Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1198
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: 165477
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:11226 original size:19 final size:21
Alignment explanation
Indices: 11202--11247 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
11192 ATTTTTATGA
11202 GATAAAAAAT-A-ATTATAAC
1 GATAAAAAATGATATTATAAC
11221 GATAAAAAATGATATTATAA-
1 GATAAAAAATGATATTATAAC
11241 G-TAAAAA
1 GATAAAAA
11248 TACATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
GATAAAAAATGATATTATAAC
Found at i:11237 original size:21 final size:18
Alignment explanation
Indices: 11196--11247 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
11186 TATTGAATTT
*
11196 TTATGAGATAAAAAATAA
1 TTATAAGATAAAAAATAA
11214 TTATAACGATAAAAAATGATA
1 TTATAA-GATAAAAAAT-A-A
11235 TTATAAG-TAAAAA
1 TTATAAGATAAAAA
11248 TACATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 2 0.07
21 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (18 bp):
TTATAAGATAAAAAATAA
Found at i:15922 original size:19 final size:19
Alignment explanation
Indices: 15898--15940 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
15888 TTTGGGTTAA
15898 AAGTGTTTTTACACTGCAG
1 AAGTGTTTTTACACTGCAG
*
15917 AAGTGTTTTTCCACTGCAG
1 AAGTGTTTTTACACTGCAG
15936 AAGTG
1 AAGTG
15941 ATGAACAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (19 bp):
AAGTGTTTTTACACTGCAG
Found at i:16284 original size:20 final size:20
Alignment explanation
Indices: 16259--16301 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16249 TTTGAAAAAA
16259 ATATTATCAATTCCACTGAT
1 ATATTATCAATTCCACTGAT
16279 ATATTATCAATTCCACTGAT
1 ATATTATCAATTCCACTGAT
16299 ATA
1 ATA
16302 AAGCTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATTATCAATTCCACTGAT
Found at i:20559 original size:124 final size:123
Alignment explanation
Indices: 20338--20592 Score: 377
Period size: 124 Copynumber: 2.1 Consensus size: 123
20328 AAATAGTGGG
* * * * *
20338 AAATCGCTTATACTAGGATGCTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
20403 TCGCTACAGTGGTCATGTGAGAAATAATTTTTTTAGACGTTTTCTGAGGAAATAGTATA
66 TCGCTACAGTGGTCATGTGAGAAATAATTTTTTTAGACG-TTTCTGAGGAAATAGTATA
* *
20462 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
* * * *
20527 TCGCTACAGTTGGTCATGT-AGGAAATAATTTTTTTTGACGTTTCTGAGTAAATAGTGTC
66 TCGCTACAG-TGGTCATGTGA-GAAATAATTTTTTTAGACGTTTCTGAGGAAATAGTATA
20586 AAATCGC
1 AAATCGC
20593 GCCCTCGTGG
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
124 91 0.77
125 27 0.23
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (123 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTGGTCATGTGAGAAATAATTTTTTTAGACGTTTCTGAGGAAATAGTATA
Found at i:31580 original size:34 final size:35
Alignment explanation
Indices: 31542--31659 Score: 123
Period size: 35 Copynumber: 3.4 Consensus size: 35
31532 AACGTGCAAG
* *
31542 AATAAAAGC-AATCTGAAGACTTAAAATTTCCATT
1 AATAAAACCAAATCTGAAGACCTAAAATTTCCATT
* ** *
31576 AATAAAACCAAAATC-AAAGAAGTAAAATTTCCATG
1 AATAAAACC-AAATCTGAAGACCTAAAATTTCCATT
** *
31611 AATAAAACCAAAAATGAAGACCTAAATTTTCCATT
1 AATAAAACCAAATCTGAAGACCTAAAATTTCCATT
*
31646 AATAAAGCCAAATC
1 AATAAAACCAAATC
31660 AAGACTAAGT
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
34 11 0.17
35 51 0.77
36 4 0.06
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (35 bp):
AATAAAACCAAATCTGAAGACCTAAAATTTCCATT
Found at i:33382 original size:254 final size:247
Alignment explanation
Indices: 32939--33423 Score: 787
Period size: 254 Copynumber: 1.9 Consensus size: 247
32929 TCAATGTATG
* *
32939 TTCATATTCAAGGTAGACTGGTTTTATATGTTTCTTTTTTACTTTAAAACCATTTTTTTTGTTTA
1 TTCATATTAAAGGTAGACTGGTTTTATATGTTTCTTTTTTACTTTAAAACCA-TATTTTTGTTTA
33004 AGGGACAGTTAATGTTGCAATATGTCTTTGCTTTTATCATATCATGAATATATATAATTGATCAA
65 AGGGACAGTTAATGTTGCAATATGTCTTTGCTTTTATCATATCATGAATATATATAATTGATCAA
* *
33069 TATTTGGGATTGAATTTCAGGATTGAATAATTTGACAAACTTGAAGTACTTGGATTTAAGTTCG-
130 TATTTGGGATTGAATTTCACGATTGAATAATTTGACAAACTTGAAATACTTGGATTTAAG-TCGC
33133 AACAGA-ATTGAAAGCATCTCAAACAAAGGTATAAGTACAGTATTTATATGTCAA
194 AACA-ACATTGAAAGCATCTCAAACAAAGGTATAAGTACAGTATTTATATGTCAA
33187 TTCATATTAAAGGTAGACTGGTTTTATATGTTTCTTTTTTACTTTAAAACCA-ATTTTTGTTTAA
1 TTCATATTAAAGGTAGACTGGTTTTATATGTTTCTTTTTTACTTTAAAACCATATTTTTGTTTAA
33251 GGGACAGTTAATGTTGCAATATGTCTTTGCTTTTATCATATCATGAATATATATATATATATAAC
66 GGGACAGTTAATGTTGCAATATGTCTTTGCTTTTATCATATCATG---A-ATATATATA-AT---
*
33316 TGATCAATATTTGGGATTGAATTTCACGATTGAATAATTTGTCAAACTTGAAATACTTGGATTTA
123 TGATCAATATTTGGGATTGAATTTCACGATTGAATAATTTGACAAACTTGAAATACTTGGATTTA
* *
33381 AGTCGCAACAACGTTGAAAGCATCTCAAACCAAGGTATAAGTA
188 AGTCGCAACAACATTGAAAGCATCTCAAACAAAGGTATAAGTA
33424 TTTGTGCGTA
Statistics
Matches: 220, Mismatches: 7, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
246 56 0.25
248 51 0.23
249 1 0.00
250 9 0.04
251 2 0.01
253 4 0.02
254 97 0.44
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (247 bp):
TTCATATTAAAGGTAGACTGGTTTTATATGTTTCTTTTTTACTTTAAAACCATATTTTTGTTTAA
GGGACAGTTAATGTTGCAATATGTCTTTGCTTTTATCATATCATGAATATATATAATTGATCAAT
ATTTGGGATTGAATTTCACGATTGAATAATTTGACAAACTTGAAATACTTGGATTTAAGTCGCAA
CAACATTGAAAGCATCTCAAACAAAGGTATAAGTACAGTATTTATATGTCAA
Found at i:35494 original size:8 final size:9
Alignment explanation
Indices: 35467--35495 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
35457 ATCCTAGTTC
35467 AATTGTTAA
1 AATTGTTAA
35476 AATTGTTAA
1 AATTGTTAA
35485 AATT-TTAA
1 AATTGTTAA
35493 AAT
1 AAT
35496 AGTTTGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (9 bp):
AATTGTTAA
Found at i:39051 original size:27 final size:29
Alignment explanation
Indices: 38997--39051 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
38987 CTCAAGTCAT
* * *
38997 TTTGTATCATGTGATATTTTACATAATTA
1 TTTGTATCATGCGATATTTTAAAAAATTA
39026 TTTGTATCAT-CGA-ATTTTAAAAAATT
1 TTTGTATCATGCGATATTTTAAAAAATT
39052 TAATATATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.48
28 2 0.09
29 10 0.43
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (29 bp):
TTTGTATCATGCGATATTTTAAAAAATTA
Found at i:41168 original size:15 final size:15
Alignment explanation
Indices: 41157--41223 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
41147 AATTTATCAT
*
41157 TATTACTATTATTAC
1 TATTATTATTATTAC
41172 TATTATTATTATTAC
1 TATTATTATTATTAC
*
41187 TATTATTATTACTAC
1 TATTATTATTATTAC
* *
41202 TACTATTATTATTAG
1 TATTATTATTATTAC
41217 TATTATT
1 TATTATT
41224 TTTTTAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:41169 original size:3 final size:3
Alignment explanation
Indices: 41150--41223 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
41140 TAATATTAAT
* * * *
41150 TTA TCA TTA TTA CTA TTA TTA CTA TTA TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
41198 CTA CTA CTA TTA TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41224 TTTTTAATCA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:42658 original size:24 final size:24
Alignment explanation
Indices: 42622--42700 Score: 61
Period size: 26 Copynumber: 3.1 Consensus size: 24
42612 TTTTTTTTAA
*
42622 AAAAAATATATGTATATAAAAATTT
1 AAAAGATA-ATGTATATAAAAATTT
***
42647 AAAAGATAATGTACATATAATGGTTT
1 AAAAGATAATGT--ATATAAAAATTT
*
42673 AAAATGACTAATATATA-AAAAATTT
1 AAAA-GA-TAATGTATATAAAAATTT
42698 AAA
1 AAA
42701 TAAATAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
24 4 0.10
25 15 0.36
26 16 0.38
27 2 0.05
28 5 0.12
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.33
Consensus pattern (24 bp):
AAAAGATAATGTATATAAAAATTT
Found at i:42731 original size:26 final size:25
Alignment explanation
Indices: 42670--42767 Score: 92
Period size: 26 Copynumber: 3.9 Consensus size: 25
42660 CATATAATGG
* *
42670 TTTAAAATGACTAATATATAAAAAA
1 TTTAAAATAAATAATATATAAAAAA
* *
42695 TTT-AAATAAATAGTATGTAAAACAA
1 TTTAAAATAAATAATATATAAAA-AA
* *
42720 TTTAAAATAAATGATAAATAAAAAAA
1 TTTAAAATAAATAATATAT-AAAAAA
* *
42746 CTTAAAACAAATAATA-ATAAAA
1 TTTAAAATAAATAATATATAAAA
42768 GAGTTTTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
24 19 0.32
25 10 0.17
26 26 0.44
27 4 0.07
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAAA
Found at i:52098 original size:29 final size:29
Alignment explanation
Indices: 52056--52113 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
52046 GGTCCGGTGT
52056 TAGTTTTTATTTGTATAGTGGAGTTTGAG
1 TAGTTTTTATTTGTATAGTGGAGTTTGAG
52085 TAGTTTTTATTTGTATAGTGGAGTTTGAG
1 TAGTTTTTATTTGTATAGTGGAGTTTGAG
52114 GATGGTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (29 bp):
TAGTTTTTATTTGTATAGTGGAGTTTGAG
Found at i:55579 original size:91 final size:91
Alignment explanation
Indices: 55424--55591 Score: 300
Period size: 91 Copynumber: 1.8 Consensus size: 91
55414 GAGATGTCCG
* * *
55424 GGGTGTTTCGATTTCAAATGTTTTCTGTAGACTGGTGATTGATTGGAGGCTTATCGTTGAGCTCA
1 GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCTCA
*
55489 CTTATGATGATGTATGATGTATGAAC
66 CTTATAATGATGTATGATGTATGAAC
55515 GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCTCA
1 GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCTCA
55580 CTTATAATGATG
66 CTTATAATGATG
55592 GTACATTCGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (91 bp):
GGGTGTTTCGATTTCAAATGTTTTCTGCACACTGGTGATTGATAGGAGGCTTATCGTTGAGCTCA
CTTATAATGATGTATGATGTATGAAC
Found at i:73785 original size:19 final size:21
Alignment explanation
Indices: 73761--73806 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
73751 ATTTTTATGA
73761 GATAAAAAAT-A-ATTATAAC
1 GATAAAAAATGATATTATAAC
73780 GATAAAAAATGATATTATAA-
1 GATAAAAAATGATATTATAAC
73800 G-TAAAAA
1 GATAAAAA
73807 TACATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
GATAAAAAATGATATTATAAC
Found at i:73796 original size:21 final size:18
Alignment explanation
Indices: 73755--73806 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
73745 TATTGAATTT
*
73755 TTATGAGATAAAAAATAA
1 TTATAAGATAAAAAATAA
73773 TTATAACGATAAAAAATGATA
1 TTATAA-GATAAAAAAT-A-A
73794 TTATAAG-TAAAAA
1 TTATAAGATAAAAA
73807 TACATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 2 0.07
21 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (18 bp):
TTATAAGATAAAAAATAA
Found at i:81157 original size:26 final size:25
Alignment explanation
Indices: 81085--81188 Score: 95
Period size: 24 Copynumber: 4.2 Consensus size: 25
81075 ACATATAATG
*
81085 GTTTAAAATGAATAATATATAAAAA
1 GTTTAAAATAAATAATATATAAAAA
* *
81110 ATTT-AAATAAATAATATGTAAAACA
1 GTTTAAAATAAATAATATATAAAA-A
* *
81135 GTTTAAAATAAATGATAAATAAAAA
1 GTTTAAAATAAATAATATATAAAAA
** * *
81160 ACTTGAAACAAATAATA-ATAAAAGA
1 GTTTAAAATAAATAATATATAAAA-A
81185 GTTT
1 GTTT
81189 TTTAAATAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
24 23 0.37
25 23 0.37
26 16 0.26
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.30
Consensus pattern (25 bp):
GTTTAAAATAAATAATATATAAAAA
Found at i:81182 original size:50 final size:50
Alignment explanation
Indices: 81085--81188 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
81075 ACATATAATG
* * * * *
81085 GTTTAAAATGAATAATATATAAAAAATTTAAATAAATAATATGTAAAACA
1 GTTTAAAATAAATAATAAATAAAAAATTGAAACAAATAATATATAAAACA
* *
81135 GTTTAAAATAAATGATAAATAAAAAACTTGAAACAAATAATA-ATAAAAGA
1 GTTTAAAATAAATAATAAATAAAAAA-TTGAAACAAATAATATATAAAACA
81185 GTTT
1 GTTT
81189 TTTAAATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
50 33 0.72
51 13 0.28
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.30
Consensus pattern (50 bp):
GTTTAAAATAAATAATAAATAAAAAATTGAAACAAATAATATATAAAACA
Found at i:85096 original size:29 final size:30
Alignment explanation
Indices: 85060--85118 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
85050 TTTTTTTTAA
*
85060 ATTACACA-AAATCAAAATTTATATATAAT
1 ATTACACATAAATCAAAATTCATATATAAT
*
85089 ATTACACATTAAATTAAAATTCATATATAA
1 ATTACACA-TAAATCAAAATTCATATATAA
85119 CTTTGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (30 bp):
ATTACACATAAATCAAAATTCATATATAAT
Found at i:88703 original size:21 final size:21
Alignment explanation
Indices: 88677--88717 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
88667 ATCTGCTCAA
* *
88677 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
88698 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
88718 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:93014 original size:240 final size:241
Alignment explanation
Indices: 92576--93015 Score: 702
Period size: 240 Copynumber: 1.8 Consensus size: 241
92566 GGCAGATTGG
* * * *
92576 TTTTACCTGTTTCTTTTTTACTTTAAAATCAATTTGGTTTAAGGAAAAGTTATTCCAATATGTCA
1 TTTTACATGTTTCTCTTTTACTTTAAAATCAATTTGGTTTAAGAAAAAGCTATTCCAATATGTCA
* * * * * *
92641 TTTGCTTTTATCTTGTGATGAAAATATAACTGATCAACATTTGGGATTGAATTTTAGAATTGAAT
66 TTTGCATTTATCTTATCATGAAAACATAACTGATCAACATTTGGGATTGAATTTCAGAATGGAAT
* **
92706 AATTTGACAAACTTGAAGTCCTTGGATTTAAGTGGGAACAAAATTGAAAGCATCTCAAACAAAGG
131 AATTTGACAAACTTGAAGTACTTGGATTTAAGTGACAACAAAATTGAAAGCATCTCAAACAAAGG
92771 TATAAATATAGTATTTATATATTATTTCATATTCAAGGTAGACTTA
196 TATAAATATAGTATTTATATATTATTTCATATTCAAGGTAGACTTA
* *
92817 TTTTACATGTTTC-CTTTTACTTTAAAATCAATTTGGTTTAAGAAAAAGCTATTGCAATATTTCA
1 TTTTACATGTTTCTCTTTTACTTTAAAATCAATTTGGTTTAAGAAAAAGCTATTCCAATATGTCA
*
92881 TTTGCATTTATCTTATCATGAAAACATAACTGATCAACATTTGGGATTGGATTTCAGAATGGAAT
66 TTTGCATTTATCTTATCATGAAAACATAACTGATCAACATTTGGGATTGAATTTCAGAATGGAAT
* * *
92946 AATTTGACAAACTTGAAGTACTTGGATTTAAGTTACAACAACATTGAAAGCATCTCAAACCAAGG
131 AATTTGACAAACTTGAAGTACTTGGATTTAAGTGACAACAAAATTGAAAGCATCTCAAACAAAGG
93011 TATAA
196 TATAA
93016 GTATTTGTGC
Statistics
Matches: 180, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
240 168 0.93
241 12 0.07
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (241 bp):
TTTTACATGTTTCTCTTTTACTTTAAAATCAATTTGGTTTAAGAAAAAGCTATTCCAATATGTCA
TTTGCATTTATCTTATCATGAAAACATAACTGATCAACATTTGGGATTGAATTTCAGAATGGAAT
AATTTGACAAACTTGAAGTACTTGGATTTAAGTGACAACAAAATTGAAAGCATCTCAAACAAAGG
TATAAATATAGTATTTATATATTATTTCATATTCAAGGTAGACTTA
Found at i:93221 original size:167 final size:167
Alignment explanation
Indices: 92945--93280 Score: 672
Period size: 167 Copynumber: 2.0 Consensus size: 167
92935 CAGAATGGAA
92945 TAATTTGACAAACTTGAAGTACTTGGATTTAAGTTACAACAACATTGAAAGCATCTCAAACCAAG
1 TAATTTGACAAACTTGAAGTACTTGGATTTAAGTTACAACAACATTGAAAGCATCTCAAACCAAG
93010 GTATAAGTATTTGTGCATGACTTTTCTGATAGAATATTATTCCAAAAGGCAATGACAGATTTTAG
66 GTATAAGTATTTGTGCATGACTTTTCTGATAGAATATTATTCCAAAAGGCAATGACAGATTTTAG
93075 TGAATTTTTATTGTAAAATTAGAGTATTATTATTTAT
131 TGAATTTTTATTGTAAAATTAGAGTATTATTATTTAT
93112 TAATTTGACAAACTTGAAGTACTTGGATTTAAGTTACAACAACATTGAAAGCATCTCAAACCAAG
1 TAATTTGACAAACTTGAAGTACTTGGATTTAAGTTACAACAACATTGAAAGCATCTCAAACCAAG
93177 GTATAAGTATTTGTGCATGACTTTTCTGATAGAATATTATTCCAAAAGGCAATGACAGATTTTAG
66 GTATAAGTATTTGTGCATGACTTTTCTGATAGAATATTATTCCAAAAGGCAATGACAGATTTTAG
93242 TGAATTTTTATTGTAAAATTAGAGTATTATTATTTAT
131 TGAATTTTTATTGTAAAATTAGAGTATTATTATTTAT
93279 TA
1 TA
93281 TGTTATATAG
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (167 bp):
TAATTTGACAAACTTGAAGTACTTGGATTTAAGTTACAACAACATTGAAAGCATCTCAAACCAAG
GTATAAGTATTTGTGCATGACTTTTCTGATAGAATATTATTCCAAAAGGCAATGACAGATTTTAG
TGAATTTTTATTGTAAAATTAGAGTATTATTATTTAT
Found at i:95321 original size:17 final size:17
Alignment explanation
Indices: 95299--95336 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
95289 TTATGAGATA
95299 AAAATAATAGTATAAAT
1 AAAATAATAGTATAAAT
*
95316 AAAATAATATTATAAAT
1 AAAATAATAGTATAAAT
95333 AAAA
1 AAAA
95337 ATACACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATAATAGTATAAAT
Found at i:103327 original size:30 final size:31
Alignment explanation
Indices: 103263--103331 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
103253 ATGTTAATGG
*
103263 GTGATTGATTTGTCACTTTTTGATAACGTTA
1 GTGACTGATTTGTCACTTTTTGATAACGTTA
* *
103294 GTGACTGATTTGTTATTTTTTGA-AA-GTTGA
1 GTGACTGATTTGTCACTTTTTGATAACGTT-A
103324 GTGACTGA
1 GTGACTGA
103332 ATTGAAACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 20 0.59
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.46
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTTGATAACGTTA
Found at i:104983 original size:27 final size:28
Alignment explanation
Indices: 104926--104983 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
104916 GATTATTTCC
*
104926 ATAGCCTAAATTATTGTAGGGGGCCTAT
1 ATAGCCTAAATTATTATAGGGGGCCTAT
104954 ATAGCCTAAATTATTATA-GGGGCCTAT
1 ATAGCCTAAATTATTATAGGGGGCCTAT
104981 ATA
1 ATA
104984 AGATCAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (28 bp):
ATAGCCTAAATTATTATAGGGGGCCTAT
Found at i:107507 original size:23 final size:21
Alignment explanation
Indices: 107473--107532 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
107463 CGAAATACAC
107473 ATATACATATAC-TTTTAATA
1 ATATACATATACATTTTAATA
*
107493 TATATACATGCATACATTTTTATA
1 -ATATACAT--ATACATTTTAATA
*
107517 ATAT-CATATATATTTT
1 ATATACATATACATTTT
107533 TTATAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 3 0.09
23 8 0.24
24 7 0.21
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATACATATACATTTTAATA
Found at i:107551 original size:22 final size:21
Alignment explanation
Indices: 107509--107549 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
107499 CATGCATACA
107509 TTTTTATAATATCATATATAT
1 TTTTTATAATATCATATATAT
*
107530 TTTTTATAAT-TTATATATAT
1 TTTTTATAATATCATATATAT
107550 ATATGCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTATAATATCATATATAT
Found at i:109058 original size:19 final size:18
Alignment explanation
Indices: 109034--109069 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
109024 AATGTTAATT
109034 TTTTAGCATTTAATTTGAA
1 TTTTAGCA-TTAATTTGAA
*
109053 TTTTAGGATTAATTTGA
1 TTTTAGCATTAATTTGA
109070 TGAGAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (18 bp):
TTTTAGCATTAATTTGAA
Found at i:117062 original size:21 final size:21
Alignment explanation
Indices: 117036--117076 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
117026 AGACGAGCAA
* *
117036 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
117057 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
117077 TTGAGCAAAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:124554 original size:22 final size:20
Alignment explanation
Indices: 124501--124560 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
124491 TTTTTAAAGA
*
124501 AATTTATGAAATTATATTTT
1 AATTTATAAAATTATATTTT
*
124521 AATATTAAAAAATTATAGTTTT
1 AAT-TTATAAAATTATA-TTTT
124543 AACTTTATAAAATT-TATT
1 AA-TTTATAAAATTATATT
124561 ATTTATCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.15
21 13 0.38
22 15 0.44
23 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTTATAAAATTATATTTT
Found at i:128012 original size:11 final size:10
Alignment explanation
Indices: 127995--128041 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
127985 TTAAAAATTA
127995 AAAATTATAT
1 AAAATTATAT
*
128005 ATAAATTATTT
1 A-AAATTATAT
128016 AAAAATTATA-
1 -AAAATTATAT
128026 AGAAATTATAT
1 A-AAATTATAT
128037 AAAAT
1 AAAAT
128042 CACATCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 1 0.03
10 13 0.42
11 16 0.52
12 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
AAAATTATAT
Found at i:128021 original size:29 final size:31
Alignment explanation
Indices: 127984--128041 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
127974 TCAGTAAATC
127984 TTTAAAAA-T-TAA-AAATTATATATAAATTA
1 TTTAAAAATTATAAGAAATTATATA-AAATTA
128013 TTTAAAAATTATAAGAAATTATATAAAAT
1 TTTAAAAATTATAAGAAATTATATAAAAT
128042 CACATCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.31
30 1 0.04
31 7 0.27
32 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTAAAAATTATAAGAAATTATATAAAATTA
Found at i:128031 original size:21 final size:22
Alignment explanation
Indices: 127992--128040 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
127982 TCTTTAAAAA
*
127992 TTAAAAATTATATATAAATTAT
1 TTAAAAATTATATAGAAATTAT
128014 TTAAAAATTATA-AGAAATTAT
1 TTAAAAATTATATAGAAATTAT
*
128035 ATAAAA
1 TTAAAA
128041 TCACATCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAAAAATTATATAGAAATTAT
Found at i:128132 original size:29 final size:29
Alignment explanation
Indices: 128100--128166 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
128090 AACCAAAAAA
*
128100 GGCCATTTTTTTCAA-AATTTATCGAAATG
1 GGCCATTTTTTT-AATAATTTACCGAAATG
* * *
128129 GGCCAGTTTTTTAATTATTTACCGGAATG
1 GGCCATTTTTTTAATAATTTACCGAAATG
128158 GGCCATTTT
1 GGCCATTTT
128167 CCGCGAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (29 bp):
GGCCATTTTTTTAATAATTTACCGAAATG
Found at i:130068 original size:13 final size:14
Alignment explanation
Indices: 130045--130081 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
130035 TTATTGTGGA
130045 TTTAATCTTTAAAT
1 TTTAATCTTTAAAT
*
130059 TTTAAT-TTTATAT
1 TTTAATCTTTAAAT
130072 TTTAATCTTT
1 TTTAATCTTT
130082 GTACAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAATCTTTAAAT
Found at i:130589 original size:35 final size:35
Alignment explanation
Indices: 130549--130643 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
130539 GGGTTAGAAT
*
130549 TTCCATTAATAAAACCAAAATCAAGGACCCAAAAA
1 TTCCATTAATAAAACCAAAATCAAGGAACCAAAAA
* * * * *
130584 TTCCATGAATAAGACGAAAAATCAA-GAACTAAAAT
1 TTCCATTAATAAAAC-CAAAATCAAGGAACCAAAAA
*
130619 TTCCATTAATAAAAACAAAATCAAG
1 TTCCATTAATAAAACCAAAATCAAG
130644 ACTAAAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
34 8 0.17
35 32 0.67
36 8 0.17
ACGTcount: A:0.55, C:0.18, G:0.07, T:0.20
Consensus pattern (35 bp):
TTCCATTAATAAAACCAAAATCAAGGAACCAAAAA
Found at i:130605 original size:70 final size:70
Alignment explanation
Indices: 130487--130643 Score: 181
Period size: 70 Copynumber: 2.2 Consensus size: 70
130477 CAATGTACAT
* * * *** *
130487 ATAAAACCAAAATCAAGGCCTAAAATTTCCAAGAAAAAAAAAACAAAATGAAGGGTTAGAATTTC
1 ATAAAACCAAAATCAAGGCCCAAAAATTCCAAGAAAAAAAAAACAAAATCAAGAACTAAAATTTC
130552 CATTA
66 CATTA
* * * **
130557 ATAAAACCAAAATCAAGGACCCAAAAATTCCATGAATAAGACGA-AAAATCAAGAACTAAAATTT
1 ATAAAACCAAAATCAAGG-CCCAAAAATTCCAAGAAAAAAAAAACAAAATCAAGAACTAAAATTT
130621 CCATTA
65 CCATTA
*
130627 ATAAAAACAAAATCAAG
1 ATAAAACCAAAATCAAG
130644 ACTAAAAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
70 55 0.75
71 18 0.25
ACGTcount: A:0.56, C:0.16, G:0.10, T:0.18
Consensus pattern (70 bp):
ATAAAACCAAAATCAAGGCCCAAAAATTCCAAGAAAAAAAAAACAAAATCAAGAACTAAAATTTC
CATTA
Found at i:137130 original size:3 final size:3
Alignment explanation
Indices: 137124--137184 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
137114 TTATTTAAGT
* * *
137124 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTG TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
137172 TTA CTA TTA TTA T
1 TTA TTA TTA TTA T
137185 ACTAATATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:149104 original size:44 final size:45
Alignment explanation
Indices: 148877--149148 Score: 194
Period size: 44 Copynumber: 6.1 Consensus size: 45
148867 GGAGCAGGTT
* * * * * *
148877 GAAGAAAACAGACCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
* * **
148922 GAAGAAAACAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
* * * * * * * *
148966 AAAGATAGCAGGTCCTGTCTTC-CTATATTGGTAGCGAAGTGGATC
1 GAAGAAAGCAGATCTTGTCTTCAC-ATACTGGTCGTGAAGTAGATC
* * * * * * * * *
149011 GAATATA-CAGAT-TTCATCTCCCCATACTGGTGGCGGAGTAGATT
1 GAAGAAAGCAGATCTT-GTCTTCACATACTGGTCGTGAAGTAGATC
* * *
149055 GAAGAAAGTAGATCTTGTCTTCACGTGCTGG-CGTGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
* * *
149099 AAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
149144 GAAGA
1 GAAGA
149149 TACAAGTCTT
Statistics
Matches: 170, Mismatches: 50, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
43 1 0.01
44 96 0.56
45 71 0.42
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (45 bp):
GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
Found at i:149165 original size:133 final size:133
Alignment explanation
Indices: 148894--149152 Score: 374
Period size: 133 Copynumber: 1.9 Consensus size: 133
148884 ACAGACCTTG
* *
148894 TCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGATCTTATCTTCATGTACTGGCGTGAA
1 TCTCCCCATACTGGTGGCGGAGTAGATCGAAGAAAACAGATCTTATCTTCACGTACTGGCGTGAA
* * * * * *
148959 GTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAATATACAGATT
66 GTAGATCAAAGAAAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGATACAGATT
149024 TCA
131 TCA
* ** * *
149027 TCTCCCCATACTGGTGGCGGAGTAGATTGAAGAAAGTAGATCTTGTCTTCACGTGCTGGCGTGAA
1 TCTCCCCATACTGGTGGCGGAGTAGATCGAAGAAAACAGATCTTATCTTCACGTACTGGCGTGAA
* * *
149092 GTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATACA
66 GTAGATCAAAGAAAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGATACA
149153 AGTCTTATCT
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
133 110 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (133 bp):
TCTCCCCATACTGGTGGCGGAGTAGATCGAAGAAAACAGATCTTATCTTCACGTACTGGCGTGAA
GTAGATCAAAGAAAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGATACAGATT
TCA
Found at i:150704 original size:3 final size:3
Alignment explanation
Indices: 150696--150739 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
150686 AAATATTTAT
150696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
150740 CTATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:152289 original size:12 final size:12
Alignment explanation
Indices: 152272--152319 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
152262 AATTAAAATT
152272 TATTATTAATAA
1 TATTATTAATAA
152284 TATTA-T--TAA
1 TATTATTAATAA
*
152293 TATTATTAATAT
1 TATTATTAATAA
152305 TATTATTAAATAA
1 TATTATT-AATAA
152318 TA
1 TA
152320 AGAAGTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 8 0.27
10 1 0.03
11 1 0.03
12 14 0.47
13 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTATTAATAA
Found at i:152293 original size:9 final size:9
Alignment explanation
Indices: 152275--152309 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
152265 TAAAATTTAT
*
152275 TATTAATAA
1 TATTATTAA
152284 TATTATTAA
1 TATTATTAA
152293 TATTATTAA
1 TATTATTAA
152302 TATTATTA
1 TATTATTA
152310 TTAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATTAA
Found at i:152745 original size:19 final size:17
Alignment explanation
Indices: 152717--152762 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
152707 ACTTATAAAC
*
152717 ATAAATATTTAAAAAAGTT
1 ATAAAAATTT-AAAAA-TT
*
152736 ATAAAAATTTTAAAATT
1 ATAAAAATTTAAAAATT
152753 ATAAAAATTT
1 ATAAAAATTT
152763 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.48
18 4 0.16
19 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAAAAATTTAAAAATT
Found at i:152756 original size:17 final size:18
Alignment explanation
Indices: 152729--152765 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
152719 AAATATTTAA
152729 AAAAGTTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
152747 AAAA-TTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
152764 AA
1 AA
152766 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAGTTATAAAAATTTT
Found at i:155432 original size:14 final size:14
Alignment explanation
Indices: 155413--155440 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
155403 CCCCGTCATT
155413 CGTGTTCACACTAG
1 CGTGTTCACACTAG
155427 CGTGTTCACACTAG
1 CGTGTTCACACTAG
155441 ATCTAATAAA
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:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
CGTGTTCACACTAG
Found at i:156672 original size:34 final size:34
Alignment explanation
Indices: 156602--156814 Score: 205
Period size: 34 Copynumber: 6.2 Consensus size: 34
156592 TGGTTTACAT
* * * * *
156602 ATAAAACCAAAACCAAGACCTAAAATTT-CAAGA
1 ATAAAAACAAAATCAAGACTTAAATTTTCCATGA
*
156635 ATAAAAACAAAATCAAGACTTAAATTTTCCATTA
1 ATAAAAACAAAATCAAGACTTAAATTTTCCATGA
* *
156669 ATAAAACCAAAATCAAGACTAAAAATTTT-CATGA
1 ATAAAAACAAAATCAAGACT-TAAATTTTCCATGA
* * * *
156703 ATAGAAACGAAATCAAGGCCTAAATTTTCCATGA
1 ATAAAAACAAAATCAAGACTTAAATTTTCCATGA
* * * *
156737 ATGAAAACAAAACCATGAATTAAACTTTTCCATGA
1 ATAAAAACAAAATCAAGACTTAAA-TTTTCCATGA
* * *
156772 ATTAAAACAAAATCAAGGCTTAAACTTCTCCATGA
1 ATAAAAACAAAATCAAGACTTAAA-TTTTCCATGA
*
156807 ATTAAAAC
1 ATAAAAAC
156815 TTTGTATGTA
Statistics
Matches: 147, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
33 31 0.21
34 62 0.42
35 54 0.37
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (34 bp):
ATAAAAACAAAATCAAGACTTAAATTTTCCATGA
Found at i:156729 original size:68 final size:66
Alignment explanation
Indices: 156602--156814 Score: 232
Period size: 68 Copynumber: 3.1 Consensus size: 66
156592 TGGTTTACAT
* *
156602 ATAAAACCAAAACCAAGACCTAAAA-TTTCAAGAATAAAAACAAAATCAAGACTTAAATTTTCCA
1 ATAAAACCAAAACCAAGA-CTAAAATTTTCATGAAT-AAAACAAAATCAAGGCTTAAATTTTCCA
*
156666 TTA
64 TGA
* * *
156669 ATAAAACCAAAATCAAGACTAAAAATTTTCATGAATAGAAACGAAATCAAGGCCTAAATTTTCCA
1 ATAAAACCAAAACCAAGACT-AAAATTTTCATGAATA-AAACAAAATCAAGGCTTAAATTTTCCA
156734 TGA
64 TGA
* * * *
156737 ATGAAAA-CAAAACCATGAATTAAACTTTTCCATGAATTAAAACAAAATCAAGGCTTAAACTTCT
1 AT-AAAACCAAAACCAAG-ACTAAAATTTT-CATGAA-TAAAACAAAATCAAGGCTTAAA-TTTT
156801 CCATGA
61 CCATGA
156807 ATTAAAAC
1 A-TAAAAC
156815 TTTGTATGTA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
66 2 0.02
67 22 0.18
68 52 0.42
69 30 0.24
70 16 0.13
71 1 0.01
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (66 bp):
ATAAAACCAAAACCAAGACTAAAATTTTCATGAATAAAACAAAATCAAGGCTTAAATTTTCCATG
A
Found at i:164454 original size:3 final size:3
Alignment explanation
Indices: 164446--164477 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
164436 TTTAAGAATA
164446 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
164478 AAATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Done.