Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 17
Found at i:1350533 original size:34 final size:33
Alignment explanation
Indices: 1350445--1350540 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1350435 AAAACAGACT
* **
1350445 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
1350479 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1350512 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1350541 CGAAACTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1350536 original size:20 final size:19
Alignment explanation
Indices: 1350478--1350545 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
1350468 GCAACGAGAG
1350478 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1350497 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1350511 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1350531 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
1350546 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1350575 original size:20 final size:19
Alignment explanation
Indices: 1350549--1350669 Score: 100
Period size: 19 Copynumber: 6.8 Consensus size: 19
1350539 CGCGAAACTA
*
1350549 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1350568 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
1350586 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
1350602 ATTTCGTATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
1350621 ATTTCGCAATGCGA--TTC
1 ATTTCGCATTGCGATTTTC
* **
1350638 -TCTCG--TTGCGATAGTC
1 ATTTCGCATTGCGATTTTC
1350654 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1350670 CTCTCGTTAC
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
14 11 0.14
16 13 0.16
17 10 0.12
18 4 0.05
19 31 0.38
20 12 0.15
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:1350644 original size:52 final size:53
Alignment explanation
Indices: 1350549--1350669 Score: 181
Period size: 52 Copynumber: 2.3 Consensus size: 53
1350539 CGCGAAACTA
* * **
1350549 ATTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTTCGCAATGCGATTCACTCGTTGCGATAGTC
* *
1350602 ATTTCGTATTGCGATTTTCA-TTTCGCAATGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCATTGCGATTTTCATTTTCGCAATGCGATTCACTCGTTGCGATAGTC
1350654 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1350670 CTCTCGTTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
52 43 0.70
53 18 0.30
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTTCATTTTCGCAATGCGATTCACTCGTTGCGATAGTC
Found at i:1350647 original size:33 final size:33
Alignment explanation
Indices: 1350610--1350684 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
1350600 TCATTTCGTA
1350610 TTGCGATTTTCATTTCGCAATGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCAATGCGATTCTCTCG
** *
1350643 TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCAATGCGATTCTCTCG
*
1350676 TTACGATTT
1 TTGCGATTT
1350685 ACAGATACTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCAATGCGATTCTCTCG
Found at i:1350697 original size:20 final size:20
Alignment explanation
Indices: 1350672--1350783 Score: 152
Period size: 20 Copynumber: 5.5 Consensus size: 20
1350662 TTGCGATTCT
* *
1350672 CTCGTTACGATTTACAGATA
1 CTCGTTGCGATTTACGGATA
* *
1350692 CTCGTTGCGATTTACGTATT
1 CTCGTTGCGATTTACGGATA
1350712 CTCGTTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
*
1350732 CGCGTTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* *
1350752 CGCTTTGCGATTTTACGGATA
1 CTCGTTGCGA-TTTACGGATA
1350773 CTCGTTGCGAT
1 CTCGTTGCGAT
1350784 AGTCAGAATC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 63 0.78
21 18 0.22
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
CTCGTTGCGATTTACGGATA
Found at i:1350801 original size:41 final size:41
Alignment explanation
Indices: 1350674--1350805 Score: 119
Period size: 40 Copynumber: 3.3 Consensus size: 41
1350664 GCGATTCTCT
* * * * * * *
1350674 CGTTACGA-TTTACAGATACTCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTTACGGATACGCGTTGCGATTCACGAATACG
* *
1350714 CGTTGCGA-TTTACGGATACGCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGGATACGCGTTGCGATTCACGAATACG
* *
1350754 CTTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CG
1 CGTTGCGATTTTACGGATACGCGTTGCGAT--TCACGAATACG
1350795 CGTTGCGATTT
1 CGTTGCGATTT
1350806 ATATGTTCGC
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 41 0.53
41 32 0.41
42 3 0.04
43 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
CGTTGCGATTTTACGGATACGCGTTGCGATTCACGAATACG
Found at i:1350815 original size:20 final size:20
Alignment explanation
Indices: 1350792--1350844 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1350782 ATAGTCAGAA
1350792 TCGCGTTGCGATTT-ATATGT
1 TCGCGTTGCGATTTCATAT-T
1350812 TCGCGTTGCGATTTTCATATT
1 TCGCGTTGCGA-TTTCATATT
1350833 T-GCGTTGCGATT
1 TCGCGTTGCGATT
1350845 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.06
20 20 0.65
21 5 0.16
22 4 0.13
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTCATATT
Found at i:1350943 original size:20 final size:19
Alignment explanation
Indices: 1350894--1350947 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1350884 ATTCTTCATA
1350894 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
1350913 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
1350934 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1350948 TTTATTTTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:1353356 original size:15 final size:15
Alignment explanation
Indices: 1353334--1353375 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1353324 CTATATCTCC
1353334 AAAA-AAATAACCTT
1 AAAATAAATAACCTT
*
1353348 AAAATAAATATCCTT
1 AAAATAAATAACCTT
*
1353363 AAACTGAAATAAC
1 AAAAT-AAATAAC
1353376 TAAAATTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 4 0.17
15 13 0.57
16 6 0.26
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATAAATAACCTT
Found at i:1362900 original size:6 final size:6
Alignment explanation
Indices: 1362889--1362939 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
1362879 GGATTGTTCG
* *
1362889 AAAGAA AAAGAA AAAGAA AAAGAA AAA-AA GACATGAA AAAGAA ATAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -A-AAGAA AAAGAA AAAGAA
1362938 AA
1 AA
1362940 CAAAACAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 2 0.05
6 32 0.84
7 2 0.05
8 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:1366087 original size:9 final size:9
Alignment explanation
Indices: 1366065--1366109 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
1366055 TCTTTATTTA
1366065 TATT-ATAT
1 TATTAATAT
1366073 TA-TAATAT
1 TATTAATAT
1366081 TATTAATAT
1 TATTAATAT
*
1366090 TATTAATTT
1 TATTAATAT
1366099 TATTAAT-T
1 TATTAATAT
1366107 TAT
1 TAT
1366110 CATTACAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
7 1 0.03
8 12 0.35
9 21 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTAATAT
Found at i:1371767 original size:17 final size:17
Alignment explanation
Indices: 1371729--1371770 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1371719 ACATGGAAAA
1371729 GATATAAGCATGTGAAC
1 GATATAAGCATGTGAAC
* *
1371746 AATATAAGCATGTGAAG
1 GATATAAGCATGTGAAC
1371763 GATATAAG
1 GATATAAG
1371771 GCCTAATCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (17 bp):
GATATAAGCATGTGAAC
Found at i:1373349 original size:76 final size:75
Alignment explanation
Indices: 1373259--1373406 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 75
1373249 TAAACTCAAA
*
1373259 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATGTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTATATGTTAGTTTAAATAGG-TTTTAGTA
1373323 TTTTAATTAATT
64 TTTTAATTAATT
* * * * *
1373335 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTATATGTTAGTTTAAATAGGTTTTAGTATT
1373400 TTAATTA
66 TTAATTA
1373407 GGATTTAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 24 0.37
76 41 0.63
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTATATGTTAGTTTAAATAGGTTTTAGTATT
TTAATTAATT
Found at i:1373408 original size:19 final size:19
Alignment explanation
Indices: 1373380--1373442 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1373370 TATATTTTAG
*
1373380 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
1373399 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
1373418 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
1373439 TTTA
1 TTTA
1373443 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:1373499 original size:21 final size:20
Alignment explanation
Indices: 1373444--1373487 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1373434 GGTATTTTAG
*
1373444 TTTAAATAG-TTTTAAGTGT
1 TTTAATTAGTTTTTAAGTGT
*
1373463 TTTAATTAGTATTTAAGATGT
1 TTTAATTAGTTTTTAAG-TGT
1373484 TTTA
1 TTTA
1373488 GCTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTAATTAGTTTTTAAGTGT
Found at i:1374100 original size:17 final size:18
Alignment explanation
Indices: 1374078--1374120 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1374068 GTTTATTTAA
*
1374078 TTATTTTTTTCTT-TCTT
1 TTATTTTATTCTTATCTT
* *
1374095 TTATTTAATTCTTATTTT
1 TTATTTTATTCTTATCTT
1374113 TTATTTTA
1 TTATTTTA
1374121 ACCACAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATTTTATTCTTATCTT
Found at i:1375838 original size:15 final size:15
Alignment explanation
Indices: 1375806--1375839 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1375796 CCAGTAGAAA
*
1375806 AAGACGCACATCAAG
1 AAGACGCACACCAAG
*
1375821 AAGACGCACACCAGG
1 AAGACGCACACCAAG
1375836 AAGA
1 AAGA
1375840 ACAAGAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.24, T:0.03
Consensus pattern (15 bp):
AAGACGCACACCAAG
Found at i:1379585 original size:21 final size:21
Alignment explanation
Indices: 1379561--1379609 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1379551 CATTTCGTTA
1379561 TATTTTTGTTTT-TATTTTTTT
1 TATTTTTGTTTTAT-TTTTTTT
*
1379582 TATTTTCGTTTTATTTTTTTT
1 TATTTTTGTTTTATTTTTTTT
1379603 TATTTTT
1 TATTTTT
1379610 TTAGCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.10, C:0.02, G:0.04, T:0.84
Consensus pattern (21 bp):
TATTTTTGTTTTATTTTTTTT
Found at i:1379593 original size:11 final size:10
Alignment explanation
Indices: 1379564--1379608 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
1379554 TTCGTTATAT
1379564 TTTTGTTTTTA
1 TTTTG-TTTTA
1379575 TTTT-TTTTA
1 TTTTGTTTTA
1379584 TTTTCGTTTTA
1 TTTT-GTTTTA
*
1379595 TTTTTTTTTA
1 TTTTGTTTTA
1379605 TTTT
1 TTTT
1379609 TTTAGCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 9 0.29
10 9 0.29
11 13 0.42
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.84
Consensus pattern (10 bp):
TTTTGTTTTA
Found at i:1379597 original size:32 final size:30
Alignment explanation
Indices: 1379553--1379611 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1379543 AGGCAACCCA
1379553 TTTCGTTATATTTTTGTTTTTATTTTTTTTAT
1 TTTCGTTATA-TTTT-TTTTTATTTTTTTTAT
*
1379585 TTTCGTTTTATTTTTTTTTATTTTTTT
1 TTTCGTTATATTTTTTTTTATTTTTTT
1379612 AGCAAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 13 0.50
31 4 0.15
32 9 0.35
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.81
Consensus pattern (30 bp):
TTTCGTTATATTTTTTTTTATTTTTTTTAT
Found at i:1381579 original size:19 final size:19
Alignment explanation
Indices: 1381551--1381613 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1381541 TGTATTTTAG
*
1381551 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
1381570 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
1381589 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
1381610 TTTA
1 TTTA
1381614 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:1381676 original size:64 final size:64
Alignment explanation
Indices: 1381542--1381676 Score: 177
Period size: 64 Copynumber: 2.1 Consensus size: 64
1381532 CTTTATCTTT
* *
1381542 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTAGATTAGTTTTTAG
* * *
1381606 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAAGAGATTTTAGCTT-GTTTTT
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTT-AGA-ATATTAGATTAGTTTTT
1381669 AG
63 AG
1381671 G-ATTTT
1 GTATTTT
1381677 GAAGGCTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
63 5 0.08
64 40 0.63
65 11 0.17
66 7 0.11
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (64 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTAGATTAGTTTTTAG
Found at i:1382269 original size:24 final size:24
Alignment explanation
Indices: 1382241--1382292 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1382231 CTTTAATTTG
* *
1382241 TTTATTTAATT-TTTTTTTCTTTCT
1 TTTATTTAATTCTTATTTT-TTTAT
1382265 TTTATTTAATTCTTATTTTTTTAT
1 TTTATTTAATTCTTATTTTTTTAT
1382289 TTTA
1 TTTA
1382293 ACCACAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTATTTAATTCTTATTTTTTTAT
Found at i:1383565 original size:13 final size:13
Alignment explanation
Indices: 1383547--1383576 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1383537 TGAGAAAGGC
1383547 GAAGTTAGCTGGA
1 GAAGTTAGCTGGA
1383560 GAAGTTAGCTGGA
1 GAAGTTAGCTGGA
1383573 GAAG
1 GAAG
1383577 ATCTCACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.40, T:0.20
Consensus pattern (13 bp):
GAAGTTAGCTGGA
Found at i:1389613 original size:85 final size:85
Alignment explanation
Indices: 1389519--1389696 Score: 252
Period size: 85 Copynumber: 2.1 Consensus size: 85
1389509 TTCTTTGAGT
* *
1389519 GTCATTGAAGTCCTCGTCATAAAT-TAAG-ATGACACACATTTGTGCGTCATAAATTTATGACAC
1 GTCATTGAAGCCCCCGTCATAAATCT--GCATGACACACATTTGTGCGTCATAAATTTATGACAC
*
1389582 GCATGTATGACTTACATTGCGC
64 GCATATATGACTTACATTGCGC
* * **
1389604 GTCATTGAAGCCCCCGTCATAAATCTGCTTGACATACATTTGTTTGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAATCTGCATGACACACATTTGTGCGTCATAAATTTATGACACGC
*
1389669 ATATATGACTTACATTGCGT
66 ATATATGACTTACATTGCGC
1389689 GTCATTGA
1 GTCATTGA
1389697 TGCACACGTC
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
84 1 0.01
85 81 0.98
86 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (85 bp):
GTCATTGAAGCCCCCGTCATAAATCTGCATGACACACATTTGTGCGTCATAAATTTATGACACGC
ATATATGACTTACATTGCGC
Found at i:1389763 original size:2 final size:2
Alignment explanation
Indices: 1389756--1389836 Score: 89
Period size: 2 Copynumber: 42.5 Consensus size: 2
1389746 TTTCGAAAAT
* * * *
1389756 TA TA TA TA TA TA TA -A TA TA GA TA CA TA TA TA AA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1389797 TA TA GA TA TA -A TA TA T- TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1389836 T
1 T
1389837 TGTAGATTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
1 4 0.06
2 61 0.94
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1391857 original size:51 final size:50
Alignment explanation
Indices: 1391789--1391885 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 50
1391779 TTCTCCTCTT
1391789 CCTTTTTCCTTTGCGGTGTCCCTTCTCCTTTAC-CCTCTTCATTTTCTTTC
1 CCTTTTTCCTTTGCGGTGTCCCTTCTCCTTT-CTCCTCTTCATTTTCTTTC
* *
1391839 CCTTTTTCCGTCTT-CGGTGTCCCTTCTTCTTTCTCCTCTTCTTTTTC
1 CCTTTTTCC-T-TTGCGGTGTCCCTTCTCCTTTCTCCTCTTCATTTTC
1391886 AACAAGTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
50 10 0.24
51 30 0.71
52 2 0.05
ACGTcount: A:0.02, C:0.36, G:0.08, T:0.54
Consensus pattern (50 bp):
CCTTTTTCCTTTGCGGTGTCCCTTCTCCTTTCTCCTCTTCATTTTCTTTC
Found at i:1399569 original size:20 final size:17
Alignment explanation
Indices: 1399518--1399567 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1399508 AAGTAAATAT
**
1399518 ATAATAAAAATAAAAAAA
1 ATAA-AAAAATAAATCAA
1399536 ATAAAAAAATAAATCAA
1 ATAAAAAAATAAATCAA
1399553 ATAAGAAAAAGTAAA
1 ATAA-AAAAA-TAAA
1399568 ATTGGTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 9 0.32
19 4 0.14
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (17 bp):
ATAAAAAAATAAATCAA
Found at i:1402238 original size:25 final size:25
Alignment explanation
Indices: 1402204--1402275 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
1402194 GAGAGAAATA
1402204 ATCCGACACATGATCTCGAGTTATT
1 ATCCGACACATGATCTCGAGTTATT
1402229 ATCCGACACATGATCTCGAGTTATT
1 ATCCGACACATGATCTCGAGTTATT
1402254 ATCCGACACATGATCTCGAGTT
1 ATCCGACACATGATCTCGAGTT
1402276 GACATCAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (25 bp):
ATCCGACACATGATCTCGAGTTATT
Found at i:1403642 original size:11 final size:11
Alignment explanation
Indices: 1403626--1403652 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1403616 ATGTTATAAG
1403626 GTTGAATGGAA
1 GTTGAATGGAA
1403637 GTTGAATGGAA
1 GTTGAATGGAA
1403648 GTTGA
1 GTTGA
1403653 TTTCAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (11 bp):
GTTGAATGGAA
Found at i:1404436 original size:24 final size:25
Alignment explanation
Indices: 1404404--1404455 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
1404394 ACATGCATGA
1404404 CATTGTACATAGATGTTTTATACAT
1 CATTGTACATAGATGTTTTATACAT
1404429 CATT-TACATAGATGTTTTATACAT
1 CATTGTACATAGATGTTTTATACAT
1404453 CAT
1 CAT
1404456 CAGGAAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (25 bp):
CATTGTACATAGATGTTTTATACAT
Found at i:1405781 original size:47 final size:43
Alignment explanation
Indices: 1405710--1405834 Score: 142
Period size: 47 Copynumber: 2.8 Consensus size: 43
1405700 TATAAAATCT
* *
1405710 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAGCAAAATA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGCAAAACA
* *
1405755 CTTACCATTTAAATTACATAAGCTCGTAAGCTTATTTTATCAATACA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGCAAAACA
* *
1405802 CTTGCCATTATTCATATGCTCGTAAGCTTATTT
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTT
1405835 GCATACTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (43 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAAAACA
Found at i:1412542 original size:47 final size:45
Alignment explanation
Indices: 1412472--1412596 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
1412462 TATAAAATCT
*
1412472 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1412517 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1412564 CTTGCCA-TTATT-CATAAGCTGGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1412597 GCATACTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
43 20 0.27
44 3 0.04
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1416698 original size:13 final size:13
Alignment explanation
Indices: 1416680--1416704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1416670 AGCCATTAGT
1416680 TTCATAATTAATA
1 TTCATAATTAATA
1416693 TTCATAATTAAT
1 TTCATAATTAAT
1416705 GTGACATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCATAATTAATA
Found at i:1418862 original size:23 final size:23
Alignment explanation
Indices: 1418835--1418896 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1418825 TCCCCTGTGG
*
1418835 GGGGGAATCGATTTCCCTTCAAA
1 GGGGGAATCGATTCCCCTTCAAA
* *
1418858 TGGGGAATCGATTCCCCTTTAAA
1 GGGGGAATCGATTCCCCTTCAAA
*
1418881 GGGGGAATCGGTTCCC
1 GGGGGAATCGATTCCC
1418897 TCATTGGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (23 bp):
GGGGGAATCGATTCCCCTTCAAA
Found at i:1422761 original size:22 final size:21
Alignment explanation
Indices: 1422719--1422758 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1422709 GAGTTTATTT
*
1422719 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1422740 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1422759 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1430743 original size:24 final size:24
Alignment explanation
Indices: 1430716--1430764 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1430706 TGCATGACAT
*
1430716 TGTATATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
*
1430740 TGTACATAGATGTTTTATCCATCA
1 TGTACATAGATGTTTTATACATCA
1430764 T
1 T
1430765 CAGGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:1436503 original size:2 final size:2
Alignment explanation
Indices: 1436496--1436527 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1436486 CAACCTTCTA
1436496 AT 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 AT
1436528 TAGAGTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1438113 original size:51 final size:50
Alignment explanation
Indices: 1438058--1438162 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 50
1438048 TCACTTTTAA
* *
1438058 ATTTCTGATTCAGCTACTATTA-TTTTAAATT-TTGCATTTTGGTCACTATTT
1 ATTTCTGATTCAACTACTA--ACTTTTAAATTCTTGCATTTTAGTCACTA-TT
* * **
1438109 ATTTCTTATTTAACTACTAACTTTTACTTTCTTGCATTTTAGTCACTATT
1 ATTTCTGATTCAACTACTAACTTTTAAATTCTTGCATTTTAGTCACTATT
1438159 ATTT
1 ATTT
1438163 TATTTTATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
49 1 0.02
50 13 0.28
51 32 0.70
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (50 bp):
ATTTCTGATTCAACTACTAACTTTTAAATTCTTGCATTTTAGTCACTATT
Found at i:1453927 original size:58 final size:57
Alignment explanation
Indices: 1453859--1454066 Score: 196
Period size: 58 Copynumber: 3.7 Consensus size: 57
1453849 AAAAAAAAAA
* *
1453859 TTAAAGAAACTAAGTCTAATTTTCAGGGGTTTCTTCATGATGATTTTCAATGAATTT
1 TTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAATTT
* * **
1453916 TTACAAGAAACTAAGTCTAATTTTTAGGGGTTTC-T--TGATG-TTTTCAAATGAGGTT
1 TTA-AAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTTTC-AATGAATTT
* * * * * *
1453971 TT--AGAAACTAAACCTGAGTTTCAGGGGTTTCTTGATGATTATCTCTAAAT-AATTT
1 TTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATGAT-TTTCAATGAATTT
** *
1454026 TTAAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCTTGATGA
1 TT-AAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGA
1454067 CAACTGAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
52 24 0.20
53 1 0.01
54 5 0.04
55 23 0.19
56 4 0.03
57 6 0.05
58 59 0.48
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (57 bp):
TTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAATTT
Found at i:1454423 original size:38 final size:38
Alignment explanation
Indices: 1454373--1454525 Score: 225
Period size: 38 Copynumber: 4.0 Consensus size: 38
1454363 GAGGGATCAA
1454373 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
* * *
1454411 TGTCTTGTTTGAGATAGTTTCACTCGAAACAGAAGATT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
*
1454449 TATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
* * * * *
1454487 TATCTCGCTTGAAACAGTTTCGCTCGAAGCAGAATATT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
1454525 T
1 T
1454526 TAAGAAGCTA
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 102 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (38 bp):
TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
Found at i:1454666 original size:41 final size:41
Alignment explanation
Indices: 1454560--1454671 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
1454550 GGGTTTCTTG
*
1454560 ATGAGTAAGTCCTTTGGGCCATC-AGTAAGTCTTTCAAGCATA
1 ATGA-TAAGTCCTTCGGGCCATCTA-TAAGTCTTTCAAGCATA
* * * *
1454602 ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCATGCA-A
1 ATG-ATAAGTCCTTCGGGCCATCTATAAGTCTTTCAAGCATA
1454643 TATGATAAGTCCTTCGGGCCATCTATAAG
1 -ATGATAAGTCCTTCGGGCCATCTATAAG
1454672 ACCTTTGGAC
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 23 0.39
42 35 0.59
43 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (41 bp):
ATGATAAGTCCTTCGGGCCATCTATAAGTCTTTCAAGCATA
Found at i:1455039 original size:58 final size:59
Alignment explanation
Indices: 1454879--1455099 Score: 228
Period size: 60 Copynumber: 3.7 Consensus size: 59
1454869 CCTCACTAGA
* * **
1454879 GGGATCAACATTTTCTTTGCTCGGTTCACAACACTTCAAATCAGCAATGCCCCACCAGAG
1 GGGAT-AACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAACACCCCACCAGAG
* * * * * * ** *
1454939 GGGATGACATTTGCTATTGCTCAATTCACAATACTTCGAATCAACAACACCATACTAGAG
1 GGGATAACATTTCCT-TTGCTCGATTCACAACACTTCAAATCAGCAACACCCCACCAGAG
* * *
1454999 GGGATAACATTT-CTTTGCTCGATTCACGACACTTCAAATCAGTAACACCCCACCATAG
1 GGGATAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAACACCCCACCAGAG
** * * *
1455057 GGGATAACATTTCCTGCGCTCGATTCATAACATTTCGAATCAG
1 GGGATAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAG
1455100 TGACGCCTCA
Statistics
Matches: 130, Mismatches: 29, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
58 46 0.35
59 34 0.26
60 50 0.38
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (59 bp):
GGGATAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAACACCCCACCAGAG
Found at i:1456410 original size:9 final size:9
Alignment explanation
Indices: 1456396--1456457 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
1456386 GTTTATTTTA
1456396 TTTTTTATT
1 TTTTTTATT
*
1456405 TTTTTT-TA
1 TTTTTTATT
1456413 TTTTTTATT
1 TTTTTTATT
* * *
1456422 GTTTTCATAG
1 TTTTTTAT-T
1456432 TTTTTTATT
1 TTTTTTATT
*
1456441 ATTTTTATT
1 TTTTTTATT
1456450 TTATTTTA
1 TT-TTTTA
1456458 AAAAAATTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
8 7 0.17
9 22 0.55
10 11 0.28
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTTTATT
Found at i:1456410 original size:11 final size:11
Alignment explanation
Indices: 1456391--1456456 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
1456381 CTTATGTTTA
1456391 TTTTATTTTTT
1 TTTTATTTTTT
*
1456402 ATTTTTTTTTATT
1 -TTTTATTTT-TT
*
1456415 TTTTATTGTTT
1 TTTTATTTTTT
** *
1456426 TCATAGTTTTT
1 TTTTATTTTTT
* *
1456437 TATTATTTTTA
1 TTTTATTTTTT
1456448 TTTTATTTT
1 TTTTATTTT
1456457 AAAAAAATTA
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
11 24 0.59
12 15 0.37
13 2 0.05
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:1456413 original size:17 final size:17
Alignment explanation
Indices: 1456391--1456451 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
1456381 CTTATGTTTA
1456391 TTTTATTTTTTATTTTT
1 TTTTATTTTTTATTTTT
1456408 TTTTATTTTTTATTGTTT
1 TTTTATTTTTTATT-TTT
** *
1456426 TCATAGTTTTTTA-TTAT
1 TTTTA-TTTTTTATTTTT
1456443 TTTTATTTT
1 TTTTATTTT
1456452 ATTTTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.11
17 19 0.51
18 7 0.19
19 7 0.19
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTTATTTTT
Found at i:1464474 original size:23 final size:23
Alignment explanation
Indices: 1464421--1464467 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1464411 AAGTATTAAC
* *
1464421 TAAAAGATT-TTAAGTACTTACTT
1 TAAAA-ATTGTTAACTACGTACTT
1464444 TAAAAATTGTTAACTACGTACTT
1 TAAAAATTGTTAACTACGTACTT
1464467 T
1 T
1464468 TACAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (23 bp):
TAAAAATTGTTAACTACGTACTT
Found at i:1464872 original size:22 final size:22
Alignment explanation
Indices: 1464831--1464873 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1464821 TTTTATTTTT
**
1464831 TTGAAAATAATTATTAAAAATC
1 TTGAAAATAAAAATTAAAAATC
1464853 TTGAAAATAAAAATTTAAAAA
1 TTGAAAATAAAAA-TTAAAAA
1464874 GTATTTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
TTGAAAATAAAAATTAAAAATC
Found at i:1465824 original size:27 final size:27
Alignment explanation
Indices: 1465786--1465841 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1465776 CTCAAAAAGG
*
1465786 CTGCCCATAACATGGTATATCGGTGCA
1 CTGCCCATAACATGGTACATCGGTGCA
*
1465813 CTGCCCATAACATGGTGCATCGGTGCA
1 CTGCCCATAACATGGTACATCGGTGCA
1465840 CT
1 CT
1465842 ATCAAGGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (27 bp):
CTGCCCATAACATGGTACATCGGTGCA
Found at i:1465958 original size:21 final size:21
Alignment explanation
Indices: 1465929--1466005 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1465919 TGCACAGCAG
1465929 GATGCATCGATGCACAGCCTT
1 GATGCATCGATGCACAGCCTT
*
1465950 GATGAATCGATGCACAGCCTT
1 GATGCATCGATGCACAGCCTT
* ***
1465971 GATGCATTGATGCACAG-AAG
1 GATGCATCGATGCACAGCCTT
1465991 GATGCATCGATGCAC
1 GATGCATCGATGCAC
1466006 TAATTGCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 14 0.29
21 35 0.71
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (21 bp):
GATGCATCGATGCACAGCCTT
Found at i:1466072 original size:42 final size:42
Alignment explanation
Indices: 1466026--1466124 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
1466016 CGGTGTTTGA
* * *
1466026 GTGCAAGGATGCACTGCATGG-TGGATCGATGCACTAGT-GCAG
1 GTGCATGGATGCACTGCAGGGATGCATCGATGCACT-GTAG-AG
* *
1466068 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGCAGGGATGCATCGATGCACTGTAGAG
1466110 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1466125 TTGACACCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 37 0.74
43 13 0.26
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGGATGCATCGATGCACTGTAGAG
Found at i:1466095 original size:21 final size:20
Alignment explanation
Indices: 1466026--1466124 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 20
1466016 CGGTGTTTGA
* *
1466026 GTGCAAGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
* *
1466046 GTGGATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
1466068 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
1466088 GATGCATGGATGCACTGTAGGG
1 G-TGCATGGATGCACTGCA-GG
1466110 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1466125 TTGACACCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 30 0.45
22 16 0.24
23 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1466236 original size:29 final size:31
Alignment explanation
Indices: 1466204--1466263 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1466194 AAACTTTAAA
*
1466204 TAAATTCAATT-AAGTCCAAAAA-CATTTTT
1 TAAATTCAATTCAAATCCAAAAACCATTTTT
1466233 TAAATTCAATTCAAATCCAAAAACCATTTTT
1 TAAATTCAATTCAAATCCAAAAACCATTTTT
1466264 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAATCCAAAAACCATTTTT
Found at i:1467564 original size:20 final size:19
Alignment explanation
Indices: 1467528--1467574 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1467518 CTAAATCCTT
*
1467528 TTTCAAAATTTCATTTTGCC
1 TTTCAAAATCTCATTTTG-C
*
1467548 TTTCAAAATCT-ATTTTTGT
1 TTTCAAAATCTCA-TTTTGC
1467567 TTTCAAAA
1 TTTCAAAA
1467575 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:1468744 original size:20 final size:22
Alignment explanation
Indices: 1468719--1468758 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1468709 TGTTGTATAT
1468719 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1468739 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1468759 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1468900 original size:20 final size:20
Alignment explanation
Indices: 1468871--1468944 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1468861 GCAGCCTTCG
*
1468871 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
1468891 TGCATCGATGCACAGCCTGGA
1 TGCATCGATGCACAG-CAGGA
* * *
1468912 TGCATTGATGCACAGAAGTA
1 TGCATCGATGCACAGCAGGA
1468932 TGCATCGATGCAC
1 TGCATCGATGCAC
1468945 TAAATACATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 28 0.61
21 18 0.39
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1468907 original size:41 final size:41
Alignment explanation
Indices: 1468862--1468944 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
1468852 TTAGTCGTTG
*
1468862 CAGCCTTCG-TGCATGGATGCACAGCAGGATGCATCGATGCA
1 CAGCC-TCGATGCATGGATGCACAGAAGGATGCATCGATGCA
* * *
1468903 CAGCCTGGATGCATTGATGCACAGAAGTATGCATCGATGCA
1 CAGCCTCGATGCATGGATGCACAGAAGGATGCATCGATGCA
1468944 C
1 C
1468945 TAAATACATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.05
41 35 0.95
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (41 bp):
CAGCCTCGATGCATGGATGCACAGAAGGATGCATCGATGCA
Found at i:1469034 original size:21 final size:21
Alignment explanation
Indices: 1468966--1469063 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
1468956 GGTGTTTGAG
* *
1468966 TGCATGGATGCAATGCATGG-
1 TGCATGGATGCACTGCAGGGA
* *
1468986 TGCATCGATGTACTAGTGCA-GG-
1 TGCATGGATG--C-ACTGCAGGGA
* *
1469008 TGCATGGATGCATTGTAGGGA
1 TGCATGGATGCACTGCAGGGA
*
1469029 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
1469050 TGCATGGATGCACT
1 TGCATGGATGCACT
1469064 TTGAGACCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
19 4 0.06
20 12 0.18
21 32 0.49
22 12 0.18
23 5 0.08
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:1469174 original size:29 final size:31
Alignment explanation
Indices: 1469142--1469201 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1469132 AAACTTTGAA
1469142 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1469171 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1469202 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1469765 original size:18 final size:19
Alignment explanation
Indices: 1469742--1469778 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1469732 CCAGTAATCA
1469742 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
1469760 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
1469779 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:1470825 original size:659 final size:656
Alignment explanation
Indices: 1469234--1471670 Score: 4142
Period size: 659 Copynumber: 3.7 Consensus size: 656
1469224 ATAGTTCAAC
1469234 ATCTTACATTACCAATAGTGGATTTTTTAGGGTATATTACCGGGAATGTCATTACCTCCATTTCC
1 ATCTTACATTACCAATAGTGGATTTTTTAGGGTATATTACCGGGAATGTCATTACCTCCATTTCC
*
1469299 TTAGGTATTGTTGGATTACCGGTATTTTGGACTAAAATGCCCTTAAATTTTTTTTCTTT-AAAAA
66 TTAGGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTT-AATTTTTTTTCTTTAAAAAA
1469363 TATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
130 TATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
*
1469428 CTATTTTAGATTTACAAAAAAAAAATCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAAT
195 CTATTTTAGATTTAC--AAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAAT
*
1469493 --AAAATTTTACACTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAATATTTATATAAAT
258 AAAAAATTTTACACTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAA-AATTATATAAAT
*
1469556 TTTATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAATAAATAT
322 TTTATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATAT
1469621 ATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGAT
387 ATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGAT
* * * * *
1469686 AATCTTATATTCATGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCCTG
452 AATATTACATTCCTGCTAAATCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCATG
1469751 GTAATCTTTTATTCCCATTGGTAATCTTACATTCCGTGAACCAAA-CA-CA-C-GTGTGTTTGGT
517 GTAATCTTTTATTCCCATTGGTAATCTTACATTCCGTGAACCAAAGCACCATCGGTGTGTTTGGT
* *
1469812 TGGGGGAATGTGAGATTCCCATGGGAATGGAATCCACATTCACCTGTTTGATTGGCCGAGAATGT
582 T-GGGGAATGTGAGATTCCCATGGGAATGGAATCCACATTCACCCGTTTGGTTGGCCGAGAATGT
*
1469877 CATTCCCGGTA
646 CATTCTCGGTA
* *
1469888 ATCTTACATTACCAATAGTGGATTTTTTTGGGGTATATTACCGGGAATGTCATTACCTCAATTTC
1 ATCTTACATTACCAATAGTGGA-TTTTTTAGGGTATATTACCGGGAATGTCATTACCTCCATTTC
*
1469953 CTTATGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTAAAAAA
65 CTTAGGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTAAAAAA
1470018 TATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
130 TATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
*
1470083 CTATTTTAGATTTACAAAAAAAGTTTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAA
195 CTATTTTAGATTTACAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAA
* *
1470148 AAAATTTTGCACTTTCATT-AAGCTTTTTCATATTTTCAATTTTGTAAAAAAATTATATAAATTT
260 AAAATTTTACACTTTCATTAAACCTTTTT-ATATTTTCAATTTTGTAAAAAAATTATATAAATTT
1470212 TATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTT-AAAAAACAAATATAT
324 TATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATAT
*
1470276 AATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGGTAA
389 AATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAA
* *
1470341 TATTACATTCCTGCTAAATCAACCAAACACAAAATACAACATTCCTAGTAATCCTATTCCATGGT
454 TATTACATTCCTGCTAAATCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCATGGT
*
1470406 AATCTTTTATTCCCATTGGTATTCTTACATTCCGTGAACCAAACGCACCATCGGGTGTGTTTGGT
519 AATCTTTTATTCCCATTGGTAATCTTACATTCCGTGAACCAAA-GCACCATC-GGTGTGTTTGGT
**
1470471 TGGGAGAATGTGAGATTCCCATGGGAATGGAATCCACATTTTCCCGTTTGGTTGGCCGAGAATGT
582 TGGG-GAATGTGAGATTCCCATGGGAATGGAATCCACATTCACCCGTTTGGTTGGCCGAGAATGT
1470536 CATTCTCGGTA
646 CATTCTCGGTA
* * * *
1470547 ATCTTACATTACCAATAGTGGATTGTTT-GGTGTATTTTACCGGAAATGTCATTACCTCCATTTT
1 ATCTTACATTACCAATAGTGGATTTTTTAGG-GTATATTACCGGGAATGTCATTACCTCCATTTC
1470611 CTTAGGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTAAAAAA
65 CTTAGGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTAAAAAA
*
1470676 TATCCTTATTTTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
130 TATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
1470741 CTATTTTAGATTTACAAACAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATA
195 CTATTTTAGATTTACAAA-AAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATA
* * *
1470806 AAAAATTTTACACTTTCATTAAACCTTTTCATATTTTCAATTTTGTAAAAAAAATATATGAATTT
259 AAAAATTTTACACTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAAATTATATAAATTT
*
1470871 TATGAATTTAAATTTTTAAAGAAAATATATTAATATTTTCCAACTTGTTAAAAAAACAAATATAT
324 TATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATAT
* * * *
1470936 AATAAAGACAATTTGGTCAAATATACATTCCAATAATATTTTATTCCTTTAACCAAACATGGTAA
389 AATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAA
* * *
1471001 TATTACATTCCTGTTAAATCAACCAAACACAAAATACAACATTCCCAGTAATCTTATTCCATTGT
454 TATTACATTCCTGCTAAATCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCATGGT
1471066 AATCTTTTATTCCCATTGGTAATCTTACATTCCGTGAACCAAATGCACCATCAGGTGTGTTTGGT
519 AATCTTTTATTCCCATTGGTAATCTTACATTCCGTGAACCAAA-GCACCATC-GGTGTGTTTGGT
*
1471131 TGAGGGAATGTGAGATTCCCATGGGAATGGAATCCACATTCCCCCGTTTGGTTGGCCGAGAATGT
582 TG-GGGAATGTGAGATTCCCATGGGAATGGAATCCACATTCACCCGTTTGGTTGGCCGAGAATGT
1471196 CATTCTCGGTA
646 CATTCTCGGTA
* *
1471207 ATCTTACATTACCAATAGTGGA-TTTTTAGGGTATTTTACAC-GGAATGTCATTACCTCCATTTT
1 ATCTTACATTACCAATAGTGGATTTTTTAGGGTATATTAC-CGGGAATGTCATTACCTCCATTTC
* * *
1471270 CTTAGGTTTTGTTGGATTACCAGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTCAAAAA
65 CTTAGGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTAAAAAA
* * *
1471335 TATCATTATTCTGTCATTGAATAATAAAAATACTAGGAAGGTTAAATTACAAATTTATCCTTAAA
130 TATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAA
*
1471400 CTATTTTAGATTTACAAAAAAAGTCTATAATTAAAATTTTATATAAAGTTCAGGGGTTAAAATAA
195 CTATTTTAGATTTACAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAA
*
1471465 AAAATTTTACACTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAAAATTACATAAATTT
260 AAAATTTTACACTTTCATTAAACCTTTTTATATTTTCAATTTTGT-AAAAAAATTATATAAATTT
*
1471530 TATGAATTTAAAATTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATAT
324 TATGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATAT
* *
1471595 AATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCTTTTAACCAAATACGATAA
389 AATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAA
*
1471660 TCTTACATTCC
454 TATTACATTCC
1471671 CACTAAACCA
Statistics
Matches: 1690, Mismatches: 73, Indels: 35
0.94 0.04 0.02
Matches are distributed among these distances:
653 224 0.13
654 106 0.06
655 209 0.12
656 2 0.00
657 3 0.00
658 273 0.16
659 568 0.34
660 303 0.18
661 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (656 bp):
ATCTTACATTACCAATAGTGGATTTTTTAGGGTATATTACCGGGAATGTCATTACCTCCATTTCC
TTAGGTATTGTTGGATTACCGGCATTTTGGACTAAAATGCCCTTAATTTTTTTTCTTTAAAAAAT
ATCCTTATTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAAC
TATTTTAGATTTACAAAAAAAGTCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAA
AAATTTTACACTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAAATTATATAAATTTTA
TGAATTTAAATTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATATAA
TAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGATAATA
TTACATTCCTGCTAAATCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCATGGTAA
TCTTTTATTCCCATTGGTAATCTTACATTCCGTGAACCAAAGCACCATCGGTGTGTTTGGTTGGG
GAATGTGAGATTCCCATGGGAATGGAATCCACATTCACCCGTTTGGTTGGCCGAGAATGTCATTC
TCGGTA
Found at i:1471077 original size:18 final size:20
Alignment explanation
Indices: 1471054--1471091 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1471044 CCCAGTAATC
1471054 TTATT-CCATT-GTAATCTT
1 TTATTCCCATTGGTAATCTT
1471072 TTATTCCCATTGGTAATCTT
1 TTATTCCCATTGGTAATCTT
1471092 ACATTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.53
Consensus pattern (20 bp):
TTATTCCCATTGGTAATCTT
Found at i:1471098 original size:20 final size:17
Alignment explanation
Indices: 1471048--1471092 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1471038 AACATTCCCA
1471048 GTAATCTTATT-CCATT
1 GTAATCTTATTCCCATT
1471064 GTAATCTTTTATTCCCATT
1 GTAATC--TTATTCCCATT
1471083 GGTAATCTTA
1 -GTAATCTTA
1471093 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
18 8 0.32
19 5 0.20
20 6 0.24
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (17 bp):
GTAATCTTATTCCCATT
Found at i:1477605 original size:36 final size:37
Alignment explanation
Indices: 1477563--1477632 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1477553 TTTTTTCCAA
* *
1477563 TCATATT-GTTTATTAATTTAA-ATTTGAGATTTTTAT
1 TCATATTAATTTATAAATTTAAGATTT-AGATTTTTAT
1477599 TCATATTAATTTATAAATTTAAGATTTAGATTTT
1 TCATATTAATTTATAAATTTAAGATTTAGATTTT
1477633 ATTTAAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 7 0.23
37 19 0.63
38 4 0.13
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (37 bp):
TCATATTAATTTATAAATTTAAGATTTAGATTTTTAT
Found at i:1482712 original size:30 final size:31
Alignment explanation
Indices: 1482660--1482723 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
1482650 ATCTTTGACT
1482660 TTTGGAAGATGATAAGGGTTAGGTGTCTTGG
1 TTTGGAAGATGATAAGGGTTAGGTGTCTTGG
*
1482691 TTTGGAATATGATAA-GGTTAGGTGTCTTGG
1 TTTGGAAGATGATAAGGGTTAGGTGTCTTGG
1482721 TTT
1 TTT
1482724 AATGGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.22, C:0.03, G:0.34, T:0.41
Consensus pattern (31 bp):
TTTGGAAGATGATAAGGGTTAGGTGTCTTGG
Found at i:1484033 original size:24 final size:24
Alignment explanation
Indices: 1484006--1484054 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1483996 TGCGTAACAT
*
1484006 TGTACATAGATGTTTTATACATCA
1 TGTACATAGAAGTTTTATACATCA
1484030 TGTACATAGAAGTTTTATACATCA
1 TGTACATAGAAGTTTTATACATCA
1484054 T
1 T
1484055 CTGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (24 bp):
TGTACATAGAAGTTTTATACATCA
Found at i:1494450 original size:168 final size:172
Alignment explanation
Indices: 1494266--1494592 Score: 396
Period size: 172 Copynumber: 1.9 Consensus size: 172
1494256 TCTAAAGGGG
* * * *
1494266 ACATTATATGTACATAAAAATGAGTTGTAAAAGTAGAGATTCTCTT-T-AAAAGAGGGTCAA-GC
1 ACATTATATATACATAAAAATGAGTTCTAAAAGCAGAGATTCT-TTATAAAAAAAGGGT-AAGGC
* * * *
1494328 ACTTTTCACAA-AA-CTTTTTCACCTTTTATAGAGAATCTTTATCATGTCATAATATCTCATC-C
64 ACTTTTCACAAGAAGCTCTTTCACCTTTTATAAAGAATCTCTATCATGCCATAATATCTCATCAC
* * *
1494390 ATTAAACATGAGATTTGTCTGTGATGAATAGTTCCCAAAAAGGA
129 ATTAAACATAAGAATTATCTGTGATGAATAGTTCCCAAAAAGGA
* * **
1494434 ACATTATCTATACATAAAATTGAGTTCTAAGCGCAGAGATTCTTTATAGAAAAAAGGGTAAGGCA
1 ACATTATATATACATAAAAATGAGTTCTAAAAGCAGAGATTCTTTATA-AAAAAAGGGTAAGGCA
* * * *
1494499 CTTTTCACAAGAAGCTCTTTCACCTTTTGTAAAGAATCTCTATTATGCCATAGTGTCTCATCACA
65 CTTTTCACAAGAAGCTCTTTCACCTTTTATAAAGAATCTCTATCATGCCATAATATCTCATCACA
* *
1494564 TTAAGCATAAGAATTATTTGTGATGAATA
130 TTAAACATAAGAATTATCTGTGATGAATA
1494593 ATTTCTTGAA
Statistics
Matches: 131, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
167 2 0.02
168 37 0.28
169 2 0.02
170 22 0.17
171 2 0.02
172 40 0.31
173 26 0.20
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (172 bp):
ACATTATATATACATAAAAATGAGTTCTAAAAGCAGAGATTCTTTATAAAAAAAGGGTAAGGCAC
TTTTCACAAGAAGCTCTTTCACCTTTTATAAAGAATCTCTATCATGCCATAATATCTCATCACAT
TAAACATAAGAATTATCTGTGATGAATAGTTCCCAAAAAGGA
Found at i:1495377 original size:32 final size:32
Alignment explanation
Indices: 1495289--1495397 Score: 105
Period size: 32 Copynumber: 3.4 Consensus size: 32
1495279 AGTGTAAATG
* * *
1495289 CTATGCATTATCTGAATATGACCCTGACATTA
1 CTATGCATTATCTGAATACGACACTGACACTA
** *
1495321 CTATGCACCATCTTAAT-CTGACACTGACACTA
1 CTATGCATTATCTGAATAC-GACACTGACACTA
*
1495353 CTATGCATTATCTGAATACAACACTG-CTACTA
1 CTATGCATTATCTGAATACGACACTGAC-ACTA
* *
1495385 TTGTGCATTATCT
1 CTATGCATTATCT
1495398 AAATGTAACA
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
31 1 0.02
32 60 0.97
33 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (32 bp):
CTATGCATTATCTGAATACGACACTGACACTA
Found at i:1495712 original size:34 final size:34
Alignment explanation
Indices: 1495668--1495736 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1495658 TGCGACTACG
1495668 CATACATATCGGAGGGCTCTAAGGCCACACAACA
1 CATACATATCGGAGGGCTCTAAGGCCACACAACA
*
1495702 CATATATATCGGAGGGCTCTAAGGCCACACAACA
1 CATACATATCGGAGGGCTCTAAGGCCACACAACA
1495736 C
1 C
1495737 TGACAATGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (34 bp):
CATACATATCGGAGGGCTCTAAGGCCACACAACA
Found at i:1496772 original size:15 final size:15
Alignment explanation
Indices: 1496762--1496796 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1496752 GGTACTCACT
1496762 GTATCACTACTCATA
1 GTATCACTACTCATA
1496777 GTATCACTACTCATA
1 GTATCACTACTCATA
1496792 GTATC
1 GTATC
1496797 GATACTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (15 bp):
GTATCACTACTCATA
Found at i:1496802 original size:15 final size:15
Alignment explanation
Indices: 1496742--1496825 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 15
1496732 GGTATTGTAA
* *
1496742 TCATAGTATTGGTAC
1 TCATAGTATCGATAC
1496757 TCACT-GTATC-ACTAC
1 TCA-TAGTATCGA-TAC
1496772 TCATAGTATC-ACTAC
1 TCATAGTATCGA-TAC
1496787 TCATAGTATCGATAC
1 TCATAGTATCGATAC
* * * * *
1496802 TAACATTATTGGTAC
1 TCATAGTATCGATAC
1496817 TCATAGTAT
1 TCATAGTAT
1496826 AAATAGTACA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
14 1 0.02
15 52 0.95
16 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (15 bp):
TCATAGTATCGATAC
Found at i:1496855 original size:20 final size:20
Alignment explanation
Indices: 1496827--1496866 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1496817 TCATAGTATA
1496827 AATAGTACAAGAACAATATC
1 AATAGTACAAGAACAATATC
* *
1496847 AATATTACAAGAATAATATC
1 AATAGTACAAGAACAATATC
1496867 GATTCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (20 bp):
AATAGTACAAGAACAATATC
Found at i:1501295 original size:32 final size:33
Alignment explanation
Indices: 1501267--1501336 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
1501257 TCTGAATGTG
* *
1501267 ACACTAACATTG-TTGTGTATTATTTGAATGCA
1 ACACTAACACTGCTTGTGCATTATTTGAATGCA
* *
1501299 ACACTGACACTGCTTTTGCATTATTTGAATGCA
1 ACACTAACACTGCTTGTGCATTATTTGAATGCA
1501332 ACACT
1 ACACT
1501337 CTACTAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (33 bp):
ACACTAACACTGCTTGTGCATTATTTGAATGCA
Found at i:1516596 original size:61 final size:61
Alignment explanation
Indices: 1516510--1516680 Score: 263
Period size: 61 Copynumber: 2.8 Consensus size: 61
1516500 AGTCTGTAAT
* **
1516510 TAGAATTTTATGTTTAGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAATTTG
1 TAGAATTTTA-GTTTTGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAATTAC
1516572 TAGAATTTTAGTTTTGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAATTAC
1 TAGAATTTTAGTTTTGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAATTAC
* *
1516633 TAGAATTTTAGTTTTGGTCC-TTGAGTTTGATTTCCTTGTAATTTAGTC
1 TAGAATTTTAGTTTT-GTCCATT-AGTTTAATTTCCTTTTAATTTAGTC
1516681 CTTAATCGAA
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
61 65 0.64
62 37 0.36
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.53
Consensus pattern (61 bp):
TAGAATTTTAGTTTTGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAATTAC
Found at i:1516703 original size:62 final size:60
Alignment explanation
Indices: 1516509--1516742 Score: 226
Period size: 61 Copynumber: 3.8 Consensus size: 60
1516499 TAGTCTGTAA
* *
1516509 TTAGAATTTTATGTTTAGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAAT-T
1 TTAGAATTTTA-GTTTTGTCC-TTAGTTTAATTTCCTTTTAATTTAGTCTCTAATAAAATAT
*
1516570 TGTAGAATTTTAGTTTTGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAAT-T
1 T-TAGAATTTTAGTTTTGTCC-TTAGTTTAATTTCCTTTTAATTTAGTCTCTAATAAAATAT
* * * * *
1516631 ACTAGAATTTTAGTTTTGGTCCTTGAGTTTGATTTCCTTGTAATTTAGTC-CTTAATCGAACTAT
1 -TTAGAATTTTAGTTTT-GTCCTT-AGTTTAATTTCCTTTTAATTTAGTCTC-TAAT-AAAATAT
* * *
1516695 TTAG-ATTTTAGGTTTAGTCCTCTAATTT-ATTTTCTTTATAATTTAGTC
1 TTAGAATTTTA-GTTTTGTCCT-TAGTTTAATTTCCTTT-TAATTTAGTC
1516743 CCTATACTTT
Statistics
Matches: 152, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
61 74 0.49
62 66 0.43
63 11 0.07
64 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (60 bp):
TTAGAATTTTAGTTTTGTCCTTAGTTTAATTTCCTTTTAATTTAGTCTCTAATAAAATAT
Found at i:1516703 original size:123 final size:124
Alignment explanation
Indices: 1516510--1516742 Score: 275
Period size: 123 Copynumber: 1.9 Consensus size: 124
1516500 AGTCTGTAAT
* *
1516510 TAGAATTTTATGTTTAGTCCATTAGTTTAATTTCCTTTTAATTTAGTCTCTAATTAAATTTGTAG
1 TAGAATTTTATGTTTAGTCCATTAGTTTAATTTCCTTGTAATTTAGTCTCTAATGAAATTTGTAG
* *
1516575 AATTTTA-GTTTTGTCCAT-TAGTTTAATTTCCTTT-TAATTTAGTCTCTAATTAAATTAC
66 AATTTTAGGTTTAGTCC-TCTAATTT-ATTTCCTTTATAATTTAGTCTCTAATTAAATTAC
* * *
1516633 TAGAATTTTA-GTTTTGGTCC-TTGAGTTTGATTTCCTTGTAATTTAGTC-CTTAATCGAACTAT
1 TAGAATTTTATG-TTTAGTCCATT-AGTTTAATTTCCTTGTAATTTAGTCTC-TAAT-GAAAT-T
*
1516695 T-TAG-ATTTTAGGTTTAGTCCTCTAATTTATTTTCTTTATAATTTAGTC
61 TGTAGAATTTTAGGTTTAGTCCTCTAATTTATTTCCTTTATAATTTAGTC
1516743 CCTATACTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
122 4 0.04
123 59 0.63
124 29 0.31
125 2 0.02
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (124 bp):
TAGAATTTTATGTTTAGTCCATTAGTTTAATTTCCTTGTAATTTAGTCTCTAATGAAATTTGTAG
AATTTTAGGTTTAGTCCTCTAATTTATTTCCTTTATAATTTAGTCTCTAATTAAATTAC
Found at i:1518220 original size:102 final size:102
Alignment explanation
Indices: 1518026--1518223 Score: 245
Period size: 102 Copynumber: 1.9 Consensus size: 102
1518016 TAGATAATAA
* * * **
1518026 TCCATTTAGAACCCATATGAGAATATACCTTCAAGTTCAAGGGAATGAAATTCATATGTGAACTT
1 TCCATTCAGAACCCATATGACAATATACCTTCAAGTTCAAGGGAAGGAAATTCATATGCCAACTT
* * ** *
1518091 GTTCAACTTCAATATCGGAATTTCATCCACACAACAG
66 GTTCAACCTCAACATCAAAATTCCATCCACACAACAG
* * *
1518128 TCCATTCAGAACCCATATGACAATATGCCTTCAAGTTCAAGGGGAAGGCAA-TCATCTGCCAACT
1 TCCATTCAGAACCCATATGACAATATACCTTCAAGTTCAA-GGGAAGGAAATTCATATGCCAACT
**
1518192 TGTTTGACCTCAACATCAAAATTCCATCCACA
65 TGTTCAACCTCAACATCAAAATTCCATCCACA
1518224 ATCAAGACAT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
102 72 0.90
103 8 0.10
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (102 bp):
TCCATTCAGAACCCATATGACAATATACCTTCAAGTTCAAGGGAAGGAAATTCATATGCCAACTT
GTTCAACCTCAACATCAAAATTCCATCCACACAACAG
Found at i:1520407 original size:51 final size:50
Alignment explanation
Indices: 1520344--1520457 Score: 156
Period size: 51 Copynumber: 2.3 Consensus size: 50
1520334 ATGATTAGAT
* * * * * *
1520344 TTATTATTTTATTAGGAATTAAGATAGAGTTATAACATTATCTTTAGTTTA
1 TTATTATTTTATTAAGAATTAAGATAAAATTAAAACAATAT-TTTAATTTA
*
1520395 TTATTATTTTATTAAGAATTAGGATAAAATTAAAACAATATTTTAATTTA
1 TTATTATTTTATTAAGAATTAAGATAAAATTAAAACAATATTTTAATTTA
1520445 TTATTATTTTATT
1 TTATTATTTTATT
1520458 CAATAGTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 21 0.38
51 35 0.62
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (50 bp):
TTATTATTTTATTAAGAATTAAGATAAAATTAAAACAATATTTTAATTTA
Found at i:1530099 original size:15 final size:15
Alignment explanation
Indices: 1530081--1530182 Score: 66
Period size: 15 Copynumber: 6.8 Consensus size: 15
1530071 ATTTTTTTGG
1530081 TATTGTATTTTATAT
1 TATTGTATTTTATAT
* * *
1530096 TATTTTAATTTCTGA-
1 TATTGTATTTTAT-AT
* *
1530111 TATTATATTTTATGT
1 TATTGTATTTTATAT
**
1530126 TATTGTATTCTT-TGC
1 TATTGTATT-TTATAT
* *
1530141 TATTATATTTTATGT
1 TATTGTATTTTATAT
1530156 TATTGTATTTTA-ATT
1 TATTGTATTTTATA-T
*
1530171 TCTTGTATTTTA
1 TATTGTATTTTA
1530183 CCATATAAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
14 2 0.03
15 63 0.93
16 3 0.04
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.65
Consensus pattern (15 bp):
TATTGTATTTTATAT
Found at i:1530182 original size:30 final size:30
Alignment explanation
Indices: 1530066--1530164 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
1530056 ATGGATCATA
* * * *
1530066 ATTGTATTTTTTTGGTATTGTATTTTATATT
1 ATTGTA-TTCTTTGCTATTATATTTTATGTT
* * *
1530097 ATTTTAATT-TCTGATATTATATTTTATGTT
1 ATTGT-ATTCTTTGCTATTATATTTTATGTT
1530127 ATTGTATTCTTTGCTATTATATTTTATGTT
1 ATTGTATTCTTTGCTATTATATTTTATGTT
1530157 ATTGTATT
1 ATTGTATT
1530165 TTAATTTCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.05
30 48 0.83
31 6 0.10
32 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.10, T:0.65
Consensus pattern (30 bp):
ATTGTATTCTTTGCTATTATATTTTATGTT
Found at i:1538672 original size:12 final size:12
Alignment explanation
Indices: 1538639--1538674 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1538629 AATTTAGTTA
1538639 TTTTATTT-ATT
1 TTTTATTTAATT
1538650 TGTTTATTTAATT
1 T-TTTATTTAATT
1538663 TTTTATTTAATT
1 TTTTATTTAATT
1538675 ATACTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.04
12 18 0.78
13 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTATTTAATT
Found at i:1538757 original size:19 final size:20
Alignment explanation
Indices: 1538729--1538778 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1538719 TTAATATTTA
*
1538729 TTATTTTATTATT-TCTCCTT
1 TTATTTTATTATTATCT-ATT
1538749 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
1538768 TTATTTTATTA
1 TTATTTTATTA
1538779 AATCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:1544861 original size:19 final size:19
Alignment explanation
Indices: 1544833--1544876 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1544823 TGTTGTCCTT
*
1544833 GTTGTTTTCTAAGGAACCC
1 GTTGTATTCTAAGGAACCC
1544852 GTTGTATTCTAAGGAACCC
1 GTTGTATTCTAAGGAACCC
*
1544871 GCTGTA
1 GTTGTA
1544877 AGTATTCGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (19 bp):
GTTGTATTCTAAGGAACCC
Found at i:1547200 original size:29 final size:30
Alignment explanation
Indices: 1547130--1547189 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1547120 CAATTTAAGG
1547130 CAAAATGGTTTTTGGACTTTAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTTAATTGAATTTA
*
1547161 CAAAATATTTTTGGAC-TTAATTGAATTTA
1 CAAAATGTTTTTGGACTTTAATTGAATTTA
1547190 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 13 0.46
30 9 0.32
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTTAATTGAATTTA
Found at i:1547298 original size:21 final size:21
Alignment explanation
Indices: 1547272--1547368 Score: 126
Period size: 21 Copynumber: 4.6 Consensus size: 21
1547262 GTGTCAAAGA
*
1547272 GCATCCATGCACCCCTACAGT
1 GCATCCATGCACCCCTGCAGT
1547293 GCATCCATGCACCCCTGCAGT
1 GCATCCATGCACCCCTGCAGT
* *
1547314 GCATCCATGCATCTCTGCAGT
1 GCATCCATGCACCCCTGCAGT
1547335 GCATCCATGCA--CCTGCATTAGT
1 GCATCCATGCACCCCTGC---AGT
1547357 GCATCCATGCAC
1 GCATCCATGCAC
1547369 TCAAAAACCG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.06
21 50 0.74
22 14 0.21
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (21 bp):
GCATCCATGCACCCCTGCAGT
Found at i:1547418 original size:20 final size:20
Alignment explanation
Indices: 1547393--1547445 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
1547383 CAATTACTGC
* *
1547393 ATCGATGTATCCGTTTGTGT
1 ATCGATGCATCCGGTTGTGT
*
1547413 ATCGATGCATCAAGGTTGTGT
1 ATCGATGCATC-CGGTTGTGT
1547434 ATCGATGCATCC
1 ATCGATGCATCC
1547446 TGCTGTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
ATCGATGCATCCGGTTGTGT
Found at i:1554294 original size:11 final size:12
Alignment explanation
Indices: 1554265--1554299 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
1554255 AATTTAGTTA
*
1554265 GTTTATTTATTT
1 GTTTATTTAATT
1554277 GTTTATTTAATT
1 GTTTATTTAATT
1554289 -TTTATTTAATT
1 GTTTATTTAATT
1554300 ATACTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
GTTTATTTAATT
Found at i:1554695 original size:83 final size:83
Alignment explanation
Indices: 1554553--1554715 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 83
1554543 ATTATTTTGA
*
1554553 TATCACAAGGTTGACATAATCTTGATTATCTGCCCAATAATTAAACCACTTTAACGGACGAGGGC
1 TATCACAAGGTTGAAATAATCTTGATTATCTGCCCAATAATTAAACCACTTTAACGGACGAGGGC
1554618 CTTCCTTGAATTAGTTGT
66 CTTCCTTGAATTAGTTGT
*
1554636 TATCACAAGGTTGAAATAATCTTGATTATCTGCCCAATAATTAAACCACTTTAATGGACGAGGGC
1 TATCACAAGGTTGAAATAATCTTGATTATCTGCCCAATAATTAAACCACTTTAACGGACGAGGGC
*
1554701 CTTTCTTGAATTAGT
66 CTTCCTTGAATTAGT
1554716 GTTTTGTAGC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (83 bp):
TATCACAAGGTTGAAATAATCTTGATTATCTGCCCAATAATTAAACCACTTTAACGGACGAGGGC
CTTCCTTGAATTAGTTGT
Found at i:1559712 original size:18 final size:18
Alignment explanation
Indices: 1559689--1559723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1559679 ACTAAAAATT
*
1559689 TGTCCCGAATGACCACTA
1 TGTCCCGAAAGACCACTA
1559707 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
1559724 TATATTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:1560429 original size:35 final size:35
Alignment explanation
Indices: 1560390--1560457 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1560380 GTTTCAAAGA
*
1560390 TGGTATCCATACCGTCCTT-AAAGTATCGGTACCCT
1 TGGTATCCATACCGTCCTTCAAA-TATCGATACCCT
* **
1560425 TGGTATCGATATTGTCCTTCAAATATCGATACC
1 TGGTATCCATACCGTCCTTCAAATATCGATACC
1560458 TCATGAATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 25 0.89
36 3 0.11
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (35 bp):
TGGTATCCATACCGTCCTTCAAATATCGATACCCT
Found at i:1570063 original size:12 final size:12
Alignment explanation
Indices: 1570046--1570081 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1570036 TTCTTCCTCT
*
1570046 AATACTAATTCC
1 AATACTAACTCC
1570058 AATACTAACTCC
1 AATACTAACTCC
1570070 AATACTAACTCC
1 AATACTAACTCC
1570082 TTGGAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.28
Consensus pattern (12 bp):
AATACTAACTCC
Found at i:1570130 original size:21 final size:20
Alignment explanation
Indices: 1570102--1570140 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1570092 CATTGCAGGA
*
1570102 ATTTATGGTTTCGACAAAAG
1 ATTTATGGCTTCGACAAAAG
*
1570122 ATTTCATGGCTTCTACAAA
1 ATTT-ATGGCTTCGACAAA
1570141 GACCCTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
ATTTATGGCTTCGACAAAAG
Found at i:1572874 original size:89 final size:89
Alignment explanation
Indices: 1572722--1572897 Score: 309
Period size: 89 Copynumber: 2.0 Consensus size: 89
1572712 CCTAACACAC
*
1572722 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTTTTATTATTTCAAATTAATTAAATCTATA
*
1572787 TTTAATTAATT-AAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
1572810 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
1572875 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
1572898 TTCGAGATTA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
88 33 0.40
89 41 0.49
90 9 0.11
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:1596313 original size:3 final size:3
Alignment explanation
Indices: 1596305--1596376 Score: 85
Period size: 3 Copynumber: 24.0 Consensus size: 3
1596295 TGCAAAAATA
* * *
1596305 AAT AAT AAT AAT AAT AAT -AT AAT AAT GAT ATT AAT AAT ATT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
1596353 AAT AAT AAT AAAT AAT -AT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT
1596377 TACGGGACAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.07
3 49 0.83
4 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1600090 original size:2 final size:2
Alignment explanation
Indices: 1600009--1600082 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1599999 TATCAATGTG
1600009 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1600051 AT 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 AT
1600083 TCATATATTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1609595 original size:24 final size:24
Alignment explanation
Indices: 1609550--1609696 Score: 145
Period size: 24 Copynumber: 6.2 Consensus size: 24
1609540 AATATTCTAA
* *
1609550 TTTATGTTCATTTA-TTGTGTTCG
1 TTTATGTTCGTTCATTTGTGTTCG
* *
1609573 TTTACGTTCGTTCGTTTGTGTTCG
1 TTTATGTTCGTTCATTTGTGTTCG
* * * *
1609597 TTAATGTTTGTTTA-TTGTGTTCA
1 TTTATGTTCGTTCATTTGTGTTCG
* * ** **
1609620 TTTATGTTTGTTTACATCCGTTCG
1 TTTATGTTCGTTCATTTGTGTTCG
1609644 TTTATGTTCGTTCATTTGTGTTCG
1 TTTATGTTCGTTCATTTGTGTTCG
*
1609668 TTTATGTTCGTTCATTTGTGTTCA
1 TTTATGTTCGTTCATTTGTGTTCG
1609692 TTTAT
1 TTTAT
1609697 TATTTAAATG
Statistics
Matches: 100, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
23 31 0.31
24 69 0.69
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTGTGTTCG
Found at i:1609655 original size:14 final size:14
Alignment explanation
Indices: 1609638--1609690 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
1609628 TGTTTACATC
1609638 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
1609652 CGTTC-ATT-TG-T
1 CGTTCGTTTATGTT
1609663 -GTTCGTTTATGTT
1 CGTTCGTTTATGTT
* *
1609676 CGTTCATTTGTGTT
1 CGTTCGTTTATGTT
1609690 C
1 C
1609691 ATTTATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 3 0.10
12 4 0.13
13 3 0.10
14 17 0.55
ACGTcount: A:0.08, C:0.15, G:0.21, T:0.57
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:1614143 original size:20 final size:20
Alignment explanation
Indices: 1614106--1614149 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1614096 TATTAACAGA
* * *
1614106 CCCCGTGGGGGTATCGATTC
1 CCCCGAGGGCGTACCGATTC
1614126 CCCCGAGGGCGTACCGATTC
1 CCCCGAGGGCGTACCGATTC
1614146 CCCC
1 CCCC
1614150 TGTTTAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.41, G:0.30, T:0.18
Consensus pattern (20 bp):
CCCCGAGGGCGTACCGATTC
Found at i:1618249 original size:18 final size:18
Alignment explanation
Indices: 1618223--1618257 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1618213 AGATTGCCCA
1618223 GGGGAACCGATTCCCCCC
1 GGGGAACCGATTCCCCCC
*
1618241 GGGGTACCGATTCCCCC
1 GGGGAACCGATTCCCCC
1618258 TGAATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (18 bp):
GGGGAACCGATTCCCCCC
Found at i:1622903 original size:63 final size:63
Alignment explanation
Indices: 1622804--1622955 Score: 277
Period size: 63 Copynumber: 2.4 Consensus size: 63
1622794 AGACTACTCT
1622804 CTCGTGAGGTTTTCACCTCCGCATGGGATAGTGGATCACACCTAGAGCTCACGCCTTATGATC
1 CTCGTGAGGTTTTCACCTCCGCATGGGATAGTGGATCACACCTAGAGCTCACGCCTTATGATC
* * *
1622867 CTCGTGAGGTTTTCACTTCCGCATGGGATAGTGGATCACTCCTGGAGCTCACGCCTTATGATC
1 CTCGTGAGGTTTTCACCTCCGCATGGGATAGTGGATCACACCTAGAGCTCACGCCTTATGATC
1622930 CTCGTGAGGTTTTCACCTCCGCATGG
1 CTCGTGAGGTTTTCACCTCCGCATGG
1622956 ACATAAGGTG
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 85 1.00
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.29
Consensus pattern (63 bp):
CTCGTGAGGTTTTCACCTCCGCATGGGATAGTGGATCACACCTAGAGCTCACGCCTTATGATC
Found at i:1624044 original size:24 final size:25
Alignment explanation
Indices: 1623996--1624046 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
1623986 ACACTCTGCA
1623996 TTTTGCATATGCATCATTTTATTATT
1 TTTTGCATATGCAT-ATTTTATTATT
1624022 TTTTGCA-ATGCAT-TTTTATTTATT
1 TTTTGCATATGCATATTTTA-TTATT
1624046 T
1 T
1624047 ATTTTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 6 0.25
25 6 0.25
26 7 0.29
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.61
Consensus pattern (25 bp):
TTTTGCATATGCATATTTTATTATT
Found at i:1627647 original size:77 final size:76
Alignment explanation
Indices: 1627557--1627720 Score: 206
Period size: 76 Copynumber: 2.1 Consensus size: 76
1627547 ATCTCACTTG
* * * *
1627557 AGATTGTTTTTCTTAAAACATA-ATTTGTCTCACTTGAGACAGTTTTTTACTCGAAACAAGAAGA
1 AGATTATTTTTCTTAAAACA-AGATTTGTCTCACTTAAGAC-GATTTTTACTCGAAACAAG-ACA
*
1627621 TTT-ATTTCATTCA
63 TTTCATTTCACTCA
* * *
1627634 ATATTATTTTTCTTAAAACAAGATTTGTCTCGCTTAAGACGATTTTTACTCGAAAGAAGACATTT
1 AGATTATTTTTCTTAAAACAAGATTTGTCTCACTTAAGACGATTTTTACTCGAAACAAGACATTT
1627699 CATTTCACTCA
66 CATTTCACTCA
*
1627710 AGATTGTTTTT
1 AGATTATTTTT
1627721 AAAGAAGAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
75 5 0.07
76 36 0.48
77 34 0.45
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (76 bp):
AGATTATTTTTCTTAAAACAAGATTTGTCTCACTTAAGACGATTTTTACTCGAAACAAGACATTT
CATTTCACTCA
Found at i:1627778 original size:39 final size:39
Alignment explanation
Indices: 1627725--1628037 Score: 500
Period size: 39 Copynumber: 8.0 Consensus size: 39
1627715 GTTTTTAAAG
*
1627725 AAGAGTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
1627764 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
1627803 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1627842 AAGATTTTAATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1 AAGATTTT-ATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
1627882 AAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
1627921 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
1627960 AAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * * *
1627999 AAGATTTTGTCTCACTTGAGATAGTTTCTCTTGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1628038 GTTTTGTCTC
Statistics
Matches: 260, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
39 222 0.85
40 38 0.15
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
Found at i:1627876 original size:118 final size:117
Alignment explanation
Indices: 1627725--1628036 Score: 516
Period size: 118 Copynumber: 2.7 Consensus size: 117
1627715 GTTTTTAAAG
*
1627725 AAGAGTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
* *
1627790 TCCCTCGAAACATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAA
66 TCTCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAA
1627842 AAGATTTTAATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGT
1 AAGATTTT-ATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGT
* *
1627907 TTCTCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
65 TTCTCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAA
* * * * *
1627960 AAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAGAAGATTTTGTCTCACTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
*
1628025 TCTCTTGAAACA
66 TCTCTCGAAACA
1628037 AGTTTTGTCT
Statistics
Matches: 183, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
117 70 0.38
118 113 0.62
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (117 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTT
TCTCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAA
Found at i:1632142 original size:21 final size:21
Alignment explanation
Indices: 1632116--1632162 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1632106 TAGCATTTTC
1632116 CAATAAACTTGAAATCCATAA
1 CAATAAACTTGAAATCCATAA
1632137 CAATAAACTTGAAATCCATAA
1 CAATAAACTTGAAATCCATAA
*
1632158 TAATA
1 CAATA
1632163 TATCAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (21 bp):
CAATAAACTTGAAATCCATAA
Found at i:1635777 original size:41 final size:40
Alignment explanation
Indices: 1635732--1635959 Score: 203
Period size: 41 Copynumber: 5.6 Consensus size: 40
1635722 CAATTGCGAA
*
1635732 GTTTGTTTTAAAAACACCACTAAAGAACT-TTCTCTTGCGGC
1 GTTTG-TTTAAAAACGCCACTAAAGAACTATTCT-TTGCGGC
* * * * *
1635773 GTTTGTTTAGAAACGCCATTATAGTACTATGT-TGTAGCGGC
1 GTTTGTTTAAAAACGCCACTAAAGAACTAT-TCT-TTGCGGC
* * ** *
1635814 GTTTGTCTAAAAACGCCAC-AATATATGTATCCTATTGCGGC
1 GTTTGTTTAAAAACGCCACTAA-AGAACTATTCT-TTGCGGC
* * *
1635855 GTTTGTTTAAAAATGCCATTAAAGAACTATTCTTTTGTGGC
1 GTTTGTTTAAAAACGCCACTAAAGAACTATTC-TTTGCGGC
* * *
1635896 GTTTGTTTAAAAACACCACTAAAGTA-GATTCTTTGGCGGC
1 GTTTGTTTAAAAACGCCACTAAAGAACTATTCTTT-GCGGC
1635936 GTTTGTTTAAAAACGCCACTAAAG
1 GTTTGTTTAAAAACGCCACTAAAG
1635960 TACTTATATG
Statistics
Matches: 147, Mismatches: 33, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
39 3 0.02
40 50 0.34
41 90 0.61
42 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (40 bp):
GTTTGTTTAAAAACGCCACTAAAGAACTATTCTTTGCGGC
Found at i:1635818 original size:82 final size:80
Alignment explanation
Indices: 1635732--1635963 Score: 243
Period size: 82 Copynumber: 2.8 Consensus size: 80
1635722 CAATTGCGAA
* * *
1635732 GTTTGTTTTAAAAACACCACTAAAGAACTTTCTCTTGCGGCGTTTGTTTAGAAACGCCATTATAG
1 GTTTG-TTTAAAAACACCACTAAAGAAGTTTCT-TTGCGGCGTTTGTTTAAAAACGCCATTAAAG
1635797 TACTATGT-TGTAGCGGC
64 TACTAT-TCTGTAGCGGC
* * * * * *
1635814 GTTTGTCTAAAAACGCCAC-AATATATGTATCCTATTGCGGCGTTTGTTTAAAAATGCCATTAAA
1 GTTTGTTTAAAAACACCACTAA-AGAAGT-TTCT-TTGCGGCGTTTGTTTAAAAACGCCATTAAA
* * * *
1635878 GAACTATTCTTTTGTGGC
63 GTACTATTCTGTAGCGGC
* * *
1635896 GTTTGTTTAAAAACACCACTAAAGTAGATTCTTTGGCGGCGTTTGTTTAAAAACGCCACTAAAGT
1 GTTTGTTTAAAAACACCACTAAAGAAGTTTCTTT-GCGGCGTTTGTTTAAAAACGCCATTAAAGT
1635961 ACT
65 ACT
1635964 TATATGTATC
Statistics
Matches: 121, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
80 4 0.03
81 49 0.40
82 66 0.55
83 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (80 bp):
GTTTGTTTAAAAACACCACTAAAGAAGTTTCTTTGCGGCGTTTGTTTAAAAACGCCATTAAAGTA
CTATTCTGTAGCGGC
Found at i:1649034 original size:3 final size:3
Alignment explanation
Indices: 1649026--1649052 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1649016 GATGCATTTA
1649026 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1649053 CTTATCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1651881 original size:3 final size:3
Alignment explanation
Indices: 1651875--1651927 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
1651865 AATAATAATA
* *
1651875 ATT ATT ATT ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1651923 ATT AT
1 ATT AT
1651928 CTCGGATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1654970 original size:16 final size:16
Alignment explanation
Indices: 1654949--1654980 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1654939 TCACTTGGTG
1654949 AACAGACTTATTATTT
1 AACAGACTTATTATTT
1654965 AACAGACTTATTATTT
1 AACAGACTTATTATTT
1654981 GGTATAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
AACAGACTTATTATTT
Found at i:1657144 original size:16 final size:16
Alignment explanation
Indices: 1657114--1657143 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1657104 CTTTTCTGTT
1657114 TCTTTTTTCTTTTTTG
1 TCTTTTTTCTTTTTTG
1657130 TCTTTTTT-TTTTTT
1 TCTTTTTTCTTTTTT
1657144 TACAGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (16 bp):
TCTTTTTTCTTTTTTG
Found at i:1660424 original size:28 final size:28
Alignment explanation
Indices: 1660382--1660506 Score: 223
Period size: 28 Copynumber: 4.5 Consensus size: 28
1660372 CTTAGTTTAT
* *
1660382 ATTATGTCATCAAGCTCGTGCTTGAAAC
1 ATTATGTCGTCAAGCCCGTGCTTGAAAC
*
1660410 ATTATGTCGTTAAGCCCGTGCTTGAAAC
1 ATTATGTCGTCAAGCCCGTGCTTGAAAC
1660438 ATTATGTCGTCAAGCCCGTGCTTGAAAC
1 ATTATGTCGTCAAGCCCGTGCTTGAAAC
1660466 ATTATGTCGTCAAGCCCGTGCTTGAAAC
1 ATTATGTCGTCAAGCCCGTGCTTGAAAC
1660494 ATTATGTCGTCAA
1 ATTATGTCGTCAA
1660507 ACTGTTGTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 93 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (28 bp):
ATTATGTCGTCAAGCCCGTGCTTGAAAC
Found at i:1663225 original size:19 final size:19
Alignment explanation
Indices: 1663201--1663240 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1663191 TTCTTTCATA
1663201 TTTTTATAATAAATAATAT
1 TTTTTATAATAAATAATAT
* **
1663220 TTTTTATTATATTTAATAT
1 TTTTTATAATAAATAATAT
1663239 TT
1 TT
1663241 ATATGTCGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATAATAAATAATAT
Found at i:1663952 original size:25 final size:24
Alignment explanation
Indices: 1663902--1663953 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1663892 AAGGTTTTTT
* * **
1663902 TAAAAAAAATAATATAATAATGAA
1 TAAAAAAAAGAAAATAATAAAAAA
1663926 TAAAAAAAACGAAAATAATAAAAAA
1 TAAAAAAAA-GAAAATAATAAAAAA
1663951 TAA
1 TAA
1663954 TATAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (24 bp):
TAAAAAAAAGAAAATAATAAAAAA
Found at i:1664235 original size:18 final size:17
Alignment explanation
Indices: 1664214--1664256 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1664204 ATATATACAT
1664214 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1664232 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1664249 ATAA-AATA
1 ATAATAATA
1664257 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1664722 original size:34 final size:34
Alignment explanation
Indices: 1664668--1664736 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1664658 GAATCCTAGC
*
1664668 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTGAATCCT
* *
1664702 AAAATTATATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTGAATCCT
1664736 A
1 A
1664737 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTATATCATATCTTTAGGAGTTTGAATCCT
Found at i:1665585 original size:105 final size:105
Alignment explanation
Indices: 1665285--1666050 Score: 1078
Period size: 105 Copynumber: 7.3 Consensus size: 105
1665275 CATTGTTCCA
* * * * ** * * *
1665285 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
1665350 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1665391 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1665451 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1665491 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1665556 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1665596 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGGGAAATTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1665661 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1665701 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1665766 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1665806 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1665871 AGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1665911 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
1665976 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1666017 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1666051 CGCAGATGGC
Statistics
Matches: 599, Mismatches: 50, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
99 1 0.00
100 80 0.13
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.01
105 400 0.67
106 81 0.14
107 4 0.01
109 21 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1666937 original size:65 final size:65
Alignment explanation
Indices: 1666833--1667013 Score: 299
Period size: 65 Copynumber: 2.8 Consensus size: 65
1666823 GACAAAATTT
1666833 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1666898 TGTTTCAAGAGAAACTATCTCAAGAGAGACGGAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
1666963 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
1667014 CTATCTCAAG
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 93 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:1667049 original size:36 final size:37
Alignment explanation
Indices: 1666965--1667049 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
1666955 AATGTTTATG
* * * **
1666965 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTCA
1667002 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTCA
1667038 TTTCAAGGGAAA
1 TTTCAAGGGAAA
1667050 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 14 0.33
37 29 0.67
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (37 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTCA
Done.