Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, 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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 56
Found at i:1357235 original size:16 final size:15
Alignment explanation
Indices: 1357209--1357239 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1357199 AGATTACCTT
1357209 TGGAAATAACATTAC
1 TGGAAATAACATTAC
1357224 TGGAATATAACATTAC
1 TGGAA-ATAACATTAC
1357240 AATGAGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TGGAAATAACATTAC
Found at i:1357517 original size:18 final size:17
Alignment explanation
Indices: 1357487--1357520 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1357477 TCATATCATT
*
1357487 ATATAAAATATAATATC
1 ATATAAAAAATAATATC
1357504 ATATGAAAAAATAATAT
1 ATAT-AAAAAATAATAT
1357521 TATGGTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATAATATC
Found at i:1358416 original size:2 final size:2
Alignment explanation
Indices: 1358409--1358438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1358399 TCTTATGGGT
1358409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1358439 AACATGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1359083 original size:2 final size:2
Alignment explanation
Indices: 1359076--1359106 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1359066 TTACGAGCTT
1359076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1359107 TTGATTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1371207 original size:3 final size:3
Alignment explanation
Indices: 1371199--1371231 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1371189 TGGGGTTAAC
1371199 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1371232 CTTTGGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1376963 original size:21 final size:21
Alignment explanation
Indices: 1376939--1376988 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1376929 CATGGTTTAC
1376939 CCATTTTCTTCATCTAGTTAT
1 CCATTTTCTTCATCTAGTTAT
1376960 CCATTTTCTTCATCTAGTTAT
1 CCATTTTCTTCATCTAGTTAT
1376981 CCATTTTC
1 CCATTTTC
1376989 CATTCAATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.26, G:0.04, T:0.52
Consensus pattern (21 bp):
CCATTTTCTTCATCTAGTTAT
Found at i:1379958 original size:17 final size:15
Alignment explanation
Indices: 1379920--1379950 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1379910 AGGGACTTAT
1379920 TTCAAGATCAGAGAA
1 TTCAAGATCAGAGAA
1379935 TTCAAGATCAGAGAA
1 TTCAAGATCAGAGAA
1379950 T
1 T
1379951 GTTCAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (15 bp):
TTCAAGATCAGAGAA
Found at i:1379970 original size:26 final size:27
Alignment explanation
Indices: 1379941--1379997 Score: 107
Period size: 26 Copynumber: 2.1 Consensus size: 27
1379931 AGAATTCAAG
1379941 ATCAGAGAATGTTCAAGAAAACAA-TA
1 ATCAGAGAATGTTCAAGAAAACAATTA
1379967 ATCAGAGAATGTTCAAGAAAACAATTA
1 ATCAGAGAATGTTCAAGAAAACAATTA
1379994 ATCA
1 ATCA
1379998 TAGGATCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (27 bp):
ATCAGAGAATGTTCAAGAAAACAATTA
Found at i:1381428 original size:24 final size:24
Alignment explanation
Indices: 1381401--1381523 Score: 176
Period size: 24 Copynumber: 5.1 Consensus size: 24
1381391 TTCTATTTGA
1381401 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1381425 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
1381449 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
1381473 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1381497 ATTTTGATATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
1381521 ATT
1 ATT
1381524 ATGTTTTGAT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 87 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1388069 original size:34 final size:36
Alignment explanation
Indices: 1388024--1388100 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
1388014 TTATTCATAA
* **
1388024 AAGAATAGCTTAAATT-AC-TATTCTTATCAACAAT
1 AAGAATGGCTTAAATTGACATATTCTTAAAAACAAT
*
1388058 AAGAATGGCTTAAATTGCCATATTCTTAAAAACAAT
1 AAGAATGGCTTAAATTGACATATTCTTAAAAACAAT
*
1388094 AATAATG
1 AAGAATG
1388101 AAGTAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 15 0.42
35 1 0.03
36 20 0.56
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (36 bp):
AAGAATGGCTTAAATTGACATATTCTTAAAAACAAT
Found at i:1389496 original size:3 final size:3
Alignment explanation
Indices: 1389488--1389556 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
1389478 TTTTCGTTAT
** *
1389488 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1389534 TTA TT- TTA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA
1389557 CGAATTTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 7 0.13
3 46 0.84
4 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1389510 original size:17 final size:18
Alignment explanation
Indices: 1389488--1389555 Score: 79
Period size: 17 Copynumber: 3.8 Consensus size: 18
1389478 TTTTCGTTAT
1389488 TTATTA-TTATTATTTTA
1 TTATTATTTATTATTTTA
1389505 TTATTA-TTATTATTATTA
1 TTATTATTTATTATT-TTA
**
1389523 TCGTTATCTTATTATTTTA
1 TTATTAT-TTATTATTTTA
1389542 TTA-TATTTATTATT
1 TTATTATTTATTATT
1389556 ACGAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
17 22 0.50
18 10 0.23
19 4 0.09
20 8 0.18
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (18 bp):
TTATTATTTATTATTTTA
Found at i:1391608 original size:22 final size:22
Alignment explanation
Indices: 1391583--1391626 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1391573 TCAAACGATG
*
1391583 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1391605 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1391627 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1397461 original size:36 final size:36
Alignment explanation
Indices: 1397416--1397535 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
1397406 ACAAAGTTGA
**
1397416 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
1397452 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
1397488 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
1397522 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
1397536 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:1397824 original size:28 final size:28
Alignment explanation
Indices: 1397787--1397912 Score: 161
Period size: 29 Copynumber: 4.5 Consensus size: 28
1397777 TCTTTTGAGG
1397787 AAAAATCTTTGAGTTTGTTCCTCTTGAA-
1 AAAAATCTTTGAGTTTGTTCCT-TTGAAT
1397815 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCC-TTTGAAT
*
1397844 AAAAATCTTGGAGTTTGTTCCTTTGGAAT
1 AAAAATCTTTGAGTTTGTTCCTTT-GAAT
* *
1397873 AAAAATCTGTGAG-TTGTTTCGTTTG-A-
1 AAAAATCTTTGAGTTTG-TTCCTTTGAAT
1397899 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
1397913 CTATTTACTT
Statistics
Matches: 88, Mismatches: 5, Indels: 11
0.85 0.05 0.11
Matches are distributed among these distances:
26 12 0.14
27 1 0.01
28 33 0.38
29 42 0.48
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (28 bp):
AAAAATCTTTGAGTTTGTTCCTTTGAAT
Found at i:1397849 original size:57 final size:56
Alignment explanation
Indices: 1397778--1397912 Score: 168
Period size: 57 Copynumber: 2.4 Consensus size: 56
1397768 AAGACAATTT
* *
1397778 CTTTTGAGGAAAAATCTTTGAGTTTGTTCCTCTT-GAA-AAAAATCTTTGAGTTTGTTC
1 CTTTTGA-AAAAAATCTTTGAGTTTGTTCCT-TTGGAATAAAAATCTGTGAG-TTGTTC
* *
1397835 CTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTGGAATAAAAATCTGTGAGTTGTTT
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTCCTTTGGAATAAAAATCTGTGAGTTGTTC
*
1397892 CGTTTG-AAAAAATCTTTGAGT
1 CTTTTGAAAAAAATCTTTGAGT
1397913 CTATTTACTT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
55 13 0.19
56 3 0.04
57 41 0.59
58 12 0.17
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (56 bp):
CTTTTGAAAAAAATCTTTGAGTTTGTTCCTTTGGAATAAAAATCTGTGAGTTGTTC
Found at i:1397924 original size:27 final size:26
Alignment explanation
Indices: 1397873--1397927 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1397863 CCTTTGGAAT
*
1397873 AAAAATCTGTGAGTTGTTTCGTTTGA
1 AAAAATCTGTGAGTTATTTCGTTTGA
*
1397899 AAAAATCTTTGAGTCTATTTAC-TTTGA
1 AAAAATCTGTGAGT-TATTT-CGTTTGA
1397926 AA
1 AA
1397928 CAAAGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.52
27 11 0.44
28 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (26 bp):
AAAAATCTGTGAGTTATTTCGTTTGA
Found at i:1398000 original size:93 final size:94
Alignment explanation
Indices: 1397865--1398092 Score: 263
Period size: 93 Copynumber: 2.4 Consensus size: 94
1397855 AGTTTGTTCC
* * *
1397865 TTTG-GAATAAAAATCTGTGAGTTGTTTCGTTTG--A-AAAAATCTTTGAGTCTATTTACTTT-G
1 TTTGTGAACAAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTT-CTTTGG
* *
1397925 AAACAAAGTTTTGTCTCTCTTGAGACAA-T
65 AAACAAAATTTTGTCTCTCTTAAGACAATT
* *
1397954 TTTGTGAA-AAAAATCTTTGAGATTGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGG
1 TTTGTGAACAAAAATCTTTGAG-TTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTTCTTTGG
*
1398018 AAACAAAATTTTGTCTCTCTTAAGATAATT
65 AAACAAAATTTTGTCTCTCTTAAGACAATT
* * *
1398048 TCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAA
1 T-TTGTG-AACAAAAATCTTTGAG-TTGTTTCTTTTGAAACAAAA
1398093 TTTTGTCTCT
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
89 16 0.14
90 14 0.12
92 5 0.04
93 44 0.37
94 2 0.02
95 4 0.03
96 2 0.02
97 31 0.26
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (94 bp):
TTTGTGAACAAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTTCTTTGGA
AACAAAATTTTGTCTCTCTTAAGACAATT
Found at i:1398386 original size:68 final size:67
Alignment explanation
Indices: 1397979--1398549 Score: 1047
Period size: 67 Copynumber: 8.5 Consensus size: 67
1397969 TTTGAGATTG
1397979 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1398044 AA
66 AA
* *
1398046 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1398111 AA
66 AA
1398113 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1398178 AA
66 AA
* *
1398180 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTGTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1398245 AA
66 AA
1398247 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1398312 AA
66 AA
1398314 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTG-TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1398379 TAA
65 TAA
1398382 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTG-TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1398447 TAA
65 TAA
*
1398450 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGTT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1398515 AA
66 AA
* *
1398517 TTTCTTTTG-AA-AAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
1398550 CTTAAAATGA
Statistics
Matches: 492, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
65 20 0.04
66 2 0.00
67 335 0.68
68 135 0.27
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:1398858 original size:67 final size:65
Alignment explanation
Indices: 1398772--1398897 Score: 189
Period size: 67 Copynumber: 1.9 Consensus size: 65
1398762 GTGATCCATC
* *
1398772 TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAGAAATTTTT
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTT-AAGACAACTTCTTTTGA-AAATTTTT
1398837 TT
64 TT
* * *
1398839 TTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAGACAACTTCTTTTGAAAAT
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAGACAACTTCTTTTGAAAAT
1398898 ACCCATCTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 4 0.07
66 15 0.28
67 35 0.65
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (65 bp):
TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAGACAACTTCTTTTGAAAATTTTTTT
Found at i:1398918 original size:66 final size:65
Alignment explanation
Indices: 1398767--1398950 Score: 176
Period size: 67 Copynumber: 2.8 Consensus size: 65
1398757 AAGATGTGAT
* * * *
1398767 CCATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAGAAA
1 CCATCTTTGAGT-TGTTTCCTTTGAAACAAAATTTTGTCTCTT-GAGACAACTTCTTTTGAGAAA
*
1398832 TT
64 TC
*** *
1398834 TTTTTTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAGACAACTTCTTTTGA-AAAT
1 CCATCTTTGAG-TTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAGACAACTTCTTTTGAGAAAT
1398898 AC
65 -C
* *
1398900 CCATCTTTGAGATTGTTT-CTATTAAAAC-AAATTTTGTATCCCTTGAGACAA
1 CCATCTTTGAG-TTGTTTCCT-TTGAAACAAAATTTTG--TCTCTTGAGACAA
1398951 TTTTTTCTAG
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
65 14 0.15
66 34 0.35
67 47 0.49
68 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (65 bp):
CCATCTTTGAGTTGTTTCCTTTGAAACAAAATTTTGTCTCTTGAGACAACTTCTTTTGAGAAATC
Found at i:1399217 original size:35 final size:36
Alignment explanation
Indices: 1399130--1399226 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
1399120 TTTGGAAAAA
** *
1399130 ATCTTTGAGTTTGTTTCT-TTGGAAACAAAATTTACC
1 ATCTTTGAGTTTGTTTCTCTT-GAAACAAAATCAAAC
1399166 ATCTTTGAGTTTGTTTCTCTTGAAACAAAA-CAAAC
1 ATCTTTGAGTTTGTTTCTCTTGAAACAAAATCAAAC
* *
1399201 ATCTTTGAGATCGTTTC-CTTTGAAAC
1 ATCTTTGAGTTTGTTTCTC-TTGAAAC
1399227 GAATTTTGTC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
34 1 0.02
35 24 0.44
36 27 0.50
37 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (36 bp):
ATCTTTGAGTTTGTTTCTCTTGAAACAAAATCAAAC
Found at i:1399538 original size:40 final size:40
Alignment explanation
Indices: 1399480--1399670 Score: 152
Period size: 40 Copynumber: 4.5 Consensus size: 40
1399470 CCAGCCGTCC
* * *
1399480 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
* ** * *
1399520 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGATC-TCT
* * * * *
1399563 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA---CCAGATCTCT
1399609 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCT
1399649 TCATCACGTATGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
1399671 CCCTTAGATA
Statistics
Matches: 119, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
40 54 0.45
42 1 0.01
43 30 0.25
44 1 0.01
46 30 0.25
47 3 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
Found at i:1399628 original size:89 final size:83
Alignment explanation
Indices: 1399470--1399630 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 83
1399460 CTAAAGATGG
* *
1399470 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
1399535 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
1399553 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
1399618 ATGAGCCGTGTCA
60 ATGAGCCGTGTCA
1399631 TTCCCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 32 0.47
84 2 0.03
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:1399694 original size:129 final size:130
Alignment explanation
Indices: 1399480--1399760 Score: 485
Period size: 129 Copynumber: 2.2 Consensus size: 130
1399470 CCAGCCGTCC
* *
1399480 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
1 TCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
1399545 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCT
* *
1399609 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCACC
1 TCATCACGTAGGAGCCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
* *
1399673 CTTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTC
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTC
1399738 T
130 T
1399739 TCATCACGTAGGAGCCGTGTCA
1 TCATCACGTAGGAGCCGTGTCA
1399761 CCTTTAGACG
Statistics
Matches: 143, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
129 109 0.76
130 34 0.24
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (130 bp):
TCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCT
Found at i:1399788 original size:43 final size:44
Alignment explanation
Indices: 1399510--1399791 Score: 172
Period size: 43 Copynumber: 6.5 Consensus size: 44
1399500 CATCCCCAGA
* * * * *
1399510 CCAGATCTCTTCATCACGTATGAGCCGTGTCAACC-ATAGA-TAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTC-ACCTTTAGACGAC
* * * * *
1399553 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG-G
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTG---TCACCTTTAGACGAC
* ***
1399599 CCAGAACTCTTCATCACGTATGAGCCGTGTCA---TTCCCCGA-
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGACGAC
* * * * *
1399639 CCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTTAGA-TAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGACGAC
* * * * * *
1399682 CCAG-CCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGC
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTG---TCACCTTTAGACGAC
*
1399729 CAAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGACGAC
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGACGAC
1399773 CCA-AACTCTTCATCACGTA
1 CCAGAACTCTTCATCACGTA
1399792 TGAGTAGTGT
Statistics
Matches: 184, Mismatches: 37, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
40 34 0.18
42 3 0.02
43 66 0.36
44 15 0.08
45 3 0.02
46 39 0.21
47 23 0.12
48 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (44 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGACGAC
Found at i:1399970 original size:3 final size:3
Alignment explanation
Indices: 1399959--1400025 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
1399949 TTTTTTTTCG
** *
1399959 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1400005 TT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
1400026 CAAATTTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1400003 original size:35 final size:35
Alignment explanation
Indices: 1399956--1400025 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1399946 GGGTTTTTTT
*
1399956 TCGTTATTTTATTATTATTATTATTA-TTATTATTA
1 TCGTTATCTTATTATT-TTATTATTATTTATTATTA
1399991 TCGTTATCTTATTATTTTATTATTATTTATTATTA
1 TCGTTATCTTATTATTTTATTATTATTTATTATTA
1400026 CAAATTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (35 bp):
TCGTTATCTTATTATTTTATTATTATTTATTATTA
Found at i:1402086 original size:22 final size:22
Alignment explanation
Indices: 1402061--1402104 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1402051 TCAAACGATG
*
1402061 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1402083 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1402105 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1410044 original size:16 final size:16
Alignment explanation
Indices: 1410011--1410049 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1410001 TAATTTATTC
*
1410011 TTTTTAATTAAAATAA
1 TTTTAAATTAAAATAA
1410027 TTGTTAAATTAAAA-AA
1 TT-TTAAATTAAAATAA
1410043 TTTTAAA
1 TTTTAAA
1410050 AACAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTTAAATTAAAATAA
Found at i:1410094 original size:16 final size:16
Alignment explanation
Indices: 1410053--1410088 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1410043 TTTTAAAAAC
*
1410053 AAAAAGAATATTTATT
1 AAAAAAAATATTTATT
1410069 AAAAAAAATATTTA-T
1 AAAAAAAATATTTATT
1410084 AAAAA
1 AAAAA
1410089 TTAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAAAAAATATTTATT
Found at i:1410893 original size:23 final size:23
Alignment explanation
Indices: 1410854--1410900 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1410844 CAAGTCAAGG
*
1410854 AGAAAATTATAAGAAAATTTTAC
1 AGAAAATTATAAGAAAATATTAC
*
1410877 AGAAATTTCATAA-AAAATATTAC
1 AGAAAATT-ATAAGAAAATATTAC
1410900 A
1 A
1410901 ACTGATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (23 bp):
AGAAAATTATAAGAAAATATTAC
Found at i:1413334 original size:14 final size:15
Alignment explanation
Indices: 1413294--1413326 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1413284 TAATTTTATT
*
1413294 TTTAGA-TTATATAA
1 TTTAGATTTATAAAA
1413308 TTTAGATTTATAAAA
1 TTTAGATTTATAAAA
1413323 TTTA
1 TTTA
1413327 TTTTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
TTTAGATTTATAAAA
Found at i:1413408 original size:14 final size:14
Alignment explanation
Indices: 1413389--1413427 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1413379 ATATAGATTT
1413389 TTAAAAAATATAAA
1 TTAAAAAATATAAA
1413403 TTAAAAAATA-AAA
1 TTAAAAAATATAAA
*
1413416 TAAAACAAATAT
1 TTAAA-AAATAT
1413428 TAACTAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
TTAAAAAATATAAA
Found at i:1415007 original size:43 final size:41
Alignment explanation
Indices: 1414927--1415142 Score: 157
Period size: 42 Copynumber: 5.1 Consensus size: 41
1414917 CGGCGATATT
* * *
1414927 AAATGCCGCAATAGGATTTGATATTTAGCGGCATTTTTCCAAA
1 AAATGCCGCAATAGG-TTTGAGATTTAGCGGCGTTTTT-CAAC
* *
1414970 AAATGCCGCAATAGGTGTTGAGGTTTACCGGCGTTTTTTC-AC
1 AAATGCCGCAATAGGT-TTGAGATTTAGCGGCG-TTTTTCAAC
* * *
1415012 AAACGCCGCAATAGGTATTAAGATTTAGCGGCGTTTTTTAAC
1 AAATGCCGCAATAGGT-TTGAGATTTAGCGGCGTTTTTCAAC
* ** * *
1415054 AAATGACGCAATAAATTTTGATAATTAGCGGCGTTTCTCTC-AC
1 AAATGCCGCAAT-AGGTTTGAGATTTAGCGGCGTTT-T-TCAAC
* ** * * *
1415097 AAACGCCGCAATAATTTTCGATATTTAGCGCCATTTTTCACAC
1 AAATGCCGCAATAGGTTT-GAGATTTAGCGGCGTTTTTCA-AC
1415140 AAA
1 AAA
1415143 CGTTATAGTA
Statistics
Matches: 140, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
41 7 0.05
42 65 0.46
43 62 0.44
44 6 0.04
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (41 bp):
AAATGCCGCAATAGGTTTGAGATTTAGCGGCGTTTTTCAAC
Found at i:1415027 original size:42 final size:42
Alignment explanation
Indices: 1414931--1415109 Score: 162
Period size: 42 Copynumber: 4.2 Consensus size: 42
1414921 GATATTAAAT
* * * * *
1414931 GCCGCAATAGG-ATTTGATATTTAGCGGCATTTTTCCAAAAAAT
1 GCCGCAATAGGTA-TTGAGATTTAGCGGCGTTTTTTC-ACAAAC
* * *
1414974 GCCGCAATAGGTGTTGAGGTTTACCGGCGTTTTTTCACAAAC
1 GCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCACAAAC
* * *
1415016 GCCGCAATAGGTATTAAGATTTAGCGGCGTTTTTTAACAAAT
1 GCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCACAAAC
* ** * * * *
1415058 GACGCAATAAATTTTGATAATTAGCGGCGTTTCTCTCACAAAC
1 GCCGCAATAGGTATTGAGATTTAGCGGCGTTT-TTTCACAAAC
1415101 GCCGCAATA
1 GCCGCAATA
1415110 ATTTTCGATA
Statistics
Matches: 109, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 65 0.60
43 44 0.40
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
GCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTTCACAAAC
Found at i:1415038 original size:85 final size:85
Alignment explanation
Indices: 1414931--1415109 Score: 200
Period size: 85 Copynumber: 2.1 Consensus size: 85
1414921 GATATTAAAT
* * * ** **
1414931 GCCGCAATAGGATTTGATATTTAGCGGCATTTTTCCAAAAAATGCCGCAATAGGTGTTGAGGTTT
1 GCCGCAATAGGATTTAAGATTTAGCGGCATTTTT-CAAAAAATGACGCAATAAATGTTGAGAATT
*
1414996 ACCGGCGTTT-TTTCACAAAC
65 ACCGGCGTTTCTCTCACAAAC
* * * * *
1415016 GCCGCAATAGG-TATTAAGATTTAGCGGCGTTTTTTAACAAATGACGCAATAAATTTTGATAATT
1 GCCGCAATAGGAT-TTAAGATTTAGCGGCATTTTTCAAAAAATGACGCAATAAATGTTGAGAATT
*
1415080 AGCGGCGTTTCTCTCACAAAC
65 ACCGGCGTTTCTCTCACAAAC
1415101 GCCGCAATA
1 GCCGCAATA
1415110 ATTTTCGATA
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
84 31 0.40
85 47 0.60
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (85 bp):
GCCGCAATAGGATTTAAGATTTAGCGGCATTTTTCAAAAAATGACGCAATAAATGTTGAGAATTA
CCGGCGTTTCTCTCACAAAC
Found at i:1416623 original size:31 final size:32
Alignment explanation
Indices: 1416562--1416629 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
1416552 TTCTGGTGTC
* * *
1416562 GGGTAGGGTCAATATCGAATCGGTATA-TTTT
1 GGGTCGGGTCAATATAGAATCGATATATTTTT
*
1416593 GGGTCGGGTCAATATAGGATCGAT-TGATTTTT
1 GGGTCGGGTCAATATAGAATCGATAT-ATTTTT
1416625 GGGTC
1 GGGTC
1416630 AAATCAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.03
31 21 0.68
32 9 0.29
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.35
Consensus pattern (32 bp):
GGGTCGGGTCAATATAGAATCGATATATTTTT
Found at i:1417466 original size:59 final size:60
Alignment explanation
Indices: 1417309--1417490 Score: 188
Period size: 60 Copynumber: 3.0 Consensus size: 60
1417299 ATATTTCTCT
* ** * **
1417309 AAACTATGACTCTCATTTTAAATTAGTAGTTAAACTTTTAAATATTCCAATTTCATCCTT
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCC
* * * * *
1417369 AAACTATGACTTTTATACTAAATTAGTCCTTAAACTTTTGAACATTCTAATTT-ATCCCC
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCC
* * * * **
1417428 AAACTATGAATCTCATTCTAAATTGGTCCCTAACCTTTTAAATC-TTTGAATTTCATCCCC
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAA-CATTCCAATTTCATCCCC
1417488 AAA
1 AAA
1417491 TTCATCCCAA
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 45 0.45
60 54 0.55
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCC
Found at i:1418565 original size:21 final size:20
Alignment explanation
Indices: 1418531--1418573 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1418521 ATTGAGTTTT
*
1418531 AAGAAAAATCAGTTCAAAGAA
1 AAGAAAAATAAGTT-AAAGAA
* *
1418552 AAGAAAGATAAGTTAAATAA
1 AAGAAAAATAAGTTAAAGAA
1418572 AA
1 AA
1418574 ATGTTTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.65, C:0.05, G:0.14, T:0.16
Consensus pattern (20 bp):
AAGAAAAATAAGTTAAAGAA
Found at i:1418803 original size:6 final size:6
Alignment explanation
Indices: 1418794--1418821 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1418784 AAACTTAAAT
1418794 TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAA
1418822 AAAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:1418897 original size:18 final size:18
Alignment explanation
Indices: 1418874--1418909 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1418864 TTAATATACC
1418874 CCTTACTTTTTATAAGGA
1 CCTTACTTTTTATAAGGA
1418892 CCTTACTTTTTATAAGGA
1 CCTTACTTTTTATAAGGA
1418910 TTAACTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
CCTTACTTTTTATAAGGA
Found at i:1419103 original size:13 final size:13
Alignment explanation
Indices: 1419085--1419110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1419075 CAAGTTTGAT
1419085 AATATTTTTAAAA
1 AATATTTTTAAAA
1419098 AATATTTTTAAAA
1 AATATTTTTAAAA
1419111 CTTAAATTTG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATTTTTAAAA
Found at i:1428791 original size:23 final size:22
Alignment explanation
Indices: 1428736--1428793 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
1428726 TTCAGCACTA
*
1428736 GGTATCGATACCCCCTTGAATG
1 GGTACCGATACCCCCTTGAATG
** *
1428758 GGTACAAATACCCCCTTTGAGTG
1 GGTACCGATACCCCC-TTGAATG
1428781 GGTACCGATACCC
1 GGTACCGATACCC
1428794 TCCACGGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGAATG
Found at i:1430873 original size:30 final size:28
Alignment explanation
Indices: 1430807--1430942 Score: 121
Period size: 30 Copynumber: 4.6 Consensus size: 28
1430797 CATTAAAAAT
*
1430807 ATATATTTTATTCTTATCTTACCTTAAA
1 ATATATTTTATTCTTATCTTAACTTAAA
*
1430835 ATTATATTTTATTCTTATTTTAACTTGAAGA
1 A-TATATTTTATTCTTATCTTAACTT-AA-A
* *
1430866 ATATATTTTAATT-TTTTATTAACTTGAAAA
1 ATATATTTT-ATTCTTATCTTAACTT--AAA
* * *
1430896 ATATAATTTATTCTTACCTTACCTTAATA
1 ATATATTTTATTCTTATCTTAACTTAA-A
*
1430925 TTTATATTTTATTCTTAT
1 -ATATATTTTATTCTTAT
1430943 AATATTTTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
28 3 0.03
29 26 0.30
30 51 0.59
31 7 0.08
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATATTTTATTCTTATCTTAACTTAAA
Found at i:1430983 original size:30 final size:30
Alignment explanation
Indices: 1430947--1431219 Score: 138
Period size: 30 Copynumber: 9.2 Consensus size: 30
1430937 TCTTATAATA
*
1430947 TTTTAAAATTAAGATAAAAATAAAATATAT
1 TTTTAAAATTAAGATAAGAATAAAATATAT
* *
1430977 TTTT-AAATTAAAATAAAAATAAAATATACAT
1 TTTTAAAATTAAGATAAGAATAAAATAT--AT
*
1431008 TTTT-AAA-TAAAATTAA-AA-AAAATATAT
1 TTTTAAAATTAAGA-TAAGAATAAAATATAT
** * *
1431035 TTTT--TGTTAAAATAAGGAT-AAAT-TAT
1 TTTTAAAATTAAGATAAGAATAAAATATAT
* * * * *
1431061 ATTTAATAATTCAAGGTATGACTAGAATATA-
1 TTTTAA-AATT-AAGATAAGAATAAAATATAT
* * *
1431092 -TTCAATAATTTAAGTTAAGAATATAATATAT
1 TTTTAA-AA-TTAAGATAAGAATAAAATATAT
* *** * * * *
1431123 GTAGCAAGTTAAAATAAAAATAAGATATATT
1 TTTTAAAATTAAGATAAGAATAAAATATA-T
*
1431154 TTTTAAAAGTTAAGATAAGATTAAAATATAT
1 TTTTAAAA-TTAAGATAAGAATAAAATATAT
* *
1431185 TTTT-AAGTTAAGATAAGATTAAAATATAT
1 TTTTAAAATTAAGATAAGAATAAAATATAT
1431214 TTTTAA
1 TTTTAA
1431220 GTTAATGGTG
Statistics
Matches: 188, Mismatches: 37, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
26 9 0.05
27 16 0.09
29 57 0.30
30 58 0.31
31 27 0.14
32 21 0.11
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTAAAATTAAGATAAGAATAAAATATAT
Found at i:1430984 original size:29 final size:29
Alignment explanation
Indices: 1430944--1431224 Score: 158
Period size: 29 Copynumber: 9.5 Consensus size: 29
1430934 TATTCTTATA
* *
1430944 ATATTTTAAAATTAAGATAAAAATAAAAT
1 ATATTTTTAAATTAAGATAAGAATAAAAT
* *
1430973 ATATTTTTAAATTAAAATAAAAATAAAAT
1 ATATTTTTAAATTAAGATAAGAATAAAAT
*
1431002 ATACATTTTTAAA-TAAAATTAA-AA-AAAAT
1 AT--ATTTTTAAATTAAGA-TAAGAATAAAAT
** * * *
1431031 ATATTTTT-TGTTAAAATAAGGATAAATT
1 ATATTTTTAAATTAAGATAAGAATAAAAT
* * * * *
1431059 ATA-TTTAATAATTCAAGGTATGACTAGAAT
1 ATATTTTTA-AATT-AAGATAAGAATAAAAT
** * * *
1431089 ATATTCAATAATTTAAGTTAAGAATATAAT
1 ATATT-TTTAAATTAAGATAAGAATAAAAT
*** * * * *
1431119 ATATGTAGCAAGTTAAAATAAAAATAAGAT
1 ATAT-TTTTAAATTAAGATAAGAATAAAAT
*
1431149 ATATTTTTTAAAAGTTAAGATAAGATTAAAAT
1 ATA-TTTTT-AAA-TTAAGATAAGAATAAAAT
* *
1431181 ATATTTTTAAGTTAAGATAAGATTAAAAT
1 ATATTTTTAAATTAAGATAAGAATAAAAT
*
1431210 ATATTTTTAAGTTAA
1 ATATTTTTAAATTAA
1431225 TGGTGAAAGT
Statistics
Matches: 196, Mismatches: 41, Indels: 30
0.73 0.15 0.11
Matches are distributed among these distances:
26 3 0.02
27 15 0.08
28 7 0.04
29 71 0.36
30 57 0.29
31 25 0.13
32 18 0.09
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATTTTTAAATTAAGATAAGAATAAAAT
Found at i:1442595 original size:20 final size:20
Alignment explanation
Indices: 1442553--1442602 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1442543 GATTTCTGGG
* * *
1442553 CAAGGGAATCGGTACCCATT
1 CAAGGGAACCGATACCCACT
*
1442573 CAAGGGAACCGATACCCCCT
1 CAAGGGAACCGATACCCACT
*
1442593 CAAGTGAACC
1 CAAGGGAACC
1442603 AGAATTTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.14
Consensus pattern (20 bp):
CAAGGGAACCGATACCCACT
Found at i:1442668 original size:23 final size:22
Alignment explanation
Indices: 1442620--1442668 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1442610 ACAGAATGTC
*
1442620 AAGG-GGGAACTGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
1442641 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
1442664 AAGGA
1 AAGGA
1442669 AAATTATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1443783 original size:31 final size:31
Alignment explanation
Indices: 1443601--1443787 Score: 304
Period size: 31 Copynumber: 6.0 Consensus size: 31
1443591 AGGGTTGAGG
* *
1443601 GTTTACCTATGTTCTTCGGAACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1443632 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1443663 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1443694 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1443725 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1443756 GATTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1443787 G
1 G
1443788 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1445441 original size:2 final size:2
Alignment explanation
Indices: 1445434--1445463 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1445424 ACTTGTTGAA
1445434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1445464 CGCAAGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1445771 original size:29 final size:29
Alignment explanation
Indices: 1445737--1445815 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
1445727 CGGTGATCGG
*
1445737 TATATTTACCGATCTAACACCGGCCAGAT
1 TATATTTCCCGATCTAACACCGGCCAGAT
* *
1445766 TATATTTCCCGATCTAATACCGGTCAGAT
1 TATATTTCCCGATCTAACACCGGCCAGAT
1445795 TATATTTCCCGATCTAACACC
1 TATATTTCCCGATCTAACACC
1445816 CGTAGCAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (29 bp):
TATATTTCCCGATCTAACACCGGCCAGAT
Found at i:1446287 original size:26 final size:25
Alignment explanation
Indices: 1446237--1446288 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
1446227 CGTTATAAGG
*
1446237 TAATTTTGTTATATTTTTTTAATTA
1 TAATTTTGTTATATTTTTATAATTA
*
1446262 TAATTATTGTT-TATTTATTATCATTA
1 TAATT-TTGTTATATTT-TTATAATTA
1446288 T
1 T
1446289 TTGAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (25 bp):
TAATTTTGTTATATTTTTATAATTA
Found at i:1446922 original size:263 final size:262
Alignment explanation
Indices: 1446451--1446980 Score: 1024
Period size: 263 Copynumber: 2.0 Consensus size: 262
1446441 TGTTATATTT
*
1446451 TCGTTCATATATAATTTATTTAATCAGATTTGTTTCAGTTATTTTTTTTGCATATATAATATTGC
1 TCGTTCATATATAATTTATTTAATCAGATTTGTTTCAGTTATTTTTTTTGCAGATATAATATTGC
1446516 CGCACTTTTAAACTCAAAGAATGACGCGACTTTCAGCTATTGTTTATTATGATGGTGAAATTCGA
66 CGCACTTTTAAACTCAAAGAATGACGCGACTTTCAGCTATTGTTTATTATGATGGTGAAATTCGA
1446581 GAAGATGAAATCGGCGTTGTTTTCGTATCAAATGAGAGTGTTAAAATATCATTCAAGAGAAACAT
131 GAAGATGAAATCGGCGTTGTTTTCGTATCAAATGAGAGTGTTAAAATATCATTCAAGAGAAACAT
1446646 AACTCTTGAGGAGCTGATAACGAAGATTTCGAGGAAGATTCATGTTGGAAGTAGTAGAAGAATGT
196 AACTCTTGAGGAGCTGATAACGAAGATTTCGAGGAAGATTCATGTTGGAAGTAGTAGAAGAATGT
1446711 CG
261 CG
1446713 TCGTTCATATATAATTTATTTAATCAGATTTGTTTCAGTTATTTTTTTTGCAGATATAATATTGC
1 TCGTTCATATATAATTTATTTAATCAGATTTGTTTCAGTTATTTTTTTTGCAGATATAATATTGC
*
1446778 CGCACTTTTAAACTCAAAGAATGGCGCGACTTTCAGCTATTGTTTTATTATGATGGTGAAATTCG
66 CGCACTTTTAAACTCAAAGAATGACGCGACTTTCAGCTATTG-TTTATTATGATGGTGAAATTCG
*
1446843 AGAAGATGAAATCGGCGTTGTTTTCGTATCAAATGAGCGTGTTAAAATATCATTCAAGAGAAACA
130 AGAAGATGAAATCGGCGTTGTTTTCGTATCAAATGAGAGTGTTAAAATATCATTCAAGAGAAACA
1446908 TAACTCTTGAGGAGCTGATAACGAAGATTTCGAGGAAGATTCATGTTGGAAGTAGTAGAAGAATG
195 TAACTCTTGAGGAGCTGATAACGAAGATTTCGAGGAAGATTCATGTTGGAAGTAGTAGAAGAATG
1446973 TCG
260 TCG
1446976 TCGTT
1 TCGTT
1446981 GCAGTACAGA
Statistics
Matches: 264, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
262 105 0.40
263 159 0.60
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (262 bp):
TCGTTCATATATAATTTATTTAATCAGATTTGTTTCAGTTATTTTTTTTGCAGATATAATATTGC
CGCACTTTTAAACTCAAAGAATGACGCGACTTTCAGCTATTGTTTATTATGATGGTGAAATTCGA
GAAGATGAAATCGGCGTTGTTTTCGTATCAAATGAGAGTGTTAAAATATCATTCAAGAGAAACAT
AACTCTTGAGGAGCTGATAACGAAGATTTCGAGGAAGATTCATGTTGGAAGTAGTAGAAGAATGT
CG
Found at i:1449867 original size:35 final size:34
Alignment explanation
Indices: 1449782--1449868 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
1449772 AATATAATTT
*
1449782 TAAATACAACAAACTTACAATAAGTATAAAATGG
1 TAAATACAACAAAATTACAATAAGTATAAAATGG
* * *
1449816 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATAAAATGG
1449854 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1449869 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATAAAATGG
Found at i:1452109 original size:111 final size:110
Alignment explanation
Indices: 1451979--1452191 Score: 374
Period size: 111 Copynumber: 1.9 Consensus size: 110
1451969 AATTAAAAAA
1451979 ATTTATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAAATTTAAAT
1 ATTTATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAAT-AATTTAAAT
1452044 T-AATAAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGAT
65 TAAATAAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGAT
*
1452089 ATTTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAATTATTACTAATAATTTAAAT
1 ATTT-ATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAAT
* *
1452154 TAAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGT
65 TAAATAAAAACATTAAAATGTTACCGTATCAGCAAAGT
1452192 ATAAAGATAT
Statistics
Matches: 98, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
110 14 0.14
111 84 0.86
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (110 bp):
ATTTATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
AAATAAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGAT
Found at i:1452306 original size:17 final size:18
Alignment explanation
Indices: 1452265--1452303 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1452255 ATTATATTAC
1452265 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
1452282 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
1452300 TAAA
1 TAAA
1452304 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:1452364 original size:10 final size:10
Alignment explanation
Indices: 1452346--1452375 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1452336 TTAAAAAGAT
*
1452346 AGAGTATTTG
1 AGAGAATTTG
1452356 AGAGAATTTG
1 AGAGAATTTG
1452366 AGAGAATTTG
1 AGAGAATTTG
1452376 GTGTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:1452552 original size:50 final size:51
Alignment explanation
Indices: 1452498--1452607 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
1452488 AGATAACCAG
* * *
1452498 GTATAGCGCGGATCA-AGGGGCGCACTATAC-CTACGTGGCGTCAAATCACC
1 GTATAGCGCGGAGCAGA-GGGCGCACTATACTCCACGTGGCGCCAAATCACC
* * * *
1452548 GTATATCGCGGGGCAGAGGGCGCGCTATACTCCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGAGCAGAGGGCGCACTATACTCCACGTGGCGCCAAATCACC
1452599 GTATAGCGC
1 GTATAGCGC
1452608 ATTGCAGGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 24 0.48
51 26 0.52
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.17
Consensus pattern (51 bp):
GTATAGCGCGGAGCAGAGGGCGCACTATACTCCACGTGGCGCCAAATCACC
Found at i:1453918 original size:42 final size:43
Alignment explanation
Indices: 1453885--1453966 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
1453875 ATATTAATGT
1453885 ATTAT-TTTAGT-ATAATTTTAATAA-A-AATATTAATTATTAC
1 ATTATATTTAGTGATAATTTTAATAATATAATATTAA-TATTAC
*
1453925 ATTATATTTATTGATAATTTTAATAATATAATATTATATATT
1 ATTATATTTAGTGATAATTTTAATAATATAATATTA-ATATT
1453967 TTATCATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 5 0.14
41 5 0.14
42 13 0.36
43 1 0.03
44 11 0.31
45 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (43 bp):
ATTATATTTAGTGATAATTTTAATAATATAATATTAATATTAC
Found at i:1454117 original size:14 final size:14
Alignment explanation
Indices: 1454098--1454137 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1454088 TACTATAATA
*
1454098 TAATATTTTTATTT
1 TAATATTTTAATTT
*
1454112 TAATATTATAATTT
1 TAATATTTTAATTT
1454126 TAAATATTTTAA
1 T-AATATTTTAA
1454138 CAATATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATATTTTAATTT
Found at i:1454156 original size:14 final size:14
Alignment explanation
Indices: 1454098--1454156 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
1454088 TACTATAATA
*
1454098 TAATATTTTTATTT
1 TAATATTATTATTT
*
1454112 TAATATTATAATTT
1 TAATATTATTATTT
*
1454126 TAA-A-TATT-TTAA
1 TAATATTATTATT-T
*
1454138 CAATATTATTATTT
1 TAATATTATTATTT
1454152 TAATA
1 TAATA
1454157 ATTAAATACT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 2 0.06
14 23 0.68
15 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATATTATTATTT
Found at i:1454190 original size:40 final size:42
Alignment explanation
Indices: 1454141--1454230 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 42
1454131 ATTTTAACAA
*
1454141 TATTATTATTTTAATAATTAAATACTATAA-TTAAAAT-ATAT
1 TATT-TTATTTTAATAATTAAATAATATAATTTAAAATAATAT
* * *
1454182 TATTTTATTTTAATAATTAATTAATATAATTTATAATAATGT
1 TATTTTATTTTAATAATTAAATAATATAATTTAAAATAATAT
1454224 TATTTTA
1 TATTTTA
1454231 ATAAAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 23 0.53
41 10 0.23
42 10 0.23
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (42 bp):
TATTTTATTTTAATAATTAAATAATATAATTTAAAATAATAT
Found at i:1454293 original size:14 final size:14
Alignment explanation
Indices: 1454202--1454295 Score: 52
Period size: 14 Copynumber: 6.9 Consensus size: 14
1454192 TAATAATTAA
1454202 TTAAT-ATAAT-TT
1 TTAATAATAATATT
* **
1454214 ATAATAATGTTATT
1 TTAATAATAATATT
* *
1454228 TTAATAA-AAAATA
1 TTAATAATAATATT
*
1454241 TTAATCATAATATTT
1 TTAATAATAATA-TT
* * *
1454256 TTATTTATAAAATT
1 TTAATAATAATATT
*
1454270 ATAGAT-ATAATATT
1 TTA-ATAATAATATT
1454284 TTAATAATAATA
1 TTAATAATAATA
1454296 ATATTGACAT
Statistics
Matches: 58, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
12 4 0.07
13 13 0.22
14 30 0.52
15 11 0.19
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (14 bp):
TTAATAATAATATT
Found at i:1454310 original size:29 final size:27
Alignment explanation
Indices: 1454224--1454307 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
1454214 ATAATAATGT
*
1454224 TATTTTAATAA-AAAATATTAATCATAA
1 TATTTTAATAATAAAATATTGA-CATAA
* * * *
1454251 TATTTTTATTTATAAAATTATAGATATAA
1 TA-TTTTAATAATAAAA-TATTGACATAA
1454280 TATTTTAATAATAATAATATTGACATAA
1 TATTTTAATAATAA-AATATTGACATAA
1454308 ATAATATTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
27 2 0.05
28 26 0.59
29 12 0.27
30 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTTTAATAATAAAATATTGACATAA
Found at i:1454367 original size:24 final size:24
Alignment explanation
Indices: 1454336--1454385 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1454326 TTTTAATATT
*
1454336 TTAAAAATAATATTA-TTATTTTA
1 TTAAAAATAATATTATTTATTGTA
1454359 TTAATAAATAATATTATTTATTGTA
1 TTAA-AAATAATATTATTTATTGTA
1454384 TT
1 TT
1454386 TGATGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTAAAAATAATATTATTTATTGTA
Found at i:1455810 original size:22 final size:22
Alignment explanation
Indices: 1455785--1455838 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1455775 GAAATTTATC
*
1455785 CCGAAGGACCTATGTATTTGTA
1 CCGAAGGACCTATGTATATGTA
* * * *
1455807 CCGAATGACTTTTGTATATGTC
1 CCGAAGGACCTATGTATATGTA
1455829 CCGAAGGACC
1 CCGAAGGACC
1455839 GCGTAGACCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (22 bp):
CCGAAGGACCTATGTATATGTA
Found at i:1458246 original size:2 final size:2
Alignment explanation
Indices: 1458239--1458264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1458229 ATTTTATACA
1458239 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1458265 GAAAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1458926 original size:20 final size:20
Alignment explanation
Indices: 1458889--1458927 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1458879 GAATTTTTTT
* *
1458889 TATTATTATTTTTTAAATAA
1 TATTATTATTATTAAAATAA
*
1458909 TATTTTTATTATTAAAATA
1 TATTATTATTATTAAAATA
1458928 GTCAAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTATTATTATTAAAATAA
Found at i:1459619 original size:34 final size:34
Alignment explanation
Indices: 1459577--1459662 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
1459567 ACTCGAACTC
*
1459577 AAAAATATTTTATATATAATTAATATAAAAAATA
1 AAAAATATTATATATATAATTAATATAAAAAATA
1459611 AAAAATATTATATATATAATTAATATAAAAAATA
1 AAAAATATTATATATATAATTAATATAAAAAATA
*
1459645 TAAAATATTATATATATA
1 AAAAATATTATATATATA
1459663 TAATCGGGGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AAAAATATTATATATATAATTAATATAAAAAATA
Found at i:1460908 original size:21 final size:21
Alignment explanation
Indices: 1460884--1460936 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1460874 ATTATGACTA
*
1460884 TCGCAATGCGATTTT-TCAATT
1 TCGCAATGCGATTTTCCCAA-T
** *
1460905 TCGCGTTGTGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
1460926 TCGCAATGCGA
1 TCGCAATGCGA
1460937 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:1460977 original size:21 final size:20
Alignment explanation
Indices: 1460926--1460977 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1460916 TTTTCCCAAT
*
1460926 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
1460946 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1460967 TCGCAATGCGA
1 TCGCAATGCGA
1460978 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1460990 original size:41 final size:41
Alignment explanation
Indices: 1460963--1461060 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
1460953 GCGAATTGGG
*
1460963 AAAATCGCAATGCGATACTGACTATCACAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* * *
1461004 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* *
1461045 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1461061 TTTCAAAGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:1460999 original size:20 final size:20
Alignment explanation
Indices: 1460966--1461040 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1460956 AATTGGGAAA
*
1460966 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1460986 ATCACAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1461007 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1461027 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1461041 ATACATAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1461016 original size:21 final size:20
Alignment explanation
Indices: 1460990--1461060 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
1460980 CTGACTATCA
1460990 CAACGCGATAATACAAAATCG
1 CAACGCGATAATAC-AAATCG
* **
1461011 CAACGCGATACTGAC-TTTCG
1 CAACGCGATAAT-ACAAATCG
*
1461031 CAACGAGATAATACATAATCG
1 CAACGCGATAATACA-AATCG
*
1461052 CAATGCGAT
1 CAACGCGAT
1461061 TTTCAAAGCG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.34
21 21 0.55
22 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
CAACGCGATAATACAAATCG
Found at i:1461257 original size:22 final size:22
Alignment explanation
Indices: 1461229--1461272 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1461219 CTCTCTCACA
1461229 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1461251 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1461273 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1461564 original size:20 final size:20
Alignment explanation
Indices: 1461539--1461587 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1461529 TTTATTCTCT
1461539 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1461559 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
1461579 TGTTGCGAT
1 CGTTGCGAT
1461588 TTTTATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1462939 original size:18 final size:18
Alignment explanation
Indices: 1462918--1462965 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1462908 TCCACTTCGG
1462918 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1462936 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1462954 GAGCCATCACCT
1 GAGCCATCACCT
1462966 GATCGGCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1463560 original size:19 final size:20
Alignment explanation
Indices: 1463517--1463561 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1463507 CGCAACACGA
1463517 AAATGACTATCACAACGCGG
1 AAATGACTATCACAACGCGG
* * *
1463537 AAATGGCTATCGCAATGC-G
1 AAATGACTATCACAACGCGG
1463556 AAATGA
1 AAATGA
1463562 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:1463652 original size:33 final size:33
Alignment explanation
Indices: 1463615--1463697 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
1463605 GCGATTTGTG
**
1463615 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
1463648 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
*
1463681 TTTCGCATTGCGATTTT
1 TTTCGCGTTGCGATTTT
1463698 CATTTCGCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.51
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
Found at i:1463662 original size:19 final size:19
Alignment explanation
Indices: 1463634--1463752 Score: 95
Period size: 19 Copynumber: 6.4 Consensus size: 19
1463624 GCGATTTTGT
*
1463634 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1463653 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
*
1463667 CGTTGCAATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1463686 CATTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
***
1463705 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1463725 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1463745 CATTGCGA
1 CGTTGCGA
1463753 AAGTAAGTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
14 7 0.09
15 3 0.04
16 2 0.02
17 2 0.02
18 3 0.04
19 37 0.46
20 24 0.30
21 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1463728 original size:20 final size:19
Alignment explanation
Indices: 1463679--1463752 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
1463669 TTGCAATTTT
* ***
1463679 CATTTCGCATTGCGATTTT
1 CATTTCGCGTTGCGATAGC
1463698 CATTTCGCGTTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1463717 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1463737 CATTTTCGCATTGCGA
1 CA-TTTCGCGTTGCGA
1463753 AAGTAAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.43
20 24 0.51
21 3 0.06
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1463763 original size:20 final size:20
Alignment explanation
Indices: 1463740--1463778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1463730 CGATAGTCAT
1463740 TTTCGCATTGCGAAAGTAAG
1 TTTCGCATTGCGAAAGTAAG
**
1463760 TTTCGTGTTGCGAAAGTAA
1 TTTCGCATTGCGAAAGTAA
1463779 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCATTGCGAAAGTAAG
Found at i:1464179 original size:21 final size:20
Alignment explanation
Indices: 1464127--1464187 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
1464117 GACTCACCTG
1464127 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
1464147 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
1464168 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
1464188 CCCACCATTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:1464214 original size:41 final size:42
Alignment explanation
Indices: 1464124--1464214 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
1464114 CCCGACTCAC
* * *
1464124 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
* *
1464166 CTATCATCCCTCAAGAGTCCCC-CCCACCATTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
1464207 CTGTCATC
1 CTGTCATC
1464215 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
Found at i:1465635 original size:14 final size:14
Alignment explanation
Indices: 1465593--1465629 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1465583 GATTGTTTAA
*
1465593 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
1465607 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
1465621 TTGATTTGT
1 TTGATTTGT
1465630 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:1465835 original size:19 final size:18
Alignment explanation
Indices: 1465807--1465957 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
1465797 CAAAACTAAA
1465807 TTCGCGTTGCGATTTTCAT
1 TTCGC-TTGCGATTTTCAT
*
1465826 TTCGCTTTGCGA--TTC-C
1 TTCGC-TTGCGATTTTCAT
*
1465842 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
*
1465859 TTCGCATTACGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
1465875 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
1465892 TTCGCGTTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
1465908 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
* **
1465925 TTCGCATTACGATAGTCAT
1 TTCGC-TTGCGATTTTCAT
1465944 TTCCGCGTTGCGAT
1 TT-CGC-TTGCGAT
1465958 AGACATTAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 17 0.17
16 20 0.20
17 20 0.20
19 34 0.34
20 9 0.09
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (18 bp):
TTCGCTTGCGATTTTCAT
Found at i:1465853 original size:33 final size:33
Alignment explanation
Indices: 1465811--1465937 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1465801 ACTAAATTCG
* *
1465811 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1465844 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1465877 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1465910 CGTTGCGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1465938 AGTCATTTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1465915 original size:14 final size:14
Alignment explanation
Indices: 1465868--1465919 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1465858 TTTCGCATTA
1465868 CGATTCTCTCGTTG
1 CGATTCTCTCGTTG
*
1465882 CGATTTTCATTTCGCGTTG
1 CGA--TTC---TCTCGTTG
1465901 CGATTCTCTCGTTG
1 CGATTCTCTCGTTG
1465915 CGATT
1 CGATT
1465920 TTCATTTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.48
16 3 0.10
17 3 0.10
19 10 0.32
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGATTCTCTCGTTG
Found at i:1465917 original size:66 final size:66
Alignment explanation
Indices: 1465811--1465937 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 66
1465801 ACTAAATTCG
*
1465811 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTC
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTC
1465876 T
66 T
*
1465877 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGAT
1465938 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTC
T
Found at i:1468281 original size:12 final size:12
Alignment explanation
Indices: 1468264--1468288 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1468254 TCTTCGGAGA
1468264 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1468276 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1468288 C
1 C
1468289 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1468422 original size:25 final size:25
Alignment explanation
Indices: 1468394--1468448 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1468384 CTGTTTCATC
* * *
1468394 ATCAAAAATTCGGGTATTGACCAAT
1 ATCAAAAATCCAGGTATTGACCAAG
*
1468419 ATC-AAAGTCCAGGTATTGACCAAG
1 ATCAAAAATCCAGGTATTGACCAAG
1468443 ATCAAA
1 ATCAAA
1468449 TTTCGAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (25 bp):
ATCAAAAATCCAGGTATTGACCAAG
Found at i:1469216 original size:20 final size:20
Alignment explanation
Indices: 1469195--1469302 Score: 171
Period size: 20 Copynumber: 5.4 Consensus size: 20
1469185 TGTATTATCT
* *
1469195 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
1469215 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
1469235 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
1469255 TGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
1469275 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
1469295 CGTTGCGA
1 CGTTGCGA
1469303 TTTTTGTATT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1469345 original size:20 final size:20
Alignment explanation
Indices: 1469190--1469344 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1469180 GATTCTGTAT
* *
1469190 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
1469210 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1469230 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
1469250 AATCGTGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1469270 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1469290 TATCGCGTTGCGATTTTTGT-AT
1 TATCGCGTTGCGA---AAGTCAG
*
1469312 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1469332 TATCGCATTGCGA
1 TATCGCGTTGCGA
1469345 TTTTCCAAAT
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.03
20 100 0.84
22 14 0.12
23 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1469378 original size:20 final size:21
Alignment explanation
Indices: 1469334--1469385 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1469324 ATAGTCAGTA
*
1469334 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1469355 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1469375 TCGCATTGCGA
1 TCGCATTGCGA
1469386 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1469427 original size:21 final size:22
Alignment explanation
Indices: 1469375--1469427 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1469365 ATTTACTTAT
1469375 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1469396 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1469417 TCGCATTGCGA
1 TCGCATTGCGA
1469428 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1471213 original size:6 final size:6
Alignment explanation
Indices: 1471204--1471266 Score: 66
Period size: 6 Copynumber: 11.5 Consensus size: 6
1471194 CGACGATAAC
*
1471204 GACGAT GACGAT GACGA- -A-GAT GACGAT GACGAT GAC--- GACGAC
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT
*
1471246 GACGAT GACGAT GATGAT GAC
1 GACGAT GACGAT GACGAT GAC
1471267 AGCGAGGAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
3 5 0.10
4 1 0.02
5 1 0.02
6 41 0.85
ACGTcount: A:0.35, C:0.17, G:0.33, T:0.14
Consensus pattern (6 bp):
GACGAT
Found at i:1471213 original size:15 final size:15
Alignment explanation
Indices: 1471189--1471259 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
1471179 ACCTGCTCAG
* *
1471189 GACGACGACGATAAC
1 GACGATGACGATGAC
1471204 GACGATGACGATGAC
1 GACGATGACGATGAC
*
1471219 GAAGATGACGAT---
1 GACGATGACGATGAC
*
1471231 GACGATGACGACGAC
1 GACGATGACGATGAC
1471246 GACGATGACGATGA
1 GACGATGACGATGA
1471260 TGATGACAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.21
15 37 0.79
ACGTcount: A:0.37, C:0.20, G:0.32, T:0.11
Consensus pattern (15 bp):
GACGATGACGATGAC
Found at i:1471219 original size:21 final size:20
Alignment explanation
Indices: 1471189--1471259 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 20
1471179 ACCTGCTCAG
*
1471189 GACGACGACGATAACGACGAT
1 GACGATGACGA-AACGACGAT
*
1471210 GACGATGACGAAGATGACGAT
1 GACGATGACGAA-ACGACGAT
*
1471231 GACGATGACGACGACGACGAT
1 GACGATGACGA-AACGACGAT
1471252 GACGATGA
1 GACGATGA
1471260 TGATGACAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.37, C:0.20, G:0.32, T:0.11
Consensus pattern (20 bp):
GACGATGACGAAACGACGAT
Found at i:1471225 original size:9 final size:9
Alignment explanation
Indices: 1471192--1471262 Score: 58
Period size: 9 Copynumber: 8.2 Consensus size: 9
1471182 TGCTCAGGAC
1471192 GACGACGAT
1 GACGACGAT
*
1471201 AACGACGAT
1 GACGACGAT
1471210 ---GACGAT
1 GACGACGAT
*
1471216 GACGAAGAT
1 GACGACGAT
* *
1471225 GACGATGAC
1 GACGACGAT
* *
1471234 GATGACGAC
1 GACGACGAT
1471243 GACGACGAT
1 GACGACGAT
*
1471252 GACGATGAT
1 GACGACGAT
1471261 GA
1 GA
1471263 TGACAGCGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 6 0.12
9 44 0.88
ACGTcount: A:0.37, C:0.18, G:0.32, T:0.13
Consensus pattern (9 bp):
GACGACGAT
Found at i:1476034 original size:60 final size:58
Alignment explanation
Indices: 1475917--1476102 Score: 171
Period size: 60 Copynumber: 3.1 Consensus size: 58
1475907 GCATCATACG
* * **
1475917 TCCCCAACCTATGACTCTCATT-TCAAATTAGTCCTTAAAATTTTAAGCATTTTAATTTCA
1 TCCCCAA-CTATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAA-TATTCCAATTTCA
* *
1475977 TCCCCTAACTATGACTCTCATTCTAAATTAGTCCTTGAACTTTTGAATATTCCAATTTTA
1 TCCCC-AACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTT-AATATTCCAATTTCA
* * * * * *
1476037 TCTCCAAACTAT-AATAGT-ATTCTAAATTGGTCCCTAAACTTTTAGATCTTCCAATTTCA
1 TC-CCCAACTATGACT-CTCATTCTAAATTAGTCCTTAAACTTTTA-ATATTCCAATTTCA
1476096 TCCCCAA
1 TCCCCAA
1476103 ATTCATCCAA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
58 5 0.05
59 38 0.36
60 55 0.52
61 7 0.07
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (58 bp):
TCCCCAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAATATTCCAATTTCA
Found at i:1476354 original size:60 final size:60
Alignment explanation
Indices: 1476268--1476384 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
1476258 AAGTTTGGGA
* **
1476268 ATTAATTTAGAATGAATATCACAGTTTGGGGATGAAAATAAAATATTTAAAA-GTTTAAAG
1 ATTAATTTAAAATGAATATCACAGTTTAAGGATGAAAATAAAATA-TTAAAATGTTTAAAG
* * * *
1476328 ATTATTTTAAAAT-AATAGTCATAGTTTAAGGATGAAATTGAAATATTAAAATGTTTA
1 ATTAATTTAAAATGAATA-TCACAGTTTAAGGATGAAAATAAAATATTAAAATGTTTA
1476385 GGGACTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 10 0.21
60 38 0.79
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.37
Consensus pattern (60 bp):
ATTAATTTAAAATGAATATCACAGTTTAAGGATGAAAATAAAATATTAAAATGTTTAAAG
Found at i:1478923 original size:54 final size:54
Alignment explanation
Indices: 1478671--1478933 Score: 341
Period size: 54 Copynumber: 4.9 Consensus size: 54
1478661 TAATTATTAC
* * *
1478671 AACTCATTAT-AATTTCCTTTG-GTTGCACACATAGTGCCAATACGGTAATTCACA
1 AACTCATTATGAA-TTCC-GTGAGTTGCACACATAGTGCCGATATGGTAATTCACA
* *
1478725 AACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCGATATGGTAATTCACA
1 AACTCATTATGAATTCCGTGAGTTGCACACATAGTGCCGATATGGTAATTCACA
** * * * *
1478779 AACTCATTATGAATTATGTGGGTTACACACATAGTGCTGATATGCTAATTCACA
1 AACTCATTATGAATTCCGTGAGTTGCACACATAGTGCCGATATGGTAATTCACA
* * * * *
1478833 AACTCATTATGAATTCCGCGAGTTGCACAGATAGTGTCAATACGGTAATTCACA
1 AACTCATTATGAATTCCGTGAGTTGCACACATAGTGCCGATATGGTAATTCACA
*
1478887 AACTCATTATGAATTCCGTGAGTTGCACACATAGTGTCGATATGGTA
1 AACTCATTATGAATTCCGTGAGTTGCACACATAGTGCCGATATGGTA
1478934 CACATAGTGT
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 179 0.98
55 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (54 bp):
AACTCATTATGAATTCCGTGAGTTGCACACATAGTGCCGATATGGTAATTCACA
Found at i:1478954 original size:18 final size:19
Alignment explanation
Indices: 1478913--1478959 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
1478903 CGTGAGTTGC
1478913 ACACATAGTGTCGATATGGT
1 ACACATAGTGTCGATA-GGT
1478933 ACACATAGTGTCGATA-GT
1 ACACATAGTGTCGATAGGT
1478951 ACACATAGT
1 ACACATAGT
1478960 ACCGATACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 11 0.41
20 16 0.59
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (19 bp):
ACACATAGTGTCGATAGGT
Found at i:1478965 original size:18 final size:18
Alignment explanation
Indices: 1478931--1478966 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1478921 TGTCGATATG
**
1478931 GTACACATAGTGTCGATA
1 GTACACATAGTACCGATA
1478949 GTACACATAGTACCGATA
1 GTACACATAGTACCGATA
1478967 CAACAATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (18 bp):
GTACACATAGTACCGATA
Found at i:1480162 original size:9 final size:8
Alignment explanation
Indices: 1480125--1480162 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
1480115 TACTTATCCT
1480125 TTTTTCCC
1 TTTTTCCC
1480133 TTTTTCCC
1 TTTTTCCC
1480141 TTTTTCCC
1 TTTTTCCC
*
1480149 TTTTCCCC
1 TTTTTCCC
1480157 TTTTTC
1 TTTTTC
1480163 AACACTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTTTCCC
Found at i:1483152 original size:15 final size:15
Alignment explanation
Indices: 1483132--1483170 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1483122 TTAACTCTTT
1483132 TGGAGCCATTCGATA
1 TGGAGCCATTCGATA
1483147 TGGAGCCATTCGATA
1 TGGAGCCATTCGATA
1483162 TGGAGCCAT
1 TGGAGCCAT
1483171 AGAAACAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (15 bp):
TGGAGCCATTCGATA
Found at i:1485435 original size:53 final size:54
Alignment explanation
Indices: 1485226--1485584 Score: 435
Period size: 54 Copynumber: 6.7 Consensus size: 54
1485216 TAACTATTAC
* *
1485226 AACTCATTAT-AATTTCCT-TGGGTTGCACATATAGTGCAGATACGGTAATTCACA
1 AACTCATTATGAA-TT-CTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
* * *
1485280 AACTCATTATGAATTCTGTGGGTTTCACACATAGTGTTGATACGGTAATTCATA
1 AACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
* *
1485334 ATCTCTTTATGAATT-TCGTGGGTTGCACACATAGTG-TCGATACGGTAATTCACA
1 AACTCATTATGAATTCT-GTGGGTTGCACACATAGTGCT-GATACGGTAATTCACA
* * * *
1485388 AACTCATTATGAATTCT-TGGGTTGTACACACAATGCTGATACAGTAATTCACA
1 AACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
* * ** * *
1485441 AACTAATTATGAATTCTGTGAGTTGCACACATAGTGCTGATA-AATAATTAAAA
1 AACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
*
1485494 AACTCATTATGAATTCTGTGAGTTGCACACATAGTG-TCGATACGGTAATTCACA
1 AACTCATTATGAATTCTGTGGGTTGCACACATAGTGCT-GATACGGTAATTCACA
* * *
1485548 AACTCATTATGAATTTTGTGAGTTGCACACGTAGTGC
1 AACTCATTATGAATTCTGTGGGTTGCACACATAGTGC
1485585 CGATGGTAAA
Statistics
Matches: 265, Mismatches: 30, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
52 1 0.00
53 97 0.37
54 164 0.62
55 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
AACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
Found at i:1485470 original size:107 final size:106
Alignment explanation
Indices: 1485247--1485584 Score: 407
Period size: 107 Copynumber: 3.2 Consensus size: 106
1485237 ATTTCCTTGG
*
1485247 GTTGCACATATAGTGCAGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTT-T-CACAC
1 GTTGCACACATAGTGCAGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGTACACAC
* * * *
1485310 ATAGTGTTGATACGGTAATTCATAATCTCTTTATGAATTTCGTGG
66 A-A-TG-TGATACGGTAATTCACAAACTCATTATGAATTT-GTGA
1485355 GTTGCACACATAGTGTC-GATACGGTAATTCACAAACTCATTATGAATTCT-TGGGTTGTACACA
1 GTTGCACACATAGTG-CAGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGTACACA
* *
1485418 CAATGCTGATACAGTAATTCACAAACTAATTATGAATTCTGTGA
65 CAATG-TGATACGGTAATTCACAAACTCATTATGAATT-TGTGA
* ** * * * * *
1485462 GTTGCACACATAGTGCTGATA-AATAATTAAAAAACTCATTATGAATTCTGTGAGTTGCACACAT
1 GTTGCACACATAGTGCAGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGTACACAC
*
1485526 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTTTGTGA
66 AATGT-GATACGGTAATTCACAAACTCATTATGAA-TTTGTGA
*
1485569 GTTGCACACGTAGTGC
1 GTTGCACACATAGTGC
1485585 CGATGGTAAA
Statistics
Matches: 203, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
106 26 0.13
107 118 0.58
108 52 0.26
109 7 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (106 bp):
GTTGCACACATAGTGCAGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGTACACAC
AATGTGATACGGTAATTCACAAACTCATTATGAATTTGTGA
Found at i:1492727 original size:257 final size:256
Alignment explanation
Indices: 1492248--1492754 Score: 685
Period size: 257 Copynumber: 2.0 Consensus size: 256
1492238 TCATGATGCC
** * *
1492248 TATTTATTGTTGTTTGATTTTACTTGGCATCTTTATGATATCAAGTACTATCACAATGTGTTGTA
1 TATTTATTGTTGTAAGATTATACTTGGCATCTTTATGATACCAAGTACTATCACAATGTGTTGTA
** * * **
1492313 TGTCGATGCATTGTAGGATGATACTGAGGTTAGAGACCTAGTACACGTTTACTCATGTTAAGCCC
66 TACCGATGCATTATAGGATGATACTGAGGTTAGAGACCTAGTACACATTTACTCATGCGAAGCCC
** * *
1492378 ATAGTGGAGACTAAGGGAAGCGTGAGACTTACACTTTAGTGATAGAACTATTGAACCTTAATTAG
131 ATAGCAGAGACTAAGGGAAGCGTGAGACTTACACTTTAGTGATAGAACCATTGAACCTTAAGTAG
* * *
1492443 GTAGCACTTGATATGGATCATGCATGTACGAACTTCTTATTATCTTGTCTTCTAGCATGAT
196 GTAGCACTTGATATGGATCATGCATGTACCAACTTCTTATTACCATGTCTTCTAGCATGAT
* * * * **
1492504 TATTTGTTGTTGTAAGATTATACTTGGCCTCTTTGTGATACCGAGTACTATCATTATGTGTTGTA
1 TATTTATTGTTGTAAGATTATACTTGGCATCTTTATGATACCAAGTACTATCACAATGTGTTGTA
* * *
1492569 TACCGATGCATTATAGGATGATGCTGAGGTTAGAGACCTATTACACATTTACTCATGGCGAGGCT
66 TACCGATGCATTATAGGATGATACTGAGGTTAGAGACCTAGTACACATTTACTCAT-GCGAAGC-
*** *
1492634 TTTTA-CAGAGACTAAGGGAAGTGTGAGACTTACACTTTAGTGATAGAACCATTGAACCTTAAGT
129 CCATAGCAGAGACTAAGGGAAGCGTGAGACTTACACTTTAGTGATAGAACCATTGAACCTTAAGT
* *
1492698 AGGTAGCACTTGATTAT-GATCATGCATGTACCTATTTCTTATTACCATGTCTTCTAG
194 AGGTAGCACTTGA-TATGGATCATGCATGTACCAACTTCTTATTACCATGTCTTCTAG
1492755 TGTGCTTTTG
Statistics
Matches: 216, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
256 105 0.49
257 106 0.49
258 5 0.02
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (256 bp):
TATTTATTGTTGTAAGATTATACTTGGCATCTTTATGATACCAAGTACTATCACAATGTGTTGTA
TACCGATGCATTATAGGATGATACTGAGGTTAGAGACCTAGTACACATTTACTCATGCGAAGCCC
ATAGCAGAGACTAAGGGAAGCGTGAGACTTACACTTTAGTGATAGAACCATTGAACCTTAAGTAG
GTAGCACTTGATATGGATCATGCATGTACCAACTTCTTATTACCATGTCTTCTAGCATGAT
Found at i:1497649 original size:26 final size:26
Alignment explanation
Indices: 1497620--1497671 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1497610 TGTAGTGACG
1497620 AAGCTACATAGGGATTAAGAGAGGTT
1 AAGCTACATAGGGATTAAGAGAGGTT
* *
1497646 AAGCTACATAGGGGTTAAGAGGGGTT
1 AAGCTACATAGGGATTAAGAGAGGTT
1497672 GTTGTCCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (26 bp):
AAGCTACATAGGGATTAAGAGAGGTT
Found at i:1505015 original size:15 final size:14
Alignment explanation
Indices: 1504972--1505005 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1504962 ATTAGGAGTA
*
1504972 TTTTTGTTATTATG
1 TTTTTATTATTATG
1504986 TTTTTATTATTATG
1 TTTTTATTATTATG
1505000 TTTTTA
1 TTTTTA
1505006 ATTTTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTTTATTATTATG
Found at i:1506769 original size:31 final size:31
Alignment explanation
Indices: 1506734--1506792 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1506724 AAAAAAAGAA
*
1506734 TAAACAATATATTTACCATTTAACTATTCAT
1 TAAACAATATATTTACCACTTAACTATTCAT
* *
1506765 TAAACTATATATTTACCACTTAATTATT
1 TAAACAATATATTTACCACTTAACTATT
1506793 TATCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAACAATATATTTACCACTTAACTATTCAT
Found at i:1506907 original size:20 final size:21
Alignment explanation
Indices: 1506877--1506915 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1506867 CAAATTACAA
*
1506877 AATTAATAAAATTAAAAGATC
1 AATTAATAAAAATAAAAGATC
1506898 AATT-ATAAAAATAAAAGA
1 AATTAATAAAAATAAAAGA
1506916 GTTAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (21 bp):
AATTAATAAAAATAAAAGATC
Found at i:1508907 original size:42 final size:42
Alignment explanation
Indices: 1508848--1508932 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1508838 CCACTTCAAC
1508848 ATGCTTTGTTCTATAATGGTGCATAGGATTATGTGAGATACT
1 ATGCTTTGTTCTATAATGGTGCATAGGATTATGTGAGATACT
1508890 ATGCTTTGTTCTATAATGGTGCATAGGATTATGTGAGATACT
1 ATGCTTTGTTCTATAATGGTGCATAGGATTATGTGAGATACT
1508932 A
1 A
1508933 ATCATTATCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (42 bp):
ATGCTTTGTTCTATAATGGTGCATAGGATTATGTGAGATACT
Found at i:1517883 original size:5 final size:5
Alignment explanation
Indices: 1517873--1517918 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
1517863 AATTCAATAA
* * *
1517873 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT ATAAT TAAAT TAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1517919 TAATTAATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AAAAT
Found at i:1517886 original size:22 final size:21
Alignment explanation
Indices: 1517846--1517910 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
1517836 TATTTTTAAA
*
1517846 AATAAAAATATTAAA-AAAATT
1 AATAAAAA-ATAAAATAAAATT
1517867 CAATAAAAAATAAAATAAAA-T
1 -AATAAAAAATAAAATAAAATT
*
1517888 AA-AATAAAATAAAATATAATT
1 AATAA-AAAATAAAATAAAATT
1517909 AA
1 AA
1517911 ATTAAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.05
20 15 0.39
21 9 0.24
22 12 0.32
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAAAAAATAAAATAAAATT
Found at i:1517919 original size:15 final size:15
Alignment explanation
Indices: 1517879--1517939 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
1517869 ATAAAAAATA
* *
1517879 AAATAAAATAAAATA
1 AAATAAAATATAATT
1517894 AAATAAAATATAATT
1 AAATAAAATATAATT
*
1517909 AAATTAAATATAATT
1 AAATAAAATATAATT
*
1517924 AATACAAAATA-AATT
1 AA-ATAAAATATAATT
1517939 A
1 A
1517940 TTAATTTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 34 0.85
16 6 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAAATATAATT
Found at i:1517923 original size:10 final size:10
Alignment explanation
Indices: 1517842--1517925 Score: 54
Period size: 10 Copynumber: 8.9 Consensus size: 10
1517832 AGCTTATTTT
*
1517842 TAAAAATAAA
1 TAAAATTAAA
*
1517852 -AATATTAAA
1 TAAAATTAAA
*
1517861 -AAAATTCAA
1 TAAAATTAAA
1517870 T-AAA--AAA
1 TAAAATTAAA
*
1517877 TAAAATAAAA
1 TAAAATTAAA
*
1517887 TAAAATAAAA
1 TAAAATTAAA
1517897 TAAAA-TATAA
1 TAAAATTA-AA
*
1517907 TTAAATTAAA
1 TAAAATTAAA
*
1517917 TATAATTAA
1 TAAAATTAA
1517926 TACAAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 18 0.31
10 33 0.56
11 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAATTAAA
Found at i:1522985 original size:30 final size:30
Alignment explanation
Indices: 1522951--1523026 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
1522941 GACTAAATTA
* *
1522951 AAATTTTAATTAAATTCGAGGACCAAAATG
1 AAATTTCAGTTAAATTCGAGGACCAAAATG
1522981 AAATTTCAGTTAAATTCGAGGACCAAAATG
1 AAATTTCAGTTAAATTCGAGGACCAAAATG
1523011 AAATTTCAGTTAAATT
1 AAATTTCAGTTAAATT
1523027 TATACCCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (30 bp):
AAATTTCAGTTAAATTCGAGGACCAAAATG
Done.