCATTGAACG
207174 GGTTGG
195 GGTTGG
*
207180 TCGATTTGTTAAGGATTTTTCTATCATAACCTTA-CCGATAATGATGTTACTCCAGAAGAATACT
1 TCGATTTGTTAAGGATTTTTCTATCATAACC-TAGCCGATAATGAAGTTACTCCAGAAGAATACT
* * **
207244 CAATTTGTCTGGACTGAGAAATGTCAGTAGAGTTTTGACCATTTAATTAAAATATTAACAGAGGC
65 CAATTTGTCTGGACTGAGAAATGTCAGCAGAGTTTTGACCAGTTAAAGAAAATATTAACAGAGGC
* * * *
207309 CTCAGTTTTGACACAACCAGAGACAGGAACAGAGTTTGTCGTTTACTGTGACGCGCCATTGAACG
130 CTCAGTTTCGACACAACCAAAGACAGGAACAGAGTTTATCGTTTACAGTGACGCGCCATTGAACG
207374 GGTTGG
195 GGTTGG
207380 GATGTGTACT
Statistics
Matches: 183, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
200 23 0.13
201 158 0.86
202 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (200 bp):
TCGATTTGTTAAGGATTTTTCTATCATAACCTAGCCGATAATGAAGTTACTCCAGAAGAATACTC
AATTTGTCTGGACTGAGAAATGTCAGCAGAGTTTTGACCAGTTAAAGAAAATATTAACAGAGGCC
TCAGTTTCGACACAACCAAAGACAGGAACAGAGTTTATCGTTTACAGTGACGCGCCATTGAACGG
GTTGG
Done.